Trajectory Optimization: OTIS 4

The latest release of the Optimal Trajectories by Implicit Simulation (OTIS4) allows users to simulate and optimize aerospace vehicle trajectories. With OTIS4, one can seamlessly generate optimal trajectories and parametric vehicle designs simultaneously. New features also allow OTIS4 to solve non-aerospace continuous time optimal control problems. The inputs and outputs of OTIS4 have been updated extensively from previous versions. Inputs now make use of objectoriented constructs, including one called a metastring. Metastrings use a greatly improved calculator and common nomenclature to reduce the user s workload. They allow for more flexibility in specifying vehicle physical models, boundary conditions, and path constraints. The OTIS4 calculator supports common mathematical functions, Boolean operations, and conditional statements. This allows users to define their own variables for use as outputs, constraints, or objective functions. The user-defined outputs can directly interface with other programs, such as spreadsheets, plotting packages, and visualization programs. Internally, OTIS4 has more explicit and implicit integration procedures, including high-order collocation methods, the pseudo-spectral method, and several variations of multiple shooting. Users may switch easily between the various methods. Several unique numerical techniques such as automated variable scaling and implicit integration grid refinement, support the integration methods. OTIS4 is also significantly more user friendly than previous versions. The installation process is nearly identical on various platforms, including Microsoft Windows, Apple OS X, and Linux operating systems. Cross-platform scripts also help make the execution of OTIS and post-processing of data easier. OTIS4 is supplied free by NASA and is subject to ITAR (International Traffic in Arms Regulations) restrictions. Users must have a Fortran compiler, and a Python interpreter is highly recommended

Xenon isotopes in Archean and Proterozoic insoluble organic matter: a robust indicator of syngenecity?

Insoluble organic materials (kerogens) isolated from ancient sedimentary rocks provide unique insights into the evolution of early life. However, establishing whether these kerogens are indeed syngenetic with the deposition of associated sedimentary host rocks, or contain contribution from episodes of secondary deposition, is not straightforward. Novel geochemical criterions are therefore required to test the syngenetic origin of Archean organic materials. On one hand, the occurrence of mass-independent fractionation of sulphur isotopes (MIF-S) provides a tool to test the Archean origin of ancient sedimentary rocks. Determining the isotope composition of sulphur within kerogens whilst limiting the contribution from associated minerals (e.g., nano-pyrites) is however challenging. On the other end, the Xe isotope composition of the Archean atmosphere has been shown to present enrichments in the light isotopes relative to its modern composition, together with a mono-isotopic deficit in ¹²⁹Xe. Given that the isotopic composition of atmospheric Xe evolved through time by mass dependent fractionation (MDF) until ∼2.5-2.0 Ga, the degree of MDF of Xe isotopes trapped in kerogens could provide a time stamp for the last chemical equilibration between organic matter and the atmosphere. However, the extent to which geological processes could affect the signature of Xe trapped in ancient kerogen remains unclear. In this contribution, we present new Ar, Kr and Xe isotopic data for four kerogens isolated from 3.4 to 1.8 Gy-old cherts and confirm that Xe isotopes from the Archean atmosphere can be retained within kerogens. However, new Xe-derived model ages are lower than expected from the ages of host rocks, indicating that initially trapped Xe components were at least partially lost and/or mixed together with some Xe carried out by younger generations of organic materials, therefore complicating the Xe-based dating method. Whilst non-null Δ³³S values and ¹²⁹Xe deficits relative to modern atmosphere constitute reliable imprints from the Archean atmosphere, using Xe isotopes to provide information on the syngenetic origin of ancient organic matter appears to be a promising - but not unequivocal - tool that calls for further analytical development

Soybean Seed Protein, Oil, and Fatty Acids are Altered by S and S + N Fertilizers Under Irrigated or Non-irrigated Environments

Information on the effect of sulfur (S) or sulfur+nitrogen (S + N) on soybean seed composition is scarce. Thus, the objective of this study was to investigate the effects of S, and S + N fertilizers on soybean [(Glycine max (L.) Merr.)] seed composition in the Early Soybean Production System (ESPS) under irrigated (I) and nonirrigated (NI) environments. Two separate field experiments were conducted from 2005 to 2007. One experiment was irrigated, and the second experiment was nonirrigated. Under I condition, S at a rate of 44.8 kg/ha alone or with N at 112 kg/ha resulted in a consistent increase in seed protein and oleic acid concentrations, and a decrease in oil and linolenic acid concentrations compared with the control (C). For example, in 2006 and compared with the C, application of S + N increased the percentage up to 11.4% and 48.5% for protein and oleic acid, respectively. However, oil concentration decreased by 3%. Protein and oleic acid increase were accompanied by a higher percentage of leaf and seed N and S. Under NI conditions, seed protein and oleic acid concentrations were significantly higher in C than in any S or S + N treatments, but the oil and linolenic acid concentrations were significantly lower. The results indicate that specific rate of S alone or S + N combined can alter seed composition under irrigated or nonirrigated conditions. This knowledge may help plant breeders to develop and release cultivars to suit specific target locations to grow new value-added soybeans or select for specific seed composition traits under specific environmental stress factors such as drought

Optical design of a high power fiber optic coupler

Fiber optic beam delivery systems are replacing conventional mirror delivery systems for many reasons (e.g., system flexibility and redundancy, stability, and ease of alignment). Commercial products are available that use of fiber optic delivery for laser surgery and materials processing. Also, pump light of dye lasers can be delivered by optical fibers. Many laser wavelengths have been transported via optical fibers; high power delivery has been reported for argon, Nd:YAG, and excimer. We have been developing fiber optic beam delivery systems for copper vapor laser light; many of the fundamental properties of these systems are applicable to other high power delivery applications. A key element of fiber optic beam delivery systems is the coupling of laser light into the optical fiber. For our application this optical coupler must be robust to a range of operating parameters and laser characteristics. We have access to a high power copper vapor laser beam that is generated by a master oscillator/power amplifier (MOPA) chain comprised of three amplifiers. The light has a pulse width of 40--50 nsec with a repetition rate of about 4 kHz. The average power (nominal) to be injected into a fiber is 200 W. (We will refer to average power in this paper.) In practice, the laser beam's direction and collimation change with time. These characteristics plus other mechanical and operational constraints make it difficult for our coupler to be opto-mechanically referenced to the laser beam. We describe specifications, design, and operation of an optical system that couples a high-power copper vapor laser beam into a large core, multimode fiber. The approach used and observations reported are applicable to fiber optic delivery applications. 6 refs., 6 figs

A Scaling Theory of Bifurcations in the Symmetric Weak-Noise Escape Problem

We consider the overdamped limit of two-dimensional double well systems perturbed by weak noise. In the weak noise limit the most probable fluctuational path leading from either point attractor to the separatrix (the most probable escape path, or MPEP) must terminate on the saddle between the two wells. However, as the parameters of a symmetric double well system are varied, a unique MPEP may bifurcate into two equally likely MPEP's. At the bifurcation point in parameter space, the activation kinetics of the system become non-Arrhenius. In this paper we quantify the non-Arrhenius behavior of a system at the bifurcation point, by using the Maslov-WKB method to construct an approximation to the quasistationary probability distribution of the system that is valid in a boundary layer near the separatrix. The approximation is a formal asymptotic solution of the Smoluchowski equation. Our analysis relies on the development of a new scaling theory, which yields `critical exponents' describing weak-noise behavior near the saddle, at the bifurcation point.Comment: LaTeX, 60 pages, 24 Postscript figures. Uses epsf macros to include the figures. A file in `uufiles' format containing the figures is separately available at ftp://platinum.math.arizona.edu/pub/papers-rsm/paperF/figures.uu and a Postscript version of the whole paper (figures included) is available at ftp://platinum.math.arizona.edu/pub/papers-rsm/paperF/paperF.p

The bracteatus pineapple genome and domestication of clonally propagated crops

Domestication of clonally propagated crops such as pineapple from South America was hypothesized to be a 'one-step operation'. We sequenced the genome of Ananas comosus var. bracteatus CB5 and assembled 513 Mb into 25 chromosomes with 29,412 genes. Comparison of the genomes of CB5, F153 and MD2 elucidated the genomic basis of fiber production, color formation, sugar accumulation and fruit maturation. We also resequenced 89 Ananas genomes. Cultivars 'Smooth Cayenne' and 'Queen' exhibited ancient and recent admixture, while 'Singapore Spanish' supported a one-step operation of domestication. We identified 25 selective sweeps, including a strong sweep containing a pair of tandemly duplicated bromelain inhibitors. Four candidate genes for self-incompatibility were linked in F153, but were not functional in self-compatible CB5. Our findings support the coexistence of sexual recombination and a one-step operation in the domestication of clonally propagated crops. This work guides the exploration of sexual and asexual domestication trajectories in other clonally propagated crops

Recurrent epimutations activate gene body promoters in primary glioblastoma

Aberrant DNA hypomethylation may play an important role in the growth rate of glioblastoma (GBM), but the functional impact on transcription remains poorly understood. We assayed the GBM methylome with MeDIP-seq and MRE-seq, adjusting for copy number differences, in a small set of non-glioma CpG island methylator phenotype (non-G-CIMP) primary tumors. Recurrent hypomethylated loci were enriched within a region of chromosome 5p15 that is specified as a cancer amplicon and also encompasses TERT, encoding telomerase reverse transcriptase, which plays a critical role in tumorigenesis. Overall, 76 gene body promoters were recurrently hypomethylated, including TERT and the oncogenes GLI3 and TP73. Recurring hypomethylation also affected previously unannotated alternative promoters, and luciferase reporter assays for three of four of these promoters confirmed strong promoter activity in GBM cells. Histone H3 lysine 4 trimethylation (H3K4me3) ChIP-seq on tissue from the GBMs uncovered peaks that coincide precisely with tumor-specific decrease of DNA methylation at 200 loci, 133 of which are in gene bodies. Detailed investigation of TP73 and TERT gene body hypomethylation demonstrated increased expression of corresponding alternate transcripts, which in TP73 encodes a truncated p73 protein with oncogenic function and in TERT encodes a putative reverse transcriptase-null protein. Our findings suggest that recurring gene body promoter hypomethylation events, along with histone H3K4 trimethylation, alter the transcriptional landscape of GBM through the activation of a limited number of normally silenced promoters within gene bodies, in at least one case leading to expression of an oncogenic protein

Does fish larval dispersal differ between high and low latitudes?

Author Posting. © The Author(s), 2013. This is the author's version of the work. It is posted here by permission of The Royal Society for personal use, not for redistribution. The definitive version was published in Proceedings of the Royal Society B Biological Sciences 280 (2013): 20130327, doi:10.1098/rspb.2013.0327.Several factors lead to expectations that the scale of larval dispersal and population connectivity of marine animals differs with latitude. We examine this expectation for demersal shorefishes, including relevant mechanisms, assumptions, and evidence. We explore latitudinal differences in: 1) biological (e.g., species composition, spawning mode, pelagic larval duration (PLD)), 2) physical (e.g., water movement, habitat fragmentation), and 3) biophysical factors (primarily temperature, which could strongly affect development, swimming ability, or feeding). Latitudinal differences exist in taxonomic composition, habitat fragmentation, temperature, and larval swimming, and each could influence larval dispersal. Nevertheless, clear evidence for latitudinal differences in larval dispersal at the level of broad faunas is lacking. For example, PLD is strongly influenced by taxon, habitat, and geographic region, but no independent latitudinal trend is present in published PLD values. Any trends in larval dispersal may be obscured by a lack of appropriate information, or use of ‘off the shelf’ information that is biased with regard to the species assemblages in areas of concern. Biases may also be introduced from latitudinal differences in taxa or spawning modes, as well as limited latitudinal sampling. We suggest research to make progress on the question of latitudinal trends in larval dispersal.TK was supported by the Norwegian Research Council through project MENUII #190286. JML was supported by ARC Discovery Grant DP110100695. JEC and RRW were supported by the Partnership for the Interdisciplinary Study of Coastal Oceans, funded by The David and Lucille Packard Foundation and the Gordon and Betty Moore Foundation.2014-03-2

The clustering of galaxies in the SDSS-III Baryon Oscillation Spectroscopic Survey: Baryon Acoustic Oscillations in the Data Release 9 Spectroscopic Galaxy Sample

We present measurements of galaxy clustering from the Baryon Oscillation Spectroscopic Survey (BOSS), which is part of the Sloan Digital Sky Survey III (SDSS-III). These use the Data Release 9 (DR9) CMASS sample, which contains 264,283 massive galaxies covering 3275 square degrees with an effective redshift z=0.57 and redshift range 0.43 < z < 0.7. Assuming a concordance Lambda-CDM cosmological model, this sample covers an effective volume of 2.2 Gpc^3, and represents the largest sample of the Universe ever surveyed at this density, n = 3 x 10^-4 h^-3 Mpc^3. We measure the angle-averaged galaxy correlation function and power spectrum, including density-field reconstruction of the baryon acoustic oscillation (BAO) feature. The acoustic features are detected at a significance of 5\sigma in both the correlation function and power spectrum. Combining with the SDSS-II Luminous Red Galaxy Sample, the detection significance increases to 6.7\sigma. Fitting for the position of the acoustic features measures the distance to z=0.57 relative to the sound horizon DV /rs = 13.67 +/- 0.22 at z=0.57. Assuming a fiducial sound horizon of 153.19 Mpc, which matches cosmic microwave background constraints, this corresponds to a distance DV(z=0.57) = 2094 +/- 34 Mpc. At 1.7 per cent, this is the most precise distance constraint ever obtained from a galaxy survey. We place this result alongside previous BAO measurements in a cosmological distance ladder and find excellent agreement with the current supernova measurements. We use these distance measurements to constrain various cosmological models, finding continuing support for a flat Universe with a cosmological constant.Comment: 33 page