Pulse Shape Discrimination of CsI(Tl) with a Photomultiplier Tube and MPPCs

In this study, we evaluate and compare the pulse shape discrimination (PSD) performance of multipixel photon counters (MPPCs, also known as silicon photomultiphers - SiPMs) with that of a typical photomultiplier tube (PMT) when testing using CsI(Tl) scintillators. We use the charge comparison method, whereby we discriminate different types of particles by the ratio of charges integrated within two time-gates (the delayed part and the entire digitized waveform). For a satisfactory PSD performance, a setup should generate many photoelectrons (p.e.) and collect their charges efficiently. The PMT setup generates more p.e. than the MPPC setup does. With the same digitizer and the same long time-gate (the entire digitized waveform), the PMT setup is also better in charge collection. Therefore, the PMT setup demonstrates better PSD performance. We subsequently test the MPPC setup using a new data acquisition (DAQ) system. Using this new DAQ, the long time-gate is extended by nearly four times the length when using the previous digitizer. With this longer time-gate, we collect more p.e. at the tail part of the pulse and almost all the charges of the total collected p.e. Thus, the PSD performance of the MPPC setup is improved significantly. This study also provides an estimation of the short time-gate (the delayed part of the digitized waveform) that can give a satisfactory PSD performance without an extensive analysis to optimize this gate

奥付

This chapter discusses a conceptual framework for integrated health and environmental assessment that combines health status, and the physical, socioeconomic and cultural environments in order to improve human health and minimize environmental impact. This concept's application in the management of human and animal excreta in Vietnam is then described

Testate amoeba response to acid deposition in a Scottish peatland

Peatlands around the world are exposed to anthropogenic or volcanogenic sulphur pollution. Impacts on peatland microbial communities have been inferred from changes in gas flux but have rarely been directly studied. In this study, the impacts of sulphuric acid deposition on peatland testate amoebae were investigated by analysis of experimental plots on a Scottish peatland almost 7 years after acid treatment. Results showed reduced concentration of live amoebae and changes in community structure which remained significant even when differences in pH were accounted for. Several possible explanations for the impacts can be proposed including taphonomic processes and changes in plant communities. Previous studies have inferred a shift from methanogenic archaea to sulphate-reducing bacteria in sulphate-treated peats; it is possible that the impacts detected here might relate to this change, perhaps through testate amoeba predation on methanotrophs

A smooth introduction to the wavefront set

The wavefront set provides a precise description of the singularities of a distribution. Because of its ability to control the product of distributions, the wavefront set was a key element of recent progress in renormalized quantum field theory in curved spacetime, quantum gravity, the discussion of time machines or quantum energy inequalitites. However, the wavefront set is a somewhat subtle concept whose standard definition is not easy to grasp. This paper is a step by step introduction to the wavefront set, with examples and motivation. Many different definitions and new interpretations of the wavefront set are presented. Some of them involve a Radon transform.Comment: 29 pages, 7 figure

How many is enough? Determining optimal count totals for ecological and palaeoecological studies of testate amoebae

Testate amoebae are increasingly used in ecological and palaeoecological studies of wetlands. To characterise the amoeba community a certain number of individuals need to be counted under the microscope. To date, most studies have aimed for 150 individuals, but that sample size is not based on adequate evidence. When testate amoeba concentrations are low, it can be difficult or impossible to reach this total. The impacts of lower count totals have never been seriously scrutinised. We investigated the impact of count size on number of taxa identified, quantitative inferences of environmental variables and the strength of the links between amoebae and environmental data in the context of predicting depth to water table. Low counts were simulated by random selection of individuals from four existing datasets. Results show progressively diminishing returns by all criteria as count size increases from low numbers to counts of 150. A higher count is required to identify all taxa than to adequately characterise the community for transfer function inference. We suggest that in most cases, it will be a more efficient use of time to count a greater number of samples to a lower count. While a count of 50 individuals may be sufficient for some samples from some sites we recommend that counts of 100 individuals should be sufficient for most samples. Counts need only be increased to 150 or more where the aim is to identify relatively minor, but still potentially ecologically relevant community changes. This approach will help reduce lack of replication and low resolution, which are common limitations in testate amoeba-based palaeoecological and ecological studies

Simulation Study of Photon-to-Digital Converter (PDC) Timing Specifications for LoLX Experiment

The Light only Liquid Xenon (LoLX) experiment is a prototype detector aimed to study liquid xenon (LXe) light properties and various photodetection technologies. LoLX is also aimed to quantify LXe's time resolution as a potential scintillator for 10~ps time-of-flight (TOF) PET. Another key goal of LoLX is to perform a time-based separation of Cerenkov and scintillation photons for new background rejection methods in LXe experiments. To achieve this separation, LoLX is set to be equipped with photon-to-digital converters (PDCs), a photosensor type that provides a timestamp for each observed photon. To guide the PDC design, we explore requirements for time-based Cerenkov separation. We use a PDC simulator, whose input is the light information from the Geant4-based LoLX simulation model, and evaluate the separation quality against time-to-digital converter (TDC) parameters. Simulation results with TDC parameters offer possible configurations supporting a good separation. Compared with the current filter-based approach, simulations show Cerenkov separation level increases from 54% to 71% when using PDC and time-based separation. With the current photon time profile of LoLX simulation, the results also show 71% separation is achievable with just 4 TDCs per PDC. These simulation results will lead to a specification guide for the PDC as well as expected results to compare against future PDC-based experimental measurements. In the longer term, the overall LoLX results will assist large LXe-based experiments and motivate the assembly of a LXe-based TOF-PET demonstrator system.Comment: 5 pages, 7 figure

Identifying hotspots for antibiotic resistance emergence and selection, and elucidating pathways to human exposure: Application of a systems-thinking approach to aquaculture systems

Aquaculture systems are highly complex, dynamic and interconnected systems influenced by environmental, biological, cultural, socio-economic and human behavioural factors. Intensification of aquaculture production is likely to drive indiscriminate use of antibiotics to treat or prevent disease and increase productivity, often to compensate for management and husbandry deficiencies. Surveillance or monitoring of antibiotic usage (ABU) and antibiotic resistance (ABR) is often lacking or absent. Consequently, there are knowledge gaps for the risk of ABR emergence and human exposure to ABR in these systems and the wider environment. The aim of this study was to use a systems-thinking approach to map two aquaculture systems in Vietnam – striped catfish and white-leg shrimp – to identify hotspots for emergence and selection of resistance, and human exposure to antibiotics and antibiotic-resistant bacteria. System mapping was conducted by stakeholders at an interdisciplinary workshop in Hanoi, Vietnam during January 2018, and the maps generated were refined until consensus. Thereafter, literature was reviewed to complement and cross-reference information and to validate the final maps. The maps and component interactions with the environment revealed the grow-out phase, where juveniles are cultured to harvest size, to be a key hotspot for emergence of ABR in both systems due to direct and indirect ABU, exposure to water contaminated with antibiotics and antibiotic-resistant bacteria, and duration of this stage. The pathways for human exposure to antibiotics and ABR were characterised as: occupational (on-farm and at different handling points along the value chain), through consumption (bacterial contamination and residues) and by environmental routes. By using systems thinking and mapping by stakeholders to identify hotspots we demonstrate the applicability of an integrated, interdisciplinary approach to characterising ABU in aquaculture. This work provides a foundation to quantify risks at different points, understand interactions between components, and identify stakeholders who can lead and implement change

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin