An Interpretable Deep Hierarchical Semantic Convolutional Neural Network for Lung Nodule Malignancy Classification

While deep learning methods are increasingly being applied to tasks such as computer-aided diagnosis, these models are difficult to interpret, do not incorporate prior domain knowledge, and are often considered as a "black-box." The lack of model interpretability hinders them from being fully understood by target users such as radiologists. In this paper, we present a novel interpretable deep hierarchical semantic convolutional neural network (HSCNN) to predict whether a given pulmonary nodule observed on a computed tomography (CT) scan is malignant. Our network provides two levels of output: 1) low-level radiologist semantic features, and 2) a high-level malignancy prediction score. The low-level semantic outputs quantify the diagnostic features used by radiologists and serve to explain how the model interprets the images in an expert-driven manner. The information from these low-level tasks, along with the representations learned by the convolutional layers, are then combined and used to infer the high-level task of predicting nodule malignancy. This unified architecture is trained by optimizing a global loss function including both low- and high-level tasks, thereby learning all the parameters within a joint framework. Our experimental results using the Lung Image Database Consortium (LIDC) show that the proposed method not only produces interpretable lung cancer predictions but also achieves significantly better results compared to common 3D CNN approaches

THYROSIM App for Education and Research Predicts Potential Health Risks of Over-the-Counter Thyroid Supplements

Background: Computer simulation tools for education and research are making increasingly effective use of the Internet and personal devices. To facilitate these activities in endocrinology and metabolism, a mechanistically based simulator of human thyroid hormone and thyrotropin (TSH) regulation dynamics was developed and further validated, and it was implemented as a facile and freely accessible web-based and personal device application: the THYROSIM app. This study elucidates and demonstrates its utility in a research context by exploring key physiological effects of over-the-counter thyroid supplements. Methods: THYROSIM has a simple and intuitive user interface for teaching and conducting simulated ?what-if? experiments. User-selectable ?experimental? test-input dosages (oral, intravenous pulses, intravenous infusions) are represented by animated graphical icons integrated with a cartoon of the hypothalamic?pituitary?thyroid axis. Simulations of familiar triiodothyronine (T3), thyroxine (T4), and TSH temporal dynamic responses to these exogenous stimuli are reported graphically, along with normal ranges on the same single interface page; and multiple sets of simulated experimental results are superimposable to facilitate comparative analyses. Results and Conclusions: This study shows that THYROSIM accurately reproduces a wide range of published clinical study data reporting hormonal kinetic responses to large and small oral hormone challenges. Simulation examples of partial thyroidectomies and malabsorption illustrate typical usage by optionally changing thyroid gland secretion and/or gut absorption rates?expressed as percentages of normal?as well as additions of oral hormone dosing, all directly on the interface, and visualizing the kinetic responses to these challenges. Classroom and patient education usage?with public health implications?is illustrated by predictive simulated responses to nonprescription thyroid health supplements analyzed previously for T3 and T4 content. Notably, it was found that T3 in supplements has potentially more serious pathophysiological effects than does T4?concomitant with low-normal TSH levels. Some preparations contain enough T3 to generate thyrotoxic conditions, with supernormal serum T3-spiking and subnormal serum T4 and TSH levels and, in some cases, with normal or low-normal range TSH levels due to thyroidal axis negative feedback. These results suggest that appropriate regulation of these products is needed.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/140268/1/thy.2015.0373.pd

Is SN 2006X from a WD + MS system with optically thick wind?

The single-degenerate channel is widely accepted as the progenitors of type Ia supernovae (SNe Ia). Following the work of Meng, Chen and Han (2009), we reproduced the birth rate and age of supernovae like SN 2006X by the single-degenerate model (WD + MS) with an optically thick wind, which may imply that the progenitor of SN 2006X is a WD + MS system.Comment: 10 pages, 2 figures, accepted for publication in New

The Big Occulting Steerable Satellite (BOSS)

Natural (such as lunar) occultations have long been used to study sources on small angular scales, while coronographs have been used to study high contrast sources. We propose launching the Big Occulting Steerable Satellite (BOSS), a large steerable occulting satellite to combine both of these techniques. BOSS will have several advantages over standard occulting bodies. BOSS would block all but about 4e-5 of the light at 1 micron in the region of interest around the star for planet detections. Because the occultation occurs outside the telescope, scattering inside the telescope does not degrade this performance. BOSS could be combined with a space telescope at the Earth-Sun L2 point to yield very long integration times, in excess of 3000 seconds. If placed in Earth orbit, integration times of 160--1600 seconds can be achieved from most major telescope sites for objects in over 90% of the sky. Applications for BOSS include direct imaging of planets around nearby stars. Planets separated by as little as 0.1--0.25 arcseconds from the star they orbit could be seen down to a relative intensity as little as 1e-9 around a magnitude 8 (or brighter) star. Other applications include ultra-high resolution imaging of compound sources, such as microlensed stars and quasars, down to a resolution as little as 0.1 milliarcseconds.Comment: 25pages, 4 figures, uses aaspp4, rotate, and epsfig. Submitted to the Astrophysical Journal. For more details see http://erebus.phys.cwru.edu/~boss

New insight into tuning magnetic phases of RMn6Sn6 kagome metals

Kagome metals with magnetic order offer the possibility of tuning topological electronic states via external control parameters such as temperature or magnetic field. ErMn$_6$Sn$_6$ (Er$166$) is a member of a group of $R166$, $R=$~rare earth, compounds hosting ferromagnetic Mn kagome nets whose magnetic moment direction and layer-to-layer magnetic correlations are strongly influenced by coupling to $R$ magnetic moments in neighboring triangular layers. Here, we use neutron diffraction and magnetization data to examine the temperature-driven transition in Er$166$ from a planar-ferrimagnetic to distorted-triple-spiral magnetic order. These data inform mean-field calculations which highlight the fragile, tunable nature of the magnetism caused by competing Mn-Mn and Mn-Er interlayer magnetic exchange couplings and Mn and Er magnetic anisotropies. This competition results in the near degeneracy of a variety of collinear, non-collinear, and non-coplanar magnetic phases which we show are readily selected and adjusted via changing temperature or magnetic field. Thermal fluctuations of the Er moment direction provide the key to this tunability.Comment: 10 pages, 7 figures, Supplementary Informatio

Cosmic-Ray Nuclei, Antiprotons and Gamma-rays in the Galaxy: a New Diffusion Model

We model the transport of cosmic ray nuclei in the Galaxy by means of a new numerical code. Differently from previous numerical models we account for a generic spatial distribution of the diffusion coefficient. We found that in the case of radially uniform diffusion, the main secondary/primary ratios (B/C, N/O and sub-Fe/Fe) and the modulated antiproton spectrum match consistently the available observations. Convection and re-acceleration do not seem to be required in the energy range we consider: $1 < E < 10^3$ GeV/nucleon. We generalize these results accounting for radial dependence of the diffusion coefficient, which is assumed to trace that of the cosmic ray sources. While this does not affect the prediction of secondary/primary ratios, the simulated longitude profile of the diffuse $\gamma$-ray emission is significantly different from the uniform case and may agree with EGRET measurements without invoking ad hoc assumptions on the galactic gas density distribution.Comment: 17 pages, 6 figures. v3: Added detailed references to nuclear cross-section networ

Graphite and Hexagonal Boron-Nitride Possess the Same Interlayer Distance. Why?

Graphite and hexagonal boron nitride (h-BN) are two prominent members of the family of layered materials possessing a hexagonal lattice. While graphite has non-polar homo-nuclear C-C intra-layer bonds, h-BN presents highly polar B-N bonds resulting in different optimal stacking modes of the two materials in bulk form. Furthermore, the static polarizabilities of the constituent atoms considerably differ from each other suggesting large differences in the dispersive component of the interlayer bonding. Despite these major differences both materials present practically identical interlayer distances. To understand this finding, a comparative study of the nature of the interlayer bonding in both materials is presented. A full lattice sum of the interactions between the partially charged atomic centers in h-BN results in vanishingly small monopolar electrostatic contributions to the interlayer binding energy. Higher order electrostatic multipoles, exchange, and short-range correlation contributions are found to be very similar in both materials and to almost completely cancel out by the Pauli repulsions at physically relevant interlayer distances resulting in a marginal effective contribution to the interlayer binding. Further analysis of the dispersive energy term reveals that despite the large differences in the individual atomic polarizabilities the hetero-atomic B-N C6 coefficient is very similar to the homo-atomic C-C coefficient in the hexagonal bulk form resulting in very similar dispersive contribution to the interlayer binding. The overall binding energy curves of both materials are thus very similar predicting practically the same interlayer distance and very similar binding energies.Comment: 18 pages, 5 figures, 2 table

A direct physical interaction between Nanog and Sox2 regulates embryonic stem cell self-renewal

Embryonic stem (ES) cell self-renewal efficiency is determined by the Nanog protein level. However, the protein partners of Nanog that function to direct self-renewal are unclear. Here, we identify a Nanog interactome of over 130 proteins including transcription factors, chromatin modifying complexes, phosphorylation and ubiquitination enzymes, basal transcriptional machinery members, and RNA processing factors. Sox2 was identified as a robust interacting partner of Nanog. The purified Nanog–Sox2 complex identified a DNA recognition sequence present in multiple overlapping Nanog/Sox2 ChIP-Seq data sets. The Nanog tryptophan repeat region is necessary and sufficient for interaction with Sox2, with tryptophan residues required. In Sox2, tyrosine to alanine mutations within a triple-repeat motif (S X T/S Y) abrogates the Nanog–Sox2 interaction, alters expression of genes associated with the Nanog-Sox2 cognate sequence, and reduces the ability of Sox2 to rescue ES cell differentiation induced by endogenous Sox2 deletion. Substitution of the tyrosines with phenylalanine rescues both the Sox2–Nanog interaction and efficient self-renewal. These results suggest that aromatic stacking of Nanog tryptophans and Sox2 tyrosines mediates an interaction central to ES cell self-renewal

Hamiltonian theory of gaps, masses and polarization in quantum Hall states: full disclosure

I furnish details of the hamiltonian theory of the FQHE developed with Murthy for the infrared, which I subsequently extended to all distances and apply it to Jain fractions \nu = p/(2ps + 1). The explicit operator description in terms of the CF allows one to answer quantitative and qualitative issues, some of which cannot even be posed otherwise. I compute activation gaps for several potentials, exhibit their particle hole symmetry, the profiles of charge density in states with a quasiparticles or hole, (all in closed form) and compare to results from trial wavefunctions and exact diagonalization. The Hartree-Fock approximation is used since much of the nonperturbative physics is built in at tree level. I compare the gaps to experiment and comment on the rough equality of normalized masses near half and quarter filling. I compute the critical fields at which the Hall system will jump from one quantized value of polarization to another, and the polarization and relaxation rates for half filling as a function of temperature and propose a Korringa like law. After providing some plausibility arguments, I explore the possibility of describing several magnetic phenomena in dirty systems with an effective potential, by extracting a free parameter describing the potential from one data point and then using it to predict all the others from that sample. This works to the accuracy typical of this theory (10 -20 percent). I explain why the CF behaves like free particle in some magnetic experiments when it is not, what exactly the CF is made of, what one means by its dipole moment, and how the comparison of theory to experiment must be modified to fit the peculiarities of the quantized Hall problem