Purpose
Mammographic breast density is an established risk marker for breast cancer and is visually assessed by radiologists in routine mammogram image reading, using four qualitative Breast Imaging ...and Reporting Data System (BI‐RADS) breast density categories. It is particularly difficult for radiologists to consistently distinguish the two most common and most variably assigned BI‐RADS categories, i.e., “scattered density” and “heterogeneously dense”. The aim of this work was to investigate a deep learning‐based breast density classifier to consistently distinguish these two categories, aiming at providing a potential computerized tool to assist radiologists in assigning a BI‐RADS category in current clinical workflow.
Methods
In this study, we constructed a convolutional neural network (CNN)‐based model coupled with a large (i.e., 22,000 images) digital mammogram imaging dataset to evaluate the classification performance between the two aforementioned breast density categories. All images were collected from a cohort of 1,427 women who underwent standard digital mammography screening from 2005 to 2016 at our institution. The truths of the density categories were based on standard clinical assessment made by board‐certified breast imaging radiologists. Effects of direct training from scratch solely using digital mammogram images and transfer learning of a pretrained model on a large nonmedical imaging dataset were evaluated for the specific task of breast density classification. In order to measure the classification performance, the CNN classifier was also tested on a refined version of the mammogram image dataset by removing some potentially inaccurately labeled images. Receiver operating characteristic (ROC) curves and the area under the curve (AUC) were used to measure the accuracy of the classifier.
Results
The AUC was 0.9421 when the CNN‐model was trained from scratch on our own mammogram images, and the accuracy increased gradually along with an increased size of training samples. Using the pretrained model followed by a fine‐tuning process with as few as 500 mammogram images led to an AUC of 0.9265. After removing the potentially inaccurately labeled images, AUC was increased to 0.9882 and 0.9857 for without and with the pretrained model, respectively, both significantly higher (P < 0.001) than when using the full imaging dataset.
Conclusions
Our study demonstrated high classification accuracies between two difficult to distinguish breast density categories that are routinely assessed by radiologists. We anticipate that our approach will help enhance current clinical assessment of breast density and better support consistent density notification to patients in breast cancer screening.
Abstract
Magnetic charge propagation in spin-ice materials has yielded a paradigm-shift in science, allowing the symmetry between electricity and magnetism to be studied. Recent work is now ...suggesting the spin-ice surface may be important in mediating the ordering and associated phase space in such materials. Here, we detail a 3D artificial spin-ice, which captures the exact geometry of bulk systems, allowing magnetic charge dynamics to be directly visualized upon the surface. Using magnetic force microscopy, we observe vastly different magnetic charge dynamics along two principal directions. For a field applied along the surface termination, local energetics force magnetic charges to nucleate over a larger characteristic distance, reducing their magnetic Coulomb interaction and producing uncorrelated monopoles. In contrast, applying a field transverse to the surface termination yields highly correlated monopole-antimonopole pairs. Detailed simulations suggest it is the difference in effective chemical potential as well as the energy landscape experienced during dynamics that yields the striking differences in monopole transport.
We present new measurements of the free-streaming of warm dark matter (WDM) from Lyman-α flux-power spectra. We use data from the medium resolution, intermediate redshift XQ-100 sample observed with ...the X-shooter spectrograph (z=3–4.2) and the high-resolution, high-redshift sample used in Viel et al. (2013) obtained with the HIRES/MIKE spectrographs (z=4.2–5.4). Based on further improved modelling of the dependence of the Lyman-α flux-power spectrum on the free-streaming of dark matter, cosmological parameters, as well as the thermal history of the intergalactic medium (IGM) with hydrodynamical simulations, we obtain the following limits, expressed as the equivalent mass of thermal relic WDM particles. The XQ-100 flux power spectrum alone gives a lower limit of 1.4 keV, the re-analysis of the HIRES/MIKE sample gives 4.1 keV while the combined analysis gives our best and significantly strengthened lower limit of 5.3 keV (all 2σ C.L.). The further improvement in the joint analysis is partly due to the fact that the two data sets have different degeneracies between astrophysical and cosmological parameters that are broken when the data sets are combined, and more importantly on chosen priors on the thermal evolution. These results all assume that the temperature evolution of the IGM can be modeled as a power law in redshift. Allowing for a nonsmooth evolution of the temperature of the IGM with sudden temperature changes of up to 5000 K reduces the lower limit for the combined analysis to 3.5 keV. A WDM with smaller thermal relic masses would require, however, a sudden temperature jump of 5000 K or more in the narrow redshift interval z=4.6–4.8, in disagreement with observations of the thermal history based on high-resolution resolution Lyman-α forest data and expectations for photo-heating and cooling in the low density IGM at these redshifts.
We report new observations of SL2S J021737-051329, a lens system consisting of a bright arc at z = 1.84435, magnified ∼17× by a massive galaxy at z = 0.65. SL2S0217 is a low-mass (M < 109 M ), ...low-metallicity (Z ∼ 1/20 Z ) galaxy, with extreme star-forming conditions that produce strong nebular UV emission lines in the absence of any apparent outflows. Here we present several notable features from rest-frame UV Keck/LRIS spectroscopy: (1) Very strong narrow emission lines are measured for C iv λλ1548, 1550, He ii λ1640, O iii λλ1661, 1666, Si iii λλ1883, 1892, and C iii λλ1907, 1909. (2) Double-peaked Ly emission is observed with a dominant blue peak and centered near the systemic velocity. (3) The low- and high-ionization absorption features indicate very little or no outflowing gas along the sight line to the lensed galaxy. The relative emission-line strengths can be reproduced with a very high ionization, low-metallicity starburst with binaries, with the exception of He ii, which indicates that an additional ionization source is needed. We rule out large contributions from active galactic nuclei and shocks to the photoionization budget, suggesting that the emission features requiring the hardest radiation field likely result from extreme stellar populations that are beyond the capabilities of current models. Therefore, SL2S0217 serves as a template for the extreme conditions that are important for reionization and thought to be more common in the early universe.
CHAOS. III. GAS-PHASE ABUNDANCES IN NGC 5457 Croxall, Kevin V.; Pogge, Richard W.; Berg, Danielle A. ...
Astrophysical journal/The Astrophysical journal,
10/2016, Letnik:
830, Številka:
1
Journal Article
Recenzirano
Odprti dostop
ABSTRACT We present Large Binocular Telescope observations of 109 H ii regions in NGC 5457 (M101) obtained with the Multi-Object Double Spectrograph. We have robust measurements of one or more ...temperature-sensitive auroral emission lines for 74 H ii regions, permitting the measurement of "direct" gas-phase abundances. Comparing the temperatures derived from the different ionic species, we find: (1) strong correlations of TN ii with TS iii and TO iii, consistent with little or no intrinsic scatter; (2) a correlation of TS iii with TO iii, but with significant intrinsic dispersion; (3) overall agreement between TN ii, TS ii, and TO ii, as expected, but with significant outliers; (4) the correlations of TN ii with TS iii and TO iii match the predictions of photoionization modeling while the correlation of TS iii with TO iii is offset from the prediction of photoionization modeling. Based on these observations, which include significantly more observations of lower excitation H ii regions, missing in many analyses, we inspect the commonly used ionization correction factors (ICFs) for unobserved ionic species and propose new empirical ICFs for S and Ar. We have discovered an unexpected population of H ii regions with a significant offset to low values in Ne/O, which defies explanation. We derive radial gradients in O/H and N/O which agree with previous studies. Our large observational database allows us to examine the dispersion in abundances, and we find intrinsic dispersions of 0.074 0.009 in O/H and 0.095 0.009 in N/O (at a given radius). We stress that this measurement of the intrinsic dispersion comes exclusively from direct abundance measurements of H ii regions in NGC 5457.
It has recently been shown that in anaerobic microorganisms the tricarboxylic acid (TCA) cycle, including the seemingly irreversible citrate synthase reaction, can be reversed and used for ...autotrophic fixation of carbon1,2. This reversed oxidative TCA cycle requires ferredoxin-dependent 2-oxoglutarate synthase instead ofthe NAD-dependent dehydrogenase as well as extremely high levels of citrate synthase (more than 7% of the proteins in the cell). In this pathway, citrate synthase replaces ATP-citrate lyase of the reductive TCA cycle, which leads to the spending of one ATP-equivalent less per one turn of the cycle. Here we show, using the thermophilic sulfur-reducing deltaproteobacterium Hippea maritima, that this route is driven by high partial pressures of CO2. These high partial pressures are especially important for the removal of the product acetyl coenzyme A (acetyl-CoA) through reductive carboxylation to pyruvate, which is catalysed by pyruvate synthase. The reversed oxidative TCA cycle may have been functioning in autotrophic CO2 fixation in a primordial atmosphere that is assumed to have been rich in CO2.
Somatic stem cells contribute to tissue ontogenesis, homeostasis, and regeneration through sequential processes. Systematic molecular analysis of stem cell behavior is challenging because classic ...approaches cannot resolve cellular heterogeneity or capture developmental dynamics. Here we provide a comprehensive resource of single-cell transcriptomes of adult hippocampal quiescent neural stem cells (qNSCs) and their immediate progeny. We further developed Waterfall, a bioinformatic pipeline, to statistically quantify singe-cell gene expression along a de novo reconstructed continuous developmental trajectory. Our study reveals molecular signatures of adult qNSCs, characterized by active niche signaling integration and low protein translation capacity. Our analyses further delineate molecular cascades underlying qNSC activation and neurogenesis initiation, exemplified by decreased extrinsic signaling capacity, primed translational machinery, and regulatory switches in transcription factors, metabolism, and energy sources. Our study reveals the molecular continuum underlying adult neurogenesis and illustrates how Waterfall can be used for single-cell omics analyses of various continuous biological processes.
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•Single-cell transcriptomes from adult NSCs form a continuous linear trajectory•Waterfall pipeline quantifies gene expression over continuous biological processes•Adult NSC-specific metabolic pathways and active niche signal integration capacity•Augmented translation capacity is the first hallmark of adult NSC activation
In vivo molecular dynamics of adult stem cells have been elusive. Shin et al. used single-cell RNA-seq and a novel bioinformatic approach named Waterfall to reconstruct somatic stem cell dynamics with unprecedented temporal resolution. The genome-wide molecular transitions they identified suggest commonalities among different somatic stem cell systems.
The evolution from microfluidic to nanofluidic systems has been accompanied by the emergence of new fluid phenomena and the potential for new nanofluidic devices. This review provides an introduction ...to the theory of nanofluidic transport, focusing on the various forces that influence the movement of both solvents and solutes through nanochannels, and reviews the applications of nanofluidic devices in separation science and energy conversion.
It was long thought that no new neurons are added to the adult brain. Similarly, neurotransmitter signaling was primarily associated with communication between differentiated neurons. Both of these ...ideas have been challenged, and a crosstalk between neurogenesis and neurotransmitter signaling is beginning to emerge. In this Review, we discuss neurotransmitter signaling as it functions at the intersection of stem cell research and regenerative medicine, exploring how it may regulate the formation of new functional neurons and outlining interactions with other signaling pathways. We consider evolutionary and cross-species comparative aspects, and integrate available results in the context of normal physiological versus pathological conditions. We also discuss the potential role of neurotransmitters in brain size regulation and implications for cell replacement therapies.
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