A Pseudolikelihood Approach for Simultaneous Analysis of Array Comparative Genomic Hybridizations (aCGH)

DNA sequence copy number has been shown to be associated with cancer development and progression. Array-based Comparative Genomic Hybridization (aCGH) is a recent development that seeks to identify the copy number ratio at large numbers of markers across the genome. Due to experimental and biological variations across chromosomes and across hybridizations, current methods are limited to analyses of single chromosomes. We propose a more powerful approach that borrows strength across chromosomes and across hybridizations. We assume a Gaussian mixture model, with a hidden Markov dependence structure, and with random effects to allow for intertumoral variation, as well as intratumoral clonal variation. For ease of computation, we base estimation on a pseudolikelihood function. The method produces quantitative assessments of the likelihood of genetic alterations at each clone, along with a graphical display for simple visual interpretation. We assess the characteristics of the method through simulation studies and through analysis of a brain tumor aCGH data set. We show that the pseudolikelihood approach is superior to existing methods both in detecting small regions of copy number alteration and in accurately classifying regions of change when intratumoral clonal variation is present

A code of conduct is imperative for ocean carbon dioxide removal research

© The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Loomis, R., Cooley, S. R., Collins, J. R., Engler, S., & Suatoni, L. A code of conduct is imperative for ocean carbon dioxide removal research. Frontiers in Marine Science, 9, (2022): 872800, https://doi.org/10.3389/fmars.2022.872800.As the impacts of rising temperatures mount and the global transition to clean energy advances only gradually, scientists and policymakers are looking towards carbon dioxide removal (CDR) methods to prevent the worst impacts of climate change. Attention has increasingly focused on ocean CDR techniques, which enhance or restore marine systems to sequester carbon. Ocean CDR research presents the risk of uncertain impacts to human and environmental welfare, yet there are no domestic regulations aimed at ensuring the safety and efficacy of this research. A code of conduct that establishes principles of responsible research, fairness, and equity is needed in this field. This article presents fifteen key components of an ocean CDR research code of conduct.JC acknowledges funding support from Bezos Earth Fund

The Cellular and Physiological Basis for Lung Repair and Regeneration: Past, Present, and Future.

The respiratory system, which includes the trachea, airways, and distal alveoli, is a complex multi-cellular organ that intimately links with the cardiovascular system to accomplish gas exchange. In this review and as members of the NIH/NHLBI-supported Progenitor Cell Translational Consortium, we discuss key aspects of lung repair and regeneration. We focus on the cellular compositions within functional niches, cell-cell signaling in homeostatic health, the responses to injury, and new methods to study lung repair and regeneration. We also provide future directions for an improved understanding of the cell biology of the respiratory system, as well as new therapeutic avenues

Detectors for the James Webb Space Telescope Near-Infrared Spectrograph I: Readout Mode, Noise Model, and Calibration Considerations

We describe how the James Webb Space Telescope (JWST) Near-Infrared Spectrograph's (NIRSpec's) detectors will be read out, and present a model of how noise scales with the number of multiple non-destructive reads sampling-up-the-ramp. We believe that this noise model, which is validated using real and simulated test data, is applicable to most astronomical near-infrared instruments. We describe some non-ideal behaviors that have been observed in engineering grade NIRSpec detectors, and demonstrate that they are unlikely to affect NIRSpec sensitivity, operations, or calibration. These include a HAWAII-2RG reset anomaly and random telegraph noise (RTN). Using real test data, we show that the reset anomaly is: (1) very nearly noiseless and (2) can be easily calibrated out. Likewise, we show that large-amplitude RTN affects only a small and fixed population of pixels. It can therefore be tracked using standard pixel operability maps.Comment: 55 pages, 10 figure

JWST Near-Infrared Detectors: Latest Test Results

The James Webb Space Telescope, an infrared-optimized space telescope being developed by NASA for launch in 2013, will utilize cutting-edge detector technology in its investigation of fundamental questions in astrophysics. JWST's near infrared spectrograph, NIRSpec utilizes two 2048 x 2048 HdCdTe arrays with Sidecar ASIC readout electronics developed by Teledyne to provide spectral coverage from 0.6 microns to 5 microns. We present recent test and calibration results for the NIRSpec flight arrays as well as data processing routines for noise reduction and cosmic ray rejection

Detector Arrays for the James Webb Space Telescope Near-Infrared Spectrograph

The James Webb Space Telescope's (JWST) Near Infrared Spectrograph (NIRSpec) incorporates two 5 micron cutoff (lambda(sub co) = 5 microns) 2048x2048 pixel Teledyne HgCdTe HAWAII-2RG sensor chip assemblies. These detector arrays, and the two Teledyne SIDECAR application specific integrated circuits that control them, are operated in space at T approx. 37 K. In this article, we provide a brief introduction to NIRSpec, its detector subsystem (DS), detector readout in the space radiation environment, and present a snapshot of the developmental status of the NIRSpec DS as integration and testing of the engineering test unit begins

Detectors for the James Webb Space Telescope Near-Infrared Spectrograph I: Readout Mode, Noise Model, and Calibration Considerations

We describe how the James Webb Space Telescope (JWST) Near-Infrared Spectrograph's (NIRSpec's) detectors will be read out, and present a model of how noise scales with the number of multiple non-destructive reads sampling-up-the-ramp. We believe that this noise model, which is validated using real and simulated test data, is applicable to most astronomical near-infrared instruments. We describe some non-ideal behaviors that have been observed in engineering grade NIRSpec detectors, and demonstrate that they are unlikely to affect NIRSpec sensitivity, operations, or calibration. These include a HAWAII-2RG reset anomaly and random telegraph noise (RTN). Using real test data, we show that the reset anomaly is: (1) very nearly noiseless and (2) can be easily calibrated out. Likewise, we show that RTN affects only a small and fixed population of pixels. It can therefore be tracked using standard pixel operability maps

James Webb Space Telescope Near-Infrared Spectrograph: Dark Performance of the First Flight Candidate Detector Arrays

The James Webb Space Telescope (JWST) Near Infrared Spectrograph (NIRSpec) incorporates two 5 micron cutoff (lambda(sub co) = 5 micron) 2048x2048 pixel Teledyne HgCdTe HAWAII-2RG sensor chip assemblies. These detector arrays, and the two Teledyne SIDECAR application specific integrated circuits that control them, are operated in space at T approx. 37 K. This article focuses on the measured performance of the first flight-candidate, and near-flight candidate, detector arrays. These are the first flight-packaged detector arrays that meet NIRSpec's challenging 6 e(-) rms total noise requirement