Performance of the CMS Cathode Strip Chambers with Cosmic Rays

The Cathode Strip Chambers (CSCs) constitute the primary muon tracking device in the CMS endcaps. Their performance has been evaluated using data taken during a cosmic ray run in fall 2008. Measured noise levels are low, with the number of noisy channels well below 1%. Coordinate resolution was measured for all types of chambers, and fall in the range 47 microns to 243 microns. The efficiencies for local charged track triggers, for hit and for segments reconstruction were measured, and are above 99%. The timing resolution per layer is approximately 5 ns

Evaluating Risk Factors for Clinical Failure Among Tigecycline-Treated Patients

Chun-Fu Huang,1 Jia-Ling Yang,2 Yu-Chung Chuang,2,&ast; Wang-Huei Sheng2,&ast; 1Department of Internal Medicine, National Taiwan University Hospital Yun-Lin Branch, Yun-Lin, Taiwan; 2Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan&ast;These authors contributed equally to this workCorrespondence: Yu-Chung Chuang, Department of Internal Medicine, National Taiwan University Hospital, 7 Chung-Shan South Road, Taipei, 100, Taiwan, Tel +886-2-23123456 ext. 63015, Fax +886-2-23971412, Email [email protected]: Clinical trials have documented that tigecycline has a higher mortality risk than other treatments; it continues to be widely used for various infections in real-world settings, where its associated risk factors for clinical failure are understudied.Patients and Methods: This retrospective analysis included a prospective 2019– 2021 cohort of tigecycline-treated patients, excluding those with multiple infection sites. We assessed the outcomes on day 28, with clinical failure defined by mortality, persistent initial infection symptoms, or the requirement for continued antimicrobial treatment. Multivariable logistic regression was used for the outcome analysis.Results: Of 253 patients included in the study, 94 experienced clinical failure. The infection foci included pneumonia (46.3%), bloodstream infection (BSI) (25.3%), and skin/soft tissue infections (10.3%). There were no significant differences in high-dose tigecycline administration or monotherapy rates between patients with favorable outcomes and those with clinical failure. A higher Charlson comorbidity index (adjusted odds ratio [aOR] = 1.20, P = 0.001), Pitt bacteremia score (aOR = 1.25, P = 0.007), and BSI (aOR = 3.94, P < 0.001) were significant predictors of clinical failure. Concomitant use of Pseudomonas aeruginosa-active fluoroquinolone (aOR = 1.97, P = 0.03) and carbapenem (aOR = 2.20, P = 0.01) was linked to increased clinical failure.Conclusion: Multiple comorbidities, BSI, and higher Pitt bacteremia scores are associated with increased risk of clinical failure in tigecycline-treated patients. These results suggest clinicians should consider alternatives to tigecycline for patients with these risk factors. When administering tigecycline, vigilant monitoring is indicated to manage potential clinical failures.Keywords: clinical response, predictors, tigecyclin

Multidrug-Resistant Elizabethkingia anophelis Bacteremia in Northern Taiwan: Focusing on Prognostic Factors and Antimicrobial Susceptibility to Minocycline and Rifampin

Wei-Lun Chuang,1,2,&amp;ast; Fu-Chieh Chang,2,3,&amp;ast; Chien-Feng Kuo,1,2 Chih-Chen Lin1,2 1Department of Infectious Diseases, MacKay Memorial Hospital, Taipei City, Taiwan; 2Infection Control Center, MacKay Memorial Hospital, Taipei City, Taiwan; 3Mackay Junior College of Medicine, Nursing, and Management, New Taipei City, Taiwan&amp;ast;These authors contributed equally to this workCorrespondence: Chih-Chen Lin, Department of Infectious Diseases, MacKay Memorial Hospital, No. 92, Sec. 2, Zhongshan N. Road, Taipei City, 104217, Taiwan, Fax +886-2-2543-3642, Email [email protected]: Elizabethkingia anophelis is an emerging multidrug-resistant pathogen associated with high mortality, particularly in healthcare-associated bacteremia. Treatment is complicated by frequent species misidentification and limited availability of effective antibiotics. This study aimed to investigate the clinical characteristics, predictors of early and late mortality, and antimicrobial resistance profiles, including associated resistance genes.Patients and Methods: A retrospective cohort study was conducted from 2018 to 2022 at a center in northern Taiwan, involving patients with E. anophelis bacteremia. Demographic and clinical data, including comorbidities and laboratory parameters, were collected. Clinical severity was assessed using the Pitt bacteremia score. Bacterial isolates were identified using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and species-specific polymerase chain reaction. Antimicrobial susceptibility was determined using broth microdilution, and resistance genes were detected by PCR.Results: The 14-day and 28-day mortality rates after admission were 35% and 40%, respectively. The 14-day mortality rate was associated with high Pitt bacteremia scores, chronic kidney disease, anemia, and hyperbilirubinemia. Anemia and high Pitt bacteremia scores were consistently associated with 28-day mortality. Most isolates were phenotypically resistant to β-lactams, fluoroquinolones, and trimethoprim-sulfamethoxazole, while susceptibility to minocycline (1.6%) and rifampin (9.5%) was preserved. The detected resistance genes included multiple determinants (blaB, blaGOB, blaCME, and dfrE), with a notable absence of arr-1.Conclusion: E. anophelis bacteremia is associated with higher mortality and multidrug resistance. Prognosis is significantly influenced by host factors and specific laboratory findings. Given the high resistance of these bacteria to traditional antibiotics, minocycline and rifampin may serve as key treatment options when susceptibility is confirmed. Further studies are needed to validate their clinical efficacy, dosing, and combination strategies.Keywords: Bacteremia mortality, antibiotic resistance genes, Pitt bacteremia score, minocycline susceptibility, rifampin efficacy, broth microdilutio

CMS: A web-based system for visualization and analysis of genome-wide methylation data of human cancers

DNA methylation of promoter CpG islands is associated with gene suppression, and its unique genome-wide profiles have been linked to tumor progression. Coupled with high-throughput sequencing technologies, it can now efficiently determine genome-wide methylation profiles in cancer cells. Also, experimental and computational technologies make it possible to find the functional relationship between cancer-specific methylation patterns and their clinicopathological parameters.Cancer methylome system (CMS) is a web-based database application designed for the visualization, comparison and statistical analysis of human cancer-specific DNA methylation. Methylation intensities were obtained from MBDCap-sequencing, pre-processed and stored in the database. 191 patient samples (169 tumor and 22 normal specimen) and 41 breast cancer cell-lines are deposited in the database, comprising about 6.6 billion uniquely mapped sequence reads. This provides comprehensive and genome-wide epigenetic portraits of human breast cancer and endometrial cancer to date. Two views are proposed for users to better understand methylation structure at the genomic level or systemic methylation alteration at the gene level. In addition, a variety of annotation tracks are provided to cover genomic information. CMS includes important analytic functions for interpretation of methylation data, such as the detection of differentially methylated regions, statistical calculation of global methylation intensities, multiple gene sets of biologically significant categories, interactivity with UCSC via custom-track data. We also present examples of discoveries utilizing the framework.CMS provides visualization and analytic functions for cancer methylome datasets. A comprehensive collection of datasets, a variety of embedded analytic functions and extensive applications with biological and translational significance make this system powerful and unique in cancer methylation research. CMS is freely accessible at: http://cbbiweb.uthscsa.edu/KMethylomes/

Neurogenic inflammation after traumatic brain injury and its potentiation of classical inflammation

Background: The neuroinflammatory response following traumatic brain injury (TBI) is known to be a key secondary injury factor that can drive ongoing neuronal injury. Despite this, treatments that have targeted aspects of the inflammatory pathway have not shown significant efficacy in clinical trials. Main body: We suggest that this may be because classical inflammation only represents part of the story, with activation of neurogenic inflammation potentially one of the key initiating inflammatory events following TBI. Indeed, evidence suggests that the transient receptor potential cation channels (TRP channels), TRPV1 and TRPA1, are polymodal receptors that are activated by a variety of stimuli associated with TBI, including mechanical shear stress, leading to the release of neuropeptides such as substance P (SP). SP augments many aspects of the classical inflammatory response via activation of microglia and astrocytes, degranulation of mast cells, and promoting leukocyte migration. Furthermore, SP may initiate the earliest changes seen in blood-brain barrier (BBB) permeability, namely the increased transcellular transport of plasma proteins via activation of caveolae. This is in line with reports that alterations in transcellular transport are seen first following TBI, prior to decreases in expression of tight-junction proteins such as claudin-5 and occludin. Indeed, the receptor for SP, the tachykinin NK1 receptor, is found in caveolae and its activation following TBI may allow influx of albumin and other plasma proteins which directly augment the inflammatory response by activating astrocytes and microglia. Conclusions: As such, the neurogenic inflammatory response can exacerbate classical inflammation via a positive feedback loop, with classical inflammatory mediators such as bradykinin and prostaglandins then further stimulating TRP receptors. Accordingly, complete inhibition of neuroinflammation following TBI may require the inhibition of both classical and neurogenic inflammatory pathways.Frances Corrigan, Kimberley A. Mander, Anna V. Leonard and Robert Vin

The tenth data release of the Sloan digital sky survey: First spectroscopic data from the SDSS-iii apache point observatory galactic evolution experiment

The Sloan Digital Sky Survey (SDSS) has been in operation since 2000 April. This paper presents the tenth public data release (DR10) from its current incarnation, SDSS-III. This data release includes the first spectroscopic data from the Apache Point Observatory Galaxy Evolution Experiment (APOGEE), along with spectroscopic data from the Baryon Oscillation Spectroscopic Survey (BOSS) taken through 2012 July. The APOGEE instrument is a near-infrared R ~ 22,500 300-fiber spectrograph covering 1:514-1:696 μm. The APOGEE survey is studying the chemical abundances and radial velocities of roughly 100,000 red giant star candidates in the bulge, bar, disk, and halo of the Milky Way. DR10 includes 178,397 spectra of 57,454 stars, each typically observed three or more times, from APOGEE. Derived quantities from these spectra (radial velocities, effective temperatures, surface gravities, and metallicities) are also included. DR10 also roughly doubles the number of BOSS spectra over those included in the ninth data release. DR10 includes a total of 1,507,954 BOSS spectra, comprising 927,844 galaxy spectra; 182,009 quasar spectra; and 159,327 stellar spectra, selected over 6373.2 deg2.This is an author-created, un-copyedited version of an article accepted for publication in The Astrophysical Journal Supplement Series. The publisher is not responsible for any errors or omissions in this version of the manuscript or any version derived from it. The Version of Record is available online at http://dx.doi.org/10.1088/0067-0049/211/2/17. The accepted version will be under embargo until the 18th March 2015

Sloan Digital Sky Survey IV: Mapping the Milky Way, Nearby Galaxies, and the Distant Universe

We describe the Sloan Digital Sky Survey IV (SDSS-IV), a project encompassing three major spectroscopic programs. The Apache Point Observatory Galactic Evolution Experiment 2 (APOGEE-2) is observing hundreds of thousands of Milky Way stars at high resolution and high signal-to-noise ratios in the near-infrared. The Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) survey is obtaining spatially resolved spectroscopy for thousands of nearby galaxies (median $z\sim 0.03$). The extended Baryon Oscillation Spectroscopic Survey (eBOSS) is mapping the galaxy, quasar, and neutral gas distributions between $z\sim 0.6$ and 3.5 to constrain cosmology using baryon acoustic oscillations, redshift space distortions, and the shape of the power spectrum. Within eBOSS, we are conducting two major subprograms: the SPectroscopic IDentification of eROSITA Sources (SPIDERS), investigating X-ray AGNs and galaxies in X-ray clusters, and the Time Domain Spectroscopic Survey (TDSS), obtaining spectra of variable sources. All programs use the 2.5 m Sloan Foundation Telescope at the Apache Point Observatory; observations there began in Summer 2014. APOGEE-2 also operates a second near-infrared spectrograph at the 2.5 m du Pont Telescope at Las Campanas Observatory, with observations beginning in early 2017. Observations at both facilities are scheduled to continue through 2020. In keeping with previous SDSS policy, SDSS-IV provides regularly scheduled public data releases; the first one, Data Release 13, was made available in 2016 July

Identification and Filtering of Uncharacteristic Noise in the CMS Hadron Calorimeter

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Sloan Digital Sky Survey IV: Mapping the Milky Way, Nearby Galaxies, and the Distant Universe

We describe the Sloan Digital Sky Survey IV (SDSS-IV), a project encompassing three major spectroscopic programs. The Apache Point Observatory Galactic Evolution Experiment 2 (APOGEE-2) is observing hundreds of thousands of Milky Way stars at high resolution and high signal-to-noise ratios in the near-infrared. The Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) survey is obtaining spatially resolved spectroscopy for thousands of nearby galaxies (median $z\sim 0.03$). The extended Baryon Oscillation Spectroscopic Survey (eBOSS) is mapping the galaxy, quasar, and neutral gas distributions between $z\sim 0.6$ and 3.5 to constrain cosmology using baryon acoustic oscillations, redshift space distortions, and the shape of the power spectrum. Within eBOSS, we are conducting two major subprograms: the SPectroscopic IDentification of eROSITA Sources (SPIDERS), investigating X-ray AGNs and galaxies in X-ray clusters, and the Time Domain Spectroscopic Survey (TDSS), obtaining spectra of variable sources. All programs use the 2.5 m Sloan Foundation Telescope at the Apache Point Observatory; observations there began in Summer 2014. APOGEE-2 also operates a second near-infrared spectrograph at the 2.5 m du Pont Telescope at Las Campanas Observatory, with observations beginning in early 2017. Observations at both facilities are scheduled to continue through 2020. In keeping with previous SDSS policy, SDSS-IV provides regularly scheduled public data releases; the first one, Data Release 13, was made available in 2016 July