Identification of rare alleles and their carriers using compressed se(que)nsing

Identification of rare variants by resequencing is important both for detecting novel variations and for screening individuals for known disease alleles. New technologies enable low-cost resequencing of target regions, although it is still prohibitive to test more than a few individuals. We propose a novel pooling design that enables the recovery of novel or known rare alleles and their carriers in groups of individuals. The method is based on a Compressed Sensing (CS) approach, which is general, simple and efficient. CS allows the use of generic algorithmic tools for simultaneous identification of multiple variants and their carriers. We model the experimental procedure and show via computer simulations that it enables the recovery of rare alleles and their carriers in larger groups than were possible before. Our approach can also be combined with barcoding techniques to provide a feasible solution based on current resequencing costs. For example, when targeting a small enough genomic region (∼100 bp) and using only ∼10 sequencing lanes and ∼10 distinct barcodes per lane, one recovers the identity of 4 rare allele carriers out of a population of over 4000 individuals. We demonstrate the performance of our approach over several publicly available experimental data sets

Direct evidence of exfoliation efficiency and graphene dispersibility of green solvents towards sustainable graphene production

Achieving a sustainable production of pristine high-quality graphene and other layered materials at a low cost is one of the bottlenecks that needs to be overcome for reaching 2D material applications at a large scale. Liquid phase exfoliation in conjunction with N-methyl-2-pyrrolidone (NMP) is recognized as the most efficient method for both the exfoliation and dispersion of graphene. Unfortunately, NMP is neither sustainable nor suitable for up-scaling production due to its adverse impact on the environment. Here, we show the real potential of green solvents by revealing the independent contributions of their exfoliation efficiency and graphene dispersibility to the graphene yield. By experimentally separating these two factors, we demonstrate that the exfoliation efficiency of a given solvent is independent of its dispersibility. Our studies revealed that isopropanol can be used to exfoliate graphite as efficiently as NMP. Our finding is corroborated by the matching ratio between the polar and dispersive energies of graphite and that of the solvent surface tension. This direct evidence of exfoliation efficiency and dispersibility of solvents paves the way to developing a deeper understanding of the real potential of sustainable graphene manufacturing at a large scale.UK Engineering and Physical Sciences Research Council (EPSRC), within the project “Sustainable and industrially scalable ultrasonic liquid phase exfoliation technologies for manufacturing 2D advanced functional materials” (EcoUltra2D), with the grant nos. EP/R031665/1; EP/R031401/1; EP/R031819/1; and EP/R031975/1. We wish to acknowledge the support of the Henry Royce Institute for advanced materials for K.L.N. through the Student Equipment Access Scheme enabling access to the Kruss GmbH K100C Surface Tensiometer facilities at the University of Manchester; EPSRC grant number EP/R00661X/1. N.G. thanks the Royal Society for financial support

Direct evidence of exfoliation efficiency and graphene dispersibility of green solvents towards sustainable graphene production

Achieving sustainable production of pristine high-quality graphene and other layered materials at low cost is one of the bottlenecks that needs to be overcome for reaching 2D materials applications at scale. Liquid Phase Exfoliation (LPE) in conjunction with N-methyl-2-pyrrolidone (NMP) is recognised as the most efficient method for both the exfoliation and dispersion of graphene. Unfortunately, NMP is neither sustainable nor suitable for up-scaling production due to its adverse impact on the environment. Here we show the real potential of green solvents by revealing the independent contributions of their exfoliation efficiency and graphene dispersibility to the graphene yield. By experimentally separating these two factors we show that the exfoliation efficiency of a given solvent is independent of its dispersibility. Here we show that isopropanol can be used to exfoliate graphite as efficiently as NMP. This finding is corroborated by the matching ratio between the polar and dispersive energy of graphite and that of the solvent surface tension. This direct evidence of exfoliation efficiency and dispersibility of solvents paves the way to developing a deeper understanding of the real potential of sustainable graphene manufacturing at scale

Direct evidence of the exfoliation efficiency and graphene dispersibility of green solvents toward sustainable graphene production

Achieving a sustainable production of pristine high-quality graphene and other layered materials at a low cost is one of the bottlenecks that needs to be overcome for reaching 2D material applications at a large scale. Liquid phase exfoliation in conjunction with N-methyl-2-pyrrolidone (NMP) is recognized as the most efficient method for both the exfoliation and dispersion of graphene. Unfortunately, NMP is neither sustainable nor suitable for up-scaling production due to its adverse impact on the environment. Here, we show the real potential of green solvents by revealing the independent contributions of their exfoliation efficiency and graphene dispersibility to the graphene yield. By experimentally separating these two factors, we demonstrate that the exfoliation efficiency of a given solvent is independent of its dispersibility. Our studies revealed that isopropanol can be used to exfoliate graphite as efficiently as NMP. Our finding is corroborated by the matching ratio between the polar and dispersive energies of graphite and that of the solvent surface tension. This direct evidence of exfoliation efficiency and dispersibility of solvents paves the way to developing a deeper understanding of the real potential of sustainable graphene manufacturing at a large scale

Probing quantum gravity using photons from a flare of the active galactic nucleus Markarian 501 observed by the MAGIC telescope

We analyze the timing of photons observed by the MAGIC telescope during a flare of the active galactic nucleus Mkn 501 for a possible correlation with energy, as suggested by some models of quantum gravity (QG), which predict a vacuum refractive index \simeq 1 + (E/M_{QGn})^n, n = 1,2. Parametrizing the delay between gamma-rays of different energies as \Delta t =\pm\tau_l E or \Delta t =\pm\tau_q E^2, we find \tau_l=(0.030\pm0.012) s/GeV at the 2.5-sigma level, and \tau_q=(3.71\pm2.57)x10^{-6} s/GeV^2, respectively. We use these results to establish lower limits M_{QG1} > 0.21x10^{18} GeV and M_{QG2} > 0.26x10^{11} GeV at the 95% C.L. Monte Carlo studies confirm the MAGIC sensitivity to propagation effects at these levels. Thermal plasma effects in the source are negligible, but we cannot exclude the importance of some other source effect.Comment: 12 pages, 3 figures, Phys. Lett. B, reflects published versio

Acute immune signatures and their legacies in severe acute respiratory syndrome coronavirus-2 infected cancer patients

Given the immune system’s importance for cancer surveillance and treatment, we have investigated how it may be affected by SARS-CoV-2 infection of cancer patients. Across some heterogeneity in tumor type, stage, and treatment, virus-exposed solid cancer patients display a dominant impact of SARS-CoV-2, apparent from the resemblance of their immune signatures to those for COVID-19+ non-cancer patients. This is not the case for hematological malignancies, with virus-exposed patients collectively displaying heterogeneous humoral responses, an exhausted T cell phenotype and a high prevalence of prolonged virus shedding. Furthermore, while recovered solid cancer patients’ immunophenotypes resemble those of nonvirus-exposed cancer patients, recovered hematological cancer patients display distinct, lingering immunological legacies. Thus, while solid cancer patients, including those with advanced disease, seem no more at risk of SARS-CoV-2-associated immune dysregulation than the general population, hematological cancer patients show complex immunological consequences of SARS-CoV-2 exposure that might usefully inform their care

International comparisons of laboratory values from the 4CE collaborative to predict COVID-19 mortality

Given the growing number of prediction algorithms developed to predict COVID-19 mortality, we evaluated the transportability of a mortality prediction algorithm using a multi-national network of healthcare systems. We predicted COVID-19 mortality using baseline commonly measured laboratory values and standard demographic and clinical covariates across healthcare systems, countries, and continents. Specifically, we trained a Cox regression model with nine measured laboratory test values, standard demographics at admission, and comorbidity burden pre-admission. These models were compared at site, country, and continent level. Of the 39,969 hospitalized patients with COVID-19 (68.6% male), 5717 (14.3%) died. In the Cox model, age, albumin, AST, creatine, CRP, and white blood cell count are most predictive of mortality. The baseline covariates are more predictive of mortality during the early days of COVID-19 hospitalization. Models trained at healthcare systems with larger cohort size largely retain good transportability performance when porting to different sites. The combination of routine laboratory test values at admission along with basic demographic features can predict mortality in patients hospitalized with COVID-19. Importantly, this potentially deployable model differs from prior work by demonstrating not only consistent performance but also reliable transportability across healthcare systems in the US and Europe, highlighting the generalizability of this model and the overall approach

Search for neutral heavy leptons produced in ZZ decays

Weak isosinglet Neutral Heavy Leptons (νm) have been searched for using data collected by the DELPHI detector corresponding to 3.3 × 106 hadronic Z0 decays at LEP1. Four separate searches have been performed, for short-lived νm production giving monojet or acollinear jet topologies, and for long-lived νm giving detectable secondary vertices or calorimeter clusters. No indication of the existence of these particles has been found, leading to an upper limit for the branching ratio BR(Z0 → νmν̄) of about 1.3 × 10-6 at 95% confidence level for νm masses between 3.5 and 50 GeV/c2. Outside this range the limit weakens rapidly with the νm mass. The results are also interpreted in terms of limits for the single production of excited neutrinos. © Springer-Verlag 1997

Outcomes from elective colorectal cancer surgery during the SARS-CoV-2 pandemic

This study aimed to describe the change in surgical practice and the impact of SARS-CoV-2 on mortality after surgical resection of colorectal cancer during the initial phases of the SARS-CoV-2 pandemic