The plasma boundary in Single Helical Axis RFP plasmas

Single Helical Axis (SHAx) states obtained in high current reversed field pinch (RFP) plasmas display, aside from a dominant mode in the m=1 spectrum, also a dominant m=0 mode, with the same toroidal mode number as the m=1 one. The two modes have a fixed phase relationship. The island chain created by the m=0 mode across the reversal surface gives rise, at shallow reversal of the toroidal field, to an X-point structure which separates the last closed flux surface from the first wall, creating a divertor-like configuration. The plasma-wall interaction is found to be related to the connection length of the field lines intercepting the wall, which displays a pattern modulated by the dominant mode toroidal periodicity. This configuration, which occurs only for shallow toroidal field reversal, could be exploited to realize an island divertor in analogy to stellarators.Comment: 12 pages, 9 figures Submitted to Nuclear Fusio

Identification and expression analysis of microRNAs and targets in the biofuel crop sugarcane

<p>Abstract</p> <p>Background</p> <p>MicroRNAs (miRNAs) are small regulatory RNAs, some of which are conserved in diverse plant genomes. Therefore, computational identification and further experimental validation of miRNAs from non-model organisms is both feasible and instrumental for addressing miRNA-based gene regulation and evolution. Sugarcane (<it>Saccharum spp</it>.) is an important biofuel crop with publicly available expressed sequence tag and genomic survey sequence databases, but little is known about miRNAs and their targets in this highly polyploid species.</p> <p>Results</p> <p>In this study, we have computationally identified 19 distinct sugarcane miRNA precursors, of which several are highly similar with their sorghum homologs at both nucleotide and secondary structure levels. The accumulation pattern of mature miRNAs varies in organs/tissues from the commercial sugarcane hybrid as well as in its corresponding founder species <it>S. officinarum </it>and <it>S. spontaneum</it>. Using sugarcane <it>MIR827 </it>as a query, we found a novel <it>MIR827 </it>precursor in the sorghum genome. Based on our computational tool, a total of 46 potential targets were identified for the 19 sugarcane miRNAs. Several targets for highly conserved miRNAs are transcription factors that play important roles in plant development. Conversely, target genes of lineage-specific miRNAs seem to play roles in diverse physiological processes, such as <it>SsCBP1</it>. <it>SsCBP1 </it>was experimentally confirmed to be a target for the monocot-specific miR528. Our findings support the notion that the regulation of <it>SsCBP1 </it>by miR528 is shared at least within graminaceous monocots, and this miRNA-based post-transcriptional regulation evolved exclusively within the monocots lineage after the divergence from eudicots.</p> <p>Conclusions</p> <p>Using publicly available nucleotide databases, 19 sugarcane miRNA precursors and one new sorghum miRNA precursor were identified and classified into 14 families. Comparative analyses between sugarcane and sorghum suggest that these two species retain homologous miRNAs and targets in their genomes. Such conservation may help to clarify specific aspects of miRNA regulation and evolution in the polyploid sugarcane. Finally, our dataset provides a framework for future studies on sugarcane RNAi-dependent regulatory mechanisms.</p

Equilibrium reconstruction for Single Helical Axis reversed field pinch plasmas

Single Helical Axis (SHAx) configurations are emerging as the natural state for high current reversed field pinch (RFP) plasmas. These states feature the presence of transport barriers in the core plasma. Here we present a method for computing the equilibrium magnetic surfaces for these states in the force-free approximation, which has been implemented in the SHEq code. The method is based on the superposition of a zeroth order axisymmetric equilibrium and of a first order helical perturbation computed according to Newcomb's equation supplemented with edge magnetic field measurements. The mapping of the measured electron temperature profiles, soft X-ray emission and interferometric density measurements on the computed magnetic surfaces demonstrates the quality of the equilibrium reconstruction. The procedure for computing flux surface averages is illustrated, and applied to the evaluation of the thermal conductivity profile. The consistency of the evaluated equilibria with Ohm's law is also discussed.Comment: Submitted to Plasma Physics and Controlled Fusio

Phosphorylation-regulated degradation of the tumor-suppressor form of PED by chaperone-mediated autophagy in lung cancer cells

PED/PEA-15 is a death effector domain (DED) family member with a variety of effects on cell growth and metabolism. To get further insight into the role of PED in cancer, we aimed to find new PED interactors. Using tandem affinity purification, we identified HSC70 (Heat Shock Cognate Protein of 70kDa)-which, among other processes, is involved in chaperone-mediated autophagy (CMA)-as a PED-interacting protein. We found that PED has two CMA-like motifs (i.e., KFERQ), one of which is located within a phosphorylation site, and demonstrate that PED is a bona fide CMA substrate and the first example in which phosphorylation modifies the ability of HSC70 to access KFERQ-like motifs and target the protein for lysosomal degradation. Phosphorylation of PED switches its function from tumor suppression to tumor promotion, and we show that HSC70 preferentially targets the unphosphorylated form of PED to CMA. Therefore, we propose that the up-regulated CMA activity characteristic of most types of cancer cell enhances oncogenesis by shifting the balance of PED function toward tumor promotion. This mechanism is consistent with the notion of a therapeutic potential for targeting CMA in cancer, as inhibition of this autophagic pathway may help restore a physiological ratio of PED form

Genetic variability and population structuring in the European Lanner Falcon Falco biarmicus feldeggii

We analysed variation in 10 polymorphic microsatellites and a variable portion of control region of mtDNA in 24 specimens from 3 populations of European Lanner Falcon Falco biarmicus feldeggii living in Sicily, continental Italy and the Balkan area to assess species' genetic diversity and population structure in the poorly investigated range of this threatened subspecies. We considered also a dataset of previously published mtDNA sequences of the other Lanner Falcon subspecies and of Hierofalco subgenus members (F. cherrug, F. rusticolus and F. jugger) to outline the genetic variation in the region on a wide-ranging basis. Regard with mtDNA we identified 6 haplotypes from our 24 European Lanner Falcon specimens, 3 of which were new and unique (1 Sicilian, 2 Balkans) and the 3 others already known and shared with other Hierofalcons. The 62.5% of our sample, including 14 of Sicilians and one Apulia specimen, belonged to haplotype H_24 shared with F. c. cherrug, F. rusticolus and F. jugger. MtDNA analyses of European Lanner Falcons showed a dispersed pattern of our specimens inside the main Hierofalco clades and haplo-groups in a way congruent to what found in recent literature. These analyses confirmed that none of the Hierofalcons form a monophyletic group, nonetheless the Lanner Falcons can be subdivided in two major Palaearctic (F. b. feldeggii, F. b. erlangeri and F. b. tanypterus) and sub-Sahara African (F. b. biarmicus and F. b. abyssinicus) clades. Microsatellites analysis yielded a first outline of population genetic structure, with genetic identity between continental Italy and Sicily and a moderate degree of differentiation of the Balkan area with Sicily and continental Italy. The 3 populations did not show significant departure from Hardy-Weinberg equilibrium, with low values of the inbreeding coefficients and had allele richness and haplotype diversity consistent with literature. Microsatellites analysis (Nm, frequency of private alleles) suggests a gene flow among the three examined populations and the connection of Sicilian population to those of mainland

Statistical features of edge turbulence in RFX-mod from Gas Puffing Imaging

Plasma density fluctuations in the edge plasma of the RFX-mod device are measured through the Gas Puffing Imaging Diagnostics. Statistical features of the signal are quantified in terms of the Probability Distribution Function (PDF), and computed for several kinds of discharges. The PDFs from discharges without particular control methods are found to be adequately described by a Gamma function, consistently with the recent results by Graves et al [J.P. Graves, et al, Plasma Phys. Control. Fusion 47, L1 (2005)]. On the other hand, pulses with external methods for plasma control feature modified PDFs. A first empirical analysis suggests that they may be interpolated through a linear combination of simple functions. An inspection of the literature shows that this kind of PDFs is common to other devices as well, and has been suggested to be due to the simultaneous presence of different mechanisms driving respectively coherent bursts and gaussian background turbulence. An attempt is made to relate differences in the PDFs to plasma conditions such as the local shift of the plasma column. A simple phenomenological model to interpret the nature of the PDF and assign a meaning to its parameters is also developed.Comment: 27 pages. Published in PPC

Expanding the medical physicist curricular and professional programme to include Artificial Intelligence

Purpose: To provide a guideline curriculum related to Artificial Intelligence (AI), for the education and training of European Medical Physicists (MPs). Materials and methods: The proposed curriculum consists of two levels: Basic (introducing MPs to the pillars of knowledge, development and applications of AI, in the context of medical imaging and radiation therapy) and Advanced. Both are common to the subspecialties (diagnostic and interventional radiology, nuclear medicine, and radiation oncology). The learning outcomes of the training are presented as knowledge, skills and competences (KSC approach). Results: For the Basic section, KSCs were stratified in four subsections: (1) Medical imaging analysis and AI Basics; (2) Implementation of AI applications in clinical practice; (3) Big data and enterprise imaging, and (4) Quality, Regulatory and Ethical Issues of AI processes. For the Advanced section instead, a common block was proposed to be further elaborated by each subspecialty core curriculum. The learning outcomes were also translated into a syllabus of a more traditional format, including practical applications. Conclusions: This AI curriculum is the first attempt to create a guideline expanding the current educational framework for Medical Physicists in Europe. It should be considered as a document to top the sub-specialties' curriculums and adapted by national training and regulatory bodies. The proposed educational program can be implemented via the European School of Medical Physics Expert (ESMPE) course modules and - to some extent - also by the national competent EFOMP organizations, to reach widely the medical physicist community in Europe.Peer reviewe

Small RNA Profile in Moso Bamboo Root and Leaf Obtained by High Definition Adapters

Moso bamboo (Phyllostachy heterocycla cv. pubescens L.) is an economically important fast-growing tree. In order to gain better understanding of gene expression regulation in this important species we used next generation sequencing to profile small RNAs in leaf and roots of young seedlings. Since standard kits to produce cDNA of small RNAs are biased for certain small RNAs, we used High Definition adapters that reduce ligation bias. We identified and experimentally validated five new microRNAs and a few other small non-coding RNAs that were not microRNAs. The biological implication of microRNA expression levels and targets of microRNAs are discussed

Search for NTRK1 proto-oncogene rearrangements in human thyroid tumours originated after therapeutic radiation

Rearrangements of NTRK1 proto-oncogene were detected in ‘spontaneous’ papillary thyroid carcinomas with a frequency varying from 5 to 25% in different studies. These rearrangements result in the formation of chimaeric genes composed of the tyrosine kinase domain of NTRK1 fused to 5′ sequences of different genes. To investigate if the NTRK1 gene plays a role in radiation-induced thyroid carcinogenesis, we looked for the presence of NTRK1 -activating rearrangements in 32 human thyroid tumours (16 follicular adenomas, 14 papillary carcinomas and two lymph-node metastases of papillary thyroid carcinomas) from patients who had received external radiation, using the reverse transcription polymerase chain reaction, Southern blot and direct sequencing techniques. These data were compared with those obtained in a series of 28 ‘spontaneous’ benign and malignant thyroid tumours, collected from patients without a history of radiation exposure and four in vitro culture cell lines derived from ‘spontaneous’ thyroid cancers. Our results concerning the radiation-associated tumours showed that only rearrangements between NTRK1 and TPM3 genes (TRK oncogene) were detected in 2/14 papillary carcinomas and in one lymph-node metastasis of one of these papillary thyroid carcinomas. All the radiation-associated adenomas were negative. In the ‘spontaneous’ tumours, only one of the 14 papillary carcinomas and one of the four in vitro culture cell lines, derived from a papillary carcinoma, presented a NTRK1 rearrangement also with the TPM3 gene. Twenty-five of this series of radiation-associated tumours were previously studied for the ras and RET/PTC oncogenes. In conclusion, our data: (a) show that the overall frequency of NTRK1 rearrangements is similar between radiation-associated (2/31: 6%) and ‘spontaneous’ epithelial thyroid tumours (2/32: 6%). The frequency, if we consider exclusively the papillary carcinomas, is in both cases 12%; (b) show that the TRK oncogene plays a role in the development of a minority of radiation-associated papillary thyroid carcinomas but not in adenomas; and (c) confirm that RET/PTC rearrangements are the major genetic alteration associated with ionizing radiation-induced thyroid tumorigenesis. © 2000 Cancer Research Campaig

A short in-frame deletion in NTRK1 tyrosine kinase domain caused by a novel splice site mutation in a patient with congenital insensitivity to pain with anhidrosis

Background: Congenital insensitivity to pain with anhidrosis (CIPA) is a rare autosomal recessive genetic disease characterized by the lack of reaction to noxious stimuli and anhidrosis. It is caused by mutations in the NTRK1 gene, which encodes the high affinity tyrosine kinase receptor I for Neurotrophic Growth Factor (NGF). -- Case Presentation: We present the case of a female patient diagnosed with CIPA at the age of 8 months. The patient is currently 6 years old and her psychomotor development conforms to her age (RMN, SPECT and psychological study are in the range of normality). PCR amplification of DNA, followed by direct sequencing, was used to investigate the presence of NTRK1 gene mutations. Reverse transcriptase (RT)-PCR amplification of RNA, followed by cloning and sequencing of isolated RT-PCR products was used to characterize the effect of the mutations on NTRK1 mRNA splicing. The clinical diagnosis of CIPA was confirmed by the detection of two splice-site mutations in NTRK1, revealing that the patient was a compound heterozygote at this gene. One of these alterations, c.574+1G > A, is located at the splice donor site of intron 5. We also found a second mutation, c.2206-2 A > G, not previously reported in the literature, which is located at the splice acceptor site of intron 16. Each parent was confirmed to be a carrier for one of the mutations by DNA sequencing analysis. It has been proposed that the c.574+1G > A mutation would cause exon 5 skipping during NTRK1 mRNA splicing. We could confirm this prediction and, more importantly, we provide evidence that the novel c.2206-2A > G mutation also disrupts normal NTRK1 splicing, leading to the use of an alternative splice acceptor site within exon 17. As a consequence, this mutation would result in the production of a mutant NTRK1 protein with a seven aminoacid in-frame deletion in its tyrosine kinase domain. --Conclusions: We present the first description of a CIPA-associated NTRK1 mutation causing a short interstitial deletion in the tyrosine kinase domain of the receptor. The possible phenotypical implications of this mutation are discussed.This investigation was supported by the Instituto de Salud Carlos III and the Fundacion Vasca de Innovacion e Investigacion Sanitarias (funds to ES)