KROME - a package to embed chemistry in astrophysical simulations

Chemistry plays a key role in many astrophysical situations regulating the cooling and the thermal properties of the gas, which are relevant during gravitational collapse, the evolution of disks and the fragmentation process. In order to simplify the usage of chemical networks in large numerical simulations, we present the chemistry package KROME, consisting of a Python pre-processor which generates a subroutine for the solution of chemical networks which can be embedded in any numerical code. For the solution of the rate equations, we make use of the high-order solver DLSODES, which was shown to be both accurate and efficient for sparse networks, which are typical in astrophysical applications. KROME also provides a large set of physical processes connected to chemistry, including photochemistry, cooling, heating, dust treatment, and reverse kinetics. The package presented here already contains a network for primordial chemistry, a small metal network appropriate for the modelling of low metallicities environments, a detailed network for the modelling of molecular clouds, a network for planetary atmospheres, as well as a framework for the modelling of the dust grain population. In this paper, we present an extended test suite ranging from one-zone and 1D-models to first applications including cosmological simulations with ENZO and RAMSES and 3D collapse simulations with the FLASH code. The package presented here is publicly available at http://kromepackage.org/ and https://bitbucket.org/krome/krome_stableComment: accepted for publication in MNRA

Order reduction approaches for the algebraic Riccati equation and the LQR problem

We explore order reduction techniques for solving the algebraic Riccati equation (ARE), and investigating the numerical solution of the linear-quadratic regulator problem (LQR). A classical approach is to build a surrogate low dimensional model of the dynamical system, for instance by means of balanced truncation, and then solve the corresponding ARE. Alternatively, iterative methods can be used to directly solve the ARE and use its approximate solution to estimate quantities associated with the LQR. We propose a class of Petrov-Galerkin strategies that simultaneously reduce the dynamical system while approximately solving the ARE by projection. This methodology significantly generalizes a recently developed Galerkin method by using a pair of projection spaces, as it is often done in model order reduction of dynamical systems. Numerical experiments illustrate the advantages of the new class of methods over classical approaches when dealing with large matrices

An astrobiological experiment to explore the habitability of tidally locked M-dwarf planets

We present a summary of a three-year academic research proposal drafted during the Sao Paulo Advanced School of Astrobiology (SPASA) to prepare for upcoming observations of tidally locked planets orbiting M-dwarf stars. The primary experimental goal of the suggested research is to expose extremophiles from analogue environments to a modified space simulation chamber reproducing the environmental parameters of a tidally locked planet in the habitable zone of a late-type star. Here we focus on a description of the astronomical analysis used to define the parameters for this climate simulation

Measuring societal awareness of the rural agrarian landscape: indicators and scale issues

The work presented in this report is part of the effort to define the landscape state and diversity indicator in the frame of COM (2006) 508 “Development of agri-environmental indicators for monitoring the integration of environmental concerns into the common agricultural policy”. The Communication classifies the indicators according to their level of development, which, for the landscape indicator is “in need of substantial improvements in order to become fully operational”. For this reason a full re-definition of the indicator has been carried out, following the initial proposal presented in the frame of the IRENA operation (“Indicator Reporting on the Integration of Environmental Concerns into Agricultural Policy”). The new proposal for the landscape state and diversity indicator is structured in three components: the first concerns the degree of naturalness, the second landscape structure, the third the societal appreciation of the rural landscape. While the first two components rely on a strong bulk of existing literature, the development of the methodology has made evident the need for further analysis of the third component, which is based on a newly proposed top-down approach. This report presents an in-depth analysis of such component of the indicator, and the effort to include a social dimension in large scale landscape assessment

Identifying breast cancer patients at risk for Central Nervous System (CNS) metastases in trials of the International Breast Cancer Study Group (IBCSG)

Background: We sought to determine whether a high-risk group could be defined among patients with operable breast cancer in whom a search of occult central nervous system (CNS) metastases was justified. Patients and methods: We evaluated data from 9524 women with early breast cancer (42% node-negative) who were randomized in International Breast Cancer Study Group clinical trials between 1978 and 1999, and treated without anthracyclines, taxanes, or trastuzumab. We identified patients whose site of first event was CNS and those who had a CNS event at any time. Results: Median follow-up was 13 years. The 10-year incidence (10-yr) of CNS relapse was 5.2% (1.3% as first recurrence). Factors predictive of CNS as first recurrence included: node-positive disease (10-yr = 2.2% for > 3 N+), estrogen receptor-negative (2.3%), tumor size > 2 cm (1.7%), tumor grade 3 (2.0%), < 35 years old (2.2%), HER2-positive (2.7%), and estrogen receptor-negative and node-positive (2.6%). The risk of subsequent CNS recurrence was elevated in patients experiencing lung metastases (10-yr = 16.4%). Conclusion: Based on this large cohort we were able to define risk factors for CNS metastases, but could not define a group at sufficient risk to justify routine screening for occult CNS metastase

Biogenesis of Pro-senescent Microparticles by Endothelial Colony Forming Cells from Premature Neonates is driven by SIRT1-Dependent Epigenetic Regulation of MKK6.

Senescent cells may exert detrimental effect on microenvironment through the secretion of soluble factors and the release of extracellular vesicles, such as microparticles, key actors in ageing and cardiovascular diseases. We previously reported that sirtuin-1 (SIRT1) deficiency drives accelerated senescence and dysfunction of endothelial colony-forming cells (ECFC) in PT neonates. Because preterm birth (PT) increases the risk for cardiovascular diseases during neonatal period as well as at adulthood, we hypothesized that SIRT1 deficiency could control the biogenesis of microparticles as part of a senescence-associated secretory phenotype (SASP) of PT-ECFC and investigated the related molecular mechanisms. Compared to control ECFC, PT-ECFC displayed a SASP associated with increased release of endothelial microparticles (EMP), mediating a paracrine induction of senescence in naïve endothelial cells. SIRT1 level inversely correlated with EMP release and drives PT-ECFC vesiculation. Global transcriptomic analysis revealed changes in stress response pathways, specifically the MAPK pathway. We delineate a new epigenetic mechanism by which SIRT1 deficiency regulates MKK6/p38 &lt;sup&gt;MAPK&lt;/sup&gt; /Hsp27 pathway to promote EMP biogenesis in senescent ECFC. These findings deepen our understanding of the role of ECFC senescence in the disruption of endothelial homeostasis and provide potential new targets towards the control of cardiovascular risk in individuals born preterm

Differential efficacy of three cycles of CMF followed by tamoxifen in patients with ER-positive and ER-negative tumors: Long-term follow up on IBCSG Trial IX

Background: The benefit of adjuvant chemotherapy in postmenopausal patients with estrogen receptor (ER)-positive lymph node-negative breast cancer is being reassessed. Patients and methods: After stratification by ER status, 1669 postmenopausal patients with operable lymph node-negative breast cancer were randomly assigned to three 28-day courses of ‘classical' CMF (cyclophosphamide, methotrexate, 5-fluorouracil) chemotherapy followed by tamoxifen for 57 months (CMF→tamoxifen) or to tamoxifen alone for 5 years. Results: ERs were positive in 81% of tumors. At a median follow-up of 13.1 years, patients with ER-positive breast cancers did not benefit from CMF [13-year disease-free survival (DFS) 64% CMF→tamoxifen, 66% tamoxifen; P = 0.99], whereas CMF substantially improved the prognosis of patients with ER-negative breast cancer (13-year DFS 73% versus 57%, P = 0.001). Similarly, breast cancer-free interval (BCFI) was identical in the ER-positive cohort but significantly improved by chemotherapy in the ER-negative cohort (13-year BCFI 80% versus 63%, P = 0.001). CMF had no influence on second nonbreast malignancies or deaths from other causes. Conclusion: CMF is not beneficial in postmenopausal patients with node-negative ER-positive breast cancer but is highly effective within the ER-negative cohort. In the future, other markers of chemotherapy response may define a subset of patients with ER-positive tumors who may benefit from adjuvant chemotherap

Menstrual cycle and timing of breast surgery in premenopausal node-positive breast cancer: Results of the International Breast Cancer Study Group (IBCSG) Trial VI

Purpose It has been postulated that breast cancer surgery performed during the follicular phase of the menstrual cycle is associated with poorer outcome. Patients and methods We tested this hypothesis by evaluating disease-free survival (DFS) for 1033 premenopausal patients who received definitive surgery either during the follicular phase (n = 358) or the luteal phase (n = 675). All patients were enrolled in a randomized trial conducted between July 1986 and April 1993. All had node positive breast cancer and randomization was stratified by estrogen receptor (ER) status. AU patients received at least three cycles of adjuvant cyclophosphamide, methotrexate, and 5-fluorouracil (CMF). The median follow-up was 60 months. Results Patients who underwent definitive surgery for breast cancer in the follicular phase had a slightly worse disease-free survival than those operated on during the luteal phase (five-year DFS percentage: 53% versus 58%; hazard ratio, 1.13; 95% confidence interval (CI), 0.94-1.38; P = 0.20). The effect was significantly greater for the subpopulation of 300 patients with ER-negative primaries (P = 0.02 interaction effect; five-year DFS percentages 42% vs. 59%; hazard ratio 1.60; 95% CI, 1.12-2.25; P 0.008). The effect of timing of surgery diminished for analyses based on lesser surgical procedures, e.g., excisional biopsies. In particular, no effect of timing was observed for fine needle aspiration procedures. Conclusion Surgical procedures which are more extensive than a fine needle aspiration biopsy might be associated with worse prognosis if conducted during the follicular phase of the menstrual cycle. This phenomenon was seen predominantly for high risk breast cancer with low levels or no estrogen receptors in the primary tumo