Doubly-charged particles at the Large Hadron Collider

In this work we investigate the production and signatures of doubly-charged particles at the Large Hadron Collider. We start with the Standard Model particle content and representations and add generic doubly-charged exotic particles. We classify these doubly-charged states according to their spin, considering scalar, fermionic and vectorial fields, and according to their SU(2)L representation, being chosen to be either trivial, fundamental, or adjoint. We write the most general interactions between them and the Standard Model sector and study their production modes and possible decay channels. We then probe how they can most likely be observed and how particles with different spin and SU(2)L representations could be possibly distinguished.Comment: 18 pages, 8 figures, 1 table; version accepted by Phys.Rev.

Automated mass spectrum generation for new physics

We describe an extension of the FeynRules package dedicated to the automatic generation of the mass spectrum associated with any Lagrangian-based quantum field theory. After introducing a simplified way to implement particle mixings, we present a new class of FeynRules functions allowing both for the analytical computation of all the model mass matrices and for the generation of a C++ package, dubbed ASperGe. This program can then be further employed for a numerical evaluation of the rotation matrices necessary to diagonalize the field basis. We illustrate these features in the context of the Two-Higgs-Doublet Model, the Minimal Left-Right Symmetric Standard Model and the Minimal Supersymmetric Standard Model.Comment: 11 pages, 1 table; version accepted by EPJ

Clinically Valuable Quality Control for PET/MRI Systems:Consensus Recommendation From the HYBRID Consortium

International audienceQuality control (QC) of medical imaging devices is essential to ensure their proper function and to gain accurate and quantitative results. Therefore, several international bodies have published QC guidelines and recommendations for a wide range of imaging modalities to ensure adequate performance of the systems. Hybrid imaging systems such as positron emission tomography/computed tomography (PET/CT) or PET/magnetic resonance imaging (PET/MRI), in particular, present additional challenges caused by differences between the combined modalities. However, despite the increasing use of this hybrid imaging modality in recent years, there are no dedicated QC recommendations for PET/MRI. Therefore, this work aims at collecting information on QC procedures across a European PET/MRI network, presenting quality assurance procedures implemented by PET/MRI vendors and achieving a consensus on PET/MRI QC procedures across imaging centers. Users of PET/MRI systems at partner sites involved in the HYBRID consortium were surveyed about local frequencies of QC procedures for PET/MRI. Although all sites indicated that they perform vendor-specific daily QC procedures, significant variations across the centers were observed for other QC tests and testing frequencies. Likewise, variations in available recommendations and guidelines and the QC procedures implemented by vendors were found. Based on the available information and our clinical expertise within this consortium, we were able to propose a minimum set of PET/MRI QC recommendations including the daily QC, cross-calibration tests, and an image quality (IQ) assessment for PET and coil checks and MR image quality tests for MRI. Together with regular checks of the PET-MRI alignment, proper PET/MRI performance can be ensured

An integrated map of structural variation in 2,504 human genomes

© 2015 Macmillan Publishers Limited. All rights reserved. Structural variants are implicated in numerous diseases and make up the majority of varying nucleotides among human genomes. Here we describe an integrated set of eight structural variant classes comprising both balanced and unbalanced variants, which we constructed using short-read DNA sequencing data and statistically phased onto haplotype blocks in 26 human populations. Analysing this set, we identify numerous gene-intersecting structural variants exhibiting population stratification and describe naturally occurring homozygous gene knockouts that suggest the dispensability of a variety of human genes. We demonstrate that structural variants are enriched on haplotypes identified by genome-wide association studies and exhibit enrichment for expression quantitative trait loci. Additionally, we uncover appreciable levels of structural variant complexity at different scales, including genic loci subject to clusters of repeated rearrangement and complex structural variants with multiple breakpoints likely to have formed through individual mutational events. Our catalogue will enhance future studies into structural variant demography, functional impact and disease association

Fast Statistical Alignment

We describe a new program for the alignment of multiple biological sequences that is both statistically motivated and fast enough for problem sizes that arise in practice. Our Fast Statistical Alignment program is based on pair hidden Markov models which approximate an insertion/deletion process on a tree and uses a sequence annealing algorithm to combine the posterior probabilities estimated from these models into a multiple alignment. FSA uses its explicit statistical model to produce multiple alignments which are accompanied by estimates of the alignment accuracy and uncertainty for every column and character of the alignment—previously available only with alignment programs which use computationally-expensive Markov Chain Monte Carlo approaches—yet can align thousands of long sequences. Moreover, FSA utilizes an unsupervised query-specific learning procedure for parameter estimation which leads to improved accuracy on benchmark reference alignments in comparison to existing programs. The centroid alignment approach taken by FSA, in combination with its learning procedure, drastically reduces the amount of false-positive alignment on biological data in comparison to that given by other methods. The FSA program and a companion visualization tool for exploring uncertainty in alignments can be used via a web interface at http://orangutan.math.berkeley.edu/fsa/, and the source code is available at http://fsa.sourceforge.net/

COVID-19 Convalescent Plasma Therapy Decreases Inflammatory Cytokines: A Randomized Controlled Trial

This study examined the role that cytokines may have played in the beneficial outcomes found when outpatient individuals infected with SARS-CoV-2 were transfused with COVID-19 convalescent plasma (CCP) early in their infection. We found that the pro-inflammatory cytokine IL-6 decreased significantly faster in patients treated early with CCP. Participants with COVID-19 treated with CCP later in the infection did not have the same effect. This decrease in IL-6 levels after early CCP treatment suggests a possible role of inflammation in COVID-19 progression. The evidence of IL-6 involvement brings insight into the possible mechanisms involved in CCP treatment mitigating SARS-CoV-2 severity

Dynamics of Inflammatory Responses After SARS-CoV-2 Infection by Vaccination Status in the USA: A Prospective Cohort Study

BACKGROUND: Cytokines and chemokines play a critical role in the response to infection and vaccination. We aimed to assess the longitudinal association of COVID-19 vaccination with cytokine and chemokine concentrations and trajectories among people with SARS-CoV-2 infection. METHODS: In this longitudinal, prospective cohort study, blood samples were used from participants enrolled in a multi-centre randomised trial assessing the efficacy of convalescent plasma therapy for ambulatory COVID-19. The trial was conducted in 23 outpatient sites in the USA. In this study, participants (aged ≥18 years) were restricted to those with COVID-19 before vaccination or with breakthrough infections who had blood samples and symptom data collected at screening (pre-transfusion), day 14, and day 90 visits. Associations between COVID-19 vaccination status and concentrations of 21 cytokines and chemokines (measured using multiplexed sandwich immunoassays) were examined using multivariate linear mixed-effects regression models, adjusted for age, sex, BMI, hypertension, diabetes, trial group, and COVID-19 waves (pre-alpha or alpha and delta). FINDINGS: Between June 29, 2020, and Sept 30, 2021, 882 participants recently infected with SARS-CoV-2 were enrolled, of whom 506 (57%) were female and 376 (43%) were male. 688 (78%) of 882 participants were unvaccinated, 55 (6%) were partly vaccinated, and 139 (16%) were fully vaccinated at baseline. After adjusting for confounders, geometric mean concentrations of interleukin (IL)-2RA, IL-7, IL-8, IL-15, IL-29 (interferon-λ), inducible protein-10, monocyte chemoattractant protein-1, and tumour necrosis factor-α were significantly lower among the fully vaccinated group than in the unvaccinated group at screening. On day 90, fully vaccinated participants had approximately 20% lower geometric mean concentrations of IL-7, IL-8, and vascular endothelial growth factor-A than unvaccinated participants. Cytokine and chemokine concentrations decreased over time in the fully and partly vaccinated groups and unvaccinated group. Log INTERPRETATION: Initially and during recovery from symptomatic COVID-19, fully vaccinated participants had lower concentrations of inflammatory markers than unvaccinated participants suggesting vaccination is associated with short-term and long-term reduction in inflammation, which could in part explain the reduced disease severity and mortality in vaccinated individuals. FUNDING: US Department of Defense, National Institutes of Health, Bloomberg Philanthropies, State of Maryland, Mental Wellness Foundation, Moriah Fund, Octapharma, HealthNetwork Foundation, and the Shear Family Foundation