High atomic weight, high-energy radiation (HZE) induces transcriptional responses shared with conventional stresses in addition to a core "DSB" response specific to clastogenic treatments.

Plants exhibit a robust transcriptional response to gamma radiation which includes the induction of transcripts required for homologous recombination and the suppression of transcripts that promote cell cycle progression. Various DNA damaging agents induce different spectra of DNA damage as well as "collateral" damage to other cellular components and therefore are not expected to provoke identical responses by the cell. Here we study the effects of two different types of ionizing radiation (IR) treatment, HZE (1 GeV Fe(26+) high mass, high charge, and high energy relativistic particles) and gamma photons, on the transcriptome of Arabidopsis thaliana seedlings. Both types of IR induce small clusters of radicals that can result in the formation of double strand breaks (DSBs), but HZE also produces linear arrays of extremely clustered damage. We performed these experiments across a range of time points (1.5-24 h after irradiation) in both wild-type plants and in mutants defective in the DSB-sensing protein kinase ATM. The two types of IR exhibit a shared double strand break-repair-related damage response, although they differ slightly in the timing, degree, and ATM-dependence of the response. The ATM-dependent, DNA metabolism-related transcripts of the "DSB response" were also induced by other DNA damaging agents, but were not induced by conventional stresses. Both Gamma and HZE irradiation induced, at 24 h post-irradiation, ATM-dependent transcripts associated with a variety of conventional stresses; these were overrepresented for pathogen response, rather than DNA metabolism. In contrast, only HZE-irradiated plants, at 1.5 h after irradiation, exhibited an additional and very extensive transcriptional response, shared with plants experiencing "extended night." This response was not apparent in gamma-irradiated plants

Genomic stability in response to high versus low linear energy transfer radiation in Arabidopsis thaliana.

Low linear energy transfer (LET) gamma rays and high LET HZE (high atomic weight, high energy) particles act as powerful mutagens in both plants and animals. DNA damage generated by HZE particles is more densely clustered than that generated by gamma rays. To understand the genetic requirements for resistance to high versus low LET radiation, a series of Arabidopsis thaliana mutants were exposed to either 1GeV Fe nuclei or gamma radiation. A comparison of effects on the germination and subsequent growth of seedlings led us to conclude that the relative biological effectiveness (RBE) of the two types of radiation (HZE versus gamma) are roughly 3:1. Similarly, in wild-type lines, loss of somatic heterozygosity was induced at an RBE of about a 2:1 (HZE versus gamma). Checkpoint and repair defects, as expected, enhanced sensitivity to both agents. The "replication fork" checkpoint, governed by ATR, played a slightly more important role in resistance to HZE-induced mutagenesis than in resistance to gamma induced mutagenesis

The Effects of Protamine on a Murine Leukemia Virus

This study indicated that: (1) i.p. inoculation of protamine into (Rauscher) leukemic mice increased their X death time, (2) protamine was more toxic for leukemic than normal mice and (3) the in vitro reaction between Rauscher virus and protamine reduced its infectivity for mice

Using eye-tracking in applied linguistics and second language research

With eye-tracking technology the eye is thought to give researchers a window into the mind. Importantly, eye-tracking has significant advantages over traditional online processing measures: chiefly that it allows for more ‘natural’ processing as it does not require a secondary task, and that it provides a very rich moment-to-moment data source. In recognition of the technology’s benefits, an ever increasing number of researchers in applied linguistics and second language research are beginning to use it. As eye-tracking gains traction in the field, it is important to ensure that it is established in an empirically sound fashion. To do this it is important for the field to come to an understanding about what eye-tracking is, what eye-tracking measures tell us, what it can be used for, and what different eye-tracking systems can and cannot do. Further, it is important to establish guidelines for designing sound research studies using the technology. The goal of the current review is to begin to address these issues

Joint super-resolution and synthesis of 1 mm isotropic MP-RAGE volumes from clinical MRI exams with scans of different orientation, resolution and contrast

Most existing algorithms for automatic 3D morphometry of human brain MRI scans are designed for data with near-isotropic voxels at approximately 1 mm resolution, and frequently have contrast constraints as well-typically requiring T1-weighted images (e.g., MP-RAGE scans). This limitation prevents the analysis of millions of MRI scans acquired with large inter-slice spacing in clinical settings every year. In turn, the inability to quantitatively analyze these scans hinders the adoption of quantitative neuro imaging in healthcare, and also precludes research studies that could attain huge sample sizes and hence greatly improve our understanding of the human brain. Recent advances in convolutional neural networks (CNNs) are producing outstanding results in super-resolution and contrast synthesis of MRI. However, these approaches are very sensitive to the specific combination of contrast, resolution and orientation of the input images, and thus do not generalize to diverse clinical acquisition protocols - even within sites. In this article, we present SynthSR, a method to train a CNN that receives one or more scans with spaced slices, acquired with different contrast, resolution and orientation, and produces an isotropic scan of canonical contrast (typically a 1 mm MP-RAGE). The presented method does not require any preprocessing, beyond rigid coregistration of the input scans. Crucially, SynthSR trains on synthetic input images generated from 3D segmentations, and can thus be used to train CNNs for any combination of contrasts, resolutions and orientations without high-resolution real images of the input contrasts. We test the images generated with SynthSR in an array of common downstream analyses, and show that they can be reliably used for subcortical segmentation and volumetry, image registration (e.g., for tensor-based morphometry), and, if some image quality requirements are met, even cortical thickness morphometry. The source code is publicly available at https://github.com/BBillot/SynthSR

Proton and Helium Spectra from the CREAM-III Flight

Primary cosmic-ray elemental spectra have been measured with the balloon-borne Cosmic Ray Energetics And Mass (CREAM) experiment since 2004. The third CREAM payload (CREAM-III) flew for 29 days during the 2007-2008 Antarctic season. Energies of incident particles above 1 TeV are measured with a calorimeter. Individual elements are clearly separated with a charge resolution of ~0.12 e (in charge units) and ~0.14 e for protons and helium nuclei, respectively, using two layers of silicon charge detectors. The measured proton and helium energy spectra at the top of the atmosphere are harder than other existing measurements at a few tens of GeV. The relative abundance of protons to helium nuclei is 9.53+-0.03 for the range of 1 TeV/n to 63 TeV/n. The ratio is considerably smaller than other measurements at a few tens of GeV/n. The spectra become softer above ~20 TeV. However, our statistical uncertainties are large at these energies and more data are needed

The Composition of M-type asteroids II: Synthesis of spectroscopic and radar observations

This work updates and expands on results of our long-term radar-driven observational campaign of main-belt asteroids (MBAs) focused on Bus-DeMeo Xc- and Xk-type objects (Tholen X and M class asteroids) using the Arecibo radar and NASA Infrared Telescope Facilities (Ockert-Bell et al. 2008; 2010; Shepard et al. 2008; 2010). Eighteen of our targets were near-simultaneously observed with radar and those observations are described in Shepard et al. (2010). We combine our near-infrared data with available visible wavelength data for a more complete compositional analysis of our targets. Compositional evidence is derived from our target asteroid spectra using two different methods, a \c{hi}2 search for spectral matches in the RELAB database and parametric comparisons with meteorites. We present four new methods of parametric comparison, including discriminant analysis. Discriminant analysis identifies meteorite type with 85% accuracy. This paper synthesizes the results of these two analog search algorithms and reconciles those results with analogs suggested from radar data (Shepard et al. 2010). We have observed 29 asteroids, 18 in conjunction with radar observations. For eighteen out of twenty-nine objects observed (62%) our compositional predictions are consistent over two or more methods applied. We find that for our Xc and Xk targets the best fit is an iron meteorite for 34% of the samples. Enstatite Chondrites were best fits for 6 of our targets (21%). Stony-iron meteorites were best fits for 2 of our targets (7%). A discriminant analysis suggests that asteroids with no absorption band can be compared to iron meteorites and asteroids with both a 0.9 and 1.9 {\mu}m absorption band can be compared to stony-iron meteorites.Comment: 30 pages, 5 figures, 10 table

Does shear wave ultrasound independently predict axillary lymph node metastasis in women with invasive breast cancer?

Shear wave elastography (SWE) shows promise as an adjunct to greyscale ultrasound examination in assessing breast masses. In breast cancer, higher lesion stiffness on SWE has been shown to be associated with features of poor prognosis. The purpose of this study was to assess whether lesion stiffness at SWE is an independent predictor of lymph node involvement. Patients with invasive breast cancer treated by primary surgery, who had undergone SWE examination were eligible. Data were retrospectively analysed from 396 consecutive patients. The mean stiffness values were obtained using the Aixplorer(®) ultrasound machine from SuperSonic Imagine Ltd. Measurements were taken from a region of interest positioned over the stiffest part of the abnormality. The average of the mean stiffness value obtained from each of two orthogonal image planes was used for analysis. Associations between lymph node involvement and mean lesion stiffness, invasive cancer size, histologic grade, tumour type, ER expression, HER-2 status and vascular invasion were assessed using univariate and multivariate logistic regression. At univariate analysis, invasive size, histologic grade, HER-2 status, vascular invasion, tumour type and mean stiffness were significantly associated with nodal involvement. Nodal involvement rates ranged from 7 % for tumours with mean stiffness <50 kPa to 41 % for tumours with a mean stiffness of >150 kPa. At multivariate analysis, invasive size, tumour type, vascular invasion, and mean stiffness maintained independent significance. Mean stiffness at SWE is an independent predictor of lymph node metastasis and thus can confer prognostic information additional to that provided by conventional preoperative tumour assessment and staging

Elemental energy spectra of cosmic rays measured by CREAM-II

We present new measurements of the energy spectra of cosmic-ray (CR) nuclei from the second flight of the balloon-borne experiment CREAM (Cosmic Ray Energetics And Mass). The instrument (CREAM-II) was comprised of detectors based on different techniques (Cherenkov light, specific ionization in scintillators and silicon sensors) to provide a redundant charge identification and a thin ionization calorimeter capable of measuring the energy of cosmic rays up to several hundreds of TeV. The data analysis is described and the individual energy spectra of C, O, Ne, Mg, Si and Fe are reported up to ~ 10^14 eV. The spectral shape looks nearly the same for all the primary elements and can be expressed as a power law in energy E^{-2.66+/-0.04}. The nitrogen absolute intensity in the energy range 100-800 GeV/n is also measured.Comment: 4 pages, 3 figures, presented at ICRC 2009, Lodz, Polan