Software Challenges For HL-LHC Data Analysis

The high energy physics community is discussing where investment is needed to prepare software for the HL-LHC and its unprecedented challenges. The ROOT project is one of the central software players in high energy physics since decades. From its experience and expectations, the ROOT team has distilled a comprehensive set of areas that should see research and development in the context of data analysis software, for making best use of HL-LHC's physics potential. This work shows what these areas could be, why the ROOT team believes investing in them is needed, which gains are expected, and where related work is ongoing. It can serve as an indication for future research proposals and cooperations

ROOT - A C++ Framework for Petabyte Data Storage, Statistical Analysis and Visualization

ROOT is an object-oriented C++ framework conceived in the high-energy physics (HEP) community, designed for storing and analyzing petabytes of data in an efficient way. Any instance of a C++ class can be stored into a ROOT file in a machine-independent compressed binary format. In ROOT the TTree object container is optimized for statistical data analysis over very large data sets by using vertical data storage techniques. These containers can span a large number of files on local disks, the web, or a number of different shared file systems. In order to analyze this data, the user can chose out of a wide set of mathematical and statistical functions, including linear algebra classes, numerical algorithms such as integration and minimization, and various methods for performing regression analysis (fitting). In particular, ROOT offers packages for complex data modeling and fitting, as well as multivariate classification based on machine learning techniques. A central piece in these analysis tools are the histogram classes which provide binning of one- and multi-dimensional data. Results can be saved in high-quality graphical formats like Postscript and PDF or in bitmap formats like JPG or GIF. The result can also be stored into ROOT macros that allow a full recreation and rework of the graphics. Users typically create their analysis macros step by step, making use of the interactive C++ interpreter CINT, while running over small data samples. Once the development is finished, they can run these macros at full compiled speed over large data sets, using on-the-fly compilation, or by creating a stand-alone batch program. Finally, if processing farms are available, the user can reduce the execution time of intrinsically parallel tasks - e.g. data mining in HEP - by using PROOF, which will take care of optimally distributing the work over the available resources in a transparent way

ROOT for the HL-LHC: data format

This document discusses the state, roadmap, and risks of the foundational components of ROOT with respect to the experiments at the HL-LHC (Run 4 and beyond). As foundational components, the document considers in particular the ROOT input/output (I/O) subsystem. The current HEP I/O is based on the TFile container file format and the TTree binary event data format. The work going into the new RNTuple event data format aims at superseding TTree, to make RNTuple the production ROOT event data I/O that meets the requirements of Run 4 and beyond

Loss of Trex1 in Dendritic Cells Is Sufficient To Trigger Systemic Autoimmunity

Defects of the intracellular enzyme 3' repair exonuclease 1 (Trex1) cause the rare autoimmune condition Aicardi-Goutières syndrome and are associated with systemic lupus erythematosus. Trex1(-/-) mice develop type I IFN-driven autoimmunity, resulting from activation of the cytoplasmic DNA sensor cyclic GMP-AMP synthase by a nucleic acid substrate of Trex1 that remains unknown. To identify cell types responsible for initiation of autoimmunity, we generated conditional Trex1 knockout mice. Loss of Trex1 in dendritic cells was sufficient to cause IFN release and autoimmunity, whereas Trex1-deficient keratinocytes and microglia produced IFN but did not induce inflammation. In contrast, B cells, cardiomyocytes, neurons, and astrocytes did not show any detectable response to the inactivation of Trex1. Thus, individual cell types differentially respond to the loss of Trex1, and Trex1 expression in dendritic cells is essential to prevent breakdown of self-tolerance ensuing from aberrant detection of endogenous DNA

Complications and Short-Term Explantation Rate Following Artificial Urinary Sphincter Implantation: Results from a Large Middle European Multi-Institutional Case Series

Background/Aims/Objectives: To analyze perioperative complication and short-term explantation rates after perineal or penoscrotal single-cuff and double-cuff artificial urinary sphincter (AUS) implantation in a large middle European multi-institutional patient cohort. Methods: 467 male patients with stress urinary incontinence underwent implantation of a perineal single-cuff (n = 152), penoscrotal single-cuff (n = 99), or perinea! double-cuff (n = 216) AUS between 2010 and 2012. Postoperative complications and 6-month explantation rates were assessed. For statistical analysis, Fisher's exact test and Kruskal Wallis rank sum test, and a multiple logistic regression model were used (p < 0.05). Results: Compared to perineal single-cuff AUS, penoscrotal single-cuff implantation led to significantly increased short-term explantation rates (8.6% (perinea)) vs. 19.2% (penoscrotal), p = 0.019). The postoperative infection rate was significantly higher after double-cuff compared to single cuff implantation (6.0% (single-cuff) vs. 13.9% (double-cuff), p = 0.019). The short-term explantation rate after primary double-cuff placement was 6.5% (p = 0.543 vs. perineal single -cuff). In multivariate analysis, the penoscrotal approach (p = 0.004), intraoperative complications (p = 0.005), postoperative bleeding (p = 0.011), and perioperative infection (p < 0.001) were independent risk factors for short-term explantation. Conclusions: Providing data from a large contemporary multi-institutional patient cohortfrom high-volume and low-volume institutions, our results reflect the current standard of care in middle Europe. We indicate that the penoscrotal approach is an independent risk factor for increased short-term explantation rates. (C) 2016 S. Karger AG, Base

Targeting Moderate and Severe Male Stress Urinary Incontinence With Adjustable Male Slings and the Perineal Artificial Urinary Sphincter: Focus on Perioperative Complications and Device Explantations

Purpose: To analyze perioperative complications and postoperative explantation rates for selected readjustable male sling systems and the perineal single-cuff artificial urinary sphincter (AUS) in a large, contemporary, multi-institutional patient cohort. Methods: Two hundred eighty-two male patients who underwent implantation between 2010 and 2012 in 13 participating institutions were included in the study (n = 127 adjustable male sling [n = 95 Argus classic, n = 32 Argus T], n = 155 AUS). Perioperative characteristics and postoperative complications were analyzed. The explantation rates of the respective devices were assessed using the Fisher exact test and the Mann-Whitney U-test. A Kaplan-Meier curve was generated. Potential features associated with device explantation were analyzed using a multiple logistic regression model (P < 0.05). Results: We found significantly increased intraoperative complication rates after adjustable male sling implantation (15.9% [adjustable male sling] vs. 4.2% [AUS], P = 0.003). The most frequent intraoperative complication was bladder perforation (n = 17). Postoperative infection rates did not vary significantly between the respective devices (P = 0.378). Device explantation rates were significantly higher after AUS implantation (9.7% [adjustable male sling] vs. 21.5% [AUS], P = 0.030). In multivariate analysis, postoperative infection was a strong independent predictor of decreased device survival (odds ratio, 6.556;P = 0.001). Conclusions: Complication profiles vary between adjustable male slings and AUS. Explantation rates are lower after adjustable male sling implantation. Any kind of postoperative infections are independent predictors of decreased device survival. There is no significant effect of the experience of the implanting institution on device survival

The Added Value of Large-Eddy and Storm-Resolving Models for Simulating Clouds and Precipitation

More than one hundred days were simulated over very large domains with fine (0.156 km to 2.5 km) grid spacing for realistic conditions to test the hypothesis that storm (kilometer) and large-eddy (hectometer) resolving simulations would provide an improved representation of clouds and precipitation in atmospheric simulations. At scales that resolve convective storms (storm-resolving for short), the vertical velocity variance becomes resolved and a better physical basis is achieved for representing clouds and precipitation. Similarly to past studies we found an improved representation of precipitation at kilometer scales, as compared to models with parameterized convection. The main precipitation features (location, diurnal cycle and spatial propagation) are well captured already at kilometer scales, and refining resolution to hectometer scales does not substantially change the simulations in these respects. It does, however, lead to a reduction in the precipitation on the time-scales considered – most notably over the ocean in the tropics. Changes in the distribution of precipitation, with less frequent extremes are also found in simulations incorporating hectometer scales. Hectometer scales appear to be more important for the representation of clouds, and make it possible to capture many important aspects of the cloud field, from the vertical distribution of cloud cover, to the distribution of cloud sizes, and to the diel (daily) cycle. Qualitative improvements, particularly in the ability to differentiate cumulus from stratiform clouds, are seen when one reduces the grid spacing from kilometer to hectometer scales. At the hectometer scale new challenges arise, but the similarity of observed and simulated scales, and the more direct connection between the circulation and the unconstrained degrees of freedom make these challenges less daunting. This quality, combined with already improved simulation as compared to more parameterized models, underpins our conviction that the use and further development of storm-resolving models offers exciting opportunities for advancing understanding of climate and climate change

Impaired DNA damage response signaling by FUS-NLS mutations leads to neurodegeneration and FUS aggregate formation

Amyotrophic lateral sclerosis (ALS) is the most frequent motor neuron disease. Cytoplasmic fused in sarcoma (FUS) aggregates are pathological hallmarks of FUS-ALS. Proper shuttling between the nucleus and cytoplasm is essential for physiological cell function. However, the initial event in the pathophysiology of FUS-ALS remains enigmatic. Using human induced pluripotent stem cell (hiPSCs)-derived motor neurons (MNs), we show that impairment of poly(ADP-ribose) polymerase (PARP)-dependent DNA damage response (DDR) signaling due to mutations in the FUS nuclear localization sequence (NLS) induces additional cytoplasmic FUS mislocalization which in turn results in neurodegeneration and FUS aggregate formation. Our work suggests that a key pathophysiologic event in ALS is upstream of aggregate formation. Targeting DDR signaling could lead to novel therapeutic routes for ameliorating ALS