CPsuperH2.3: an Updated Tool for Phenomenology in the MSSM with Explicit CP Violation

We describe the Fortran code CPsuperH2.3, which incorporates the following updates compared with its predecessor CPsuperH2.0. It implements improved calculations of the Higgs-boson masses and mixing including stau contributions and finite threshold effects on the tau-lepton Yukawa coupling. It incorporates the LEP limits on the processes e^+ e^- to H_i Z, H_i H_j and the CMS limits on H_i to tau^+ tau^- obtained from 4.6/fb of data at a centre-of-mass energy of 7 TeV. It also includes the decay mode H_i to Z gamma and the Schiff-moment contributions to the electric dipole moments of Mercury and Radium225, with several calculational options for the case of Mercury. These additions make CPsuperH2.3 a suitable tool for analyzing possible CP-violating effects in the MSSM in the era of the LHC and a new generation of EDM experimentsComment: 31 pages, 10 eps figures, 7 tables; H to Z gamma and SM BRs included; To appear in CPC; Typos in Eq.(A.2) corrected;The program may be obtained from http://www.hep.man.ac.uk/u/jslee/CPsuperH.html, or by contacting the first author at [email protected]; A comment added after Eq.(15) and a typo in Eq.(A.4) correcte

Automated line scan analysis to quantify biosensor activity at the cell edge

Biosensors are valuable tools used to image the subcellular localization and kinetics of protein activity in living cells. Signaling at the edge of motile cells that regulates cell protrusion and retraction is important in many aspects of cell physiology, and frequently studied using biosensors. However, quantitation and interpretation is limited by the heterogeneity of this signaling behavior; automated analytical approaches are required to systematically extract large data sets from biosensor studies for statistical analysis. Here we describe an automated analysis to relate the velocity at specific points along the cell edge with biosensor activity in adjoining regions. Time series of biosensor images are processed to interpolate a smooth edge of the cell at each time point. Profiles of biosensor activity (‘line scans’) are then calculated along lines perpendicular to the cell edge. An energy minimization method is used to calculate a velocity associated with each line scan. Sorting line scans by the proximal velocity has generated novel biological insights, as exemplified by analysis of the Src merobody biosensor. With the large data sets that can be generated automatically by this program, conclusions can be drawn that are not apparent from qualitative or ‘manual’ quantitative techniques. Our ‘LineScan’ software includes a graphical user interface (GUI) to facilitate application in other studies. It is available at hahnlab.com and is exemplified here in a study using the RhoC FLARE biosensor

Topological self-similarity on the random binary-tree model

Asymptotic analysis on some statistical properties of the random binary-tree model is developed. We quantify a hierarchical structure of branching patterns based on the Horton-Strahler analysis. We introduce a transformation of a binary tree, and derive a recursive equation about branch orders. As an application of the analysis, topological self-similarity and its generalization is proved in an asymptotic sense. Also, some important examples are presented

Super AutoDipole

The publicly available package for an automated dipole subtraction, AutoDipole, is extended to include the SUSY dipoles in the MSSM. All fields in the SM and the MSSM are available. The code is checked against the analytical expressions for a simple process. The extended package makes it possible to compute the QCD NLO corrections to SUSY multi-parton processes like the stop pair production plus jets at the LHC.Comment: 16 pages, 1 figure, v2: a few typos to match the published version in Eur. Phys. J.

Simulating quantum repeater strategies for multiple satellites

A global quantum repeater network involving satellite based links is likely to have advantages over fiber based networks in terms of long distance communication, since the photon losses in vacuum scale only polynomially with the distance compared to the exponential losses in optical fibers. To simulate the performance of such networks, we have introduced a scheme of large scale event based Monte Carlo simulation of quantum repeaters with multiple memories that can faithfully represent loss and imperfections in these memories. In this work, we identify the quantum key distribution rates achievable in various satellite and ground station geometries for feasible experimental parameters. The power and flexibility of the simulation toolbox allows us to explore various strategies and parameters, some of which only arise in these more complex, multi satellite repeater scenarios. As a primary result, we conclude that key rates in the kHz range are reasonably attainable for intercontinental quantum communication with three satellites, only one of which carries a quantum memor

Survival, pathologic response, and genomics in CALGB 40601 (Alliance), a neoadjuvant Phase III trial of paclitaxel-trastuzumab with or without lapatinib in HER2-positive breast cancer

PURPOSE CALGB 40601 assessed whether dual versus single human epidermal growth factor receptor 2 (HER2) -targeting drugs added to neoadjuvant chemotherapy increased pathologic complete response (pCR). Here, we report relapse-free survival (RFS), overall survival (OS), and gene expression signatures that predict pCR and survival. PATIENTS AND METHODS Three hundred five women with untreated stage II and III HER2-positive breast cancer were randomly assigned to receive weekly paclitaxel combined with trastuzumab plus lapatinib (THL), trastuzumab (TH), or lapatinib (TL). The primary end point was pCR, and secondary end points included RFS, OS, and gene expression analyses. mRNA sequencing was performed on 264 pretreatment samples. RESULTS One hundred eighteen patients were randomly allocated to THL, 120 to TH, and 67 to TL. At more than 7 years of follow-up, THL had significantly better RFS and OS than did TH (RFS hazard ratio, 0.32; 95% CI, 0.14 to 0.71; P 5.005; OS hazard ratio, 0.34; 95% CI, 0.12 to 0.94; P 5.037), with no difference between TH and TL. Of 688 previously described gene expression signatures, significant associations were found in 215 with pCR, 45 with RFS, and only 22 with both pCR and RFS (3.2%). Specifically, eight immune signatures were significantly correlated with a higher pCR rate and better RFS. Among patients with residual disease, the immunoglobulin G signature was an independent, good prognostic factor, whereas the HER2-enriched signature, which was associated with a higher pCR rate, showed a significantly shorter RFS. CONCLUSION In CALGB 40601, dual HER2-targeting resulted in significant RFS and OS benefits. Integration of intrinsic subtype and immune signatures allowed for the prediction of pCR and RFS, both overall and within the residual disease group. These approaches may provide means for rational escalation and de-escalation treatment strategies in HER2-positive breast cancer

The Kuiper Belt and Other Debris Disks

We discuss the current knowledge of the Solar system, focusing on bodies in the outer regions, on the information they provide concerning Solar system formation, and on the possible relationships that may exist between our system and the debris disks of other stars. Beyond the domains of the Terrestrial and giant planets, the comets in the Kuiper belt and the Oort cloud preserve some of our most pristine materials. The Kuiper belt, in particular, is a collisional dust source and a scientific bridge to the dusty "debris disks" observed around many nearby main-sequence stars. Study of the Solar system provides a level of detail that we cannot discern in the distant disks while observations of the disks may help to set the Solar system in proper context.Comment: 50 pages, 25 Figures. To appear in conference proceedings book "Astrophysics in the Next Decade

Shrinking a large dataset to identify variables associated with increased risk of Plasmodium falciparum infection in Western Kenya

Large datasets are often not amenable to analysis using traditional single-step approaches. Here, our general objective was to apply imputation techniques, principal component analysis (PCA), elastic net and generalized linear models to a large dataset in a systematic approach to extract the most meaningful predictors for a health outcome. We extracted predictors for Plasmodium falciparum infection, from a large covariate dataset while facing limited numbers of observations, using data from the People, Animals, and their Zoonoses (PAZ) project to demonstrate these techniques: data collected from 415 homesteads in western Kenya, contained over 1500 variables that describe the health, environment, and social factors of the humans, livestock, and the homesteads in which they reside. The wide, sparse dataset was simplified to 42 predictors of P. falciparum malaria infection and wealth rankings were produced for all homesteads. The 42 predictors make biological sense and are supported by previous studies. This systematic data-mining approach we used would make many large datasets more manageable and informative for decision-making processes and health policy prioritization