HZTool and Rivet: Toolkit and Framework for the Comparison of Simulated Final States and Data at Colliders

A common problem in particle physics is the requirement to reproduce comparisons between data and theory when the theory is a (general purpose) Monte Carlo simulation and the data are measurements of final state observables in high energy collisions. The complexity of the experiments, the obervables and the models all contribute to making this a highly non-trivial task. We describe an existing library of Fortran routines, HZTool, which enables, for each measurement of interest, a comparable prediction to be produced from any given Monte Carlo generator. The HZTool library is being maintained by CEDAR, with subroutines for various measurements contributed by a number of authors within and outside the CEDAR collaboration. We also describe the outline design and current status of a replacement for HZTool, to be called Rivet (Robust Independent Validation of Experiment and Theory). This will use an object-oriented design, implemented in C++, together with standard interfaces (such as HepMC and AIDA) to make the new framework more flexible and extensible than the Fortran HZTool.Comment: Contribution to CHEP06 conferenc

HepForge: A lightweight development environment for HEP software

Setting up the infrastructure to manage a software project can become a task as significant writing the software itself. A variety of useful open source tools are available, such as Web-based viewers for version control systems, "wikis" for collaborative discussions and bug-tracking systems, but their use in high-energy physics, outside large collaborations, is insubstantial. Understandably, physicists would rather do physics than configure project management tools. We introduce the CEDAR HepForge system, which provides a lightweight development environment for HEP software. Services available as part of HepForge include the above-mentioned tools as well as mailing lists, shell accounts, archiving of releases and low-maintenance Web space. HepForge also exists to promote best-practice software development methods and to provide a central repository for re-usable HEP software and phenomenology codes.Comment: 3 pages, 0 figures. To be published in proceedings of CHEP06. Refers to the HepForge facility at http://hepforge.cedar.ac.u

HepData and JetWeb: HEP data archiving and model validation

The CEDAR collaboration is extending and combining the JetWeb and HepData systems to provide a single service for tuning and validating models of high-energy physics processes. The centrepiece of this activity is the fitting by JetWeb of observables computed from Monte Carlo event generator events against their experimentally determined distributions, as stored in HepData. Caching the results of the JetWeb simulation and comparison stages provides a single cumulative database of event generator tunings, fitted against a wide range of experimental quantities. An important feature of this integration is a family of XML data formats, called HepML.Comment: 4 pages, 0 figures. To be published in proceedings of CHEP0

Sensitivity of stratospheric inorganic chlorine to differences in transport

International audienceCorrectly modeling stratospheric inorganic chlorine (Cly) is crucial for modeling the past and future evolution of stratospheric ozone. However, comparisons of the chemistry climate models used in the latest international assessment of stratospheric ozone depletion have shown large differences in the modeled Cly, with these differences explaining many of the differences in the simulated evolution of ozone over the next century. Here in, we examine the role of transport in determining the simulated Cly using three simulations from the same off-line chemical transport model that have the same lower tropospheric boundary conditions and the same chemical solver, but differing resolution and/or meteorological fields. These simulations show that transport plays a key role in determining the Cly distribution, and that Cly depends on both the time scales and pathways of transport. The time air spends in the stratosphere (e.g., the mean age) is an important transport factor determining stratospheric Cly, but the relationship between mean age and Cly is not simple. Lower stratospheric Cly depends on the fraction of air that has been in the upper stratosphere, and transport differences between models having the same mean age can result in differences in the fraction of organic chlorine converted into Cly. Differences in transport pathways result in differences in vertical profiles of CFCs, and comparisons of observed and modeled CFC profiles provide a stringent test of transport pathways in models

Transport and modeling of stratospheric inorganic chlorine

International audienceCorrectly modeling stratospheric inorganic chlorine (Cly) is crucial for modeling the past and future evolution of stratospheric ozone. However, comparisons of the chemistry climate models used in the latest international assessment of stratospheric ozone depletion have shown large differences in the modeled Cly, with these differences explaining differences in the simulated evolution of ozone over the next century. Here in, we examine the role of transport in determining the simulated Cly using three simulations from the same off-line chemical transport model that have the same lower tropospheric boundary conditions and the same chemical solver, but differing resolution and/or meteorological fields. These simulations show that transport plays a key role in determining the Cly distribution, and that Cly depends on both the time scales and pathways of transport. The time air spends in the stratosphere (e.g., the mean age) is an important transport factor determining stratospheric Cly, but the relationship between mean age and Cly is not simple. Lower stratospheric Cly depends on the fraction of air that has been in the upper stratosphere, and transport differences between models having the same mean age can result in differences in the fraction of organic chlorine converted into Cly. Differences in transport pathways result in differences in vertical profiles of CFCs, and comparisons of observed and modeled CFC profiles provides a stringent test of transport pathways in models

Screening for gestational diabetes : a systematic review and economic evaluation

Background Screening for gestational diabetes mellitus (GDM) has been controversial, with some expert bodies advising universal screening, others selective screening, and yet others advising against screening at all. This has partly been a result of debate about the definition of GDM, and partly because of the profusion of different tests available, both for screening and definite diagnosis. In the UK, there is no national policy on screening, and a variety of practices exist in different parts of the country. There have also been doubts about the treatment of GDM, and particularly about management of minor degrees of glucose elevation, which are better described as glucose intolerance rather than true diabetes. Objectives To provide an updated review of current knowledge, to clarify research needs, and to assist with policy making in the interim, pending future research. Methods A literature review was carried out, with a particular focus on screening methods and costs, and an appraisal of screening for GDM against the criteria for assessing screening programmes used by the UK National Screening Committee (NSC). Results There is still debate about what is meant by GDM – the threshold for diagnosis is not soundly based; the terms GDM and impaired glucose tolerance are not used in a standard fashion in pregnancy; there is almost certainly a continuum of risk to the baby, rather than there being separate normal and abnormal groups; and the key risk factor in most women may be maternal overweight, with glucose intolerance being an associate of that. In addition there are some rare genetic conditions, which affect a few women, such as glucokinase and hepatic nuclear factor disorders. GDM is usually defined according to divergence from normal glucose levels, but glucose levels are usually raised in pregnancy, and so diagnosis by normal levels in non-pregnant women may misclassify many normal pregnant women as abnormal. This may lead to anxiety and the inconvenience of extra investigations and ‘disease’ care. The Caesarean section rate appears to be increased by the diagnosis alone. Ideally, the condition should be defined by the incidence of adverse effects. However, the most common reported complication of GDM is ‘macrosomia’ in the baby. This is usually defined by arbitrary weight cut-offs (usually a birth weight of 4000 g, but sometimes 4500 g), but such neat thresholds fail to distinguish between larger than average healthy babies and those that have the abnormal growth patterns associated with high insulin levels in the womb. Screening for GDM fails to meet some of the NSC criteria. A number of screening tests have been used but some, such as glycosylated haemoglobin and fructosamine, have proved unsatisfactory and can be discarded. Others, such as urine testing or random blood glucose, are far from satisfactory, although they may be cheap to do. There is marked international variation. Risk factors such as weight, age and family history are useful for selective screening but some patients with GDM would be missed. Fasting plasma glucose (FPG) is convenient and reliable, but some pregnant women have normal fasting levels but raised levels of glucose after meals, and would be missed by screening based on FPG alone. Glucose challenge tests (GCTs) are based on glucose levels after a glucose drink, but also have shortcomings. The definitive diagnosis is usually by oral glucose tolerance test (OGTT), but the glucose load and timing vary in different countries; taking a 75 g glucose load is unnatural, makes some women sick, and the reproducibility of the test is poor. More natural methods such as test meals have been used, but not widely. Conclusions Interim conclusions There are clearly some women whose glucose levels rise sufficiently in pregnancy to cause harm to their babies. However, there are also many women with lower levels of glucose intolerance whose babies are not at risk, but who may suffer anxiety and inconvenience as a result of being classed as abnormal. On balance, the present evidence suggests that we should not have universal screening, but a highly selective policy, based on age and overweight. The best test at present, for those deemed to need testing, is probably the GCT, preferably combined with an FPG. The benefits of a follow-up OGTT are doubtful

An evaluation of genotyping by sequencing (GBS) to map the <em>Breviaristatum-e (ari-e)</em> locus in cultivated barley

ABSTRACT: We explored the use of genotyping by sequencing (GBS) on a recombinant inbred line population (GPMx) derived from a cross between the two-rowed barley cultivar ‘Golden Promise’ (ari-e.GP/Vrs1) and the six-rowed cultivar ‘Morex’ (Ari-e/vrs1) to map plant height. We identified three Quantitative Trait Loci (QTL), the first in a region encompassing the spike architecture gene Vrs1 on chromosome 2H, the second in an uncharacterised centromeric region on chromosome 3H, and the third in a region of chromosome 5H coinciding with the previously described dwarfing gene Breviaristatum-e (Ari-e). BACKGROUND: Barley cultivars in North-western Europe largely contain either of two dwarfing genes; Denso on chromosome 3H, a presumed ortholog of the rice green revolution gene OsSd1, or Breviaristatum-e (ari-e) on chromosome 5H. A recessive mutant allele of the latter gene, ari-e.GP, was introduced into cultivation via the cv. ‘Golden Promise’ that was a favourite of the Scottish malt whisky industry for many years and is still used in agriculture today. RESULTS: Using GBS mapping data and phenotypic measurements we show that ari-e.GP maps to a small genetic interval on chromosome 5H and that alternative alleles at a region encompassing Vrs1 on 2H along with a region on chromosome 3H also influence plant height. The location of Ari-e is supported by analysis of near-isogenic lines containing different ari-e alleles. We explored use of the GBS to populate the region with sequence contigs from the recently released physically and genetically integrated barley genome sequence assembly as a step towards Ari-e gene identification. CONCLUSIONS: GBS was an effective and relatively low-cost approach to rapidly construct a genetic map of the GPMx population that was suitable for genetic analysis of row type and height traits, allowing us to precisely position ari-e.GP on chromosome 5H. Mapping resolution was lower than we anticipated. We found the GBS data more complex to analyse than other data types but it did directly provide linked SNP markers for subsequent higher resolution genetic analysis

A Microcantilever Device to Assess the Effect of Force on the Lifetime of Selectin-Carbohydrate Bonds

A microcantilever technique was used to apply force to receptor-ligand molecules involved in leukocyte rolling on blood vessel walls. E-selectin was adsorbed onto 3-μm-diameter, 4-mm-long glass fibers, and the selectin ligand, sialyl Lewisx, was coupled to latex microspheres. After binding, the microsphere and bound fiber were retracted using a computerized loading protocol that combines hydrodynamic and Hookean forces on the fiber to produce a range of force loading rates (force/time), rf. From the distribution of forces at failure, the average force was determined and plotted as a function of ln rf. The slope and intercept of the plot yield the unstressed reverse reaction rate, kro , and a parameter that describes the force dependence of reverse reaction rates, ro. The ligand was titrated so adhesion occurred in ~30% of tests, implying that \u3e80% of adhesive events involve single bonds. Monte Carlo simulations show that this level of multiple bonding has little effect on parameter estimation. The estimates are ro = 0.048 and 0.016 nm and kro = 0.72 and 2.2 s-1 for loading rates in the ranges 200–1000 and 1000–5000 pN s-1, respectively. Levenberg-Marquardt fitting across all values of rf gives ro = 0.034 nm and kro = 0.82 s-1. The values of these parameters are in the range required for rolling, as suggested by adhesive dynamics simulations

Bath generated work extraction and inversion-free gain in two-level systems

The spin-boson model, often used in NMR and ESR physics, quantum optics and spintronics, is considered in a solvable limit to model a spin one-half particle interacting with a bosonic thermal bath. By applying external pulses to a non-equilibrium initial state of the spin, work can be extracted from the thermalized bath. It occurs on the timescale \T_2 inherent to transversal (`quantum') fluctuations. The work (partly) arises from heat given off by the surrounding bath, while the spin entropy remains constant during a pulse. This presents a violation of the Clausius inequality and the Thomson formulation of the second law (cycles cost work) for the two-level system. Starting from a fully disordered state, coherence can be induced by employing the bath. Due to this, a gain from a positive-temperature (inversion-free) two-level system is shown to be possible.Comment: 4 pages revte