Study of the electron trigger efficiency of the CMS Experiment using test beam data

A study of the electron identification and selection efficiency of the L1 Trigger algorithm has been performed using the combined ECAL/HCAL test beam data. A detailed discussion of the electron isolation and its impact on the selection efficiency is presented. The L1 electron algorithm is studied for different beam energies and the results indicate that efficiencies of 98% or more can be achieved for electrons with energies between 15 and 100 GeV. The fraction of charged hadrons with energies from 3 up to 100 GeV rejected by the L1 electron trigger algorithm is estimated to be larger than 93%.Comment: 22 pages, 14 figure

Idiopathic calcium nephrolithiasis with pure calcium oxalate composition: clinical correlates of the calcium oxalate dihydrate/monohydrate (COD/COM) stone ratio

Pure calcium oxalate is the most frequent type of idiopathic kidney stone composition. Fourier transform infrared spectroscopy (FT-IR) allows to detect the ratio of calcium oxalate dihydrate (COD) and monohydrate (COM) crystals in stones, but the clinical significance of this parameter remains uncertain. The objective of this observational study was to verify the association of clinical and laboratory parameters of kidney stone disease with COD/COM ratio in a group of 465 (322 M, age 46 ± 14) patients suffering from idiopathic calcium nephrolithiasis with pure calcium oxalate stones (≥ 97%). Each participant underwent a complete clinical examination, serum chemistry, 24-h urine collection for the determination of the profile of lithogenic risk, and had stones analyzed by FT-IR. Most (62%) of the stones had a COD/COM ratio ≤ 0.25, and the urine chemistry of the corresponding patients showed a low prevalence of urinary metabolic abnormalities. With increasing COD/COM ratio intervals (0–0.25, 0.26–0.50, 0.51–0.75, 0.76–1), a significant association was observed for the number of urological procedures, serum calcium, 24-h urinary calcium excretion, prevalence of hypercalciuria and relative calcium oxalate supersaturation, and a negative trend was detected for the age of the first stone episode (all p values < 0.05). A linear regression model showed that the only parameters significantly associated with COD/COM ratio were 24-h urinary calcium excretion (standardized β = 0.464, p < 0.001) and urine pH (standardized β = 0.103, p = 0.013). In pure calcium oxalate idiopathic stones, COD/COM ratio may reflect the presence of urinary metabolic risk factors, and represent a guide for the prescription of urinary analyses

Using XDAQ in Application Scenarios of the CMS Experiment

XDAQ is a generic data acquisition software environment that emerged from a rich set of of use-cases encountered in the CMS experiment. They cover not the deployment for multiple sub-detectors and the operation of different processing and networking equipment as well as a distributed collaboration of users with different needs. The use of the software in various application scenarios demonstrated the viability of the approach. We discuss two applications, the tracker local DAQ system for front-end commissioning and the muon chamber validation system. The description is completed by a brief overview of XDAQ.Comment: Conference CHEP 2003 (Computing in High Energy and Nuclear Physics, La Jolla, CA

The CMS Event Builder

The data acquisition system of the CMS experiment at the Large Hadron Collider will employ an event builder which will combine data from about 500 data sources into full events at an aggregate throughput of 100 GByte/s. Several architectures and switch technologies have been evaluated for the DAQ Technical Design Report by measurements with test benches and by simulation. This paper describes studies of an EVB test-bench based on 64 PCs acting as data sources and data consumers and employing both Gigabit Ethernet and Myrinet technologies as the interconnect. In the case of Ethernet, protocols based on Layer-2 frames and on TCP/IP are evaluated. Results from ongoing studies, including measurements on throughput and scaling are presented. The architecture of the baseline CMS event builder will be outlined. The event builder is organised into two stages with intelligent buffers in between. The first stage contains 64 switches performing a first level of data concentration by building super-fragments from fragments of 8 data sources. The second stage combines the 64 super-fragments into full events. This architecture allows installation of the second stage of the event builder in steps, with the overall throughput scaling linearly with the number of switches in the second stage. Possible implementations of the components of the event builder are discussed and the expected performance of the full event builder is outlined.Comment: Conference CHEP0

Commissioning of the CMS High Level Trigger

The CMS experiment will collect data from the proton-proton collisions delivered by the Large Hadron Collider (LHC) at a centre-of-mass energy up to 14 TeV. The CMS trigger system is designed to cope with unprecedented luminosities and LHC bunch-crossing rates up to 40 MHz. The unique CMS trigger architecture only employs two trigger levels. The Level-1 trigger is implemented using custom electronics, while the High Level Trigger (HLT) is based on software algorithms running on a large cluster of commercial processors, the Event Filter Farm. We present the major functionalities of the CMS High Level Trigger system as of the starting of LHC beams operations in September 2008. The validation of the HLT system in the online environment with Monte Carlo simulated data and its commissioning during cosmic rays data taking campaigns are discussed in detail. We conclude with the description of the HLT operations with the first circulating LHC beams before the incident occurred the 19th September 2008

The gut–muscle axis in older subjects with low muscle mass and performance: a proof of concept study exploring fecal microbiota composition and function with shotgun metagenomics sequencing

The gut microbiota could influence the pathophysiology of age‐related sarcopenia through multiple mechanisms implying modulation of chronic inflammation and anabolic resistance. The aim of this study was to compare the fecal microbiota composition and functionality, assessed by shotgun metagenomics sequencing, between two groups of elderly outpatients, differing only for the presence of primary sarcopenia. Five sarcopenic elderly subjects and twelve non‐sarcopenic controls, classified according to lower limb function and bioimpedance‐derived skeletal muscle index, provided a stool sample, which was analyzed with shotgun metagenomics approaches, to determine the overall microbiota composition, the representation of bacteria at the species level, and the prediction of bacterial genes involved in functional metabolic pathways. Sarcopenic subjects displayed different fecal microbiota compositions at the species level, with significant depletion of two species known for their metabolic capacity of producing short‐chain fatty acids (SCFAs), Faecalibacterium prausnitzii and Roseburia inulinivorans, and of Alistipes shahii. Additionally, their fecal metagenome had different representation of genes belonging to 108 metabolic pathways, namely, depletion of genes involved in SCFA synthesis, carotenoid and isoflavone biotransformation, and amino acid interconversion. These results support the hypothesis of an association between microbiota and sarcopenia, indicating novel possible mediators, whose clinical relevance should be investigated in future studies

Evidences for lipid involvement in SARS-CoV-2 cytopathogenesis

The pathogenesis of SARS-CoV-2 remains to be completely understood, and detailed SARS-CoV-2 cellular cytopathic effects requires definition. We performed a comparative ultrastructural study of SARS-CoV-1 and SARS-CoV-2 infection in Vero E6 cells and in lungs from deceased COVID-19 patients. SARS-CoV-2 induces rapid death associated with profound ultrastructural changes in Vero cells. Type II pneumocytes in lung tissue showed prominent altered features with numerous vacuoles and swollen mitochondria with presence of abundant lipid droplets. The accumulation of lipids was the most striking finding we observed in SARS-CoV-2 infected cells, both in vitro and in the lungs of patients, suggesting that lipids can be involved in SARS-CoV-2 pathogenesis. Considering that in most cases, COVID-19 patients show alteration of blood cholesterol and lipoprotein homeostasis, our findings highlight a peculiar important topic that can suggest new approaches for pharmacological treatment to contrast the pathogenicity of SARS-CoV-2

Retrospective screening of solid organ donors in Italy, 2009, reveals unpredicted circulation of West Nile virus

Since the occurrence of West Nile virus (WNV) infection in humans in 2008 in Italy, concerns have been raised about the potential risks associated with solid organ transplantation (SOT). A nationwide retrospective survey showed that 1.2% of SOT donors in 2009 were WNV-seropositive and demonstrated that human WNV infection is distributed throughout several Italian regions. Transmission of WNV or other arboviruses through SOT is a possibility and risk assessment should be carried out before SOT to avoid infection through transplantatation