138 research outputs found
Physics-assisted Generative Adversarial Network for X-Ray Tomography
X-ray tomography is capable of imaging the interior of objects in three
dimensions non-invasively, with applications in biomedical imaging, materials
science, electronic inspection, and other fields. The reconstruction process
can be an ill-conditioned inverse problem, requiring regularization to obtain
satisfactory reconstructions. Recently, deep learning has been adopted for
tomographic reconstruction. Unlike iterative algorithms which require a
distribution that is known a priori, deep reconstruction networks can learn a
prior distribution through sampling the training distributions. In this work,
we develop a Physics-assisted Generative Adversarial Network (PGAN), a two-step
algorithm for tomographic reconstruction. In contrast to previous efforts, our
PGAN utilizes maximum-likelihood estimates derived from the measurements to
regularize the reconstruction with both known physics and the learned prior.
Synthetic objects with spatial correlations are integrated circuits (IC) from a
proposed model CircuitFaker. Compared with maximum-likelihood estimation, PGAN
can reduce the photon requirement with limited projection angles to achieve a
given error rate. We further attribute the improvement to the learned prior by
reconstructing objects created without spatial correlations. The advantages of
using a prior from deep learning in X-ray tomography may further enable
low-photon nanoscale imaging.Comment: arXiv admin note: text overlap with arXiv:2111.0801
A Tabletop X-Ray Tomography Instrument for Nanometer-Scale Imaging: Integration of a Scanning Electron Microscope with a Transition-Edge Sensor Spectrometer
X-ray nanotomography is a powerful tool for the characterization of nanoscale
materials and structures, but is difficult to implement due to competing
requirements on X-ray flux and spot size. Due to this constraint,
state-of-the-art nanotomography is predominantly performed at large synchrotron
facilities. Compact X-ray nanotomography tools operated in standard analysis
laboratories exist, but are limited by X-ray optics and destructive sample
preparation techniques. We present a laboratory-scale nanotomography instrument
that achieves nanoscale spatial resolution while changing the limitations of
conventional tomography tools. The instrument combines the electron beam of a
scanning electron microscope (SEM) with the precise, broadband X-ray detection
of a superconducting transition-edge sensor (TES) microcalorimeter. The
electron beam generates a highly focused X-ray spot in a metal target, while
the TES spectrometer isolates target photons with high signal-to-noise. This
combination of a focused X-ray spot, energy-resolved X-ray detection, and
unique system geometry enable nanoscale, element-specific X-ray imaging in a
compact footprint. The proof-of-concept for this approach to X-ray
nanotomography is demonstrated by imaging 160 nm features in three dimensions
in a Cu-SiO2 integrated circuit, and a path towards finer resolution and
enhanced imaging capabilities is discussed.Comment: The following article has been submitted to Physical Review Applie
A tabletop x-ray tomography instrument for nanometer-scale imaging: demonstration of the 1,000-element transition-edge sensor subarray
We report on the 1,000-element transition-edge sensor (TES) x-ray
spectrometer implementation of the TOMographic Circuit Analysis Tool (TOMCAT).
TOMCAT combines a high spatial resolution scanning electron microscope (SEM)
with a highly efficient and pixelated TES spectrometer to reconstruct
three-dimensional maps of nanoscale integrated circuits (ICs). A 240-pixel
prototype spectrometer was recently used to reconstruct ICs at the 130 nm
technology node, but to increase imaging speed to more practical levels, the
detector efficiency needs to be improved. For this reason, we are building a
spectrometer that will eventually contain 3,000 TES microcalorimeters read out
with microwave superconducting quantum interference device (SQUID)
multiplexing, and we currently have commissioned a 1,000 TES subarray. This
still represents a significant improvement from the 240-pixel system and allows
us to begin characterizing the full spectrometer performance. Of the 992
maximimum available readout channels, we have yielded 818 devices, representing
the largest number of TES x-ray microcalorimeters simultaneously read out to
date. These microcalorimeters have been optimized for pulse speed rather than
purely energy resolution, and we measure a FWHM energy resolution of 14 eV at
the 8.0 keV Cu K line.Comment: 5 pages, 4 figures, submitted to IEEE Transactions on Applied
Superconductivit
Acceleration of Relativistic Protons during the 20 January 2005 Flare and CME
The origin of relativistic solar protons during large flare/CME events has
not been uniquely identified so far.We perform a detailed comparative analysis
of the time profiles of relativistic protons detected by the worldwide network
of neutron monitors at Earth with electromagnetic signatures of particle
acceleration in the solar corona during the large particle event of 20 January
2005. The intensity-time profile of the relativistic protons derived from the
neutron monitor data indicates two successive peaks. We show that microwave,
hard X-ray and gamma-ray emissions display several episodes of particle
acceleration within the impulsive flare phase. The first relativistic protons
detected at Earth are accelerated together with relativistic electrons and with
protons that produce pion decay gamma-rays during the second episode. The
second peak in the relativistic proton profile at Earth is accompanied by new
signatures of particle acceleration in the corona within approximatively 1
solar radius above the photosphere, revealed by hard X-ray and microwave
emissions of low intensity, and by the renewed radio emission of electron beams
and of a coronal shock wave. We discuss the observations in terms of different
scenarios of particle acceleration in the corona.Comment: 22 pages, 5 figure
The North American tree-ring fire-scar network
Fire regimes in North American forests are diverse and modern fire records are often too short to capture important patterns, trends, feedbacks, and drivers of variability. Tree-ring fire scars provide valuable perspectives on fire regimes, including centuries-long records of fire year, season, frequency, severity, and size. Here, we introduce the newly compiled North American tree-ring fire-scar network (NAFSN), which contains 2562 sites, >37,000 fire-scarred trees, and covers large parts of North America. We investigate the NAFSN in terms of geography, sample depth, vegetation, topography, climate, and human land use. Fire scars are found in most ecoregions, from boreal forests in northern Alaska and Canada to subtropical forests in southern Florida and Mexico. The network includes 91 tree species, but is dominated by gymnosperms in the genus Pinus. Fire scars are found from sea level to >4000-m elevation and across a range of topographic settings that vary by ecoregion. Multiple regions are densely sampled (e.g., >1000 fire-scarred trees), enabling new spatial analyses such as reconstructions of area burned. To demonstrate the potential of the network, we compared the climate space of the NAFSN to those of modern fires and forests; the NAFSN spans a climate space largely representative of the forested areas in North America, with notable gaps in warmer tropical climates. Modern fires are burning in similar climate spaces as historical fires, but disproportionately in warmer regions compared to the historical record, possibly related to under-sampling of warm subtropical forests or supporting observations of changing fire regimes. The historical influence of Indigenous and non-Indigenous human land use on fire regimes varies in space and time. A 20th century fire deficit associated with human activities is evident in many regions, yet fire regimes characterized by frequent surface fires are still active in some areas (e.g., Mexico and the southeastern United States). These analyses provide a foundation and framework for future studies using the hundreds of thousands of annually- to sub-annually-resolved tree-ring records of fire spanning centuries, which will further advance our understanding of the interactions among fire, climate, topography, vegetation, and humans across North America
Anchored enrichment dataset for true flies (order Diptera) reveals insights into the phylogeny of flower flies (family Syrphidae)
Background: Anchored hybrid enrichment is a form of next-generation sequencing that uses oligonucleotide probes to target conserved regions of the genome flanked by less conserved regions in order to acquire data useful for phylogenetic inference from a broad range of taxa. Once a probe kit is developed, anchored hybrid enrichment is superior to traditional PCR-based Sanger sequencing in terms of both the amount of genomic data that can be recovered and effective cost. Due to their incredibly diverse nature, importance as pollinators, and historical instability with regard to subfamilial and tribal classification, Syrphidae (flower flies or hoverflies) are an ideal candidate for anchored hybrid enrichment-based phylogenetics, especially since recent molecular phylogenies of the syrphids using only a few markers have resulted in highly unresolved topologies. Over 6200 syrphids are currently known and uncovering their phylogeny will help us to understand how these species have diversified, providing insight into an array of ecological processes, from the development of adult mimicry, the origin of adult migration, to pollination patterns and the evolution of larval resource utilization. Results: We present the first use of anchored hybrid enrichment in insect phylogenetics on a dataset containing 30 flower fly species from across all four subfamilies and 11 tribes out of 15. To produce a phylogenetic hypothesis, 559 loci were sampled to produce a final dataset containing 217,702 sites. We recovered a well resolved topology with bootstrap support values that were almost universally >95 %. The subfamily Eristalinae is recovered as paraphyletic, with the strongest support for this hypothesis to date. The ant predators in the Microdontinae are sister to all other syrphids. Syrphinae and Pipizinae are monophyletic and sister to each other. Larval predation on soft-bodied hemipterans evolved only once in this family. Conclusions: Anchored hybrid enrichment was successful in producing a robustly supported phylogenetic hypothesis for the syrphids. Subfamilial reconstruction is concordant with recent phylogenetic hypotheses, but with much higher support values. With the newly designed probe kit this analysis could be rapidly expanded with further sampling, opening the door to more comprehensive analyses targeting problem areas in syrphid phylogenetics and ecology.Peer reviewe
Genetic variants in novel pathways influence blood pressure and cardiovascular disease risk.
Blood pressure is a heritable trait influenced by several biological pathways and responsive to environmental stimuli. Over one billion people worldwide have hypertension (≥140 mm Hg systolic blood pressure or ≥90 mm Hg diastolic blood pressure). Even small increments in blood pressure are associated with an increased risk of cardiovascular events. This genome-wide association study of systolic and diastolic blood pressure, which used a multi-stage design in 200,000 individuals of European descent, identified sixteen novel loci: six of these loci contain genes previously known or suspected to regulate blood pressure (GUCY1A3-GUCY1B3, NPR3-C5orf23, ADM, FURIN-FES, GOSR2, GNAS-EDN3); the other ten provide new clues to blood pressure physiology. A genetic risk score based on 29 genome-wide significant variants was associated with hypertension, left ventricular wall thickness, stroke and coronary artery disease, but not kidney disease or kidney function. We also observed associations with blood pressure in East Asian, South Asian and African ancestry individuals. Our findings provide new insights into the genetics and biology of blood pressure, and suggest potential novel therapeutic pathways for cardiovascular disease prevention
Association of genetic variation with systolic and diastolic blood pressure among African Americans: the Candidate Gene Association Resource study
The prevalence of hypertension in African Americans (AAs) is higher than in other US groups; yet, few have performed genome-wide association studies (GWASs) in AA. Among people of European descent, GWASs have identified genetic variants at 13 loci that are associated with blood pressure. It is unknown if these variants confer susceptibility in people of African ancestry. Here, we examined genome-wide and candidate gene associations with systolic blood pressure (SBP) and diastolic blood pressure (DBP) using the Candidate Gene Association Resource (CARe) consortium consisting of 8591 AAs. Genotypes included genome-wide single-nucleotide polymorphism (SNP) data utilizing the Affymetrix 6.0 array with imputation to 2.5 million HapMap SNPs and candidate gene SNP data utilizing a 50K cardiovascular gene-centric array (ITMAT-Broad-CARe [IBC] array). For Affymetrix data, the strongest signal for DBP was rs10474346 (P= 3.6 × 10−8) located near GPR98 and ARRDC3. For SBP, the strongest signal was rs2258119 in C21orf91 (P= 4.7 × 10−8). The top IBC association for SBP was rs2012318 (P= 6.4 × 10−6) near SLC25A42 and for DBP was rs2523586 (P= 1.3 × 10−6) near HLA-B. None of the top variants replicated in additional AA (n = 11 882) or European-American (n = 69 899) cohorts. We replicated previously reported European-American blood pressure SNPs in our AA samples (SH2B3, P= 0.009; TBX3-TBX5, P= 0.03; and CSK-ULK3, P= 0.0004). These genetic loci represent the best evidence of genetic influences on SBP and DBP in AAs to date. More broadly, this work supports that notion that blood pressure among AAs is a trait with genetic underpinnings but also with significant complexit
Testing the AGN Radio and Neutrino correlation using the MOJAVE catalog and 10 years of IceCube Data
New genetic loci link adipose and insulin biology to body fat distribution.
Body fat distribution is a heritable trait and a well-established predictor of adverse metabolic outcomes, independent of overall adiposity. To increase our understanding of the genetic basis of body fat distribution and its molecular links to cardiometabolic traits, here we conduct genome-wide association meta-analyses of traits related to waist and hip circumferences in up to 224,459 individuals. We identify 49 loci (33 new) associated with waist-to-hip ratio adjusted for body mass index (BMI), and an additional 19 loci newly associated with related waist and hip circumference measures (P < 5 × 10(-8)). In total, 20 of the 49 waist-to-hip ratio adjusted for BMI loci show significant sexual dimorphism, 19 of which display a stronger effect in women. The identified loci were enriched for genes expressed in adipose tissue and for putative regulatory elements in adipocytes. Pathway analyses implicated adipogenesis, angiogenesis, transcriptional regulation and insulin resistance as processes affecting fat distribution, providing insight into potential pathophysiological mechanisms
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