Adaptor Template Oligo-Mediated Sequencing (ATOM-Seq) is a new ultra-sensitive UMI-based NGS library preparation technology for use with cfDNA and cfRNA

Liquid biopsy testing utilising Next Generation Sequencing (NGS) is rapidly moving towards clinical adoption for personalised oncology. However, before NGS can fulfil its potential any novel testing approach must identify ways of reducing errors, allowing separation of true low-frequency mutations from procedural artefacts, and be designed to improve upon current technologies. Popular NGS technologies typically utilise two DNA capture approaches; PCR and ligation, which have known limitations and seem to have reached a development plateau with only small, stepwise improvements being made. To maximise the ultimate utility of liquid biopsy testing we have developed a highly versatile approach to NGS: Adaptor Template Oligo Mediated Sequencing (ATOM-Seq). ATOM-Seq's strengths and versatility avoid the major limitations of both PCR- and ligation-based approaches. This technology is ligation free, simple, efficient, flexible, and streamlined, and it offers novel advantages that make it perfectly suited for use on highly challenging clinical material. Using reference and clinical materials, we demonstrate detection of known SNVs down to allele frequencies of 0.1% using as little as 20–25 ng of cfDNA, as well as the ability to detect fusions from RNA. We illustrate ATOM-Seq’s suitability for clinical testing by showing high concordance rates between paired cfDNA and FFPE clinical samples

The Effects of Warming-Shifted Plant Phenology on Ecosystem Carbon Exchange Are Regulated by Precipitation in a Semi-Arid Grassland

BACKGROUND: The longer growing season under climate warming has served as a crucial mechanism for the enhancement of terrestrial carbon (C) sink over the past decades. A better understanding of this mechanism is critical for projection of changes in C cycling of terrestrial ecosystems. METHODOLOGY/PRINCIPAL FINDINGS: A 4-year field experiment with day and night warming was conducted to examine the responses of plant phenology and their influences on plant coverage and ecosystem C cycling in a temperate steppe in northern China. Greater phenological responses were observed under night than day warming. Both day and night warming prolonged the growing season by advancing phenology of early-blooming species but without changing that of late-blooming species. However, no warming response of vegetation coverage was found for any of the eight species. The variances in species-level coverage and ecosystem C fluxes under different treatments were positively dependent upon the accumulated precipitation within phenological duration but not the length of phenological duration. CONCLUSIONS/SIGNIFICANCE: These plants' phenology is more sensitive to night than day warming, and the warming effects on ecosystem C exchange via shifting plant phenology could be mediated by precipitation patterns in semi-arid grasslands

Global Assessment of Extinction Risk to Populations of Sockeye Salmon Oncorhynchus nerka

BACKGROUND: Concern about the decline of wild salmon has attracted the attention of the International Union for the Conservation of Nature (IUCN). The IUCN applies quantitative criteria to assess risk of extinction and publishes its results on the Red List of Threatened Species. However, the focus is on the species level and thus may fail to show the risk to populations. The IUCN has adapted their criteria to apply to populations but there exist few examples of this type of assessment. We assessed the status of sockeye salmon Oncorhynchus nerka as a model for application of the IUCN population-level assessments and to provide the first global assessment of the status of an anadromous Pacific salmon. METHODS/PRINCIPAL FINDINGS: We found from demographic data that the sockeye salmon species is not presently at risk of extinction. We identified 98 independent populations with varying levels of risk within the species' range. Of these, 5 (5%) are already extinct. We analyzed the risk for 62 out of 93 extant populations (67%) and found that 17 of these (27%) are at risk of extinction. The greatest number and concentration of extinct and threatened populations is in the southern part of the North American range, primarily due to overfishing, freshwater habitat loss, dams, hatcheries, and changing ocean conditions. CONCLUSIONS/SIGNIFICANCE: Although sockeye salmon are not at risk at the species-level, about one-third of the populations that we analyzed are at risk or already extinct. Without an understanding of risk to biodiversity at the level of populations, the biodiversity loss in salmon would be greatly underrepresented on the Red List. We urge government, conservation organizations, scientists and the public to recognize this limitation of the Red List. We also urge recognition that about one-third of sockeye salmon global population diversity is at risk of extinction or already extinct

Arousal increases neural gain via the locus coeruleus-norepinephrine system in younger adults but not in older adults

In younger adults, arousal amplifies attentional focus to the most salient or goal-relevant information while suppressing other information. A computational model of how the locus coeruleus-norepinephrine (LC-NE) system can implement this increased selectivity under arousal and an fMRI study comparing how arousal affects younger and older adults’ processing indicate that the amplification of salient stimuli and the suppression of non-salient stimuli are separate processes, with aging affecting suppression without impacting amplification under arousal. In the fMRI study, arousal increased processing of salient stimuli and decreased processing of non-salient stimuli for younger adults. In contrast, for older adults, arousal increased processing of both low and high salience stimuli, generally increasing excitatory responses to visual stimuli. Older adults also showed decline in LC functional connectivity with frontoparietal networks that coordinate attentional selectivity. Thus, among older adults, arousal increases the potential for distraction from non-salient stimuli

Wittgenstein’s Revenge: How Semantic Algorithms Can Help Survey Research Escape Smedslund’s Labyrinth

Empirical research has shown how semantic algorithms can often predict the statistics of survey data a priori, particularly in topics like “leadership” and “motivation.” In those cases, the survey data reflect the language usages of respondents, not the attitudes toward the topics in question. While this fact seems to bewilder researchers, it opens a computational tool for exploring our semantic construction of psychological reality. Using Dennett’s concept “competence without comprehension,” this article discusses how humans are trapped in a semantic network that we ourselves struggle to understand. Since Smedslund’s work and the language algorithms have common roots in formal logics, the computational algorithms may help us explore the cognitively challenging area of a priori assumptions in psychological research. There may be a computational way to test and explore Smedslund’s ideas of “pseudo-empiricality,” helping science explore the complex area among empirical, logical, and psychological phenomena