2,005 research outputs found
Numerical algebraic geometry for model selection and its application to the life sciences
Researchers working with mathematical models are often confronted by the
related problems of parameter estimation, model validation, and model
selection. These are all optimization problems, well-known to be challenging
due to non-linearity, non-convexity and multiple local optima. Furthermore, the
challenges are compounded when only partial data is available. Here, we
consider polynomial models (e.g., mass-action chemical reaction networks at
steady state) and describe a framework for their analysis based on optimization
using numerical algebraic geometry. Specifically, we use probability-one
polynomial homotopy continuation methods to compute all critical points of the
objective function, then filter to recover the global optima. Our approach
exploits the geometric structures relating models and data, and we demonstrate
its utility on examples from cell signaling, synthetic biology, and
epidemiology.Comment: References added, additional clarification
The Effects of Diffuse Ionized Gas and Spatial Resolution on Metallicity Gradients: TYPHOON Two-Dimensional Spectrophotometry of M83
We present a systematic study of the diffuse ionized gas (DIG) in M83 and its
effects on the measurement of metallicity gradients at varying resolution
scales. Using spectrophotometric data cubes of M83 obtained at the 2.5m duPont
telescope at Las Campanas Observatory as part of the TYPHOON program, we
separate the HII regions from the DIG using the [SII]/H ratio, HIIphot
(HII finding algorithm) and the H surface brightness. We find that the
contribution to the overall H luminosity is approximately equal for the
HII and DIG regions. The data is then rebinned to simulate low-resolution
observations at varying resolution scales from 41 pc up to 1005 pc. Metallicity
gradients are measured using five different metallicity diagnostics at each
resolution. We find that all metallicity diagnostics used are affected by the
inclusion of DIG to varying degrees. We discuss the reasons of why the
metallicity gradients are significantly affected by DIG using the HII dominance
and emission line ratio radial profiles. We find that applying the
[SII]/H cut will provide a closer estimate of the true metallicity
gradient up to a resolution of 1005 pc for all metallicity diagnostics used in
this study.Comment: 26 pages, 12 figures + Appendix/Supplementary Material, accepted for
publication by MNRA
Starburst-AGN mixing: TYPHOON observations of NGC 1365, NGC 1068, and the effect of spatial resolution on the AGN fraction
We demonstrate a robust method of resolving the star-formation and AGN
contributions to emission lines using two very well known AGN systems: NGC
1365, and NGC 1068, using the high spatial resolution data from the
TYPHOON/PrISM survey. We expand the previous method of calculating the AGN
fraction by using theoretical-based model grids rather than empirical points.
The high spatial resolution of the TYPHOON/PrISM observations show evidence of
both star formation and AGN activity occurring in the nuclei of the two
galaxies. We rebin the data to the lower resolutions, typically found in other
integral field spectroscopy surveys such as SAMI, MaNGA, and CALIFA. The
results show that when rebinned from the native resolution of TYPHOON (< 200
pc/pixel) to 1 kpc/pixel, the effects include a roughly 3 kpc increase in the
radius of measured AGN activity, and a factor of 2 to 7 increase in the
detection of low surface brightness features such as shocks. All of this
information is critical, because information on certain physical processes may
be lost at varying resolutions. We make recommendations for analysing data at
current IFU survey resolutions.Comment: 30 pages, 28 figures, accepted for publication by MNRA
Vibrational modes in nanocrystalline iron under high pressure
The phonon density of states (DOS) of nanocrystalline 57Fe was measured using nuclear resonant inelastic x-ray scattering (NRIXS) at pressures up to 28 GPa in a diamond anvil cell. The nanocrystalline material exhibited an enhancement in its DOS at low energies by a factor of 2.2. This enhancement persisted throughout the entire pressure range, although it was reduced to about 1.7 after decompression. The low-energy regions of the spectra were fitted to the function AEn, giving values of n close to 2 for both the bulk control sample and the nanocrystalline material, indicative of nearly three-dimensional vibrational dynamics. At higher energies, the van Hove singularities observed in both samples were coincident in energy and remained so at all pressures, indicating that the forces conjugate to the normal coordinates of the nanocrystalline materials are similar to the interatomic potentials of bulk crystals
Flow network controlled shape transformation of a thin membrane through differential fluid storage and surface expansion
The mechanical properties of a thin, planar material, perfused by an embedded
flow network, can be changed locally and globally by the fluid transport and
storage, resulting in small or large-scale deformation, such as out-of-plane
buckling. Fluid absorption and storage eventually cause the material to locally
swell. Different parts can hydrate and swell unevenly, prompting a differential
expansion of the surface. In order to computationally study the hydraulically
induced differential swelling and buckling of such a membrane, we develop a
network model that describes both the membrane shape and fluid movement,
coupling mechanics with hydrodynamics. We simulate the time-dependent fluid
distribution in the flow network based on a spatially explicit resistor network
model with local fluid-storage capacitance. The shape of the surface is modeled
by a spring network produced by a tethered mesh discretization, in which local
bond rest lengths are adjusted instantaneously according to associated local
fluid content in the capacitors in a quasi-static way. We investigate the
effects of various designs of the flow network, including overall hydraulic
traits (resistance and capacitance) and hierarchical architecture (arrangement
of major and minor veins), on the specific dynamics of membrane shape
transformation. To quantify these effects, we explore the correlation between
local Gaussian curvature and relative stored fluid content in each hierarchy by
using linear regression, which reveals that stronger correlations could be
induced by less densely connected major veins. This flow-controlled mechanism
of shape transformation was inspired by the blooming of flowers through the
unfolding of petals. It can potentially offer insights for other reversible
motions observed in plants induced by differential turgor and water transport
through the xylem vessels, as well as engineering applications
Azimuthal variations of gas-phase oxygen abundance in NGC 2997
13 pages, 17 figures, accepted to A&A Reproduced with permission from Astronomy & Astrophysics. © 2018 ESO.The azimuthal variation of the HII region oxygen abundance in spiral galaxies is a key observable for understanding how quickly oxygen produced by massive stars can be dispersed within the surrounding interstellar medium. Observational constraints on the prevalence and magnitude of such azimuthal variations remain rare in the literature. Here, we report the discovery of pronounced azimuthal variations of HII region oxygen abundance in NGC 2997, a spiral galaxy at approximately 11.3 Mpc. Using 3D spectroscopic data from the TYPHOON Program, we study the HII region oxygen abundance at a physical resolution of 125 pc. Individual HII regions or complexes are identified in the 3D optical data and their strong emission line fluxes measured to constrain their oxygen abundances. We find 0.06 dex azimuthal variations in the oxygen abundance on top of a radial abundance gradient that is comparable to those seen in other star-forming disks. At a given radial distance, the oxygen abundances are highest in the spiral arms and lower in the inter-arm regions, similar to what has been reported in NGC 1365 using similar observations. We discuss whether the azimuthal variations could be recovered when the galaxy is observed at worse physical resolutions and lower signal-to-noise ratios.Peer reviewe
A Symposium on Donor‐Specific Antibodies after Transplantation Introduction
Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/106818/1/j.1399-3046.2011.01521.x.pd
Lymphocyte Phenotype during Therapy for Acute Graft-versus-Host Disease: A Brief Report from BMT-CTN 0302
AbstractAlthough significant strides have been made in understanding the biology of graft-versus-host disease (GVHD) and its prevention over the last 4 decades, little is known about the different populations of lymphocytes and the changes in response to treatment for this condition. BMT-CTN 0302 was a randomized phase II clinical trial in the Blood and Marrow Transplant Clinical Trials Network that assessed the efficacy of combination therapy with steroids plus pentostatin, mycophenolate mofetil, etanercept, or denileukin diftitox in patients with acute GVHD. Patients enrolled in the study underwent blood analysis by flow cytometry on days 0, 14, and 28 of therapy to enumerate the number of total lymphocytes, T cells, B cells, and lymphocytes expressing activation markers. Baseline total lymphocyte counts and subpopulations were similar in the 4 treatment arms. Responding patients had a smaller decrease in total CD45+ cell count (P = .005) compared with nonresponding patients at day 28. On univariate analysis, those who developed chronic GVHD had significantly higher CD8+ cell counts at day 14 compared with those without it (P = .005). There was no significant association between baseline lymphocyte count and survival. On univariate analysis, among the patients with higher lymphocyte counts at days 14 and 28, there was a trend toward better survival at day 180, although this trend did not reach the predetermined threshold for significance. We found no significant differences in lymphocyte total or subpopulation counts among the 4 treatment arms, and no notable influence on outcomes
- …