Effects of the equilibrium model on impurity transport in tokamaks

Gyrokinetic simulations of ion temperature gradient mode and trapped electron mode driven impurity transport in a realistic tokamak geometry are presented and compared with results using simplified geometries. The gyrokinetic results, obtained with the GENE code in both linear and non-linear modes are compared with data and analysis for a dedicated impurity injection discharge at JET. The impact of several factors on heat and particle transport is discussed, lending special focus to tokamak geometry and rotational shear. To this end, results using s-alpha and concentric circular equilibria are compared with results with magnetic geometry from a JET experiment. To further approach experimental conditions, non-linear gyrokinetic simulations are performed with collisions and a carbon background included. The impurity peaking factors, computed by finding local density gradients corresponding to zero particle flux, are discussed. The impurity peaking factors are seen to be reduced by a factor of ~2 in realistic geometry compared with the simplified geometries, due to a reduction of the convective pinch. It is also seen that collisions reduce the peaking factor for low-Z impurities, while increasing it for high charge numbers, which is attributed to a shift in the transport spectra towards higher wavenumbers with the addition of collisions. With the addition of roto-diffusion, an overall reduction of the peaking factors is observed, but this decrease is not sufficient to explain the flat carbon profiles seen at JET.Comment: 19 pages, 9 figures (17 subfigures

En kritisk litteraturgjennomgang: Beskytter cricoidtrykk mot aspirasjon ved endotrakeal intubasjon av ikke fastende pasient?

Master i spesialsykepleie - Nord universitet 202

Fluid and gyrokinetic modelling of particle transport in plasmas with hollow density profiles

Hollow density profiles occur in connection with pellet fuelling and L to H transitions. A positive density gradient could potentially stabilize the turbulence or change the relation between convective and diffusive fluxes, thereby reducing the turbulent transport of particles towards the center, making the fuelling scheme inefficient. In the present work, the particle transport driven by ITG/TE mode turbulence in regions of hollow density profiles is studied by fluid as well as gyrokinetic simulations. The fluid model used, an extended version of the Weiland transport model, Extended Drift Wave Model (EDWM), incorporates an arbitrary number of ion species in a multi-fluid description, and an extended wavelength spectrum. The fluid model, which is fast and hence suitable for use in predictive simulations, is compared to gyrokinetic simulations using the code GENE. Typical tokamak parameters are used based on the Cyclone Base Case. Parameter scans in key plasma parameters like plasma β, R/LT , and magnetic shear are investigated. It is found that β in particular has a stabilizing effect in the negative R/Ln region, both nonlinear GENE and EDWM show a decrease in inward flux for negative R/Ln and a change of direction from inward to outward for positive R/Ln . This might have serious consequences for pellet fuelling of high β plasmas

Identifying Structural Variation in Haploid Microbial Genomes from Short-Read Resequencing Data Using Breseq

Mutations that alter chromosomal structure play critical roles in evolution and disease, including in the origin of new lifestyles and pathogenic traits in microbes. Large-scale rearrangements in genomes are often mediated by recombination events involving new or existing copies of mobile genetic elements, recently duplicated genes, or other repetitive sequences. Most current software programs for predicting structural variation from short-read DNA resequencing data are intended primarily for use on human genomes. They typically disregard information in reads mapping to repeat sequences, and significant post-processing and manual examination of their output is often required to rule out false-positive predictions and precisely describe mutational events. Results: We have implemented an algorithm for identifying structural variation from DNA resequencing data as part of the breseq computational pipeline for predicting mutations in haploid microbial genomes. Our method evaluates the support for new sequence junctions present in a clonal sample from split-read alignments to a reference genome, including matches to repeat sequences. Then, it uses a statistical model of read coverage evenness to accept or reject these predictions. Finally, breseq combines predictions of new junctions and deleted chromosomal regions to output biologically relevant descriptions of mutations and their effects on genes. We demonstrate the performance of breseq on simulated Escherichia coli genomes with deletions generating unique breakpoint sequences, new insertions of mobile genetic elements, and deletions mediated by mobile elements. Then, we reanalyze data from an E. coli K-12 mutation accumulation evolution experiment in which structural variation was not previously identified. Transposon insertions and large-scale chromosomal changes detected by breseq account for similar to 25% of spontaneous mutations in this strain. In all cases, we find that breseq is able to reliably predict structural variation with modest read-depth coverage of the reference genome (>40-fold). Conclusions: Using breseq to predict structural variation should be useful for studies of microbial epidemiology, experimental evolution, synthetic biology, and genetics when a reference genome for a closely related strain is available. In these cases, breseq can discover mutations that may be responsible for important or unintended changes in genomes that might otherwise go undetected.U.S. National Institutes of Health R00-GM087550U.S. National Science Foundation (NSF) DEB-0515729NSF BEACON Center for the Study of Evolution in Action DBI-0939454Cancer Prevention & Research Institute of Texas (CPRIT) RP130124University of Texas at Austin startup fundsUniversity of Texas at AustinCPRIT Cancer Research TraineeshipMolecular Bioscience

Preclinical efficacy of hK2 targeted [177Lu]hu11B6 for prostate cancer theranostics

Androgen ablating drugs increase life expectancy in men with metastatic prostate cancer, but resistance inevitably develops. In a majority of these recurrent tumors, the androgen axis is reactivated in the form of increased androgen receptor (AR) expression. Targeting proteins that are expressed as a down-stream effect of AR activity is a promising rationale for management of this disease. The humanized IgG1 antibody hu11B6 internalizes into prostate and prostate cancer (PCa) cells by binding to the catalytic cleft of human kallikrein 2 (hK2), a prostate specific enzyme governed by the AR-pathway. In a previous study, hu11B6 conjugated with Actinium-225 (225Ac), a high linear energy transfer (LET) radionuclide, was shown to generate an AR-upregulation driven feed-forward mechanism that is believed to enhance therapeutic efficacy. We assessed the efficacy of hu11B6 labeled with a low LET beta-emitter, Lutetium-177 (177Lu) and investigated whether similar tumor killing and AR-enhancement is produced. Moreover, single-photon emission computed tomography (SPECT) imaging of 177Lu is quantitatively accurate and can be used to perform treatment planning. [177Lu]hu11B6 therefore has significant potential as a theranostic agent. Materials and Methods: Subcutaneous PCa xenografts (LNCaP s.c.) were grown in male mice. Biokinetics at 4-336 h post injection and uptake as a function of the amount of hu11B6 injected at 72 h were studied. Over a 30 to 120-day treatment period the therapeutic efficacy of different activities of [177Lu]hu11B6 were assessed by volumetric tumor measurements, blood cell counts, molecular analysis of the tumor as well as SPECT/CT imaging. Organ specific mean absorbed doses were calculated, using a MIRD-scheme, based on biokinetic data and rodent specific S-factors from a modified MOBY phantom. Tumor tissues of treated xenografts were immunohistochemically (IHC) stained for Ki-67 (proliferation) and AR, SA-β-gal activity (senescence) and analyzed by digital autoradiography (DAR). Results: Organ-to-blood and tumor-to-blood ratios were independent of hu11B6 specific activity except for the highest amount of antibody (150 µg). Tumor accumulation of [177Lu]hu11B6 peaked at 168 h with a specific uptake of 29 ± 9.1 percent injected activity per gram (%IA/g) and low accumulation in normal organs except in the submandibular gland (15 ± 4.5 %IA/g), attributed to a cross-reaction with mice kallikreins in this organ, was seen. However, SPECT imaging with therapeutic amounts of [177Lu]hu11B6 revealed no peak in tumor accumulation at 7 d, probably due to cellular retention of 177Lu and decreasing tumor volumes. For [177Lu]hu11B6 treated mice, tumor decrements of up to 4/5 of the initial tumor volume and reversible myelotoxicity with a nadir at 12 d were observed after a single injection. Tumor volume reduction correlated with injected activity and the absorbed dose. IHC revealed retained expression of AR throughout treatment and that Ki-67 staining reached a nadir at 9-14 d which coincided with high SA- β-gal activity (14 d). Quantification of nuclei staining showed that Ki-67 expression correlated negatively with activity uptake. AR expression levels in cells surviving therapy compared to previous timepoints and to controls at 30 d were significantly increased (p = 0.017). Conclusions: This study shows that hu11B6 labeled with the low LET beta-emitting radionuclide 177Lu can deliver therapeutic absorbed doses to prostate cancer xenografts with transient hematological side-effects. The tumor response correlated with the absorbed dose both on a macro and a small scale dosimetric level. Analysis of AR staining showed that AR protein levels increased late in the study suggesting a therapeutic mechanism, a feed forward mechanism coupled to AR driven response to DNA damage or clonal lineage selection, similar to that reported in high LET alpha-particle therapy using 225Ac labeled hu11B6, however emerging at a later timepoint

Soil organic matter molecular composition and state of decomposition in three locations of the European Arctic

Increased mineralization of the organic matter (OM) stored in permafrost is expected to constitute the largest additional global warming potential from terrestrial ecosystems exposed to a warmer climate. Chemical composition of permafrost OM is thought to be a key factor controlling the sensitivity of decomposition to warming. Our objective was to characterise OM from permafrost soils of the European Arctic: two mineral soils—Adventdalen, Svalbard, Norway and Vorkuta, northwest Russia— and a ‘‘palsa’’ (ice-cored peat mound patterning in heterogeneous permafrost landscapes) soil in Neiden, northern Norway, in terms of molecular composition and state of decomposition. At all sites, the OM stored in the permafrost was at an advanced stage of decomposition, although somewhat less so in the palsa peat. By comparing permafrost and active layers, we found no consistent effect of depth or permafrost on soil organic matter (SOM) chemistry across sites. The permafrost-affected palsa peat displayed better preservation of plant material in the deeper layer, as indicated by increasing contribution of lignin carbon to total carbon with depth, associated to decreasing acid (Ac) to aldehyde (Al) ratio of the syringyl (S) and vanillyl (V) units, and increasing S/V and contribution of plant-derived sugars. By contrast, in Adventdalen, the Ac/Al ratio of lignin and the Alkyl C to O-alkyl C ratio in the NMR spectra increased with depth, which suggests less oxidized SOM in the active layer compared to the permafrost layer. In Vorkuta, SOM characteristics in the permafrost profile did not change substantially with depth, probably due to mixing of soil layers by cryoturbation. The composition and state of decomposition of SOM appeared to be site-specific, in particular bound to the prevailing organic or mineral nature of soil when attempting to predict the SOM proneness to degradation. The occurrence of processes such as palsa formation in organic soils and cryoturbation should be considered when up-scaling and predicting the responses of OM to climate change in arctic soils.acceptedVersio

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I denna uppsats undersöks hur räntan påverkar priset på bostäder på den svenska marknaden, och hur ett avskaffat ränteavdrag skulle påverka prisutvecklingen på lång sikt och på kort sikt. Teorin säger att bostadspriset styrs av en mängd olika faktorer och är trögrörligt vid förändringar av de förklarande faktorerna. Räntekostnader gör bostadsinvesteringar och bostadsinnehav dyrare och har ett negativt samband på priset. I uppsatsens första del ges en beskrivning av bolånemarknaden och svenska hushålls lån och skuldsättning. Detta görs för att ge en bild av ränteavdragets omfattningen och betydelse för olika grupper, och för att kunna ge en mer detaljerad analys av hur ett avskaffat ränteavdrag skulle påverka bostadspriser och hushållens skuldsättning. Metoden som används är ekonometrisk regression baserad på tidigare vedertagna metoder för undersökningar av bostadsmarknader. Dels undersöks ett långsiktigt linjärt samband mellan ränta och bostadspriset genom Engle-Grangers kointegrationstest, och dels konstrueras en modell som avser att beskriva prisdynamiken på kortare sikt. Datan är sekundärdata från SCB, Macrobond och Valueguard där ett månadsprisindex mellan åren 2005-2014 på bostadsrätter och småhus används som den förklarade variabeln. Som förklarande variabler används ränta, inkomst och finansiella tillgångar. Resultaten visar att kointegrationstest för att skatta det långsiktiga sambandet mellan räntan och priset är olämplig för perioden vi har undersökt. Den kortsiktiga prissättningsmodellen visar att räntan har ett negativt samband på priset, men att förändringen i priset sker med en fördröjning. Detta resultat styrker teorin om att priser på bostadsmarknaden är trögrörliga. Till skillnad från tidigare studier på svenska bostadsmarknaden inkluderas i denna undersökning bostadsrätter och underlaget består av månatlig data istället för kvartalsdata. Vi får således fler observationer att använda till ekonometrisk analys och kan undersöka dynamiken på en allt snabbare bostadsmarknad

Community Seismic Network

The article describes the design of the Community Seismic Network, which is a dense open seismic network based on low cost sensors. The inputs are from sensors hosted by volunteers from the community by direct connection to their personal computers, or through sensors built into mobile devices. The server is cloud-based for robustness and to dynamically handle the load of impulsive earthquake events. The main product of the network is a map of peak acceleration, delivered within seconds of the ground shaking. The lateral variations in the level of shaking will be valuable to first responders, and the waveform information from a dense network will allow detailed mapping of the rupture process. Sensors in buildings may be useful for monitoring the state-of-health of the structure after major shaking

Particle transport in ion and electron scale turbulence

Micro turbulent modes have important and non-trivial effects on transport in tokamaks. This paper deals with transport of main ions and impurities in ion and electron scale turbulence, driven by ion and electron temperature gradients, and trapped electrons. Using the gyrokinetic Vlasov code GENE, results are obtained from both nonlinear and quasi-linear simulations. The transport properties are quantified by calculating the gradient of zero particle flux for steady state in source free regions of the plasma. The results are compared and contrasted with results obtained using a computationally efficient fluid model. Of particular interest are conditions of steep gradients, relevant to e.g. transport barrier conditions. Further, results from a simple s–α geometry are compared with results obtained using a JET-like magnetic equilibrium, and the effects on transport investigated