Sub-electron noise charge-coupled devices

A charge coupled device designed for celestial spectroscopy has achieved readout noise as low as 0.6 electrons rms. A nondestructive output circuit was operated in a special manner to read a single pixel multiple times. Off-chip electronics averaged the multiple values, reducing the random noise by the square root of the number of readouts. Charge capacity was measured to be 500,000 electrons. The device format is 1600 pixels horizontal by 64 pixels vertical. Pixel size is 28 microns square. Two output circuits are located at opposite ends of the 1600 bit CCD register. The device was thinned and operated backside illuminated at -110 degrees C. Output circuit design, layout, and operation are described. Presented data includes the photon transfer curve, noise histograms, and bar-target images down to 3 electrons signal. The test electronics are described, and future improvements are discussed

Habitat associations of Golden-winged Warblers and Blue-winged Warblers during the non-breeding season

The Golden-winged Warbler (Vermivora chyrsoptera) and Blue-winged Warbler (Vermivora cyanoptera) are both Neotropical migratory species of elevated conservation concern that overlap in distribution on their Central American wintering grounds, yet the extent to which they overlap in terms of habitat use is unknown, potentially hindering conservation efforts. We surveyed these two species along habitat and elevational gradients within a coffee-growing landscape during 2016 and 2017 in Yoro, Honduras. We used playback with a mobbing track known to enhance detections of female warblers, since examining sexual habitat segregation was another objective of our study. Habitat occupied by these two species differed, with male Golden-winged Warblers occurring in landscapes dominated by humid forest/coffee (forest with some dense shade coffee, which were indistinguishable with remote sensing at our sites) at higher elevations than male Blue-winged Warblers, which were positively associated with the amount of agriculture in the landscape. Six of seven female Golden-winged Warblers were encountered in shade coffee, however, this association was not significant, likely due to small sample size and low detectability. The association between male Golden-winged Warblers and humid forest/coffee and elevation, and contrasts in habitat use between male and female Golden-winged Warblers, are consistent with prior research in the region. Furthermore, the landscape associations of these non-breeding Vermivora species mirror their breeding landscape associations, with Golden-winged Warblers occupying more forested landscapes and Blue-winged Warblers occupying more agricultural landscapes. The use of shade coffee by female Golden-winged Warblers and Blue-winged Warblers suggests agroforestry could be a promising tool for conserving wintering populations of these species, although this result should be viewed with caution given that use of shade coffee is reported to elevate predation risk in other migratory species, and may not provide habitat for forest-dependent resident birds

Prior specification in Bayesian occupancy modelling improves analysis of species occurrence data

Multi-species biodiversity indicators are increasingly used to assess progress towards the 2020 ‘Aichi’ targets of the Convention on Biological Diversity. However, most multi-species indicators are biased towards a few well-studied taxa for which suitable abundance data are available. Consequently, many taxonomic groups are poorly represented in current measures of biodiversity change, particularly invertebrates. Alternative data sources, including opportunistic occurrence data, when analysed appropriately, can provide robust estimates of occurrence over time and increase the taxonomic coverage of such measures of population change. Occupancy modelling has been shown to produce robust estimates of species occurrence and trends through time. So far, this approach has concentrated on well-recorded taxa and performs poorly where recording intensity is low. Here, we show that the use of weakly informative priors in a Bayesian occupancy model framework greatly improves the precision of occurrence estimates associated with current model formulations when analysing low-intensity occurrence data, although estimated trends can be sensitive to the choice of prior when data are extremely sparse at either end of the recording period. Specifically, three variations of a Bayesian occupancy model, each with a different focus on information sharing among years, were compared using British ant data from the Bees, Wasps and Ants Recording Society and tested in a simulation experiment. Overall, the random walk model, which allows the sharing of information between the current and previous year, showed improved precision and low bias when estimating species occurrence and trends. The use of the model formulation described here will enable a greater range of datasets to be analysed, covering more taxa, which will significantly increase taxonomic representation of measures of biodiversity change

New advancements in charge-coupled device technology: sub-electron noise and 4096x4096 pixel CCDs

This paper reports on two new advancements in CCD technology. The first area of development has produced a special purpose CCD designed for ultra low-signal level imaging and spectroscopy applications that require sub-electron read noise floors. A nondestructive output circuit operating near its 1/f noise regime is clocked in a special manner to read a single pixel multiple times. Off-chip electronics average the multiple values, reducing the random noise by the square-root of the number of samples taken. Noise floors below 0.5 electrons rms are reported. The second development involves the design and performance of a high resolution imager of 4096 x 4096 pixels, the largest CCD manufactured in terms of pixel count. The device utilizes a 7.5-micron pixel fabricated with three-level poly-silicon to achieve high yield

Sub-electron noise charge-coupled devices

A charge coupled device designed for celestial spectroscopy has achieved readout noise as low as 0.6 electrons rms. A nondestructive output circuit was operated in a special manner to read a single pixel multiple times. Off-chip electronics averaged the multiple values, reducing the random noise by the square root of the number of readouts. Charge capacity was measured to be 500,000 electrons. The device format is 1600 pixels horizontal by 64 pixels vertical. Pixel size is 28 microns square. Two output circuits are located at opposite ends of the 1600 bit CCD register. The device was thinned and operated backside illuminated at -110 degrees C. Output circuit design, layout, and operation are described. Presented data includes the photon transfer curve, noise histograms, and bar-target images down to 3 electrons signal. The test electronics are described, and future improvements are discussed

Alzheimer's genetic risk effects on cerebral blood flow are spatially consistent and proximal to gene expression across the lifespan

Cerebrovascular dysregulation is a hallmark feature of Alzheimer’s disease (AD), where alterations in cerebral blood flow (CBF) are observed decades prior to symptom onset. Genome-wide association studies (GWAS) show that AD has a polygenic aetiology, providing a tool for studying AD susceptibility across the lifespan. Here, we ascertain whether AD genetic risk effects on CBF previously observed (Chandler et al., 2019) remain consistent across the lifespan. We further provide a causal mechanism to AD genetic risk scores (AD-GRS) effects by establishing spatial convergence between AD-GRS associated regional reductions in CBF and mRNA expression of the proximal AD transcripts using independent data from the Allen Brain Atlas. We analysed grey matter (GM) CBF in a young cohort (N=75; aged 18-35) and an older cohort (N=90; aged 55-85). Critically, we observed that AD-GRS was negatively associated with whole brain GM CBF in the older cohort (standardised β −0.38 [−0.68 – −0.09], P = 0.012), consistent with our prior observation in younger healthy adults (Chandler et al., 2019). We then demonstrate that the regional impact of AD-GRS on GM CBF was spatially consistent across the younger and older samples (r = 0.233, P = 0.035). Finally, we show that CBF across the cortex was related to the regional expression of the genes proximal to SNP’s used to estimate AD-GRS in both younger and older cohorts (ZTWO-TAILED = −1.99, P= 0.047; ZTWO-TAILED = −2.153 P = 0.032, respectively). These observations collectively demonstrate that AD risk alleles have a negative influence on brain vascular function and likely contribute to cerebrovascular changes preceding the onset of clinical symptoms, potentially driven by regional expression of proximal AD risk genes across the brain. Our observations suggest that reduced CBF is an early antecedent of AD and a key modifiable target for therapeutic intervention in individuals with a higher cumulative genetic risk for AD. This study will further enable identification of key molecular processes that underpin AD genetic risk related reductions in CBF that could be targeted decades prior to the onset of neurodegeneration

Deep-sea microbes as tools to refine the rules of innate immune pattern recognition.

The assumption of near-universal bacterial detection by pattern recognition receptors is a foundation of immunology. The limits of this pattern recognition concept, however, remain undefined. As a test of this hypothesis, we determined whether mammalian cells can recognize bacteria that they have never had the natural opportunity to encounter. These bacteria were cultivated from the deep Pacific Ocean, where the genus Moritella was identified as a common constituent of the culturable microbiota. Most deep-sea bacteria contained cell wall lipopolysaccharide (LPS) structures that were expected to be immunostimulatory, and some deep-sea bacteria activated inflammatory responses from mammalian LPS receptors. However, LPS receptors were unable to detect 80% of deep-sea bacteria examined, with LPS acyl chain length being identified as a potential determinant of immunosilence. The inability of immune receptors to detect most bacteria from a different ecosystem suggests that pattern recognition strategies may be defined locally, not globally.R01 AI093589 - NIAID NIH HHS; P30 DK034854 - NIDDK NIH HHS; U19 AI133524 - NIAID NIH HHS; R01 AI147314 - NIAID NIH HHS; R01 AI116550 - NIAID NIH HHS; R37 AI116550 - NIAID NIH HHS; R01 AI123820 - NIAID NIH HHSAccepted manuscrip