The Architecture of MEG Simulation and Analysis Software

MEG (Mu to Electron Gamma) is an experiment dedicated to search for the $\mu^+ \rightarrow e^+\gamma$ decay that is strongly suppressed in the Standard Model but predicted in several Super Symmetric extensions of it at an accessible rate. MEG is a small-size experiment ($\approx 50-60$ physicists at any time) with a life span of about 10 years. The limited human resource available, in particular in the core offline group, emphasized the importance of reusing software and exploiting existing expertise. Great care has been devoted to provide a simple system that hides implementation details to the average programmer. That allowed many members of the collaboration to contribute to the development of the software of the experiment with limited programming skill. The offline software is based on two frameworks: {\bf REM} in FORTRAN 77 used for the event generation and detector simulation package {\bf GEM}, based on GEANT 3, and {\bf ROME} in C++ used in the readout simulation {\bf Bartender} and in the reconstruction and analysis program {\bf Analyzer}. Event display in the simulation is based on GEANT 3 graphic libraries and in the reconstruction on ROOT graphic libraries. Data are stored in different formats in various stage of the processing. The frameworks include utilities for input/output, database handling and format conversion transparent to the user.Comment: Presented at the IEEE NSS Knoxville, 2010 Revised according to referee's remarks Accepted by European Physical Journal Plu

A noninvasive multi-analyte diagnostic assay: Combining protein and DNA markers to stratify bladder cancer patients

Purpose: The authors recently reported the development of a noninvasive diagnostic assay using urinary matrix metalloproteinases (MMPs) as monitors of disease-free status and bladder cancer in high-risk populations. Using an approach called clinical intervention determining diagnostic (CIDD), they identified with high confidence those patients who could be excluded from additional intervention. To maximize performance, MMPs were combined with DNAbased markers and CIDD was applied to a population of patients undergoing monitoring for recurrence. Patients and methods: Urine samples were obtained from 323 patients, 48 of whom had a recurrence and 275 of whom did not have cancer upon cytoscopic evaluation. Twist1 and Nid2 methylation status was determined using methylation-specific polymerase chain reaction, FGFR3 mutational status by quantitative PCR, and MMP levels by enzyme-linked immunosorbent assay. Results: Using a combination of these DNA and protein markers, the authors identified with high confidence (97% negative predicted value) those patients who do not have cancer. Cutoffs were adjusted such that at 92% sensitivity, 51% of disease-free patients might be triaged from receiving further tests. Conclusion: The multi-analyte diagnostic readout assay described here is the first to combine protein and DNA biomarkers into one assay for optimal clinical performance. Using this approach, the detection of FGFR3 mutations and Twist1 and Nid2 methylation in the urine of patients undergoing bladder cancer recurrence screening increase the sensitivity and negative predictive value at an established MMP protein cutoff. This noninvasive urinary diagnostic assay could lead to the more efficient triage of patients undergoing recurrence monitoring

Study of relativistic bound states for scalar theories in Bethe-Salpeter and Dyson-Schwinger formalism

The Bethe-Salpeter equation for Wick-Cutkosky like models is solved in dressed ladder approximation. The bare vertex truncation of the Dyson-Schwinger equations for propagators is combined with the dressed ladder Bethe-Salpeter equation for the scalar S-wave bound state amplitudes. With the help of spectral representation the results are obtained directly in Minkowski space. We give a new analytic formula for the resulting equation simplifying the numerical treatment. The bare ladder approximation of Bethe-Salpeter equation is compared with the one with dressed ladder. The elastic electromagnetic form factors is calculated within the relativistic impulse approximation.Comment: 30 pages, 10 figures, accepted for publication in Phys. Rev.

Monitoring of the accelerator beam distributions for internal target facilities

We describe a direct method for monitoring the geometrical dimensions of a synchrotron beam at the target position for internal target installations. The method allows for the observation of the proton beam size as well as the position of the beam relative to the target. As a first demonstration of the technique, we present results obtained by means of the COSY-11 detection system installed at the cooler synchrotron COSY. The influence of the stochastic cooling on the COSY proton beam dimensions is also investigated.Comment: 7 pages, 8 figures, Submitted to Nucl. Inst. & Meth.

Broken symmetry states and divergent resistance in suspended bilayer graphene

Graphene [1] and its bilayer have generated tremendous excitement in the physics community due to their unique electronic properties [2]. The intrinsic physics of these materials, however, is partially masked by disorder, which can arise from various sources such as ripples [3] or charged impurities [4]. Recent improvements in quality have been achieved by suspending graphene flakes [5,6], yielding samples with very high mobilities and little charge inhomogeneity. Here we report the fabrication of suspended bilayer graphene devices with very little disorder. We observe fully developed quantized Hall states at magnetic fields of 0.2 T, as well as broken symmetry states at intermediate filling factors $\nu = 0$, $\pm 1$, $\pm 2$ and $\pm 3$. The devices exhibit extremely high resistance in the $\nu = 0$ state that grows with magnetic field and scales as magnetic field divided by temperature. This resistance is predominantly affected by the perpendicular component of the applied field, indicating that the broken symmetry states arise from many-body interactions.Comment: 23 pages, including 4 figures and supplementary information; accepted to Nature Physic

Literature-based discovery of diabetes- and ROS-related targets

Abstract Background Reactive oxygen species (ROS) are known mediators of cellular damage in multiple diseases including diabetic complications. Despite its importance, no comprehensive database is currently available for the genes associated with ROS. Methods We present ROS- and diabetes-related targets (genes/proteins) collected from the biomedical literature through a text mining technology. A web-based literature mining tool, SciMiner, was applied to 1,154 biomedical papers indexed with diabetes and ROS by PubMed to identify relevant targets. Over-represented targets in the ROS-diabetes literature were obtained through comparisons against randomly selected literature. The expression levels of nine genes, selected from the top ranked ROS-diabetes set, were measured in the dorsal root ganglia (DRG) of diabetic and non-diabetic DBA/2J mice in order to evaluate the biological relevance of literature-derived targets in the pathogenesis of diabetic neuropathy. Results SciMiner identified 1,026 ROS- and diabetes-related targets from the 1,154 biomedical papers (http://jdrf.neurology.med.umich.edu/ROSDiabetes/). Fifty-three targets were significantly over-represented in the ROS-diabetes literature compared to randomly selected literature. These over-represented targets included well-known members of the oxidative stress response including catalase, the NADPH oxidase family, and the superoxide dismutase family of proteins. Eight of the nine selected genes exhibited significant differential expression between diabetic and non-diabetic mice. For six genes, the direction of expression change in diabetes paralleled enhanced oxidative stress in the DRG. Conclusions Literature mining compiled ROS-diabetes related targets from the biomedical literature and led us to evaluate the biological relevance of selected targets in the pathogenesis of diabetic neuropathy.http://deepblue.lib.umich.edu/bitstream/2027.42/78315/1/1755-8794-3-49.xmlhttp://deepblue.lib.umich.edu/bitstream/2027.42/78315/2/1755-8794-3-49-S7.XLShttp://deepblue.lib.umich.edu/bitstream/2027.42/78315/3/1755-8794-3-49-S10.XLShttp://deepblue.lib.umich.edu/bitstream/2027.42/78315/4/1755-8794-3-49-S8.XLShttp://deepblue.lib.umich.edu/bitstream/2027.42/78315/5/1755-8794-3-49-S3.XLShttp://deepblue.lib.umich.edu/bitstream/2027.42/78315/6/1755-8794-3-49-S1.XLShttp://deepblue.lib.umich.edu/bitstream/2027.42/78315/7/1755-8794-3-49-S4.XLShttp://deepblue.lib.umich.edu/bitstream/2027.42/78315/8/1755-8794-3-49-S2.XLShttp://deepblue.lib.umich.edu/bitstream/2027.42/78315/9/1755-8794-3-49-S12.XLShttp://deepblue.lib.umich.edu/bitstream/2027.42/78315/10/1755-8794-3-49-S11.XLShttp://deepblue.lib.umich.edu/bitstream/2027.42/78315/11/1755-8794-3-49-S9.XLShttp://deepblue.lib.umich.edu/bitstream/2027.42/78315/12/1755-8794-3-49-S5.XLShttp://deepblue.lib.umich.edu/bitstream/2027.42/78315/13/1755-8794-3-49-S6.XLShttp://deepblue.lib.umich.edu/bitstream/2027.42/78315/14/1755-8794-3-49.pdfPeer Reviewe

Mortality and Cardiovascular Disease among Older Live Kidney Donors

Over the past two decades, live kidney donation by older individuals (≥55 years) has become more common. Given the strong associations of older age with cardiovascular disease (CVD), nephrectomy could make older donors vulnerable to death and cardiovascular events. We performed a cohort study among older live kidney donors who were matched to healthy older individuals in the Health and Retirement Study. The primary outcome was mortality ascertained through national death registries. Secondary outcomes ascertained among pairs with Medicare coverage included death or CVD ascertained through Medicare claims data. During the period from 1996 to 2006, there were 5717 older donors in the United States. We matched 3368 donors 1:1 to older healthy nondonors. Among donors and matched pairs, the mean age was 59 years; 41% were male and 7% were black race. In median follow-up of 7.8 years, mortality was not different between donors and matched pairs (p = 0.21). Among donors with Medicare, the combined outcome of death/CVD (p = 0.70) was also not different between donors and nondonors. In summary, carefully selected older kidney donors do not face a higher risk of death or CVD. These findings should be provided to older individuals considering live kidney donation

The iCanCope pain self-management application for adolescents with juvenile idiopathic arthritis: A pilot randomized controlled trial

Objectives: To evaluate the feasibility and preliminary effectiveness of iCanCope with Pain (iCanCope), a smartphone-based pain self-management program, in adolescents with JIA. iCanCope featured symptom tracking, goal-setting, pain coping skills and social support. Methods: A two-arm pilot randomized controlled trial was used to evaluate the iCanCope app compared with a version with symptom tracking only. Primary (feasibility) outcomes were: participant accrual/attrition rates, success of app deployment, acceptability and adherence. Secondary (preliminary effectiveness) outcomes were: pain intensity, pain-related activity limitations and health-related quality of life. Outcomes were assessed at baseline and 8 weeks. Adherence was defined as the proportion of completed symptom reports: \u27low\u27 (≤24%); \u27low-moderate\u27 (25-49%); \u27high-moderate\u27 (50-75%); or \u27high\u27 (76-100%). Linear mixed models were applied for preliminary effectiveness analyses as per intention-to-treat. Results: Adolescents (N = 60) were recruited from three paediatric rheumatology centres. Rates of accrual and attrition were 82 and 13%, respectively. Both apps were deployed with high success (over 85%) and were rated as highly acceptable. Adherence was similar for both groups, with most participants demonstrating moderate-to-high adherence. Both groups exhibited a clinically meaningful reduction in pain intensity (≥1 point) that did not statistically differ between groups. There were no significant changes in activity limitations or health-related quality of life. Conclusion: The iCanCope pilot randomized controlled trial was feasible to implement in a paediatric rheumatology setting. Both apps were deployed successfully, with high acceptability, and were associated with moderate-to-high adherence. Preliminary reductions in pain intensity warrant a future trial to evaluate effectiveness of iCanCope in improving health outcomes in adolescents with JIA

Renal cell carcinoma in tuberous sclerosis complex

Renal cell carcinoma (RCC) occurs in 2% to 4% of patients with tuberous sclerosis complex (TSC). Previous reports have noted a variety of histologic appearances in these cancers, but the full spectrum of morphologic and molecular features has not been fully elucidated. We encountered 46 renal epithelial neoplasms from 19 TSC patients and analyzed their clinical, pathologic, and molecular features, enabling separation of these 46 tumors into 3 groups. The largest subset of tumors (n=24) had a distinct morphologic, immunologic, and molecular profile, including prominent papillary architecture and uniformly deficient succinate dehydrogenase subunit B (SDHB) expression prompting the novel term "TSC-associated papillary RCC (PRCC)." The second group (n=15) were morphologically similar to a hybrid oncocytic/chromophobe tumor (HOCT), whereas the last 7 renal epithelial neoplasms of group 3 remained unclassifiable. The TSC-associated PRCCs had prominent papillary architecture lined by clear cells with delicate eosinophilic cytoplasmic thread-like strands that occasionally appeared more prominent and aggregated to form eosinophilic globules. All 24 (100%) of these tumors were International Society of Urological Pathology (ISUP) nucleolar grade 2 or 3 with mostly basally located nuclei. Tumor cells from 17 of 24 TSC-associated PRCCs showed strong, diffuse labeling for carbonic anhydrase IX (100%), CK7 (94%), vimentin (88%), and CD10 (83%) and were uniformly negative for SDHB, TFE3, and AMACR. Gains of chromosomes 7 and 17 were found in 2 tumors, whereas chromosome 3p deletion and TFE3 translocations were not detected. In this study, we reported a sizable cohort of renal tumors seen in TSC and were able to identify them as different morphotypes, which may help to expand the morphologic spectrum of TSC-associated RCC