FMRI Clustering and False Positive Rates

Recently, Eklund et al. (2016) analyzed clustering methods in standard FMRI packages: AFNI (which we maintain), FSL, and SPM [1]. They claimed: 1) false positive rates (FPRs) in traditional approaches are greatly inflated, questioning the validity of "countless published fMRI studies"; 2) nonparametric methods produce valid, but slightly conservative, FPRs; 3) a common flawed assumption is that the spatial autocorrelation function (ACF) of FMRI noise is Gaussian-shaped; and 4) a 15-year-old bug in AFNI's 3dClustSim significantly contributed to producing "particularly high" FPRs compared to other software. We repeated simulations from [1] (Beijing-Zang data [2], see [3]), and comment on each point briefly.Comment: 3 pages, 1 figure. A Letter accepted in PNA

Combining yield potential and drought resilience in a spring wheat diversity panel

Pressures of population growth and climate change require the development of resilient higher yielding crops, particularly to drought. A spring wheat diversity panel was developed to combine high‐yield potential with resilience. To assess performance under drought, which in many environments is intermittent and dependent on plant development, 150 lines were grown with drought imposed for 10 days either at jointing or at anthesis stages in Obregon, Mexico. Both drought treatments strongly reduced grain numbers compared with the fully irrigated check. Best performers under drought at jointing had more grain than poor performers, while best performers under drought at anthesis had larger grain than poor performers. Most high‐yielding lines were high yielding in one drought environment only. However, some of the best‐performing lines displayed yield potential and resilience across two environments (28 lines), particularly for yield under well‐watered and drought at jointing, where yield was most related to grain numbers. Strikingly, only three lines were high yielding across all three environments, and interestingly, these lines had high grain numbers. Among parameters measured in leaves and grain, leaf relative water content did not correlate with yield, and proline was negatively correlated with yield; there were small but significant relationships between leaf sugars and yield. This study provides a valuable resource for further crosses and for elucidating genes and mechanisms that may contribute to grain number and grain filling conservation to combine yield potential and drought resilience

Three dimensional reconstructed MRI of an acrylic meniscal cartilage phantom: the effect of acquisition slice thickness upon accuracy of volume measurement

AUSTRALI

The Remarkably Featureless High Resolution X-ray Spectrum of Mrk 478

An observation of Mrk 478 using the Chandra Low Energy Transmission Grating Spectrometer is presented. The source exhibited 30-40% flux variations on timescales of order 10000 s together with a slow decline in the spectral softness over the full 80 ks observation. The 0.15--3.0 keV spectrum is well fitted by a single power law with photon index of Gamma = 2.91 +/- 0.03. Combined with high energy data from BeppoSAX, the spectrum from 0.15 to 10 keV is well fit as the sum of two power laws with Gamma = 3.03 +/- 0.04, which dominates below 2 keV and 1.4 +/- 0.2, which dominates above 2 keV (quoting 90% confidence uncertainties). No significant emission or absorption features are detected in the high resolution spectrum, supporting our previous findings using the Extreme Ultraviolet Explorer but contradicting the claims of emission lines by Hwang & Bowyer (1997). There is no evidence of a warm absorber, as found in the high resolution spectra of many Sy 1 galaxies including others classified as narrow line Sy 1 galaxies such as Mrk 478. We suggest that the X-ray continuum may result from Comptonization of disk thermal emission in a hot corona through a range of optical depths.Comment: 21 pages, 7 figures; accepted for publication in the Astronomical Journa

A Dynamical Study of the Black Hole X-ray Binary Nova Muscae 1991

We present a dynamical study of the Galactic black hole binary system Nova Muscae 1991 (GS/GRS 1124-683). We utilize 72 high resolution Magellan Echellette (MagE) spectra and 72 strictly simultaneous V-band photometric observations; the simultaneity is a unique and crucial feature of this dynamical study. The data were taken on two consecutive nights and cover the full 10.4-hour orbital cycle. The radial velocities of the secondary star are determined by cross-correlating the object spectra with the best-match template spectrum obtained using the same instrument configuration. Based on our independent analysis of five orders of the echellette spectrum, the semi-amplitude of the radial velocity of the secondary is measured to be K_2 = 406.8+/-2.7 km/s, which is consistent with previous work, while the uncertainty is reduced by a factor of 3. The corresponding mass function is f(M) = 3.02+/-0.06 M_\odot. We have also obtained an accurate measurement of the rotational broadening of the stellar absorption lines (v sin i = 85.0+/-2.6 km/s) and hence the mass ratio of the system q = 0.079+/-0.007. Finally, we have measured the spectrum of the non-stellar component of emission that veils the spectrum of the secondary. In a future paper, we will use our veiling-corrected spectrum of the secondary and accurate values of K_2 and q to model multi-color light curves and determine the systemic inclination and the mass of the black hole.Comment: ApJ accepted version; minor revision; added a subsection about systematic uncertaintie

Identifying Important Parameters in the Inflammatory Process with a Mathematical Model of Immune Cell Influx and Macrophage Polarization

In an inflammatory setting, macrophages can be polarized to an inflammatory M1 phenotype or to an anti-inflammatory M2 phenotype, as well as existing on a spectrum between these two extremes. Dysfunction of this phenotypic switch can result in a population imbalance that leads to chronic wounds or disease due to unresolved inflammation. Therapeutic interventions that target macrophages have therefore been proposed and implemented in diseases that feature chronic inflammation such as diabetes mellitus and atherosclerosis. We have developed a model for the sequential influx of immune cells in the peritoneal cavity in response to a bacterial stimulus that includes macrophage polarization, with the simplifying assumption that macrophages can be classified as M1 or M2. With this model, we were able to reproduce the expected timing of sequential influx of immune cells and mediators in a general inflammatory setting. We then fit this model to in vivo experimental data obtained from a mouse peritonitis model of inflammation, which is widely used to evaluate endogenous processes in response to an inflammatory stimulus. Model robustness is explored with local structural and practical identifiability of the proposed model a posteriori. Additionally, we perform sensitivity analysis that identifies the population of apoptotic neutrophils as a key driver of the inflammatory process. Finally, we simulate a selection of proposed therapies including points of intervention in the case of delayed neutrophil apoptosis, which our model predicts will result in a sustained inflammatory response. Our model can therefore provide hypothesis testing for therapeutic interventions that target macrophage phenotype and predict outcomes to be validated by subsequent experimentation

Identifying Important Parameters in the Inflammatory Process with a Mathematical Model of Immune Cell Influx and Macrophage Polarization

In an inflammatory setting, macrophages can be polarized to an inflammatory M1 phenotype or to an anti-inflammatory M2 phenotype, as well as existing on a spectrum between these two extremes. Dysfunction of this phenotypic switch can result in a population imbalance that leads to chronic wounds or disease due to unresolved inflammation. Therapeutic interventions that target macrophages have therefore been proposed and implemented in diseases that feature chronic inflammation such as diabetes mellitus and atherosclerosis. We have developed a model for the sequential influx of immune cells in the peritoneal cavity in response to a bacterial stimulus that includes macrophage polarization, with the simplifying assumption that macrophages can be classified as M1 or M2. With this model, we were able to reproduce the expected timing of sequential influx of immune cells and mediators in a general inflammatory setting. We then fit this model to in vivo experimental data obtained from a mouse peritonitis model of inflammation, which is widely used to evaluate endogenous processes in response to an inflammatory stimulus. Model robustness is explored with local structural and practical identifiability of the proposed model a posteriori. Additionally, we perform sensitivity analysis that identifies the population of apoptotic neutrophils as a key driver of the inflammatory process. Finally, we simulate a selection of proposed therapies including points of intervention in the case of delayed neutrophil apoptosis, which our model predicts will result in a sustained inflammatory response. Our model can therefore provide hypothesis testing for therapeutic interventions that target macrophage phenotype and predict outcomes to be validated by subsequent experimentation

Tomography of X-ray Nova Muscae 1991: Evidence for ongoing mass transfer and stream-disc overflow

We present a spectroscopic analysis of the black hole binary Nova Muscae 1991 in quiescence using data obtained in 2009 with MagE on the Magellan Clay telescope and in 2010 with IMACS on the Magellan Baade telescope at the Las Campanas Observatory. Emission from the disc is observed in H alpha, H beta and Ca II (8662 A). A prominent hotspot is observed in the Doppler maps of all three emission lines. The existence of this spot establishes ongoing mass transfer from the donor star in 2009-2010 and, given its absence in the 1993-1995 observations, demonstrates the presence of a variable hotspot in the system. We find the radial distance to the hotspot from the black hole to be consistent with the circularization radius. Our tomograms are suggestive of stream-disc overflow in the system. We also detect possible Ca II (8662 A) absorption from the donor star.Comment: 10 pages, 11 figures, 1 table. Accepted for publication in MNRA

Differences Between The Optical/Uv Spectra Of X-Ray Bright And X-Ray Faint QSOs

We contrast measurements of composite optical and ultraviolet (UV) spectra constructed from samples of QSOs defined by their soft X-ray brightness. X-ray bright (XB) composites show stronger emission lines in general, but particularly from the narrow line region. The difference in the [OIII]/Hbeta ratio is particularly striking, and even more so when blended FeII emission is properly subtracted. The correlation of this ratio with X-ray brightness were principal components of QSO spectral diversity found by Boroson & Green (1992). We find here that other, much weaker narrow optical forbidden lines ([OII] and NeV) are enhanced by factors of 2 to 3 in our XB composites, and that narrow line emission is also strongly enhanced in the XB UV composite. Broad permitted line fluxes are slightly larger for all XB spectra, but the narrow/broad line ratio stays similar or increases strongly with X-ray brightness for all strong permitted lines except Hbeta. Spectral differences between samples divided by their relative X-ray brightness (as measured by alpha_{ox}) exceed those seen between complementary samples divided by luminosity or radio loudness. We propose that the Baldwin effect may be a secondary correlation to the primary relationship between alpha_{ox} and emission line equivalent width. We conclude that either 1) equivalent width depends strongly on the SHAPE of the ionizing continuum, as crudely characterized here by alpha_{ox} or 2) both equivalent width and alpha_{ox} are related to some third parameter characterizing the QSO physics. One such possibility is intrinsic warm absorption; a soft X-ray absorber situated between the broad and narrow line regions can successfully account for many of the properties observed.Comment: 16 pages including 3 figures, AAS latex, plus 4 tables totaling 5 pages, to appear in ApJ Vol. 498, May 1, 199