Validating Dose Uncertainty Estimates Produced by AUTODIRECT: An Automated Program to Evaluate Deformable Image Registration Accuracy.

Deformable image registration is a powerful tool for mapping information, such as radiation therapy dose calculations, from one computed tomography image to another. However, deformable image registration is susceptible to mapping errors. Recently, an automated deformable image registration evaluation of confidence tool was proposed to predict voxel-specific deformable image registration dose mapping errors on a patient-by-patient basis. The purpose of this work is to conduct an extensive analysis of automated deformable image registration evaluation of confidence tool to show its effectiveness in estimating dose mapping errors. The proposed format of automated deformable image registration evaluation of confidence tool utilizes 4 simulated patient deformations (3 B-spline-based deformations and 1 rigid transformation) to predict the uncertainty in a deformable image registration algorithm's performance. This workflow is validated for 2 DIR algorithms (B-spline multipass from Velocity and Plastimatch) with 1 physical and 11 virtual phantoms, which have known ground-truth deformations, and with 3 pairs of real patient lung images, which have several hundred identified landmarks. The true dose mapping error distributions closely followed the Student t distributions predicted by automated deformable image registration evaluation of confidence tool for the validation tests: on average, the automated deformable image registration evaluation of confidence tool-produced confidence levels of 50%, 68%, and 95% contained 48.8%, 66.3%, and 93.8% and 50.1%, 67.6%, and 93.8% of the actual errors from Velocity and Plastimatch, respectively. Despite the sparsity of landmark points, the observed error distribution from the 3 lung patient data sets also followed the expected error distribution. The dose error distributions from automated deformable image registration evaluation of confidence tool also demonstrate good resemblance to the true dose error distributions. Automated deformable image registration evaluation of confidence tool was also found to produce accurate confidence intervals for the dose-volume histograms of the deformed dose

First radial velocity results from the MINiature Exoplanet Radial Velocity Array (MINERVA)

The MINiature Exoplanet Radial Velocity Array (MINERVA) is a dedicated observatory of four 0.7m robotic telescopes fiber-fed to a KiwiSpec spectrograph. The MINERVA mission is to discover super-Earths in the habitable zones of nearby stars. This can be accomplished with MINERVA's unique combination of high precision and high cadence over long time periods. In this work, we detail changes to the MINERVA facility that have occurred since our previous paper. We then describe MINERVA's robotic control software, the process by which we perform 1D spectral extraction, and our forward modeling Doppler pipeline. In the process of improving our forward modeling procedure, we found that our spectrograph's intrinsic instrumental profile is stable for at least nine months. Because of that, we characterized our instrumental profile with a time-independent, cubic spline function based on the profile in the cross dispersion direction, with which we achieved a radial velocity precision similar to using a conventional "sum-of-Gaussians" instrumental profile: 1.8 m s$^{-1}$ over 1.5 months on the RV standard star HD 122064. Therefore, we conclude that the instrumental profile need not be perfectly accurate as long as it is stable. In addition, we observed 51 Peg and our results are consistent with the literature, confirming our spectrograph and Doppler pipeline are producing accurate and precise radial velocities.Comment: 22 pages, 9 figures, submitted to PASP, Peer-Reviewed and Accepte

The DEEP2 Galaxy Redshift Survey: Design, Observations, Data Reduction, and Redshifts

We describe the design and data sample from the DEEP2 Galaxy Redshift Survey, the densest and largest precision-redshift survey of galaxies at z ~ 1 completed to date. The survey has conducted a comprehensive census of massive galaxies, their properties, environments, and large-scale structure down to absolute magnitude M_B = -20 at z ~ 1 via ~90 nights of observation on the DEIMOS spectrograph at Keck Observatory. DEEP2 covers an area of 2.8 deg^2 divided into four separate fields, observed to a limiting apparent magnitude of R_AB=24.1. Objects with z < 0.7 are rejected based on BRI photometry in three of the four DEEP2 fields, allowing galaxies with z > 0.7 to be targeted ~2.5 times more efficiently than in a purely magnitude-limited sample. Approximately sixty percent of eligible targets are chosen for spectroscopy, yielding nearly 53,000 spectra and more than 38,000 reliable redshift measurements. Most of the targets which fail to yield secure redshifts are blue objects that lie beyond z ~ 1.45. The DEIMOS 1200-line/mm grating used for the survey delivers high spectral resolution (R~6000), accurate and secure redshifts, and unique internal kinematic information. Extensive ancillary data are available in the DEEP2 fields, particularly in the Extended Groth Strip, which has evolved into one of the richest multiwavelength regions on the sky. DEEP2 surpasses other deep precision-redshift surveys at z ~ 1 in terms of galaxy numbers, redshift accuracy, sample number density, and amount of spectral information. We also provide an overview of the scientific highlights of the DEEP2 survey thus far. This paper is intended as a handbook for users of the DEEP2 Data Release 4, which includes all DEEP2 spectra and redshifts, as well as for the publicly-available DEEP2 DEIMOS data reduction pipelines. [Abridged]Comment: submitted to ApJS; data products available for download at http://deep.berkeley.edu/DR4

Biogenetically-Inspired Total Synthesis of Epidithiodiketopiperazines and Related Alkaloids

Natural products chemistry has historically been the prime arena for the discovery of new chemical transformations and the fountain of insights into key biological processes. It remains a fervent incubator of progress in the fields of chemistry and biology and an exchange mediating the flow of ideas between these allied fields of science. It is with this ethos that our group has taken an interest in and pursued the synthesis of a complex family of natural products termed the dimeric epipolythiodiketopiperazine (ETP) alkaloids. We present here an Account of the highly complex target molecules to which we pegged our ambitions, our systematic and relentless efforts toward those goals, the chemistry we developed in their pursuit, and the insight we have gained for their translational potential as potent anticancer molecules.National Institute of General Medical Sciences (U.S.) (Grant GM089732)Amgen Inc

Prototype Testing Results of Charged Particle Detectors and Critical Subsystems for the ESRA Mission to GTO

The Experiment for Space Radiation Analysis (ESRA) is the latest of a series of Demonstration and Validation (DemVal) missions built by the Los Alamos National Laboratory, with the focus on testing a new generation of plasma and energetic paritcle sensors along with critical subsystems. The primary motivation for the ESRA payloads is to minimize size, weight, power, and cost while still providing necessary mission data. These new instruments will be demonstrated by ESRA through ground-based testing and on-orbit operations to increase their technology readiness level such that they can support the evolution of technology and mission objectives. This project will leverage a commercial off-the-shelf CubeSat avionics bus and commercial satellite ground networks to reduce the cost and timeline associated with traditional DemVal missions. The system will launch as a ride share with the DoD Space Test Program to be inserted in Geosynchronous Transfer Orbit (GTO) and allow observations of the Earth\u27s radiation belts. The ESRA CubeSat consists of two science payloads and several subsystems: the Wide field-of-view Plasma Spectrometer, the Energetic Charged Particle telescope, high voltage power supply, payload processor, flight software architecture, and distributed processor module. The ESRA CubeSat will provide measurements of the plasma and energetic charged particle populations in the GTO environment for ions ranging from ~100 eV to ~1000 MeV and electrons with energy ranging from 100 keV to 20 MeV. ESRA will utilize a commercial 12U bus and demonstrate a low-cost, rapidly deployable spaceflight platform with sufficient SWAP to enable efficient measurements of the charged particle populations in the dynamic radiation belts

Characterizing the Cool KOIs III. KOI-961: A Small Star with Large Proper Motion and Three Small Planets

We present the characterization of the star KOI 961, an M dwarf with transit signals indicative of three short-period exoplanets, originally discovered by the Kepler Mission. We proceed by comparing KOI 961 to Barnard's Star, a nearby, well-characterized mid-M dwarf. By comparing colors, optical and near-infrared spectra, we find remarkable agreement between the two, implying similar effective temperatures and metallicities. Both are metal-poor compared to the Solar neighborhood, have low projected rotational velocity, high absolute radial velocity, large proper motion and no quiescent H-alpha emission--all of which is consistent with being old M dwarfs. We combine empirical measurements of Barnard's Star and expectations from evolutionary isochrones to estimate KOI 961's mass (0.13 +/- 0.05 Msun), radius (0.17 +/- 0.04 Rsun) and luminosity (2.40 x 10^(-3.0 +/- 0.3) Lsun). We calculate KOI 961's distance (38.7 +/- 6.3 pc) and space motions, which, like Barnard's Star, are consistent with a high scale-height population in the Milky Way. We perform an independent multi-transit fit to the public Kepler light curve and significantly revise the transit parameters for the three planets. We calculate the false-positive probability for each planet-candidate, and find a less than 1% chance that any one of the transiting signals is due to a background or hierarchical eclipsing binary, validating the planetary nature of the transits. The best-fitting radii for all three planets are less than 1 Rearth, with KOI 961.03 being Mars-sized (Rp = 0.57 +/- 0.18 Rearth), and they represent some of the smallest exoplanets detected to date.Comment: Accepted to Ap

The DEEP2 Galaxy Redshift Survey: Design, Observations, Data Reduction, and Redshifts

We describe the design and data analysis of the DEEP2 Galaxy Redshift Survey, the densest and largest high-precision redshift survey of galaxies at z approx. 1 completed to date. The survey was designed to conduct a comprehensive census of massive galaxies, their properties, environments, and large-scale structure down to absolute magnitude MB = 20 at z approx. 1 via approx.90 nights of observation on the Keck telescope. The survey covers an area of 2.8 Sq. deg divided into four separate fields observed to a limiting apparent magnitude of R(sub AB) = 24.1. Objects with z approx. 0.7 to be targeted approx. 2.5 times more efficiently than in a purely magnitude-limited sample. Approximately 60% of eligible targets are chosen for spectroscopy, yielding nearly 53,000 spectra and more than 38,000 reliable redshift measurements. Most of the targets that fail to yield secure redshifts are blue objects that lie beyond z approx. 1.45, where the [O ii] 3727 Ang. doublet lies in the infrared. The DEIMOS 1200 line mm(exp 1) grating used for the survey delivers high spectral resolution (R approx. 6000), accurate and secure redshifts, and unique internal kinematic information. Extensive ancillary data are available in the DEEP2 fields, particularly in the Extended Groth Strip, which has evolved into one of the richest multiwavelength regions on the sky. This paper is intended as a handbook for users of the DEEP2 Data Release 4, which includes all DEEP2 spectra and redshifts, as well as for the DEEP2 DEIMOS data reduction pipelines. Extensive details are provided on object selection, mask design, biases in target selection and redshift measurements, the spec2d two-dimensional data-reduction pipeline, the spec1d automated redshift pipeline, and the zspec visual redshift verification process, along with examples of instrumental signatures or other artifacts that in some cases remain after data reduction. Redshift errors and catastrophic failure rates are assessed through more than 2000 objects with duplicate observations. Sky subtraction is essentially photon-limited even under bright OH sky lines; we describe the strategies that permitted this, based on high image stability, accurate wavelength solutions, and powerful B-spline modeling methods. We also investigate the impact of targets that appear to be single objects in ground-based targeting imaging but prove to be composite in Hubble Space Telescope data; they constitute several percent of targets at z approx. 1, approaching approx. 5%-10% at z > 1.5. Summary data are given that demonstrate the superiority of DEEP2 over other deep high-precision redshift surveys at z approx. 1 in terms of redshift accuracy, sample number density, and amount of spectral information. We also provide an overview of the scientific highlights of the DEEP2 survey thus far

The DEEP2 Galaxy Redshift Survey: Design, Observations, Data Reduction, and Redshifts

We describe the design and data analysis of the DEEP2 Galaxy Redshift Survey, the densest and largest high-precision redshift survey of galaxies at z ~ 1 completed to date. The survey was designed to conduct a comprehensive census of massive galaxies, their properties, environments, and large-scale structure down to absolute magnitude M_B = −20 at z ~ 1 via ~90 nights of observation on the Keck telescope. The survey covers an area of 2.8 deg^2 divided into four separate fields observed to a limiting apparent magnitude of R_(AB) = 24.1. Objects with z ≾0.7 are readily identifiable using BRI photometry and rejected in three of the four DEEP2 fields, allowing galaxies with z > 0.7 to be targeted ~2.5 times more efficiently than in a purely magnitude-limited sample. Approximately 60% of eligible targets are chosen for spectroscopy, yielding nearly 53,000 spectra and more than 38,000 reliable redshift measurements. Most of the targets that fail to yield secure redshifts are blue objects that lie beyond z ~ 1.45, where the [O ii] 3727 Å doublet lies in the infrared. The DEIMOS 1200 line mm^(−1) grating used for the survey delivers high spectral resolution (R ~ 6000), accurate and secure redshifts, and unique internal kinematic information. Extensive ancillary data are available in the DEEP2 fields, particularly in the Extended Groth Strip, which has evolved into one of the richest multiwavelength regions on the sky. This paper is intended as a handbook for users of the DEEP2 Data Release 4, which includes all DEEP2 spectra and redshifts, as well as for the DEEP2 DEIMOS data reduction pipelines. Extensive details are provided on object selection, mask design, biases in target selection and redshift measurements, the spec2d two-dimensional data-reduction pipeline, the spec1d automated redshift pipeline, and the zspec visual redshift verification process, along with examples of instrumental signatures or other artifacts that in some cases remain after data reduction. Redshift errors and catastrophic failure rates are assessed through more than 2000 objects with duplicate observations. Sky subtraction is essentially photon-limited even under bright OH sky lines; we describe the strategies that permitted this, based on high image stability, accurate wavelength solutions, and powerful B-spline modeling methods. We also investigate the impact of targets that appear to be single objects in ground-based targeting imaging but prove to be composite in Hubble Space Telescope data; they constitute several percent of targets at z ~ 1, approaching ~5%–10% at z > 1.5. Summary data are given that demonstrate the superiority of DEEP2 over other deep high-precision redshift surveys at z ~ 1 in terms of redshift accuracy, sample number density, and amount of spectral information. We also provide an overview of the scientific highlights of the DEEP2 survey thus far

The Long-Baseline Neutrino Experiment: Exploring Fundamental Symmetries of the Universe

The preponderance of matter over antimatter in the early Universe, the dynamics of the supernova bursts that produced the heavy elements necessary for life and whether protons eventually decay --- these mysteries at the forefront of particle physics and astrophysics are key to understanding the early evolution of our Universe, its current state and its eventual fate. The Long-Baseline Neutrino Experiment (LBNE) represents an extensively developed plan for a world-class experiment dedicated to addressing these questions. LBNE is conceived around three central components: (1) a new, high-intensity neutrino source generated from a megawatt-class proton accelerator at Fermi National Accelerator Laboratory, (2) a near neutrino detector just downstream of the source, and (3) a massive liquid argon time-projection chamber deployed as a far detector deep underground at the Sanford Underground Research Facility. This facility, located at the site of the former Homestake Mine in Lead, South Dakota, is approximately 1,300 km from the neutrino source at Fermilab -- a distance (baseline) that delivers optimal sensitivity to neutrino charge-parity symmetry violation and mass ordering effects. This ambitious yet cost-effective design incorporates scalability and flexibility and can accommodate a variety of upgrades and contributions. With its exceptional combination of experimental configuration, technical capabilities, and potential for transformative discoveries, LBNE promises to be a vital facility for the field of particle physics worldwide, providing physicists from around the globe with opportunities to collaborate in a twenty to thirty year program of exciting science. In this document we provide a comprehensive overview of LBNE's scientific objectives, its place in the landscape of neutrino physics worldwide, the technologies it will incorporate and the capabilities it will possess.Comment: Major update of previous version. This is the reference document for LBNE science program and current status. Chapters 1, 3, and 9 provide a comprehensive overview of LBNE's scientific objectives, its place in the landscape of neutrino physics worldwide, the technologies it will incorporate and the capabilities it will possess. 288 pages, 116 figure