Vortex Structure Around a Magnetic Dot in Planar Superconductors

The problem of the giant vortex state around a magnetic dot which is embedded in a superconducting film is investigated. The full non-linear, self-consistent Ginzburg-Landau equations are solved numerically in order to calculate the free energy, the order parameter of the host superconductor, the internal magnetic field due to the supercurrents, the corresponding current density, the magnetization probed in the vicinity of the dot, and the normal electron density as a function of the various parameters of the system. We find that, as we increase the magnetic moment of the dot, higher flux quanta vortex states become energetically more favorable, as they can better compete with the external magnetic field via the Meissner effect. In addition to that, they progressively become closer to each other in energy with direct experimental consequences, i.e. physical quantities like magnetization may fluctuate when measured, for example, as a function of a uniform external magnetic field.Comment: text 21 pages (REVTEX), 8 figures available upon reques

Effects of columnar disorder on flux-lattice melting in high-temperature superconductors

The effect of columnar pins on the flux-lines melting transition in high-temperature superconductors is studied using Path Integral Monte Carlo simulations. We highlight the similarities and differences in the effects of columnar disorder on the melting transition in YBa$_2$Cu$_3$O$_{7-\delta}$ (YBCO) and the highly anisotropic Bi$_2$Sr$_2$CaCu$_2$O$_{8+\delta}$ (BSCCO) at magnetic fields such that the mean separation between flux-lines is smaller than the penetration length. For pure systems, a first order transition from a flux-line solid to a liquid phase is seen as the temperature is increased. When adding columnar defects to the system, the transition temperature is not affected in both materials as long as the strength of an individual columnar defect (expressed as a flux-line defect interaction) is less than a certain threshold for a given density of randomly distributed columnar pins. This threshold strength is lower for YBCO than for BSCCO. For higher strengths the transition line is shifted for both materials towards higher temperatures, and the sharp jump in energy, characteristic of a first order transition, gives way to a smoother and gradual rise of the energy, characteristic of a second order transition. Also, when columnar defects are present, the vortex solid phase is replaced by a pinned Bose glass phase and this is manifested by a marked decrease in translational order and orientational order as measured by the appropriate structure factors. For BSCCO, we report an unusual rise of the translational order and the hexatic order just before the melting transition. No such rise is observed in YBCO.Comment: 32 pages, 13 figures, revte

Integrative genomic analyses reveal an androgen-driven somatic alteration landscape in early-onset prostate cancer

Early-onset prostate cancer (EO-PCA) represents the earliest clinical manifestation of prostate cancer. To compare the genomic alteration landscapes of EO-PCA with "classical" (elderly-onset) PCA, we performed deep sequencing-based genomics analyses in 11 tumors diagnosed at young age, and pursued comparative assessments with seven elderly-onset PCA genomes. Remarkable age-related differences in structural rearrangement (SR) formation became evident, suggesting distinct disease pathomechanisms. Whereas EO-PCAs harbored a prevalence of balanced SRs, with a specific abundance of androgen-regulated ETS gene fusions including TMPRSS2:ERG, elderly-onset PCAs displayed primarily non-androgen-associated SRs. Data from a validation cohort of > 10,000 patients showed age-dependent androgen receptor levels and a prevalence of SRs affecting androgen-regulated genes, further substantiating the activity of a characteristic "androgen-type" pathomechanism in EO-PCA

Dietary phenethylisothiocyanate attenuates bowel inflammation in mice

<p>Abstract</p> <p>Background</p> <p>Phenethylisothiocyanate (PEITC) is produced by Brassica food plants. PEO is a <b>P</b>EITC <b>E</b>ssential <b>O</b>il containing >95% natural PEITC. PEITC is known to produce various health benefits but its effect in alleviation of ulcerative colitis signs is unknown.</p> <p>Results</p> <p>In two efficacy studies (acute and chronic) oral administration of PEO was effective at remitting acute and chronic signs of ulcerative colitis (UC) in mice. Disease activity, histology and biochemical characteristics were measured in the treated animals and were compared with appropriate controls. PEO treatment significantly improved body weights and stool consistency as well as decreased intestinal bleeding. PEO treatment also reduced mucosal inflammation, depletion of goblet cells and infiltration of inflammatory cells. Attenuation of proinflammatory interleukin1β production was observed in the colons of PEO-treated animals. Expression analyses were also carried out for immune function related genes, transcription factors and cytokines in lipopolysaccharide-activated mouse macrophage cells. PEO likely affects an intricate network of immune signaling genes including a novel concentration dependent reduction of total cellular Signal Transducer and Activator of Transcription 1 (STAT1) as well as nuclear phosphorylated-STAT1 (activated form of STAT1). A PEO-concentration dependent decrease of mRNA of C-X-C motif ligand 10 (a STAT1 responsive chemokine) and Interleukin 6 were also observed.</p> <p>Conclusions</p> <p>PEO might be a promising candidate to develop as a treatment for ulcerative colitis patients. The disease attenuation by PEO is likely associated with suppression of activation of STAT1 transcription and inhibition of pro-inflammatory cytokines.</p

Primary Postnatal Dorsal Root Ganglion Culture from Conventionally Slaughtered Calves

Neurological disorders in ruminants have an important impact on veterinary health, but very few host-specific in vitro models have been established to study diseases affecting the nervous system. Here we describe a primary neuronal dorsal root ganglia (DRG) culture derived from calves after being conventionally slaughtered for food consumption. The study focuses on the in vitro characterization of bovine DRG cell populations by immunofluorescence analysis. The effects of various growth factors on neuron viability, neurite outgrowth and arborisation were evaluated by morphological analysis. Bovine DRG neurons are able to survive for more than 4 weeks in culture. GF supplementation is not required for neuronal survival and neurite outgrowth. However, exogenously added growth factors promote neurite outgrowth. DRG cultures from regularly slaughtered calves represent a promising and sustainable host specific model for the investigation of pain and neurological diseases in bovines

Pan-cancer analysis of whole genomes

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale(1-3). Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter(4); identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation(5,6); analyses timings and patterns of tumour evolution(7); describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity(8,9); and evaluates a range of more-specialized features of cancer genomes(8,10-18).Peer reviewe

Autothermal reforming of palm empty fruit bunch bio-oil: thermodynamic modelling

This work focuses on thermodynamic analysis of the autothermal reforming of palm empty fruit bunch (PEFB) bio-oil for the production of hydrogen and syngas. PEFB bio-oil composition was simulated using bio-oil surrogates generated from a mixture of acetic acid, phenol, levoglucosan, palmitic acid and furfural. A sensitivity analysis revealed that the hydrogen and syngas yields were not sensitive to actual bio-oil composition, but were determined by a good match of molar elemental composition between real bio-oil and surrogate mixture. The maximum hydrogen yield obtained under constant reaction enthalpy and pressure was about 12 wt% at S/C = 1 and increased to about 18 wt% at S/C = 4; both yields occurring at equivalence ratio Φ of 0.31. The possibility of generating syngas with varying H2 and CO content using autothermal reforming was analysed and application of this process to fuel cells and Fischer-Tropsch synthesis is discussed. Using a novel simple modelling methodology, reaction mechanisms were proposed which were able to account for equilibrium product distribution. It was evident that different combinations of reactions could be used to obtain the same equilibrium product concentrations. One proposed reaction mechanism, referred to as the ‘partial oxidation based mechanism’ involved the partial oxidation reaction of the bio-oil to produce hydrogen, with the extent of steam reforming and water gas shift reactions varying depending on the amount of oxygen used. Another proposed mechanism, referred to as the ‘complete oxidation based mechanism’ was represented by thermal decomposition of about 30% of bio-oil and hydrogen production obtained by decomposition, steam reforming, water gas shift and carbon gasification reactions. The importance of these mechanisms in assisting in the eventual choice of catalyst to be used in a real ATR of PEFB bio-oil process was discussed

Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing

Chromothripsis is a mutational phenomenon characterized by massive, clustered genomic rearrangements that occurs in cancer and other diseases. Recent studies in selected cancer types have suggested that chromothripsis may be more common than initially inferred from low-resolution copy-number data. Here, as part of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA), we analyze patterns of chromothripsis across 2,658 tumors from 38 cancer types using whole-genome sequencing data. We find that chromothripsis events are pervasive across cancers, with a frequency of more than 50% in several cancer types. Whereas canonical chromothripsis profiles display oscillations between two copy-number states, a considerable fraction of events involve multiple chromosomes and additional structural alterations. In addition to non-homologous end joining, we detect signatures of replication-associated processes and templated insertions. Chromothripsis contributes to oncogene amplification and to inactivation of genes such as mismatch-repair-related genes. These findings show that chromothripsis is a major process that drives genome evolution in human cancer