631 research outputs found
Effect of hyperfine structure on atomic frequency combs in Pr:YSO
Quantum memory will be a key component in future quantum networks, and atomic
frequency combs (AFCs) in rare-earth-doped crystals are one promising platform
for realizing this technology. We theoretically and experimentally investigate
the formation of AFCs in Pr3+:Y2SiO5, with an overall bandwidth of 120 MHz and
tooth spacing ranging from 0.1 MHz to 20 MHz, showing agreement between our
calculations and measurements. We observe that the echo efficiency depends
crucially on the AFC tooth spacing. Our results suggest approaches to
developing a high-efficiency AFC quantum memory.Comment: 20 pages, 7 figure
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
EvoChromo: towards a synthesis of chromatin biology and evolution
Over the past few years, interest in chromatin and its evolution has grown. To further advance these interests, we organized a workshop with the support of The Company of Biologists to debate the current state of knowledge regarding the origin and evolution of chromatin. This workshop led to prospective views on the development of a new field of research that we term ‘EvoChromo’. In this short Spotlight article, we define the breadth and expected impact of this new area of scientific inquiry on our understanding of both chromatin and evolution
Spatio-temporal Models of Lymphangiogenesis in Wound Healing
Several studies suggest that one possible cause of impaired wound healing is
failed or insufficient lymphangiogenesis, that is the formation of new
lymphatic capillaries. Although many mathematical models have been developed to
describe the formation of blood capillaries (angiogenesis), very few have been
proposed for the regeneration of the lymphatic network. Lymphangiogenesis is a
markedly different process from angiogenesis, occurring at different times and
in response to different chemical stimuli. Two main hypotheses have been
proposed: 1) lymphatic capillaries sprout from existing interrupted ones at the
edge of the wound in analogy to the blood angiogenesis case; 2) lymphatic
endothelial cells first pool in the wound region following the lymph flow and
then, once sufficiently populated, start to form a network. Here we present two
PDE models describing lymphangiogenesis according to these two different
hypotheses. Further, we include the effect of advection due to interstitial
flow and lymph flow coming from open capillaries. The variables represent
different cell densities and growth factor concentrations, and where possible
the parameters are estimated from biological data. The models are then solved
numerically and the results are compared with the available biological
literature.Comment: 29 pages, 9 Figures, 6 Tables (39 figure files in total
Effect of Algorithm-Based Therapy vs Usual Care on Clinical Success and Serious Adverse Events in Patients with Staphylococcal Bacteremia: A Randomized Clinical Trial
Importance: The appropriate duration of antibiotics for staphylococcal bacteremia is unknown. Objective: To test whether an algorithm that defines treatment duration for staphylococcal bacteremia vs standard of care provides noninferior efficacy without increasing severe adverse events. Design, Setting, and Participants: A randomized trial involving adults with staphylococcal bacteremia was conducted at 16 academic medical centers in the United States (n = 15) and Spain (n = 1) from April 2011 to March 2017. Patients were followed up for 42 days beyond end of therapy for those with Staphylococcus aureus and 28 days for those with coagulase-negative staphylococcal bacteremia. Eligible patients were 18 years or older and had 1 or more blood cultures positive for S aureus or coagulase-negative staphylococci. Patients were excluded if they had known or suspected complicated infection at the time of randomization. Interventions: Patients were randomized to algorithm-based therapy (n = 255) or usual practice (n = 254). Diagnostic evaluation, antibiotic selection, and duration of therapy were predefined for the algorithm group, whereas clinicians caring for patients in the usual practice group had unrestricted choice of antibiotics, duration, and other aspects of clinical care. Main Outcomes and Measures: Coprimary outcomes were (1) clinical success, as determined by a blinded adjudication committee and tested for noninferiority within a 15% margin; and (2) serious adverse event rates in the intention-to-treat population, tested for superiority. The prespecified secondary outcome measure, tested for superiority, was antibiotic days among per-protocol patients with simple or uncomplicated bacteremia. Results: Among the 509 patients randomized (mean age, 56.6 [SD, 16.8] years; 226 [44.4%] women), 480 (94.3%) completed the trial. Clinical success was documented in 209 of 255 patients assigned to algorithm-based therapy and 207 of 254 randomized to usual practice (82.0% vs 81.5%; difference, 0.5% [1-sided 97.5% CI, -6.2% to ∞]). Serious adverse events were reported in 32.5% of algorithm-based therapy patients and 28.3% of usual practice patients (difference, 4.2% [95% CI, -3.8% to 12.2%]). Among per-protocol patients with simple or uncomplicated bacteremia, mean duration of therapy was 4.4 days for algorithm-based therapy vs 6.2 days for usual practice (difference, -1.8 days [95% CI, -3.1 to -0.6]). Conclusions and Relevance: Among patients with staphylococcal bacteremia, the use of an algorithm to guide testing and treatment compared with usual care resulted in a noninferior rate of clinical success. Rates of serious adverse events were not significantly different, but interpretation is limited by wide confidence intervals. Further research is needed to assess the utility of the algorithm. Trial Registration: ClinicalTrials.gov Identifier: NCT01191840
Distinct Effects of Unfractionated Heparin versus Bivalirudin on Circulating Angiogenic Peptides
Background: Human studies of therapeutic angiogenesis, stem-cell, and progenitor-cell therapy have failed to demonstrate consistent clinical benefit. Recent studies have shown that heparin increases circulating levels of anti-angiogenic peptides. Given the widely prevalent use of heparin in percutaneous and surgical procedures including those performed as part of studies examining the benefit of therapeutic angiogenesis and cell-based therapy, we compared the effects of unfractionated heparin (UFH) on angiogenic peptides with those of bivalirudin, a relatively newer anticoagulant whose effects on angiogenic peptides have not been studied. Methodology/Principal Findings: We measured soluble fms-like tyrosine kinase-1 (sFLT1), placental growth factor (PlGF), vascular endothelial growth factor (VEGF), and soluble Endoglin (sEng) serum levels by enzyme linked immunosorbent assays (ELISA) in 16 patients undergoing elective percutaneous coronary intervention. Compared to baseline values, sFLT1 and PlGF levels increased by 26296313 % and 253654%, respectively, within 30 minutes of UFH therapy (p,0.01 for both; n = 8). VEGF levels decreased by 93.265 % in patients treated with UFH (p,0.01 versus baseline). No change in sEng levels were observed after UFH therapy. No changes in sFLT1, PlGF, VEGF, or sEng levels were observed in any patients receiving bivalirudin (n = 8). To further explore the direct effect of anticoagulation on circulating angiogenic peptides, adult, male wild-type mice received venous injections of clinically dosed UFH or bivalirudin. Compared to saline controls, sFLT1 an
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
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
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
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