Digital pulse-shape discrimination of fast neutrons and gamma rays

Discrimination of the detection of fast neutrons and gamma rays in a liquid scintillator detector has been investigated using digital pulse-processing techniques. An experimental setup with a 252Cf source, a BC-501 liquid scintillator detector, and a BaF2 detector was used to collect waveforms with a 100 Ms/s, 14 bit sampling ADC. Three identical ADC's were combined to increase the sampling frequency to 300 Ms/s. Four different digital pulse-shape analysis algorithms were developed and compared to each other and to data obtained with an analogue neutron-gamma discrimination unit. Two of the digital algorithms were based on the charge comparison method, while the analogue unit and the other two digital algorithms were based on the zero-crossover method. Two different figure-of-merit parameters, which quantify the neutron-gamma discrimination properties, were evaluated for all four digital algorithms and for the analogue data set. All of the digital algorithms gave similar or better figure-of-merit values than what was obtained with the analogue setup. A detailed study of the discrimination properties as a function of sampling frequency and bit resolution of the ADC was performed. It was shown that a sampling ADC with a bit resolution of 12 bits and a sampling frequency of 100 Ms/s is adequate for achieving an optimal neutron-gamma discrimination for pulses having a dynamic range for deposited neutron energies of 0.3-12 MeV. An investigation of the influence of the sampling frequency on the time resolution was made. A FWHM of 1.7 ns was obtained at 100 Ms/s.Comment: 26 pages, 14 figures, submitted to Nuclear Instruments and Methods in Physics Research

Practical evaluation of SEEK and OpenBIS for biological data management in SynthSys; second report.

Author contributions: ET and TZ modified and configured the software; KT provided servers and services; TZ and AJM wrote the report with input from all authors.The objective of this joint project between University Information Services (IS) and the School of Biological Sciences (SBS) is to evaluate the provision of Biological Data Management systems and their integration with University Research Data Management solutions. The long-term aim is to comply with the University and Funder data mandates, while also adding value to ongoing research in SBS and the wider University. The benefits from streamlining data management would help to balance the School and user investment in establishing and adopting data management systems

Comparative transcriptome in large-scale human and cattle populations

Cross-species comparison of transcriptomes is important for elucidating evolutionary molecular mechanisms underpinning phenotypic variation between and within species, yet to date it has been essentially limited to model organisms with relatively small sample sizes. Here, we systematically analyze and compare 10,830 and 4866 publicly available RNA-seq samples in humans and cattle, respectively, representing 20 common tissues. Focusing on 17,315 orthologous genes, we demonstrate that mean/median gene expression, inter-individual variation of expression, expression quantitative trait loci, and gene co-expression networks are generally conserved between humans and cattle. By examining large-scale genome-wide association studies for 46 human traits (average n = 327,973) and 45 cattle traits (average n = 24,635), we reveal that the heritability of complex traits in both species is significantly more enriched in transcriptionally conserved than diverged genes across tissues. In summary, our study provides a comprehensive comparison of transcriptomes between humans and cattle, which might help decipher the genetic and evolutionary basis of complex traits in both species.https://doi.org/10.1186/s13059-022-02745-

SARS-CoV-2 susceptibility and COVID-19 disease severity are associated with genetic variants affecting gene expression in a variety of tissues

Variability in SARS-CoV-2 susceptibility and COVID-19 disease severity between individuals is partly due to genetic factors. Here, we identify 4 genomic loci with suggestive associations for SARS-CoV-2 susceptibility and 19 for COVID-19 disease severity. Four of these 23 loci likely have an ethnicity-specific component. Genome-wide association study (GWAS) signals in 11 loci colocalize with expression quantitative trait loci (eQTLs) associated with the expression of 20 genes in 62 tissues/cell types (range: 1:43 tissues/gene), including lung, brain, heart, muscle, and skin as well as the digestive system and immune system. We perform genetic fine mapping to compute 99% credible SNP sets, which identify 10 GWAS loci that have eight or fewer SNPs in the credible set, including three loci with one single likely causal SNP. Our study suggests that the diverse symptoms and disease severity of COVID-19 observed between individuals is associated with variants across the genome, affecting gene expression levels in a wide variety of tissue types

A first update on mapping the human genetic architecture of COVID-19

peer reviewe

Whole-genome sequencing reveals host factors underlying critical COVID-19

Critical COVID-19 is caused by immune-mediated inflammatory lung injury. Host genetic variation influences the development of illness requiring critical care1 or hospitalization2,3,4 after infection with SARS-CoV-2. The GenOMICC (Genetics of Mortality in Critical Care) study enables the comparison of genomes from individuals who are critically ill with those of population controls to find underlying disease mechanisms. Here we use whole-genome sequencing in 7,491 critically ill individuals compared with 48,400 controls to discover and replicate 23 independent variants that significantly predispose to critical COVID-19. We identify 16 new independent associations, including variants within genes that are involved in interferon signalling (IL10RB and PLSCR1), leucocyte differentiation (BCL11A) and blood-type antigen secretor status (FUT2). Using transcriptome-wide association and colocalization to infer the effect of gene expression on disease severity, we find evidence that implicates multiple genes—including reduced expression of a membrane flippase (ATP11A), and increased expression of a mucin (MUC1)—in critical disease. Mendelian randomization provides evidence in support of causal roles for myeloid cell adhesion molecules (SELE, ICAM5 and CD209) and the coagulation factor F8, all of which are potentially druggable targets. Our results are broadly consistent with a multi-component model of COVID-19 pathophysiology, in which at least two distinct mechanisms can predispose to life-threatening disease: failure to control viral replication; or an enhanced tendency towards pulmonary inflammation and intravascular coagulation. We show that comparison between cases of critical illness and population controls is highly efficient for the detection of therapeutically relevant mechanisms of disease

Detection of explosive substances by tomographic inspection using neutron and gamma-ray spectroscopy.

In recent years the detection and identification of hazardous materials has become increasingly important. This work discusses research and development of a technique which is capable of detecting and imaging hidden explosives. It is proposed to utilise neutron interrogation of the substances under investigation facilitating the detection of emitted gamma radiation and scattered neutrons. Pulsed fast neutron techniques are attractive because they can be used to determine the concentrations of the light elements (hydrogen, carbon, nitrogen, and oxygen) which can be the primary components of explosive materials. Using segmented High Purity Ge (HPGe) detectors and digital pulse processing [R.J. Cooper, G. Turk, A.J. Boston, H.C. Boston, J.R. Cresswell, A.R. Mather, P.J. Nolan, C.J. Hall, I. Lazarus, J. Simpson, A. Berry, T. Beveridge, J. Gillam, R.A. Lewis, in: Proceedings of the 7th International Conference on Position Sensitive Detectors, Nuclear Instruments and Methods A, in press; I. Lazarus, D.E. Appelbe, A. J. Boston, P.J. Coleman-Smith, J.R. Cresswell, M. Descovich, S.A.A. Gros, M. Lauer, J. Norman, C.J. Pearson, V.F.E. Pucknell, J.A. Sampson, G. Turk, J.J. Valiente-Dobón, IEEE Trans. Nucl. Sci., 51 (2004) 1353; R.J. Cooper, A.J. Boston, H.C. Boston, J.R. Cresswell, A.N. Grint, A.R. Mather, P.J. Nolan, D.P. Scraggs, G. Turk, C.J. Hall, I. Lazarus, A. Berry, T. Beveridge, J. Gillam, R.A. Lewis, in: Proceedings of the 11th International Symposium on Radiation Measurements and Application, 2006. [1-3]] the scatter path of incident photons can be reconstructed to determine the origin of the gamma-rays without the need for mechanical collimation by applying the Compton camera principle [V. Schonfelder, A. Hirner, K. Schneider, Nucl. Instr. and Meth. 107 (1973) 385; R.W. Todd, J.M. Nightingale, D.B. Everett, Nature 251 (1974) 132. [4,5]]. In addition, it is proposed to utilise the scattered neutrons which recoil from the materials being assayed, detecting them with a fast neutron detector providing data for inversion to tomographic images. In this paper, we present our approach to the design and implementation of a system for the efficient screening of goods in luggage and cargo containers. The simulation in a Monte Carlo framework using GEANT4 has been carried out for the imaging of gamma-ray events using the Compton camera design which will be discussed. The results of Compton camera measurements using HPGe detectors and the subsequent reconstructed images will also be presented. © 2007 Elsevier B.V. All rights reserved

The empirical characterization of organic liquid scintillation detectors by the normalized average of digitized pulse shapes.

The application of the digital acquisition of pulses from a liquid scintillator to detector characterization is described. Experimental data for a mixed neutron/γ-ray field have been recorded digitally. An empirical method for the characterization of liquid scintillation detectors, in terms of their pulse shape, has been developed which is quick and easy. It provides generic pulses shapes for use in pulse-shape discrimination and that can be used to derive analytical descriptions of each pulse via an accepted six-parameter formulism. The distributions of the neutron and γ-ray components arising as a result of discrimination via pulse gradient analysis (PGA) follow a bi-Gaussian trend and exhibit degrees of both kurtosis and skew