Classification of Radiology Reports Using Neural Attention Models

The electronic health record (EHR) contains a large amount of multi-dimensional and unstructured clinical data of significant operational and research value. Distinguished from previous studies, our approach embraces a double-annotated dataset and strays away from obscure "black-box" models to comprehensive deep learning models. In this paper, we present a novel neural attention mechanism that not only classifies clinically important findings. Specifically, convolutional neural networks (CNN) with attention analysis are used to classify radiology head computed tomography reports based on five categories that radiologists would account for in assessing acute and communicable findings in daily practice. The experiments show that our CNN attention models outperform non-neural models, especially when trained on a larger dataset. Our attention analysis demonstrates the intuition behind the classifier's decision by generating a heatmap that highlights attended terms used by the CNN model; this is valuable when potential downstream medical decisions are to be performed by human experts or the classifier information is to be used in cohort construction such as for epidemiological studies

The Black Hole to Bulge Mass Relation in Active Galactic Nuclei

The masses of the central black holes in Active Galactic Nuclei (AGNs) can be estimated using the broad emission-lines as a probe of the virial mass. Using reverberation mapping to determine the size of the Broad Line Region (BLR) and the width of the variable component of the line profile H$\beta$ line it is possible to find quite accurate virial mass estimates for AGNs with adequate data. Compiling a sample of AGNs with reliable central masses and bulge magnitudes we find an average black-hole-to-bulge mass ratio of 0.0003, a factor of 20 less than the value found for normal galaxies and for bright quasars. This lower ratio is more consistent with the back hole mass density predicted from quasar light, and is similar to the central black hole/bulge mass ratio in our Galaxy. We argue that the black hole/bulge mass ratio actually has a significantly larger range than indicated by mssive black holes detected in normal galaxies (using stellar dynamics) and in bright quasars, which may be biased towards large black holes. We derive a scenario of black hole growth that explains the observed distribution.Comment: 12 pages LaTeX, including 2 revised figures, revised table. Revised version to be published in the Astrophysical Journal (Letters) Ap.J.Lett. 51

Deformation and crystallization of Zr-based amorphous alloys in homogeneous flow regime

The purpose of this study is to experimentally investigate the interaction of inelastic deformation and microstructural changes of two Zr-based bulk metallic glasses (BMGs): Zr_(41.25)Ti_(13.75)Cu_(12.5)Ni_(10)Be_(22.5) (commercially designated as Vitreloy 1 or Vit1) and Zr_(46.75)Ti_(8.25)Cu_(7.5)Ni_(10)Be_(27.5) (Vitreloy 4, Vit4). High-temperature uniaxial compression tests were performed on the two Zr alloys at various strain rates, followed by structural characterization using differential scanning calorimetry (DSC) and transmission electron microscopy (TEM). Two distinct modes of mechanically induced atomic disordering in the two alloys were observed, with Vit1 featuring clear phase separation and crystallization after deformation as observed with TEM, while Vit4 showing only structural relaxation with no crystallization. The influence of the structural changes on the mechanical behaviors of the two materials was further investigated by jump-in-strain-rate tests, and flow softening was observed in Vit4. A free volume theory was applied to explain the deformation behaviors, and the activation volumes were calculated for both alloys

The Cosmic Density of Massive Black Holes from Galaxy Velocity Dispersions

Supermassive black holes are thought to be relics of quasars, and their numbers and masses are therefore related to the quasar luminosity function and its evolution with redshift. We have used the relationship between black hole mass and bulge velocity dispersion (the M_bullet - sigma relation) to make an improved estimate of the mass density and mass spectrum of supermassive black holes. Uncertainties in the M_bullet - sigma relation have little effect on the mass density. We find a mass density of (4.8 +/- 1.6) h^2 x 10^5 M_sun Mpc^-3. Some of the variance in published density estimates comes from the use of different values of the Hubble constant.Comment: To appear in the December 2002 issue of The Astronomical Journa

Identification and characterization of small compound inhibitors of human FATP2

Fatty acid transport proteins (FATPs) are bifunctional proteins, which transport long chain fatty acids into cells and activate very long chain fatty acids by esterification with coenzyme A. In an effort to understand the linkage between cellular fatty acid transport and the pathology associated with excessive accumulation of exogenous fatty acids, we targeted FATP-mediated fatty acid transport in a high throughput screen of more than 100,000 small diverse chemical compounds in yeast expressing human FATP2 (hsFATP2). Compounds were selected for their ability to depress the transport of the fluorescent long chain fatty acid analogue, C1-BODIPY-C12. Among 234 hits identified in the primary screen, 5 compounds, each representative of a structural class, were further characterized in the human Caco-2 and HepG2 cell lines, each of which normally expresses FATP2, and in 3T3-L1 adipocytes, which do not. These compounds were effective in inhibiting uptake with IC50s in the low micromolar range in both Caco-2 and HepG2 cells. Inhibition of transport was highly specific for fatty acids and there were no effects of these compounds on cell viability, trans-epithelial electrical resistance, glucose transport, or long chain acyl-CoA synthetase activity. The compounds were less effective when tested in 3T3-L1 adipocytes suggesting selectivity of inhibition. These results suggest fatty acid transport can be inhibited in a FATP-specific manner without causing cellular toxicity

Adaptive design of a clinical decision support tool: What the impact on utilization rates means for future CDS research

© The Author(s) 2019. OBJECTIVE: We employed an agile, user-centered approach to the design of a clinical decision support tool in our prior integrated clinical prediction rule study, which achieved high adoption rates. To understand if applying this user-centered process to adapt clinical decision support tools is effective in improving the use of clinical prediction rules, we examined utilization rates of a clinical decision support tool adapted from the original integrated clinical prediction rule study tool to determine if applying this user-centered process to design yields enhanced utilization rates similar to the integrated clinical prediction rule study. MATERIALS & METHODS: We conducted pre-deployment usability testing and semi-structured group interviews at 6 months post-deployment with 75 providers at 14 intervention clinics across the two sites to collect user feedback. Qualitative data analysis is bifurcated into immediate and delayed stages; we reported on immediate-stage findings from real-time field notes used to generate a set of rapid, pragmatic recommendations for iterative refinement. Monthly utilization rates were calculated and examined over 12 months. RESULTS: We hypothesized a well-validated, user-centered clinical decision support tool would lead to relatively high adoption rates. Then 6 months post-deployment, integrated clinical prediction rule study tool utilization rates were substantially lower than anticipated based on the original integrated clinical prediction rule study trial (68%) at 17% (Health System A) and 5% (Health System B). User feedback at 6 months resulted in recommendations for tool refinement, which were incorporated when possible into tool design; however, utilization rates at 12 months post-deployment remained low at 14% and 4% respectively. DISCUSSION: Although valuable, findings demonstrate the limitations of a user-centered approach given the complexity of clinical decision support. CONCLUSION: Strategies for addressing persistent external factors impacting clinical decision support adoption should be considered in addition to the user-centered design and implementation of clinical decision support

Faint AGN and the Ionizing Background

We determine the evolution of the faint, high-redshift, optical luminosity function (LF) of AGN implied by several observationally-motivated models of the ionizing background. Our results depend crucially on whether we use the total ionizing rate measured by the proximity effect technique or the lower determination from the flux decrement distribution of Ly alpha forest lines. Assuming a faint-end LF slope of 1.58 and the SDSS estimates of the bright-end slope and normalization, we find that the LF must break at M_B*=-24.2,-22.3, -20.8 at z=3,4, 5 if we adopt the lower ionization rate and assume no stellar contribution to the background. The break must occur at M_B*=-20.6,-18.7, -18.7 for the proximity effect background estimate. These values brighten by as much as ~2 mag if high-z galaxies contribute to the background with an escape fraction of ionizing photons consistent with recent estimates: f_e=0.16. By comparing to faint AGN searches, we find that the typically-quoted proximity effect estimates of the background imply an over-abundance of faint AGN (even with f_e=1). Even adopting the lower bound on proximity effect measurements, the stellar escape fraction must be high: f_e>0.2. Conversely, the lower flux- decrement-derived background requires a limited stellar contribution: f_e<0.05. Our derived LFs together with the locally-estimated black hole density suggest that the efficiency of converting mass to light in optically-unobscured AGN is somewhat lower than expected, <0.05. Comparison with similar estimates based on X-ray counts suggests that more than half of all AGN are obscured in the UV/optical. We also derive lower limits on typical AGN lifetimes and obtain >10^7 yrs for favored cases.Comment: 19 pages, 16 figures. Accepted by Astrophysical Journa

Numerical determination of the material properties of porous dust cakes

The formation of planetesimals requires the growth of dust particles through collisions. Micron-sized particles must grow by many orders of magnitude in mass. In order to understand and model the processes during this growth, the mechanical properties, and the interaction cross sections of aggregates with surrounding gas must be well understood. Recent advances in experimental (laboratory) studies now provide the background for pushing numerical aggregate models onto a new level. We present the calibration of a previously tested model of aggregate dynamics. We use plastic deformation of surface asperities as the physical model to bring critical velocities for sticking into accordance with experimental results. The modified code is then used to compute compression strength and the velocity of sound in the aggregate at different densities. We compare these predictions with experimental results and conclude that the new code is capable of studying the properties of small aggregates.Comment: Accepted for publication in A&

Massive Ellipticals at High Redshift: NICMOS Imaging of Z~1 Radio Galaxies

We present deep, continuum images of eleven high-redshift (0.811 < z < 1.875) 3CR radio galaxies observed with NICMOS. Our images probe the rest-frame optical light where stars are expected to dominate the galaxy luminosity. The rest-frame UV light of eight of these galaxies demonstrates the well-known ``alignment effect''. Most of the radio galaxies have rounder, more symmetric morphologies at rest-frame optical wavelengths. Here we show the most direct evidence that in most cases the stellar hosts are normal elliptical galaxies with de Vaucouleurs law light profiles. For a few galaxies very faint traces of the UV-bright aligned component are also visible in the infrared images. We derive both the effective radius and surface-brightness for nine of eleven sample galaxies by fitting surface-brightness models to them. We find their sizes are similar to those of local FRII radio source hosts and are in general larger than other local galaxies. The derived host galaxy luminosities are very high and lie at the bright end of luminosity functions constructed at similar redshifts. The galaxies in our sample are also brighter than the rest-frame size--surface-brightness locus defined by the low-redshift sources. Passive evolution roughly aligns the z ~ 1 galaxies with the low-redshift samples. The optical host is sometimes centered on a local minimum in the rest-frame UV emission, suggesting the presence of substantial dust obscuration. We also see good evidence of nuclear point sources in three galaxies. Overall, our results are consistent with the hypothesis that these galaxies have already formed the bulk of their stars at redshifts greater than z >~ 2, and that the AGN phenomenon takes place within otherwise normal, perhaps passively evolving, galaxies. (abridged)Comment: 28 pages, 14 figures, accepted to ApJ. Uses AASTEX and emulateapj

The influence of iron status and genetic polymorphisms in the HFE gene on the risk for postoperative complications after bariatric surgery: a prospective cohort study in 1,064 patients

<p>Abstract</p> <p>Background</p> <p>Gastric bypass surgery is a highly effective therapy for long-term weight loss in severely obese patients, but carries significant perioperative risks including infection, wound dehiscence, and leaks from staple breakdown. Iron status can affect immune function and wound healing, thus may influence peri-operative complications. Common mutations in the HFE gene, the gene responsible for the iron overload disorder hereditary hemochromatosis, may impact iron status.</p> <p>Methods</p> <p>We analyzed 1064 extremely obese Caucasian individuals who underwent open and laparoscopic Roux-n-Y gastric bypass surgery at the Geisinger Clinic. Serum iron, ferritin, transferrin, and iron binding capacity were measured pre-operatively. All patients had intra-operative liver biopsies and were genotyped for the C282Y and H63D mutations in the HFE gene. Associations between surgical complications and serum iron measures, HFE gene status, and liver iron histology were determined.</p> <p>Results</p> <p>We found that increased serum iron and transferrin saturation were present in patients with any post-operative complication, and that increased serum ferritin was also increased in patients with major complications. Increased serum transferrin saturation was also associated with wound complications in open RYGB, and transferrin saturation and ferritin with prolonged lengths of stay. The presence of 2 or more HFE mutations was associated with overall complications as well as wound complications in open RYGB. No differences were found in complication rates between those with stainable liver iron and those without.</p> <p>Conclusion</p> <p>Serum iron status and HFE genotype may be associated with complications following RYGB surgery in the extremely obese.</p