Perspective:Dietary Biomarkers of Intake and Exposure - Exploration with Omics Approaches

While conventional nutrition research has yielded biomarkers such as doubly labeled water for energy metabolism and 24-h urinary nitrogen for protein intake, a critical need exists for additional, equally robust biomarkers that allow for objective assessment of specific food intake and dietary exposure. Recent advances in high-throughput MS combined with improved metabolomics techniques and bioinformatic tools provide new opportunities for dietary biomarker development. In September 2018, the NIH organized a 2-d workshop to engage nutrition and omics researchers and explore the potential of multiomics approaches in nutritional biomarker research. The current Perspective summarizes key gaps and challenges identified, as well as the recommendations from the workshop that could serve as a guide for scientists interested in dietary biomarkers research. Topics addressed included study designs for biomarker development, analytical and bioinformatic considerations, and integration of dietary biomarkers with other omics techniques. Several clear needs were identified, including larger controlled feeding studies, testing a variety of foods and dietary patterns across diverse populations, improved reporting standards to support study replication, more chemical standards covering a broader range of food constituents and human metabolites, standardized approaches for biomarker validation, comprehensive and accessible food composition databases, a common ontology for dietary biomarker literature, and methodologic work on statistical procedures for intake biomarker discovery. Multidisciplinary research teams with appropriate expertise are critical to moving forward the field of dietary biomarkers and producing robust, reproducible biomarkers that can be used in public health and clinical research

Effects of protein on glycemic and incretin responses and gastric emptying after oral glucose in healthy subjects

© 2007 American Society for NutritionBackgroundDietary interventions represent a promising therapeutic strategy to optimize postprandial glycemia. The addition of protein to oral glucose has been reported to improve the glycemic profile.ObjectiveThe aim of the current study was to evaluate the mechanisms by which protein supplementation lowers the blood glucose response to oral glucose.DesignNine healthy men were studied on 3 d each in a random order. Subjects consumed 300-mL drinks containing either 50 g glucose (Glucose), 30 g gelatin (Protein), or 50 g glucose with 30 g gelatin (Glucose + Protein) in water labeled with 150 mg [(13)C]acetate. Blood and breath samples were subsequently collected for 3 h to measure blood glucose and plasma insulin, glucagon-like peptide 1 (GLP-1), and glucose-dependent insulinotropic polypeptide (GIP) concentrations and gastric half-emptying time, which was calculated from (13)CO(2) excretion.ResultsThe blood glucose response was less after Glucose + Protein than after Glucose (P ConclusionsIn healthy humans, the addition of protein to oral glucose lowers postprandial blood glucose concentrations acutely, predominantly by slowing gastric emptying, although protein also stimulates incretin hormones and non-glucose-dependent insulin release

Citizen scientists track a charismatic carnivore: Mapping the spread and impact of the South African Mantis (Miomantidae, Miomantis caffra) in Australia

The recent integration of citizen science with modern technology has greatly increased its applications and has allowed more people than ever to contribute to research across all areas of science. In particular, citizen science has been instrumental in the detection and monitoring of novel introduced species across the globe. This study provides the first records of Miomantis caffra Saussure, 1871, the South African Mantis, from the Australian mainland and uses records from four different citizen science and social media platforms in conjunction with museum records to track the spread of the species through the country. A total of 153 wild mantises and oothecae were observed across four states and territories (New South Wales, Norfolk Island, Victoria, and Western Australia) between 2009 and 2021. The large number of observations of the species in Victoria and the more recent isolated observations in other states and territories suggest that the species initially arrived in Geelong via oothecae attached to plants or equipment, likely from the invasive population in New Zealand. From there it established and spread outwards to Melbourne and eventually to other states and territories, both naturally and with the aid of human transport. We also provide a comparison of M. caffra to similar native mantises, specifically Pseudomantis albofimbriata (Stål, 1860), and comment on the potential impact and further spread of the species within Australia. Finally, we reiterate the many benefits of engaging directly with citizen scientists in biodiversity research and comment on the decision to include them in all levels of this research investigation

Citizen scientists track a charismatic carnivore: Mapping the spread and impact of the South African Mantis (Miomantidae, Miomantis caffra) in Australia

The recent integration of citizen science with modern technology has greatly increased its applications and has allowed more people than ever to contribute to research across all areas of science. In particular, citizen science has been instrumental in the detection and monitoring of novel introduced species across the globe. This study provides the first records of Miomantis caffra Saussure, 1871, the South African Mantis, from the Australian mainland and uses records from four different citizen science and social media platforms in conjunction with museum records to track the spread of the species through the country. A total of 153 wild mantises and oothecae were observed across four states and territories (New South Wales, Norfolk Island, Victoria, and Western Australia) between 2009 and 2021. The large number of observations of the species in Victoria and the more recent isolated observations in other states and territories suggest that the species initially arrived in Geelong via oothecae attached to plants or equipment, likely from the invasive population in New Zealand. From there it established and spread outwards to Melbourne and eventually to other states and territories, both naturally and with the aid of human transport. We also provide a comparison of M. caffra to similar native mantises, specifically Pseudomantis albofimbriata (Stål, 1860), and comment on the potential impact and further spread of the species within Australia. Finally, we reiterate the many benefits of engaging directly with citizen scientists in biodiversity research and comment on the decision to include them in all levels of this research investigation

Perspective: Dietary Biomarkers of Intake and Exposure—Exploration with Omics Approaches

While conventional nutrition research has yielded biomarkers such as doubly labeled water for energy metabolism and 24-h urinary nitrogen for protein intake, a critical need exists for additional, equally robust biomarkers that allow for objective assessment of specific food intake and dietary exposure. Recent advances in high-throughput MS combined with improved metabolomics techniques and bioinformatic tools provide new opportunities for dietary biomarker development. In September 2018, the NIH organized a 2-d workshop to engage nutrition and omics researchers and explore the potential of multiomics approaches in nutritional biomarker research. The current Perspective summarizes key gaps and challenges identified, as well as the recommendations from the workshop that could serve as a guide for scientists interested in dietary biomarkers research. Topics addressed included study designs for biomarker development, analytical and bioinformatic considerations, and integration of dietary biomarkers with other omics techniques. Several clear needs were identified, including larger controlled feeding studies, testing a variety of foods and dietary patterns across diverse populations, improved reporting standards to support study replication, more chemical standards covering a broader range of food constituents and human metabolites, standardized approaches for biomarker validation, comprehensive and accessible food composition databases, a common ontology for dietary biomarker literature, and methodologic work on statistical procedures for intake biomarker discovery. Multidisciplinary research teams with appropriate expertise are critical to moving forward the field of dietary biomarkers and producing robust, reproducible biomarkers that can be used in public health and clinical research

DUNE Offline Computing Conceptual Design Report

International audienceThis document describes Offline Software and Computing for the Deep Underground Neutrino Experiment (DUNE) experiment, in particular, the conceptual design of the offline computing needed to accomplish its physics goals. Our emphasis in this document is the development of the computing infrastructure needed to acquire, catalog, reconstruct, simulate and analyze the data from the DUNE experiment and its prototypes. In this effort, we concentrate on developing the tools and systems thatfacilitate the development and deployment of advanced algorithms. Rather than prescribing particular algorithms, our goal is to provide resources that are flexible and accessible enough to support creative software solutions as HEP computing evolves and to provide computing that achieves the physics goals of the DUNE experiment

Highly-parallelized simulation of a pixelated LArTPC on a GPU

The rapid development of general-purpose computing on graphics processing units (GPGPU) is allowing the implementation of highly-parallelized Monte Carlo simulation chains for particle physics experiments. This technique is particularly suitable for the simulation of a pixelated charge readout for time projection chambers, given the large number of channels that this technology employs. Here we present the first implementation of a full microphysical simulator of a liquid argon time projection chamber (LArTPC) equipped with light readout and pixelated charge readout, developed for the DUNE Near Detector. The software is implemented with an end-to-end set of GPU-optimized algorithms. The algorithms have been written in Python and translated into CUDA kernels using Numba, a just-in-time compiler for a subset of Python and NumPy instructions. The GPU implementation achieves a speed up of four orders of magnitude compared with the equivalent CPU version. The simulation of the current induced on $10^3$ pixels takes around 1 ms on the GPU, compared with approximately 10 s on the CPU. The results of the simulation are compared against data from a pixel-readout LArTPC prototype

DUNE Offline Computing Conceptual Design Report

This document describes Offline Software and Computing for the Deep Underground Neutrino Experiment (DUNE) experiment, in particular, the conceptual design of the offline computing needed to accomplish its physics goals. Our emphasis in this document is the development of the computing infrastructure needed to acquire, catalog, reconstruct, simulate and analyze the data from the DUNE experiment and its prototypes. In this effort, we concentrate on developing the tools and systems thatfacilitate the development and deployment of advanced algorithms. Rather than prescribing particular algorithms, our goal is to provide resources that are flexible and accessible enough to support creative software solutions as HEP computing evolves and to provide computing that achieves the physics goals of the DUNE experiment

Highly-parallelized simulation of a pixelated LArTPC on a GPU

The rapid development of general-purpose computing on graphics processing units (GPGPU) is allowing the implementation of highly-parallelized Monte Carlo simulation chains for particle physics experiments. This technique is particularly suitable for the simulation of a pixelated charge readout for time projection chambers, given the large number of channels that this technology employs. Here we present the first implementation of a full microphysical simulator of a liquid argon time projection chamber (LArTPC) equipped with light readout and pixelated charge readout, developed for the DUNE Near Detector. The software is implemented with an end-to-end set of GPU-optimized algorithms. The algorithms have been written in Python and translated into CUDA kernels using Numba, a just-in-time compiler for a subset of Python and NumPy instructions. The GPU implementation achieves a speed up of four orders of magnitude compared with the equivalent CPU version. The simulation of the current induced on $10^3$ pixels takes around 1 ms on the GPU, compared with approximately 10 s on the CPU. The results of the simulation are compared against data from a pixel-readout LArTPC prototype