Characterizing the Rigidly Rotating Magnetosphere Stars HD 345439 and HD 23478

The SDSS III APOGEE survey recently identified two new $\sigma$ Ori E type candidates, HD 345439 and HD 23478, which are a rare subset of rapidly rotating massive stars whose large (kGauss) magnetic fields confine circumstellar material around these systems. Our analysis of multi-epoch photometric observations of HD 345439 from the KELT, SuperWASP, and ASAS surveys reveals the presence of a $\sim$0.7701 day period in each dataset, suggesting the system is amongst the faster known $\sigma$ Ori E analogs. We also see clear evidence that the strength of H-alpha, H I Brackett series lines, and He I lines also vary on a $\sim$0.7701 day period from our analysis of multi-epoch, multi-wavelength spectroscopic monitoring of the system from the APO 3.5m telescope. We trace the evolution of select emission line profiles in the system, and observe coherent line profile variability in both optical and infrared H I lines, as expected for rigidly rotating magnetosphere stars. We also analyze the evolution of the H I Br-11 line strength and line profile in multi-epoch observations of HD 23478 from the SDSS-III APOGEE instrument. The observed periodic behavior is consistent with that recently reported by Sikora and collaborators in optical spectra.Comment: Accepted in ApJ

Limitations of phase-sorting based pencil beam scanned 4D proton dose calculations under irregular motion.

Objective.4D dose calculation (4DDC) for pencil beam scanned (PBS) proton therapy is typically based on phase-sorting of individual pencil beams onto phases of a single breathing cycle 4DCT. Understanding the dosimetric limitations and uncertainties of this approach is essential, especially for the realistic treatment scenario with irregular free breathing motion.Approach.For three liver and three lung cancer patient CTs, the deformable multi-cycle motion from 4DMRIs was used to generate six synthetic 4DCT(MRI)s, providing irregular motion (11/15 cycles for liver/lung; tumor amplitudes ∼4-18 mm). 4DDCs for two-field plans were performed, with the temporal resolution of the pencil beam delivery (4-200 ms) or with 8 phases per breathing cycle (500-1000 ms). For the phase-sorting approach, the tumor center motion was used to determine the phase assignment of each spot. The dose was calculated either using the full free breathing motion or individually repeating each single cycle. Additionally, the use of an irregular surrogate signal prior to 4DDC on a repeated cycle was simulated. The CTV volume with absolute dose differences >5% (Vdosediff>5%) and differences in CTVV95%andD5%-D95%compared to the free breathing scenario were evaluated.Main results.Compared to 4DDC considering the full free breathing motion with finer spot-wise temporal resolution, 4DDC based on a repeated single 4DCT resulted inVdosediff>5%of on average 34%, which resulted in an overestimation ofV95%up to 24%. However, surrogate based phase-sorting prior to 4DDC on a single cycle 4DCT, reduced the averageVdosediff>5%to 16% (overestimationV95%up to 19%). The 4DDC results were greatly influenced by the choice of reference cycle (Vdosediff>5%up to 55%) and differences due to temporal resolution were much smaller (Vdosediff>5%up to 10%).Significance.It is important to properly consider motion irregularity in 4D dosimetric evaluations of PBS proton treatments, as 4DDC based on a single 4DCT can lead to an underestimation of motion effects

Numerical investigation of mesh size convergence rate of the finite element method in MESFET simulation

The mesh size convergence rate of the finite element method in two-dimensional GaAs MESFET simulation has been investigated numerically. The equations governing MESFET operation and the finite element formulation of these equations are summarized. The presence of corner singularities at the gate contact endpoints is noteworthy, for such singularities are known to determine the convergence rate in linear model problems. The local potential and electron concentration solutions are obtained in the neighborhood of these singularities and used to estimate a lower bound on the convergence rate for the nonlinear problem. The rate of convergence of the MESFET problem is tabulated for three mesh sequences and discussed. The common source output characteristic of a 0.25 [mu]m gate length GaAs MESFET is calculated and compared to the characteristic of a MESFET fabricated in our laboratory. Considerable discrepancy between the two is obtained; reasons for this are hypothesized.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/24366/1/0000635.pd

Microwave device investigations

Several tasks were active during this report period: (1) noise modulation in avalanche-diode devices; (2) schottky-barrier microwave devices; (3) intermodulation products in IMPATT diode amplifiers; (4) harmonic generation using Read-diode varactors; and (5) fabrication of GaAs Schottky-barrier IMPATT diodes

A survey of cost-sensitive decision tree induction algorithms

The past decade has seen a significant interest on the problem of inducing decision trees that take account of costs of misclassification and costs of acquiring the features used for decision making. This survey identifies over 50 algorithms including approaches that are direct adaptations of accuracy based methods, use genetic algorithms, use anytime methods and utilize boosting and bagging. The survey brings together these different studies and novel approaches to cost-sensitive decision tree learning, provides a useful taxonomy, a historical timeline of how the field has developed and should provide a useful reference point for future research in this field

Ontology mapping for semantically enabled applications

In this review, we provide a summary of recent progress in ontology mapping (OM) at a crucial time when biomedical research is under a deluge of an increasing amount and variety of data. This is particularly important for realising the full potential of semantically enabled or enriched applications and for meaningful insights, such as drug discovery, using machine-learning technologies. We discuss challenges and solutions for better ontology mappings, as well as how to select ontologies before their application. In addition, we describe tools and algorithms for ontology mapping, including evaluation of tool capability and quality of mappings. Finally, we outline the requirements for an ontology mapping service (OMS) and the progress being made towards implementation of such sustainable services

Diverting phenylpropanoid pathway flux from sinapine to produce industrially useful 4-vinyl derivatives of hydroxycinnamic acids in Brassicaceous oilseeds

Sinapine (sinapoylcholine) is an antinutritive phenolic compound that can account for up to 2% of seed weight in brassicaceous oilseed crops and reduces the suitability of their protein-rich seed meal for use as animal feed. Sinapine biosynthesis draws on hydroxycinnamic acid precursors produced by the phenylpropanoid pathway. The 4-vinyl derivatives of several hydroxycinnamic acids have industrial applications. For example, 4-vinyl phenol (4-hydroxystyrene) is a building block for a range of synthetic polymers applied in resins, inks, elastomers, and coatings. Here we have expressed a modified bacterial phenolic acid decarboxylase (PAD) in developing seed of Camelina sativa to redirect phenylpropanoid pathway flux from sinapine biosynthesis to the production of 4-vinyl phenols. PAD expression led to a ∼95% reduction in sinapine content in seeds of both glasshouse and field grown C. sativa and to an accumulation of 4-vinyl derivatives of hydroxycinnamic acids, primarily as glycosides. The most prevalent aglycone was 4-vinyl phenol, but 4-vinyl guaiacol, 6-hydroxy-4-vinyl guaiacol and 4-vinylsyringol (Canolol) were also detected. The molar quantity of 4-vinyl phenol glycosides was more than twice that of sinapine in wild type seeds. PAD expression was not associated with an adverse effect on seed yield, harvest index, seed morphology, storage oil content or germination in either glasshouse or field experiments. Our data show that expression of PAD in brassicaceous oilseeds can supress sinapine accumulation, diverting phenylpropanoid pathway flux into 4-vinyl phenol derivatives, thereby also providing a non-petrochemical source of this class of industrial chemicals

A motion model-guided 4D dose reconstruction for pencil beam scanned proton therapy.

Objective.4D dose reconstruction in proton therapy with pencil beam scanning (PBS) typically relies on a single pre-treatment 4DCT (p4DCT). However, breathing motion during the fractionated treatment can vary considerably in both amplitude and frequency. We present a novel 4D dose reconstruction method combining delivery log files with patient-specific motion models, to account for the dosimetric effect of intra- and inter-fractional breathing variability.Approach.Correlation between an external breathing surrogate and anatomical deformations of the p4DCT is established using principal component analysis. Using motion trajectories of a surface marker acquired during the dose delivery by an optical tracking system, deformable motion fields are retrospectively reconstructed and used to generate time-resolved synthetic 4DCTs ('5DCTs') by warping a reference CT. For three abdominal/thoracic patients, treated with respiratory gating and rescanning, example fraction doses were reconstructed using the resulting 5DCTs and delivery log files. The motion model was validated beforehand using leave-one-out cross-validation (LOOCV) with subsequent 4D dose evaluations. Moreover, besides fractional motion, fractional anatomical changes were incorporated as proof of concept.Main results.For motion model validation, the comparison of 4D dose distributions for the original 4DCT and predicted LOOCV resulted in 3%/3 mm gamma pass rates above 96.2%. Prospective gating simulations on the p4DCT can overestimate the target dose coverage V95%by up to 2.1% compared to 4D dose reconstruction based on observed surrogate trajectories. Nevertheless, for the studied clinical cases treated with respiratory-gating and rescanning, an acceptable target coverage was maintained with V95%remaining above 98.8% for all studied fractions. For these gated treatments, larger dosimetric differences occurred due to CT changes than due to breathing variations.Significance.To gain a better estimate of the delivered dose, a retrospective 4D dose reconstruction workflow based on motion data acquired during PBS proton treatments was implemented and validated, thus considering both intra- and inter-fractional motion and anatomy changes

A Coordinated X-ray and Optical Campaign on the Nearest Massive Eclipsing Binary, Delta Ori Aa: I. Overview of the X-ray Spectrum

We present an overview of four phase-constrained Chandra HETGS X-ray observations of Delta Ori A. Delta Ori A is actually a triple system which includes the nearest massive eclipsing spectroscopic binary, Delta Ori Aa, the only such object which can be observed with little phase-smearing with the Chandra gratings. Since the fainter star, Delta Ori Aa2, has a much lower X-ray luminosity than the brighter primary, Delta Ori A provides a unique system with which to test the spatial distribution of the X-ray emitting gas around Delta Ori Aa1 via occultation by the photosphere of and wind cavity around the X-ray dark secondary. Here we discuss the X-ray spectrum and X-ray line profiles for the combined observation, having an exposure time of nearly 500 ksec and covering nearly the entire binary orbit. Companion papers discuss the X-ray variability seen in the Chandra spectra, present new space-based photometry and ground-based radial velocities simultaneous with the X-ray data to better constrain the system parameters, and model the effects of X-rays on the optical and UV spectrum. We find that the X-ray emission is dominated by embedded wind shock emission from star Aa1, with little contribution from the tertiary star Ab or the shocked gas produced by the collision of the wind of Aa1 against the surface of Aa2. We find a similar temperature distribution to previous X-ray spectrum analyses. We also show that the line half-widths are about $0.3-0.5\times$ the terminal velocity of the wind of star Aa1. We find a strong anti-correlation between line widths and the line excitation energy, which suggests that longer-wavelength, lower-temperature lines form farther out in the wind. Our analysis also indicates that the ratio of the intensities of the strong and weak lines of \ion{Fe}{17} and \ion{Ne}{10} are inconsistent with model predictions, which may be an effect of resonance scatteringComment: accepted by ApJ; revised according to ApJ proo

A Coordinated X-ray and Optical Campaign of the Nearby Massive Binary δ\delta Orionis Aa: II. X-ray Variability

We present time-resolved and phase-resolved variability studies of an extensive X-ray high-resolution spectral dataset of the $\delta$ Orionis Aa binary system. The four observations, obtained with Chandra ACIS HETGS, have a total exposure time of ~479 ks and provide nearly complete binary phase coverage. Variability of the total X-ray flux in the range 5-25 $\AA$ is confirmed, with maximum amplitude of about +/-15% within a single ~125 ks observation. Periods of 4.76d and 2.04d are found in the total X-ray flux, as well as an apparent overall increase in flux level throughout the 9-day observational campaign. Using 40 ks contiguous spectra derived from the original observations, we investigate variability of emission line parameters and ratios. Several emission lines are shown to be variable, including S XV, Si XIII, and Ne IX. For the first time, variations of the X-ray emission line widths as a function of the binary phase are found in a binary system, with the smallest widths at phase=0.0 when the secondary $\delta$ Orionis Aa2 is at inferior conjunction. Using 3D hydrodynamic modeling of the interacting winds, we relate the emission line width variability to the presence of a wind cavity created by a wind-wind collision, which is effectively void of embedded wind shocks and is carved out of the X-ray-producing primary wind, thus producing phase-locked X-ray variability.Comment: 36 pages, 14 Tables, 19 Figures, accepted by ApJ, one of 4 related papers to be published togethe