Circulating DNA: Diagnostic Tool and Predictive Marker for Overall Survival of NSCLC Patients

PURPOSE: The purpose of our study was to determine whether the amounts of circulating DNA (cDNA) could discriminate between NSCLC patients and healthy individuals and assess its value as a prognostic marker of this disease. METHODS: We conducted a study of 309 individuals and the cDNA levels were assessed through real-time PCR methodology. RESULTS: We found increased cDNA levels in NSCLC patients compared to control individuals. We also found a decreased overall survival time in patients presenting high cDNA levels, when compared to lower cDNA concentrations. CONCLUSIONS: Quantification of cDNA may be a good tool for NSCLC detection with potential for clinical applicability

Report of Working Group on Widely Distributed Stocks (WGWIDE).

As a consequence of the impact of the COVID pandemic on international travel which prevented the traditional meeting from taking place, the Working Group on Widely Distributed Stocks (WGWIDE) met online via WebEx hosted by ICES. Prior to the 2020 meeting, the generic ToRs for species and regional working groups were re-prioritised by ACOM to allow the WG to focus primarily on those ToRs most applicable to the provision of advice. WGWIDE reports on the status and considerations for management of Northeast Atlantic mackerel, blue whiting, Western and North Sea horse mackerel, Northeast Atlantic boarfish, Norwegian springspawning herring, striped red mullet (Subareas 6, 8 and Divisions 7.a-c, e-k and 9.a), and red gurnard (Subareas 3, 4, 5, 6, 7, and 8) stocks. Northeast Atlantic (NEA) Mackerel. This stock is highly migratory and widely distributed throughout the Northeast Atlantic with significant fisheries is most ICES subareas. A diverse range of fleets from smaller artisanal, handline vessels to large (100m+) factory freezer vessels and modern RSW trawlers and purse seiners take part in what is one of the most valuable European fisheries. The assessment conducted in 2020 is an update assessment, based on the configuration agreed during the most recent inter-benchmark exercise in 2019 and incorporates the most recent data available from sampling of the commercial catch in 2019, the final 2019 egg survey SSB estimate, an updated recruitment index and tagging time series along with 2020 survey data from the IESSNS swept area survey. Advice is given based on stock reference points which were updated during a management strategy evaluation carried out in 2020. Following a strong increase from 2007 to 2014, SSB has been declining although it remains well above MSY Btrigger. Fishing mortality has been below FMSY since 2016. There have been a number of large year classes since 2001 with above average recruitment over much of the most recent decade. Blue Whiting. This pelagic gadoid is widely distributed in the eastern part of the North Atlantic. The 2020 update assessment followed the protocol from the most recent inter-benchmark in 2016 and used preliminary catch data from 2020. Due to the cancellation of the 2020 acoustic survey, this data was not available. The effect on the assessment was minimal and limited to increases in uncertainty of the terminal year estimates. The SSB continues to decrease from the most recent maximum in 2017 mainly due to below average recruitment since 2017, although it remains above MSY Btrigger. Fishing mortality has been above FMSY since 2014. Norwegian Spring Spawning Herring. This is one of the largest herring stocks in the world. It is highly migratory, spawning along the Norwegian coast and feeding throughout much of the Norwegian Sea. The 2020 assessment is based on an implementation of the XSAM assessment model introduced at the benchmark in 2016. This years’ assessment indicates that the stock is continuing to decline from the peak in 2008 of 7Mt to just above MSY Btrigger due to successive years of average or below average recruitment. Catch advice for 2021 is given on the basis of the agreed management plan and represents a substantial increase over the 2020 advice due to an upward revision in the estimate of the 2016 year-class which is considered to be the most significant year-class since 2004

Insights into Land Plant Evolution Garnered from the Marchantia polymorpha Genome.

The evolution of land flora transformed the terrestrial environment. Land plants evolved from an ancestral charophycean alga from which they inherited developmental, biochemical, and cell biological attributes. Additional biochemical and physiological adaptations to land, and a life cycle with an alternation between multicellular haploid and diploid generations that facilitated efficient dispersal of desiccation tolerant spores, evolved in the ancestral land plant. We analyzed the genome of the liverwort Marchantia polymorpha, a member of a basal land plant lineage. Relative to charophycean algae, land plant genomes are characterized by genes encoding novel biochemical pathways, new phytohormone signaling pathways (notably auxin), expanded repertoires of signaling pathways, and increased diversity in some transcription factor families. Compared with other sequenced land plants, M. polymorpha exhibits low genetic redundancy in most regulatory pathways, with this portion of its genome resembling that predicted for the ancestral land plant. PAPERCLIP

Testing a prediction model for the H-mode density pedestal against JET-ILW pedestals

The neutral ionisation model proposed by Groebner et al (2002 Phys. Plasmas 9 2134) to determine the plasma density profile in the H-mode pedestal, is extended to include charge exchange processes in the pedestal stimulated by the ideas of Mahdavi et al (2003 Phys. Plasmas 10 3984). The model is then tested against JET H-mode pedestal data, both in a 'standalone' version using experimental temperature profiles and also by incorporating it in the Europed version of EPED. The model is able to predict the density pedestal over a wide range of conditions with good accuracy. It is also able to predict the experimentally observed isotope effect on the density pedestal that eludes simpler neutral ionization models

Shattered pellet injection experiments at JET in support of the ITER disruption mitigation system design

A series of experiments have been executed at JET to assess the efficacy of the newly installed shattered pellet injection (SPI) system in mitigating the effects of disruptions. Issues, important for the ITER disruption mitigation system, such as thermal load mitigation, avoidance of runaway electron (RE) formation, radiation asymmetries during thermal quench mitigation, electromagnetic load control and RE energy dissipation have been addressed over a large parameter range. The efficiency of the mitigation has been examined for the various SPI injection strategies. The paper summarises the results from these JET SPI experiments and discusses their implications for the ITER disruption mitigation scheme

The role of ETG modes in JET-ILW pedestals with varying levels of power and fuelling

We present the results of GENE gyrokinetic calculations based on a series of JET-ITER-like-wall (ILW) type I ELMy H-mode discharges operating with similar experimental inputs but at different levels of power and gas fuelling. We show that turbulence due to electron-temperature-gradient (ETGs) modes produces a significant amount of heat flux in four JET-ILW discharges, and, when combined with neoclassical simulations, is able to reproduce the experimental heat flux for the two low gas pulses. The simulations plausibly reproduce the high-gas heat fluxes as well, although power balance analysis is complicated by short ELM cycles. By independently varying the normalised temperature gradients (omega(T)(e)) and normalised density gradients (omega(ne )) around their experimental values, we demonstrate that it is the ratio of these two quantities eta(e) = omega(Te)/omega(ne) that determines the location of the peak in the ETG growth rate and heat flux spectra. The heat flux increases rapidly as eta(e) increases above the experimental point, suggesting that ETGs limit the temperature gradient in these pulses. When quantities are normalised using the minor radius, only increases in omega(Te) produce appreciable increases in the ETG growth rates, as well as the largest increases in turbulent heat flux which follow scalings similar to that of critical balance theory. However, when the heat flux is normalised to the electron gyro-Bohm heat flux using the temperature gradient scale length L-Te, it follows a linear trend in correspondence with previous work by different authors

Comparing pedestal structure in JET-ILW H-mode plasmas with a model for stiff ETG turbulent heat transport

A predictive model for the electron temperature profile of the H-mode pedestal is described, and its results are compared with the pedestal structure of JET-ILW plasmas. The model is based on a scaling for the gyro-Bohm normalized, turbulent electron heat flux qe/qe,gB resulting from electron temperature gradient (ETG) turbulence, derived from results of nonlinear gyrokinetic (GK) calculations for the steep gradient region. By using the local temperature gradient scale length L-Te in the normalization, the dependence of q(e)/q(e,g)B on the normalized gradients R/L-Te and R/(Lne) can be represented by a unified scaling with the parameter eta(e) = L-ne/L-Te, to which the linear stability of ETG turbulence is sensitive when the density gradient is sufficiently steep. For a prescribed density profile, the value of R/L-Te determined from this scaling, required to maintain a constant electron heat flux qe across the pedestal, is used to calculate the temperature profile. Reasonable agreement with measurements is found for different cases, the model providing an explanation of the relative widths and shifts of the T-e and n(e) profiles, as well as highlighting the importance of the separatrix boundary conditions. Other cases showing disagreement indicate conditions where other branches of turbulence might dominate.This article is part of a discussion meeting issue "H-mode transition and pedestal studies in fusion plasmas'

New H-mode regimes with small ELMs and high thermal confinement in the Joint European Torus

New H-mode regimes with high confinement, low core impurity accumulation, and small edge-localized mode perturbations have been obtained in magnetically confined plasmas at the Joint European Torus tokamak. Such regimes are achieved by means of optimized particle fueling conditions at high input power, current, and magnetic field, which lead to a self-organized state with a strong increase in rotation and ion temperature and a decrease in the edge density. An interplay between core and edge plasma regions leads to reduced turbulence levels and outward impurity convection. These results pave the way to an attractive alternative to the standard plasmas considered for fusion energy generation in a tokamak with a metallic wall environment such as the ones expected in ITER.& nbsp;Published under an exclusive license by AIP Publishing

Spectroscopic camera analysis of the roles of molecularly assisted reaction chains during detachment in JET L-mode plasmas

The roles of the molecularly assisted ionization (MAI), recombination (MAR) and dissociation (MAD) reaction chains with respect to the purely atomic ionization and recombination processes were studied experimentally during detachment in low-confinement mode (L-mode) plasmas in JET with the help of experimentally inferred divertor plasma and neutral conditions, extracted previously from filtered camera observations of deuterium Balmer emission, and the reaction coefficients provided by the ADAS, AMJUEL and H2VIBR atomic and molecular databases. The direct contribution of MAI and MAR in the outer divertor particle balance was found to be inferior to the electron-atom ionization (EAI) and electron-ion recombination (EIR). Near the outer strike point, a strong atom source due to the D+2-driven MAD was, however, observed to correlate with the onset of detachment at outer strike point temperatures of Te,osp = 0.9-2.0 eV via increased plasma-neutral interactions before the increasing dominance of EIR at Te,osp < 0.9 eV, followed by increasing degree of detachment. The analysis was supported by predictions from EDGE2D-EIRENE simulations which were in qualitative agreement with the experimental observations

Disruption prediction at JET through deep convolutional neural networks using spatiotemporal information from plasma profiles

In view of the future high power nuclear fusion experiments, the early identification of disruptions is a mandatory requirement, and presently the main goal is moving from the disruption mitigation to disruption avoidance and control. In this work, a deep-convolutional neural network (CNN) is proposed to provide early detection of disruptive events at JET. The CNN ability to learn relevant features, avoiding hand-engineered feature extraction, has been exploited to extract the spatiotemporal information from 1D plasma profiles. The model is trained with regularly terminated discharges and automatically selected disruptive phase of disruptions, coming from the recent ITER-like-wall experiments. The prediction performance is evaluated using a set of discharges representative of different operating scenarios, and an in-depth analysis is made to evaluate the performance evolution with respect to the considered experimental conditions. Finally, as real-time triggers and termination schemes are being developed at JET, the proposed model has been tested on a set of recent experiments dedicated to plasma termination for disruption avoidance and mitigation. The CNN model demonstrates very high performance, and the exploitation of 1D plasma profiles as model input allows us to understand the underlying physical phenomena behind the predictor decision