LibCPIXE: a PIXE simulation open-source library for multilayered samples

Most particle induced X-ray emission (PIXE) data analysis codes are not focused on handling multilayered samples. We have developed an open-source library called "LibCPIXE", for PIXE data analysis. It is written in standard C and implements functions for simulating X-ray yields of PIXE spectra taken from arbitrary samples, including multilayered targets. The library is designed to be fast, portable, modular and scalable, as well as to facilitate its incorporation into any existing program. In order to demonstrate the capabilities of the library, a program called CPIXE was developed and used to analyze various real samples involving both bulk and layered samples. Just as the library, the CPIXE source code is freely available under the General Public License. We demonstrate that it runs both under GNU/Linux systems as well as under MS Windows. There is in principle no limitation to port it to other platforms

Application of Minimal Subtraction Renormalization to Crossover Behavior near the 3^3He Liquid-Vapor Critical Point

Parametric expressions are used to calculate the isothermal susceptibility, specific heat, order parameter, and correlation length along the critical isochore and coexistence curve from the asymptotic region to crossover region. These expressions are based on the minimal-subtraction renormalization scheme within the $\phi^4$ model. Using two adjustable parameters in these expressions, we fit the theory globally to recently obtained experimental measurements of isothermal susceptibility and specific heat along the critical isochore and coexistence curve, and early measurements of coexistence curve and light scattering intensity along the critical isochore of $^3$He near its liquid-vapor critical point. The theory provides good agreement with these experimental measurements within the reduced temperature range $|t| \le 2\times 10^{-2}$

Genomic and protein expression analysis reveals flap endonuclease 1 (FEN1) as a key biomarker in breast and ovarian cancer

FEN1 has key roles in Okazaki fragment maturation during replication, long patch base excision repair, rescue of stalled replication forks, maintenance of telomere stability and apoptosis. FEN1 may be dysregulated in breast and ovarian cancers and have clinicopathological significance in patients. We comprehensively investigated FEN1 mRNA expression in multiple cohorts of breast cancer [training set (128), test set (249), external validation (1952)]. FEN1 protein expression was evaluated in 568 oestrogen receptor (ER) negative breast cancers, 894 ER positive breast cancers and 156 ovarian epithelial cancers. FEN1 mRNA overexpression was highly significantly associated with high grade (p= 4.89 x 10 - 57) , high mitotic index (p= 5.25 x 10 - 28), pleomorphism (p= 6.31 x 10-19), ER negative (p= 9.02 x 10-35 ), PR negative (p= 9.24 x 10-24 ), triple negative phenotype (p= 6.67 x 10-21) , PAM50.Her2 (p=5.19 x 10-13 ), PAM50.Basal (p=2.7 x 10-41), PAM50.LumB (p=1.56 x 10-26), integrative molecular cluster 1 (intClust.1) ( p=7.47 x 10-12), intClust.5 (p=4.05 x 10-12) and intClust. 10 (p=7.59 x 10-38 ) breast cancers. FEN1 mRNA overexpression is associated with poor breast cancer specific survival in univariate (p=4.4 x 10-16) and multivariate analysis (p=9.19 x 10-7). At the protein level, in ER positive tumours , FEN1 overexpression remains significantly linked to high grade, high mitotic index and pleomorphism (ps< 0.01). In ER negative tumours, high FEN1 is significantly associated with pleomorphism, tumour type, lymphovascular invasion, triple negative phenotype, EGFR and HER2 expression (ps<0.05). In ER positive as well as in ER negative tumours, FEN1 protein over expression is associated with poor survival in univariate and multivariate analysis (ps<0.01). In ovarian epithelial cancers , similarly, FEN1 overexpression is associated with high grade, high stage and poor survival (ps<0.05). We conclude that FEN1 is a promising biomarker in breast and ovarian epithelial cancer

Higgs-Boson Production Induced by Bottom Quarks

Bottom quark-induced processes are responsible for a large fraction of the LHC discovery potential, in particular for supersymmetric Higgs bosons. Recently, the discrepancy between exclusive and inclusive Higgs boson production rates has been linked to the choice of an appropriate bottom factorization scale. We investigate the process kinematics at hadron colliders and show that it leads to a considerable decrease in the bottom factorization scale. This effect is the missing piece needed to understand the corresponding higher order results. Our results hold generally for charged and for neutral Higgs boson production at the LHC as well as at the Tevatron. The situation is different for single top quark production, where we find no sizeable suppression of the factorization scale. Turning the argument around, we can specify how large the collinear logarithms are, which can be resummed using the bottom parton picture.Comment: 18 page

Understanding Helical Magnetic Dynamo Spectra with a Nonlinear Four-Scale Theory

Recent MHD dynamo simulations for magnetic Prandtl number $>1$ demonstrate that when MHD turbulence is forced with sufficient kinetic helicity, the saturated magnetic energy spectrum evolves from having a single peak below the forcing scale to become doubly peaked with one peak at the system (=largest) scale and one at the forcing scale. The system scale field growth is well modeled by a recent nonlinear two-scale nonlinear helical dynamo theory in which the system and forcing scales carry magnetic helicity of opposite sign. But a two-scale theory cannot model the shift of the small-scale peak toward the forcing scale. Here I develop a four-scale helical dynamo theory which shows that the small-scale helical magnetic energy first saturates at very small scales, but then successively saturates at larger values at larger scales, eventually becoming dominated by the forcing scale. The transfer of the small scale peak to the forcing scale is completed by the end of the kinematic growth regime of the large scale field, and does not depend on magnetic Reynolds number $R_M$ for large $R_M$. The four-scale and two-scale theories subsequently evolve almost identically, and both show significant field growth on the system and forcing scales that is independent of $R_M$. In the present approach, the helical and nonhelical parts of the spectrum are largely decoupled. Implications for fractionally helical turbulence are discussed.Comment: 19 Pages, LaTex, (includes 4 figs at the end), in press, MNRA

Charged Higgs Boson Production in Bottom-Gluon Fusion

We compute the complete next-to-leading order SUSY-QCD corrections for the associated production of a charged Higgs boson with a top quark via bottom-gluon fusion. We investigate the applicability of the bottom parton description in detail. The higher order corrections can be split into real and virtual corrections for a general two Higgs doublet model and into additional massive supersymmetric loop contributions. We find that the perturbative behavior is well under control. The supersymmetric contributions consist of the universal bottom Yukawa coupling corrections and non-factorizable diagrams. Over most of the relevant supersymmetric parameter space the Yukawa coupling corrections are sizeable, while the remaining supersymmetric loop contributions are negligible.Comment: 18 pages, v2: some discussions added, v3: published versio

Progress in operational modeling in support of oil spill response

Following the 2010 Deepwater Horizon accident of a massive blow-out in the Gulf of Mexico, scientists from government, industry, and academia collaborated to advance oil spill modeling and share best practices in model algorithms, parameterizations, and application protocols. This synergy was greatly enhanced by research funded under the Gulf of Mexico Research Initiative (GoMRI), a 10-year enterprise that allowed unprecedented collection of observations and data products, novel experiments, and international collaborations that focused on the Gulf of Mexico, but resulted in the generation of scientific findings and tools of broader value. Operational oil spill modeling greatly benefited from research during the GoMRI decade. This paper provides a comprehensive synthesis of the related scientific advances, remaining challenges, and future outlook. Two main modeling components are discussed: Ocean circulation and oil spill models, to provide details on all attributes that contribute to the success and limitations of the integrated oil spill forecasts. These forecasts are discussed in tandem with uncertainty factors and methods to mitigate them. The paper focuses on operational aspects of oil spill modeling and forecasting, including examples of international operational center practices, observational needs, communication protocols, and promising new methodologies

Simulations of galactic dynamos

We review our current understanding of galactic dynamo theory, paying particular attention to numerical simulations both of the mean-field equations and the original three-dimensional equations relevant to describing the magnetic field evolution for a turbulent flow. We emphasize the theoretical difficulties in explaining non-axisymmetric magnetic fields in galaxies and discuss the observational basis for such results in terms of rotation measure analysis. Next, we discuss nonlinear theory, the role of magnetic helicity conservation and magnetic helicity fluxes. This leads to the possibility that galactic magnetic fields may be bi-helical, with opposite signs of helicity and large and small length scales. We discuss their observational signatures and close by discussing the possibilities of explaining the origin of primordial magnetic fields.Comment: 28 pages, 15 figure, to appear in Lecture Notes in Physics "Magnetic fields in diffuse media", Eds. E. de Gouveia Dal Pino and A. Lazaria

Role of carbonate burial in Blue Carbon budgets

Calcium carbonates (CaCO 3 ) often accumulate in mangrove and seagrass sediments. As CaCO 3 production emits CO 2 , there is concern that this may partially offset the role of Blue Carbon ecosystems as CO 2 sinks through the burial of organic carbon (C org ). A global collection of data on inorganic carbon burial rates (C inorg , 12% of CaCO 3 mass) revealed global rates of 0.8 TgC inorg yr −1 and 15–62 TgC inorg yr −1 in mangrove and seagrass ecosystems, respectively. In seagrass, CaCO 3 burial may correspond to an offset of 30% of the net CO 2 sequestration. However, a mass balance assessment highlights that the C inorg burial is mainly supported by inputs from adjacent ecosystems rather than by local calcification, and that Blue Carbon ecosystems are sites of net CaCO 3 dissolution. Hence, CaCO 3 burial in Blue Carbon ecosystems contribute to seabed elevation and therefore buffers sea-level rise, without undermining their role as CO 2 sinks. © 2019, The Author(s)