Colour Reconnection - Models and Tests

Recent progress on colour reconnection within the Pythia framework is presented. A new model is introduced, based on the SU(3) structure of QCD and a minimization of the potential string energy. The inclusion of the epsilon structure of SU(3) gives a new baryon production mechanism and makes it possible simultaneously to describe hyperon production at both $e^+e^-$ and pp colliders. Finally, predictions for $e^+e^-$ colliders, both past and potential future ones, are presented.Comment: 6 pages, 5 figures. To appear in the proceedings of the The European Physical Society Conference on High Energy Physics, 22-29 July 2015 in Vienna, Austri

String Formation Beyond Leading Colour

We present a new model for the hadronisation of multi-parton systems, in which colour correlations beyond leading $N_C$ are allowed to influence the formation of confining potentials (strings). The multiplet structure of $SU(3)$ is combined with a minimisation of the string potential energy, to decide between which partons strings should form, allowing also for "baryonic" configurations (e.g., two colours can combine coherently to form an anticolour). In $e^+e^-$collisions, modifications to the leading-colour picture are small, suppressed by both colour and kinematics factors. But in $pp$ collisions, multi-parton interactions increase the number of possible subleading connections, counteracting their naive $1/N_C^2$ suppression. Moreover, those that reduce the overall string lengths are kinematically favoured. The model, which we have implemented in the PYTHIA 8 generator, is capable of reaching agreement not only with the important \left(n_\mathrm{charged}) distribution but also with measured rates (and ratios) of kaons and hyperons, in both $ee$ and $pp$ collisions. Nonetheless, the shape of their $p_\perp$ spectra remains challenging to explain.Comment: 48 pages, 22 figure

Recent Pythia 8 developments: Hard diffraction, Colour reconnection and γγ\gamma\gamma collisions

An overview of recent developments in \pythia~8 is given. First the new hard diffraction model, which is implemented as a part of the multiparton interactions (MPI) framework, is discussed. Then the new colour reconnection model, which includes beyond leading colour effects that can become important when MPI are present, is briefly reviewed. As a last topic an introduction is given to our implementation of photon-photon collisions. In particular photon PDFs, required modifications for the initial state radiation algorithm and beam remnant handling with photon beams is discussed.Comment: Contribution to proceedings of 7th International Workshop on Multiple Partonic Interactions at the LHC, 23 - 27 November 2015, Miramare, Trieste, Ital

Mass-Spectrometry Based Proteome Comparison of Extracellular Vesicle Isolation Methods:Comparison of ME-kit, Size-Exclusion Chromatography, and High-Speed Centrifugation

Extracellular vesicles (EVs) are small membrane-enclosed particles released by cells under various conditions specific to cells’ biological states. Hence, mass-spectrometry (MS) based proteome analysis of EVs in plasma has gained much attention as a method to discover novel protein biomarkers. MS analysis of EVs in plasma is challenging and EV isolation is usually necessary. Therefore, we compared differences in abundance, subtypes, and contamination for EVs isolated by high-speed centrifugation, size exclusion chromatography (SEC), and peptide-affinity precipitation (PAP/ME kit) for subsequent MS-based proteome analysis. Successful EV isolation was evaluated by nanoparticle-tracking analysis, immunoblotting, and transmission electron microscopy, while EV abundance, EV subtypes, and contamination was evaluated by label-free tandem MS. High-speed centrifugation and SEC isolates showed high EV abundance at the expense of contamination by non-EV proteins and lipoproteins, respectively. These two methods also resulted in EVs of a similar type, however, with smaller EVs in SEC isolates. PAP isolates had a relatively low EV abundance and high contamination. We consider high-speed centrifugation and SEC suitable as EV isolation for MS biomarker studies, where the choice between the two should depend on the scientific questions and whether the focus is on larger or smaller EVs or a combination of both

An Introduction to PYTHIA 8.2

The PYTHIA program is a standard tool for the generation of events in high-energy collisions, comprising a coherent set of physics models for the evolution from a few-body hard process to a complex multiparticle final state. It contains a library of hard processes, models for initial- and final-state parton showers, matching and merging methods between hard processes and parton showers, multiparton interactions, beam remnants, string fragmentation and particle decays. It also has a set of utilities and several interfaces to external programs. PYTHIA 8.2 is the second main release after the complete rewrite from Fortran to C++, and now has reached such a maturity that it offers a complete replacement for most applications, notably for LHC physics studies. The many new features should allow an improved description of data.Comment: 45 page

Distribution of Stromal Cell Subsets in Cultures from Distinct Ocular Surface Compartments

Purpose: To reveal the phenotypic differences between human ocular surface stromal cells (hOSSCs) cultured from the corneal, limbal, and scleral compartments. Methods: A comparative analysis of cultured hOSSCs derived from four unrelated donors was conducted by multichromatic flow cytometry for six distinct CD antigens, including the CD73, CD90, CD105, CD166, CD146, and CD34. Results: The hOSSCs, as well as the reference cells, displayed phenotypical profiles that were similar in high expression of the hallmark mesenchymal stem cell markers CD73, CD90, and CD105, and also the cancer stem cell marker CD166. Notably, there was considerable variation regarding the expression of CD34, where the highest levels were found in the corneal and scleral compartments. The multi-differentiation potential marker CD146 was also expressed highly variably, ranging from 9% to 89%, but the limbal stromal and endometrial mesenchymal stem cells significantly surpassed their counterparts within the ocular and reference groups, respectively. The use of six markers enabled investigation of 64 possible variants, however, just four variants accounted for almost 90% of all hOSSCs, with the co-expression of CD73, CD90, CD105, and CD166 and a combination of CD146 and CD34. The limbal compartment appeared unique in that it displayed greatest immunophenotype diversity and harbored the highest proportion of the CD146+CD34- pericyte-like forms, but, interestingly, the pericyte-like cells were also found in the avascular cornea. Conclusions: Our findings confirm that the hOSSCs exhibit an immunophenotype consistent with that of MSCs, further highlight the phenotypical heterogeneity in stroma from distinct ocular surface compartments, and finally underscore the uniqueness of the limbal region.&nbsp

The nonlinear time-dependent response of isotactic polypropylene

Tensile creep tests, tensile relaxation tests and a tensile test with a constant rate of strain are performed on injection-molded isotactic polypropylene at room temperature in the vicinity of the yield point. A constitutive model is derived for the time-dependent behavior of semi-crystalline polymers. A polymer is treated as an equivalent network of chains bridged by permanent junctions. The network is modelled as an ensemble of passive meso-regions (with affine nodes) and active meso-domains (where junctions slip with respect to their positions in the bulk medium with various rates). The distribution of activation energies for sliding in active meso-regions is described by a random energy model. Adjustable parameters in the stress--strain relations are found by fitting experimental data. It is demonstrated that the concentration of active meso-domains monotonically grows with strain, whereas the average potential energy for sliding of junctions and the standard deviation of activation energies suffer substantial drops at the yield point. With reference to the concept of dual population of crystalline lamellae, these changes in material parameters are attributed to transition from breakage of subsidiary (thin) lamellae in the sub-yield region to fragmentation of primary (thick) lamellae in the post-yield region of deformation.Comment: 29 pages, 12 figure

Global Research Alliance N2O chamber methodology guidelines: Design considerations

Terrestrial ecosystems, both natural ecosystems and agroecosystems, generate greenhouse gases (GHGs). The chamber method is the most common method to quantify GHG fluxes from soil–plant systems and to better understand factors affecting their generation and mitigation. The objective of this study was to review and synthesize literature on chamber designs (non‐flow‐through, non‐steady‐state chamber) and associated factors that affect GHG nitrous oxide (N2O) flux measurement when using chamber methods. Chamber design requires consideration of many facets that include materials, insulation, sealing, venting, depth of placement, and the need to maintain plant growth and activity. Final designs should be tailored, and bench tested, in order to meet the nuances of the experimental objectives and the ecosystem under study while reducing potential artifacts. Good insulation, to prevent temperature fluctuations and pressure changes, and a high‐quality seal between base and chamber are essential. Elimination of pressure differentials between headspace and atmosphere through venting should be performed, and designs now exist to eliminate Venturi effects of earlier tube‐type vent designs. The use of fans within the chamber headspace increases measurement precision but may alter the flux. To establish best practice recommendations when using fans, further data are required, particularly in systems containing tall plants, to systematically evaluate the effects that fan speed, position, and mixing rate have on soil gas flux.Peer reviewe