The universal instability in optimised stellarators

In tokamaks and neoclassically optimised stellarators, like Wendelstein 7-X (W7-X) and the Helically Symmetric Experiment, turbulent transport is expected to be the dominant transport mechanism. Among the electrostatic instabilities that drive turbulence, the trapped-electron mode (TEM) has been shown both analytically and in simulations to be absent over large ranges of parameter space in quasi-isodynamic stellarator configurations with the maximum- property. It has been proposed that the reduction of the linear TEM growth rate in such configurations may lead to the passing-electron-driven universal instability, which is often subdominant to the TEM, becoming the fastest-growing instability over some range of parameter space. Here, we show through gyrokinetic simulations using the Gene code, that the universal instability is dominant in a variety of stellarator geometries over a range of parameter space typically occupied by the TEM, but most consequentially in devices which possess beneficial TEM stability properties like W7-X, which locally satisfies the maximum- property for deeply trapped particles in the regions of worst curvature. We find that the universal instability exists at long perpendicular wavelengths and, as a result, dominates the potential fluctuation amplitude in nonlinear simulations. In W7-X, universal modes are found to differ in parallel mode structure from trapped-particle modes, which may impact turbulence localisation in experiments.</p

Improving QPF by blending techniques at the Meteorological Service of Catalonia

The current operational very short-term and short-term quantitative precipitation forecast (QPF) at the Meteorological Service of Catalonia (SMC) is made by three different methodologies: Advection of the radar reflectivity field (ADV), Identification, tracking and forecasting of convective structures (CST) and numerical weather prediction (NWP) models using observational data assimilation (radar, satellite, etc.). These precipitation forecasts have different characteristics, lead time and spatial resolutions. The objective of this study is to combine these methods in order to obtain a single and optimized QPF at each lead time. This combination (blending) of the radar forecast (ADV and CST) and precipitation forecast from NWP model is carried out by means of different methodologies according to the prediction horizon. Firstly, in order to take advantage of the rainfall location and intensity from radar observations, a phase correction technique is applied to the NWP output to derive an additional corrected forecast (MCO). To select the best precipitation estimation in the first and second hour (t+1 h and t+2 h), the information from radar advection (ADV) and the corrected outputs from the model (MCO) are mixed by using different weights, which vary dynamically, according to indexes that quantify the quality of these predictions. This procedure has the ability to integrate the skill of rainfall location and patterns that are given by the advection of radar reflectivity field with the capacity of generating new precipitation areas from the NWP models. From the third hour (t+3 h), as radar-based forecasting has generally low skills, only the quantitative precipitation forecast from model is used. This blending of different sources of prediction is verified for different types of episodes (convective, moderately convective and stratiform) to obtain a robust methodology for implementing it in an operational and dynamic wa

Recurrent epimutations activate gene body promoters in primary glioblastoma

Aberrant DNA hypomethylation may play an important role in the growth rate of glioblastoma (GBM), but the functional impact on transcription remains poorly understood. We assayed the GBM methylome with MeDIP-seq and MRE-seq, adjusting for copy number differences, in a small set of non-glioma CpG island methylator phenotype (non-G-CIMP) primary tumors. Recurrent hypomethylated loci were enriched within a region of chromosome 5p15 that is specified as a cancer amplicon and also encompasses TERT, encoding telomerase reverse transcriptase, which plays a critical role in tumorigenesis. Overall, 76 gene body promoters were recurrently hypomethylated, including TERT and the oncogenes GLI3 and TP73. Recurring hypomethylation also affected previously unannotated alternative promoters, and luciferase reporter assays for three of four of these promoters confirmed strong promoter activity in GBM cells. Histone H3 lysine 4 trimethylation (H3K4me3) ChIP-seq on tissue from the GBMs uncovered peaks that coincide precisely with tumor-specific decrease of DNA methylation at 200 loci, 133 of which are in gene bodies. Detailed investigation of TP73 and TERT gene body hypomethylation demonstrated increased expression of corresponding alternate transcripts, which in TP73 encodes a truncated p73 protein with oncogenic function and in TERT encodes a putative reverse transcriptase-null protein. Our findings suggest that recurring gene body promoter hypomethylation events, along with histone H3K4 trimethylation, alter the transcriptional landscape of GBM through the activation of a limited number of normally silenced promoters within gene bodies, in at least one case leading to expression of an oncogenic protein

Lipid and fatty acid composition of parasitic caligid copepods belonging to the genus Lepeophtheirus

Sea lice are copepod ectoparasites that constitute a major barrier to the sustainability and economic viability of marine finfish aquaculture operations worldwide. In particular, the salmon louse, Lepeophtheirus salmonis, poses a considerable problem for salmoniculture in the northern hemisphere. The free-swimming nauplii and infective copepodids of L. salmonis are lecithotrophic, subsisting principally on maternally-derived lipid reserves. However, the lipids and fatty acids of sea lice have been sparsely studied and therefore the present project aimed to investigate the lipid and fatty acid composition of sea lice of the genus Lepeophtheirus obtained from a variety of fish hosts. Total lipid was extracted from eggs and adult female Lepeophtheirus salmonis obtained from both wild and farmed Atlantic salmon (Salmo salar L.) sampled at two time points, in the mid 1990’s and in 2009. In addition, L. salmonis from wild sea trout (Salmo trutta L.) and L. hippoglossi from wild Atlantic halibut (Hippoglossus hippoglossus L.) were sampled and analyzed. The lipids of both females and egg strings of Lepeophtheirus were characterized by triacylglycerol (TAG) as the major neutral (storage) lipid with phosphatidylcholine and phosphatidylethanolamine as the major polar (membrane) lipids. The major fatty acids were 22:6n-3 (DHA), 18:1n-9 and 16:0, with lesser amounts of 20:5n-3, 22:5n-3 and 18:0. L. salmonis sourced from farmed salmon were characterized by higher levels of 18:2n-6 and 18:3n-3 than lice from wild salmon. Egg strings had higher levels of TAG and lower DHA compared to females, whereas L. hippoglossi had lower levels of TAG and higher DHA than L. salmonis. The results demonstrate that the fatty acid compositions of lice obtained from wild and farmed salmon differ and that changes to the lipid and fatty acid composition of feeds for farmed salmon influence the louse compositions

Biochar versus hydrochar as growth media constituents for ornamental plant cultivation

[EN] Biochar and hydrochar have been proposed as novel materials for providing soilless growth media. However, much more knowledge is required before reliable advice can be given on the use of these materials for this purpose. Depending on the material and the technology applied (pyrolysis or hydrothermal carbonization), phytotoxicity and greenhouse gas emissions have been found for certain chars. In this study, our aim was to assess the feasibility of three chars as substrate constituents. We compared two biochars, one from forest waste and the other from olive mill waste, and a hydrochar from forest waste. We studied how chars affected substrate characteristics, plant performance, water economy and respiratory CO2 emission. Substrates containing biochar from forest waste showed the best characteristics, with good air/water relationships and adequate electrical conductivity. Those with biochar from olive mill waste were highly saline and, consequently, low quality. The substrates with hydrochar retained too much water and were poorly aerated, presenting high CO2 concentrations due to high respiratory activity. Plants performed well only when grown in substrates containing a maximum of 25 % biochar from forest waste or hydrochar. After analyzing the char characteristics, we concluded that biochar from forest waste could be safely used as a substrate constituent and is environmentally friendly when applied due to its low salinity and low CO2 emission. However, biochar from olive mill waste and hydrochar need to be improved before they can be used as substrate constituents.This study was funded by the Polytechnic University of Valencia (Projects on New Multidisciplinary Research; PAID-05-12). We thank Molly Marcus-McBride for supervising the English.Fornes Sebastiá, F.; Belda Navarro, RM. (2018). Biochar versus hydrochar as growth media constituents for ornamental plant cultivation. Scientia Agricola (Online). 75(4):304-312. https://doi.org/10.1590/1678-992X-2017-0062S304312754Abad, M., Noguera, P., & Burés, S. (2001). National inventory of organic wastes for use as growing media for ornamental potted plant production: case study in Spain. Bioresource Technology, 77(2), 197-200. doi:10.1016/s0960-8524(00)00152-8Bargmann, I., Martens, R., Rillig, M. C., Kruse, A., & Kücke, M. (2013). Hydrochar amendment promotes microbial immobilization of mineral nitrogen. Journal of Plant Nutrition and Soil Science, 177(1), 59-67. doi:10.1002/jpln.201300154Bargmann, I., Rillig, M. C., Buss, W., Kruse, A., & Kuecke, M. (2013). Hydrochar and Biochar Effects on Germination of Spring Barley. Journal of Agronomy and Crop Science, 199(5), 360-373. doi:10.1111/jac.12024Bedussi, F., Zaccheo, P., & Crippa, L. (2015). Pattern of pore water nutrients in planted and non-planted soilless substrates as affected by the addition of biochars from wood gasification. Biology and Fertility of Soils, 51(5), 625-635. doi:10.1007/s00374-015-1011-6Belda, R. M., Lidón, A., & Fornes, F. (2016). Biochars and hydrochars as substrate constituents for soilless growth of myrtle and mastic. Industrial Crops and Products, 94, 132-142. doi:10.1016/j.indcrop.2016.08.024Costello, R. C., & Sullivan, D. M. (2013). Determining the pH Buffering Capacity of Compost Via Titration with Dilute Sulfuric Acid. Waste and Biomass Valorization, 5(3), 505-513. doi:10.1007/s12649-013-9279-yFernandes, C., & Corá, J. E. (2004). Bulk density and relationship air/water of horticultural substrate. Scientia Agricola, 61(4), 446-450. doi:10.1590/s0103-90162004000400015Fornes, F., Belda, R. M., Carrión, C., Noguera, V., García-Agustín, P., & Abad, M. (2007). Pre-conditioning ornamental plants to drought by means of saline water irrigation as related to salinity tolerance. Scientia Horticulturae, 113(1), 52-59. doi:10.1016/j.scienta.2007.01.008Fornes, F., Belda, R. M., & Lidón, A. (2015). Analysis of two biochars and one hydrochar from different feedstock: focus set on environmental, nutritional and horticultural considerations. Journal of Cleaner Production, 86, 40-48. doi:10.1016/j.jclepro.2014.08.057Fornes, F., & Belda, R. M. (2017). Acidification with nitric acid improves chemical characteristics and reduces phytotoxicity of alkaline chars. Journal of Environmental Management, 191, 237-243. doi:10.1016/j.jenvman.2017.01.026Fornes, F., Belda, R. M., Fernández de Córdova, P., & Cebolla-Cornejo, J. (2017). Assessment of biochar and hydrochar as minor to major constituents of growing media for containerized tomato production. Journal of the Science of Food and Agriculture, 97(11), 3675-3684. doi:10.1002/jsfa.8227Fornes, F., Carrión, C., García-de-la-Fuente, R., Puchades, R., & Abad, M. (2010). Leaching composted lignocellulosic wastes to prepare container media: Feasibility and environmental concerns. Journal of Environmental Management, 91(8), 1747-1755. doi:10.1016/j.jenvman.2010.03.017GARCIADELAFUENTE, R., CARRION, C., BOTELLA, S., FORNES, F., NOGUERA, V., & ABAD, M. (2007). Biological oxidation of elemental sulphur added to three composts from different feedstocks to reduce their pH for horticultural purposes. Bioresource Technology, 98(18), 3561-3569. doi:10.1016/j.biortech.2006.11.008Genty, B., Briantais, J.-M., & Baker, N. R. (1989). The relationship between the quantum yield of photosynthetic electron transport and quenching of chlorophyll fluorescence. Biochimica et Biophysica Acta (BBA) - General Subjects, 990(1), 87-92. doi:10.1016/s0304-4165(89)80016-9Hoitink, H. A. J., Stone, A. G., & Han, D. Y. (1997). Suppression of Plant Diseases by Composts. HortScience, 32(2), 184-187. doi:10.21273/hortsci.32.2.184Libra, J. A., Ro, K. S., Kammann, C., Funke, A., Berge, N. D., Neubauer, Y., … Emmerich, K.-H. (2011). Hydrothermal carbonization of biomass residuals: a comparative review of the chemistry, processes and applications of wet and dry pyrolysis. Biofuels, 2(1), 71-106. doi:10.4155/bfs.10.81Mazuela, P., Salas, M. del C., & Urrestarazu, M. (2005). Vegetable Waste Compost as Substrate for Melon. Communications in Soil Science and Plant Analysis, 36(11-12), 1557-1572. doi:10.1081/css-200059054Méndez, A., Paz-Ferreiro, J., Gil, E., & Gascó, G. (2015). The effect of paper sludge and biochar addition on brown peat and coir based growing media properties. Scientia Horticulturae, 193, 225-230. doi:10.1016/j.scienta.2015.07.032Nieto, A., Gascó, G., Paz-Ferreiro, J., Fernández, J. M., Plaza, C., & Méndez, A. (2016). The effect of pruning waste and biochar addition on brown peat based growing media properties. Scientia Horticulturae, 199, 142-148. doi:10.1016/j.scienta.2015.12.012Sáez, J. A., Belda, R. M., Bernal, M. P., & Fornes, F. (2016). Biochar improves agro-environmental aspects of pig slurry compost as a substrate for crops with energy and remediation uses. Industrial Crops and Products, 94, 97-106. doi:10.1016/j.indcrop.2016.08.035Smith, B. R., Fisher, P. R., & Argo, W. R. (2004). Growth and Pigment Content of Container-grown Impatiens and Petunia in Relation to Root Substrate pH and Applied Micronutrient Concentration. HortScience, 39(6), 1421-1425. doi:10.21273/hortsci.39.6.1421Solaiman, Z. M., Murphy, D. V., & Abbott, L. K. (2011). Biochars influence seed germination and early growth of seedlings. Plant and Soil, 353(1-2), 273-287. doi:10.1007/s11104-011-1031-4Steiner, C., & Harttung, T. (2014). Biochar as a growing media additive and peat substitute. Solid Earth, 5(2), 995-999. doi:10.5194/se-5-995-2014Tian, Y., Sun, X., Li, S., Wang, H., Wang, L., Cao, J., & Zhang, L. (2012). Biochar made from green waste as peat substitute in growth media for Calathea rotundifola cv. Fasciata. Scientia Horticulturae, 143, 15-18. doi:10.1016/j.scienta.2012.05.018Vaughn, S. F., Eller, F. J., Evangelista, R. L., Moser, B. R., Lee, E., Wagner, R. E., & Peterson, S. C. (2015). Evaluation of biochar-anaerobic potato digestate mixtures as renewable components of horticultural potting media. Industrial Crops and Products, 65, 467-471. doi:10.1016/j.indcrop.2014.10.04

Understanding TERT promoter mutations: a common path to immortality

Telomerase (TERT) activation is a fundamental step in tumorigenesis. By maintaining telomere length, telomerase relieves a main barrier on cellular lifespan, enabling limitless proliferation driven by oncogenes. The recently discovered, highly recurrent mutations in the promoter of TERT are found in over 50 cancer types, and are the most common mutation in many cancers. Transcriptional activation of TERT, via promoter mutation or other mechanisms, is the rate-limiting step in production of active telomerase. Although TERT is expressed in stem cells, it is naturally silenced upon differentiation. Thus, the presence of TERT promoter mutations may shed light on whether a particular tumor arose from a stem cell or more differentiated cell type. It is becoming clear that TERT mutations occur early during cellular transformation, and activate the TERT promoter by recruiting transcription factors that do not normally regulate TERT gene expression. This review highlights the fundamental and widespread role of TERT promoter mutations in tumorigenesis, including recent progress on their mechanism of transcriptional activation. These somatic promoter mutations, along with germline variation in the TERT locus also appear to have significant value as biomarkers of patient outcome. Understanding the precise molecular mechanism of TERT activation by promoter mutation and germline variation may inspire novel cancer cell-specific targeted therapies for a large number of cancer patients.Support was provided from a generous gift from the Dabbiere family(RJB,AM,JFC), the Hana Jabsheh Research Initiative (RJB,AM,JFC), and NIH grants NCI P50CA097257 (RJB,AM,JFC), P01CA118816-06 (RJB,AM,JFC), R01HG003008 (HTR), and R01CA163336 (JSS). Additional support was provided from the Sontag Foundation Distinguished Scientist Award (JSS), Fundação para a Ciência e Tecnologia SFRH/BD/88220/2012 (AXM), IF/00601/2012 (BMC), Programa Operacional Regional do Norte (ON.2—O Novo Norte) (BMC), Quadro de Referência Estratégico Nacional (BMC), and Fundo Europeu de Desenvolvimento Regional (BMC).info:eu-repo/semantics/publishedVersio

Endothelial cells create a stem cell niche in glioblastoma by providing NOTCH ligands that nurture self-renewal of cancer stem-like cells

One important function of endothelial cells in glioblastoma multiforme (GBM) is to create a niche that helps promote self-renewal of cancer stem-like cells (CSLC). However, the underlying molecular mechanism for this endothelial function is not known. Since activation of NOTCH signaling has been found to be required for propagation of GBM CSLCs, we hypothesized that the GBM endothelium may provide the source of NOTCH ligands. Here, we report a corroboration of this concept with a demonstration that NOTCH ligands are expressed in endothelial cells adjacent to NESTIN and NOTCH receptor-positive cancer cells in primary GBMs. Coculturing human brain microvascular endothelial cells (hBMEC) or NOTCH ligand with GBM neurospheres promoted GBM cell growth and increased CSLC self-renewal. Notably, RNAi-mediated knockdown of NOTCH ligands in hBMECs abrogated their ability to induce CSLC self-renewal and GBM tumor growth, both in vitro and in vivo. Thus, our findings establish that NOTCH activation in GBM CSLCs is driven by juxtacrine signaling between tumor cells and their surrounding endothelial cells in the tumor microenvironment, suggesting that targeting both CSLCs and their niche may provide a novel strategy to deplete CSLCs and improve GBM treatment

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types

Thermographic imaging in sports and exercise medicine: a Delphi study and consensus statement on the measurement of human skin temperature

The importance of using infrared thermography (IRT) to assess skin temperature (tsk) is increasing in clinical settings. Recently, its use has been increasing in sports and exercise medicine; however, no consensus guideline exists to address the methods for collecting data in such situations. The aim of this study was to develop a checklist for the collection of tsk using IRT in sports and exercise medicine. We carried out a Delphi study to set a checklist based on consensus agreement from leading experts in the field. Panelists (n = 24) representing the areas of sport science (n = 8; 33%), physiology (n = 7; 29%), physiotherapy (n = 3; 13%) and medicine (n = 6; 25%), from 13 different countries completed the Delphi process. An initial list of 16 points was proposed which was rated and commented on by panelists in three rounds of anonymous surveys following a standard Delphi procedure. The panel reached consensus on 15 items which encompassed the participants’ demographic information, camera/room or environment setup and recording/analysis of tsk using IRT. The results of the Delphi produced the checklist entitled “Thermographic Imaging in Sports and Exercise Medicine (TISEM)” which is a proposal to standardize the collection and analysis of tsk data using IRT. It is intended that the TISEM can also be applied to evaluate bias in thermographic studies and to guide practitioners in the use of this technique