PSACNN: Pulse Sequence Adaptive Fast Whole Brain Segmentation

With the advent of convolutional neural networks~(CNN), supervised learning methods are increasingly being used for whole brain segmentation. However, a large, manually annotated training dataset of labeled brain images required to train such supervised methods is frequently difficult to obtain or create. In addition, existing training datasets are generally acquired with a homogeneous magnetic resonance imaging~(MRI) acquisition protocol. CNNs trained on such datasets are unable to generalize on test data with different acquisition protocols. Modern neuroimaging studies and clinical trials are necessarily multi-center initiatives with a wide variety of acquisition protocols. Despite stringent protocol harmonization practices, it is very difficult to standardize the gamut of MRI imaging parameters across scanners, field strengths, receive coils etc., that affect image contrast. In this paper we propose a CNN-based segmentation algorithm that, in addition to being highly accurate and fast, is also resilient to variation in the input acquisition. Our approach relies on building approximate forward models of pulse sequences that produce a typical test image. For a given pulse sequence, we use its forward model to generate plausible, synthetic training examples that appear as if they were acquired in a scanner with that pulse sequence. Sampling over a wide variety of pulse sequences results in a wide variety of augmented training examples that help build an image contrast invariant model. Our method trains a single CNN that can segment input MRI images with acquisition parameters as disparate as $T_1$-weighted and $T_2$-weighted contrasts with only $T_1$-weighted training data. The segmentations generated are highly accurate with state-of-the-art results~(overall Dice overlap$=0.94$), with a fast run time~($\approx$ 45 seconds), and consistent across a wide range of acquisition protocols.Comment: Typo in author name corrected. Greves -> Grev

ALICE: Study of Financial Hardship-Louisiana

Through a series of new, standardized measurements, the United Way ALICE Reports present a broad picture of financial insecurity at the county and town level, and the reasons for why. What we found was startling -- the size of the workforce in each state that is struggling financially is much higher than traditional federal poverty guidelines suggest. The United Way ALICE Project is a grassroots movement stimulating a fresh, nonpartisan national dialogue about how to reverse the trend and improve conditions for this growing population of families living paycheck to paycheck

ALICE: Study of Financial Hardship-Pacific Northwest: Idaho, Oregon and Washington

Through a series of new, standardized measurements, the United Way ALICE Reports present a broad picture of financial insecurity at the county and town level, and the reasons for why. What we found was startling -- the size of the workforce in each state that is struggling financially is much higher than traditional federal poverty guidelines suggest. The United Way ALICE Project is a grassroots movement stimulating a fresh, nonpartisan national dialogue about how to reverse the trend and improve conditions for this growing population of families living paycheck to paycheck

Learning the Effect of Registration Hyperparameters with HyperMorph

We introduce HyperMorph, a framework that facilitates efficient hyperparameter tuning in learning-based deformable image registration. Classical registration algorithms perform an iterative pair-wise optimization to compute a deformation field that aligns two images. Recent learning-based approaches leverage large image datasets to learn a function that rapidly estimates a deformation for a given image pair. In both strategies, the accuracy of the resulting spatial correspondences is strongly influenced by the choice of certain hyperparameter values. However, an effective hyperparameter search consumes substantial time and human effort as it often involves training multiple models for different fixed hyperparameter values and may lead to suboptimal registration. We propose an amortized hyperparameter learning strategy to alleviate this burden by learning the impact of hyperparameters on deformation fields. We design a meta network, or hypernetwork, that predicts the parameters of a registration network for input hyperparameters, thereby comprising a single model that generates the optimal deformation field corresponding to given hyperparameter values. This strategy enables fast, high-resolution hyperparameter search at test-time, reducing the inefficiency of traditional approaches while increasing flexibility. We also demonstrate additional benefits of HyperMorph, including enhanced robustness to model initialization and the ability to rapidly identify optimal hyperparameter values specific to a dataset, image contrast, task, or even anatomical region, all without the need to retrain models. We make our code publicly available at http://hypermorph.voxelmorph.net.Comment: Accepted for publication at the Journal of Machine Learning for Biomedical Imaging (MELBA) at https://www.melba-journal.or

Evidence for Black Hole Growth in Local Analogs to Lyman Break Galaxies

We have used XMM-Newton to observe six Lyman Break Analogs (LBAs): members of the rare population of local galaxies that have properties that are very similar to distant Lyman Break Galaxies. Our six targets were specifically selected because they have optical emission-line properties that are intermediate between starbursts and Type 2 (obscured) AGN. Our new X-ray data provide an important diagnostic of the presence of an AGN. We find X-ray luminosities of order 10^{42} erg/s and ratios of X-ray to far-IR luminosities that are higher than values in pure starburst galaxies by factors ranging from ~ 3 to 30. This strongly suggests the presence of an AGN in at least some of the galaxies. The ratios of the luminosities of the hard (2-10 keV) X-ray to [O III]\lambda 5007 emission-line are low by about an order-of-magnitude compared to Type 1 AGN, but are consistent with the broad range seen in Type 2 AGN. Either the AGN hard X-rays are significantly obscured or the [O III] emission is dominated by the starburst. We searched for an iron emission line at ~ 6.4 keV, which is a key feature of obscured AGN, but only detected emission at the ~ 2\sigma level. Finally, we find that the ratios of the mid-infrared (24\mu m) continuum to [O III]\lambda 5007 luminosities in these LBAs are higher than the values for Type 2 AGN by an average of 0.8 dex. Combining all these clues, we conclude that an AGN is likely to be present, but that the bolometric luminosity is produced primarily by an intense starburst. If these black holes are radiating at the Eddington limit, their masses would lie in the range of 10^5 to 10^6 M_{sun}. These objects may offer ideal local laboratories to investigate the processes by which black holes grew in the early universe.Comment: Accepted for publication in Ap

Diaphragm Abnormalities in Patients with End-Stage Heart Failure: NADPH Oxidase Upregulation and Protein Oxidation

Patients with heart failure (HF) have diaphragm abnormalities that contribute to disease morbidity and mortality. Studies in animals suggest that reactive oxygen species (ROS) cause diaphragm abnormalities in HF. However, the effects of HF on ROS sources, antioxidant enzymes, and protein oxidation in the diaphragm of humans is unknown. NAD(P)H oxidase, especially the Nox2 isoform, is an important source of ROS in the diaphragm. Our main hypothesis was that diaphragm from patients with HF have heightened Nox2 expression and p47phox phosphorylation (marker of enzyme activation) that is associated with elevated protein oxidation. We collected diaphragm biopsies from patients with HF and brain-dead organ donors (controls). Diaphragm mRNA levels of Nox2 subunits were increased 2.5–4.6-fold over controls (p \u3c 0.05). Patients also had increased protein levels of Nox2 subunits (p47phox, p22phox, and p67phox) and total p47phox phosphorylation, while phospho-to-total p47phox levels were unchanged. The antioxidant enzyme catalase was increased in patients, whereas glutathione peroxidase and superoxide dismutases were unchanged. Among markers of protein oxidation, carbonyls were increased by ~40% (p \u3c 0.05) and 4-hydroxynonenal and 3-nitrotyrosines were unchanged in patients with HF. Overall, our findings suggest that Nox2 is an important source of ROS in the diaphragm of patients with HF and increases in levels of antioxidant enzymes are not sufficient to maintain normal redox homeostasis. The net outcome is elevated diaphragm protein oxidation that has been shown to cause weakness in animals

CARMA Survey Toward Infrared-bright Nearby Galaxies (STING): Molecular Gas Star Formation Law in NGC4254

This study explores the effects of different assumptions and systematics on the determination of the local, spatially resolved star formation law. Using four star formation rate (SFR) tracers (H\alpha with azimuthally averaged extinction correction, mid-infrared 24 micron, combined H\alpha and mid-infrared 24 micron, and combined far-ultraviolet and mid-infrared 24 micron), several fitting procedures, and different sampling strategies we probe the relation between SFR and molecular gas at various spatial resolutions and surface densities within the central 6.5 kpc in the disk of NGC4254. We find that in the high surface brightness regions of NGC4254 the form of the molecular gas star formation law is robustly determined and approximately linear and independent of the assumed fraction of diffuse emission and the SFR tracer employed. When the low surface brightness regions are included, the slope of the star formation law depends primarily on the assumed fraction of diffuse emission. In such case, results range from linear when the fraction of diffuse emission in the SFR tracer is ~30% or less (or when diffuse emission is removed in both the star formation and the molecular gas tracer), to super-linear when the diffuse fraction is ~50% and above. We find that the tightness of the correlation between gas and star formation varies with the choice of star formation tracer. The 24 micron SFR tracer by itself shows the tightest correlation with the molecular gas surface density, whereas the H\alpha corrected for extinction using an azimuthally-averaged correction shows the highest dispersion. We find that for R<0.5R_25 the local star formation efficiency is constant and similar to that observed in other large spirals, with a molecular gas depletion time ~2 Gyr.Comment: accepted for publication in ApJ, vol 729, March 10 2011 issue; 30 pages; 14 figures; revised version includes referee's comments; results unchange

Modeling the Influence of Vitamin D Deficiency on Cigarette Smoke-Induced Emphysema

Chronic obstructive pulmonary disease (COPD) is a major cause of morbidity and mortality worldwide. While the primary risk factor for COPD is cigarette smoke exposure, vitamin D deficiency has been epidemiologically implicated as a factor in the progressive development of COPD-associated emphysema. Because of difficulties inherent to studies involving multiple risk factors in the progression of COPD in humans, we developed a murine model in which to study the separate and combined effects of vitamin D deficiency and cigarette smoke exposure. During a 16-week period, mice were exposed to one of four conditions, control diet breathing room air (CD-NS), control diet with cigarette smoke exposure (CD-CSE), vitamin D deficient diet breathing room air (VDD-NS) or vitamin D deficient diet with cigarette smoke exposure (VDD-CSE). At the end of the exposure period, the lungs were examined by a pathologist and separately by morphometric analysis. In parallel experiments, mice were anesthetized for pulmonary function testing followed by sacrifice and analysis. Emphysema (determined by an increase in alveolar mean linear intercept length) was more severe in the VDD-CSE mice compared to control animals and animals exposed to VDD or CSE alone. The VDD-CSE and the CD-CSE mice had increased total lung capacity and increased static lung compliance. There was also a significant increase in the matrix metalloproteinase-9: tissue inhibitor of metalloproteinases-1 (TIMP-1) ratio in VDD-CSE mice compared with all controls. Alpha-1 antitrypsin (A1AT) expression was reduced in VDD-CSE mice as well. In summary, vitamin D deficiency, when combined with cigarette smoke exposure, seemed to accelerate the appearance of emphysemas, perhaps by virtue of an increased protease-antiprotease ratio in the combined VDD-CSE animals. These results support the value of our mouse model in the study of COPD

The Extreme Hosts of Extreme Supernovae

We use GALEX ultraviolet (UV) and optical integrated photometry of the hosts of seventeen luminous supernovae (LSNe, having peak M_V < -21) and compare them to a sample of 26,000 galaxies from a cross-match between the SDSS DR4 spectral catalog and GALEX interim release 1.1. We place the LSNe hosts on the galaxy NUV-r versus M_r color magnitude diagram (CMD) with the larger sample to illustrate how extreme they are. The LSN hosts appear to favor low-density regions of the galaxy CMD falling on the blue edge of the blue cloud toward the low luminosity end. From the UV-optical photometry, we estimate the star formation history of the LSN hosts. The hosts have moderately low star formation rates (SFRs) and low stellar masses (M_*) resulting in high specific star formation rates (sSFR). Compared with the larger sample, the LSN hosts occupy low-density regions of a diagram plotting sSFR versus M_* in the area having higher sSFR and lower M_*. This preference for low M_*, high sSFR hosts implies the LSNe are produced by an effect having to do with their local environment. The correlation of mass with metallicity suggests that perhaps wind-driven mass loss is the factor that prevents LSNe from arising in higher-mass, higher-metallicity hosts. The massive progenitors of the LSNe (>100 M_sun), by appearing in low-SFR hosts, are potential tests for theories of the initial mass function that limit the maximum mass of a star based on the SFR.Comment: 8 pages, 3 figures, 2 tables, accepted to ApJ, amended references and updated SN designation

The ACS Nearby Galaxy Survey Treasury II. Young Stars and their Relation to Halpha and UV Emission Timescales in the M81 Outer Disk

We have obtained resolved stellar photometry from Hubble Space Telescope (HST) Advanced Camera for Surveys (ACS) observations of a field in the outer disk of M81 as part of the ACS Nearby Galaxy Survey Treasury (ANGST). Motivated by the recent discovery of extended UV (XUV) disks around many nearby spiral galaxies, we use the observed stellar population to derive the recent star formation histories of five ~0.5 kpc-sized regions within this field. These regions were selected on the basis of their UV luminosity from GALEX and include two HII regions, two regions which are UV-bright but Halpha-faint, and one "control" region faint in both UV and Halpha. We estimate our effective SFR detection limit at ~2 x 10^-4 Msun/yr, which is lower than that of GALEX for regions of this size. As expected, the HII regions contain massive main sequence stars (in the mass range 18-27 Msun, based on our best extinction estimates), while similar massive main sequence stars are lacking in the UV-bright/Halpha-faint regions. The observations are consistent with stellar ages 16 Myr in the UV-bright/Halpha-faint regions. All regions but the control have formed ~10^4 Msun of stars over the past ~65 Myr. Thus, our results, for at least one small area in the outer disk of M81, are consistent with an age difference being sufficient to explain the observed discrepancy between star-forming regions detected in Halpha and those detected exclusively in UV. However, our data cannot conclusively rule out other explanations, such as a strongly truncated initial mass function (IMF).Comment: 18 pages, 12 figures, accepted for publication in ApJ, paper with full resolution figures available: http://www.nearbygalaxies.org/papers/M81_Halpha_uv.pd