Delaunay triangulation and computational fluid dynamics meshes

In aerospace computational fluid dynamics (CFD) calculations, the Delaunay triangulation of suitable quadrilateral meshes can lead to unsuitable triangulated meshes. Here, we present case studies which illustrate the limitations of using structured grid generation methods which produce points in a curvilinear coordinate system for subsequent triangulations for CFD applications. We discuss conditions under which meshes of quadrilateral elements may not produce a Delaunay triangulation suitable for CFD calculations, particularly with regard to high aspect ratio, skewed quadrilateral elements

Yanagi: Transcript Segment Library Construction for RNA-Seq Quantification

Analysis of differential alternative splicing from RNA-seq data is complicated by the fact that many RNA-seq reads map to multiple transcripts, and that annotated transcripts from a given gene are often a small subset of many possible complete transcripts for that gene. Here we describe Yanagi, a tool which segments a transcriptome into disjoint regions to create a segments library from a complete transcriptome annotation that preserves all of its consecutive regions of a given length L while distinguishing annotated alternative splicing events in the transcriptome. In this paper, we formalize this concept of transcriptome segmentation and propose an efficient algorithm for generating segment libraries based on a length parameter dependent on specific RNA-Seq library construction. The resulting segment sequences can be used with pseudo-alignment tools to quantify expression at the segment level. We characterize the segment libraries for the reference transcriptomes of Drosophila melanogaster and Homo sapiens. Finally, we demonstrate the utility of quantification using a segment library based on an analysis of differential exon skipping in Drosophila melanogaster and Homo sapiens. The notion of transcript segmentation as introduced here and implemented in Yanagi will open the door for the application of lightweight, ultra-fast pseudo-alignment algorithms in a wide variety of analyses of transcription variation

An extreme ultraviolet spectrometer experiment for the Shuttle Get Away Special Program

An extreme ultraviolet (EUV) spectrometer experiment operated successfully during the STS-7 mission in an experiment to measure the global and diurnal variation of the EUV airglow. The spectrometer is an F 3.5 Wadsworth mount with mechanical collimator, a 75 x 75 mm grating, and a bare microchannel plate detector providing a spectral resolution of 7 X FWHM. Read-out of the signal is through discrete channels or resistive anode techniques. The experiment includes a microcomputer, 20 Mbit tape recorder, and a 28V, 40 Ahr silver-zinc battery. It is the first GAS payload to use an opening door. The spectrometer's 0.1 x 4.2 deg field of view is pointed vertically out of the shuttle bay. During the STS-7 flight data were acquired continuously for a period of 5 hours and 37 minutes, providing spectra of the 570 A to 850 A wavelength region of the airglow. Five diurnal cycles of the 584 A emission of neutral helium and the 834 A emission of ionized atomic oxygen were recorded. The experiment also recorded ion events and pressure pulses associated with thruster firings. The experiment is to fly again on Mission 41-F

Class I Gap-formation in Highly-viscous Glass-ionomer Restorations: Delayed vs Immediate Polishing

This in vitro study evaluated the effects of delayed versus immediate polishing to permit maturation of interfacial gap-formation around highly viscous conventional glass-ionomer cement (HV-GIC) in Class I restorations, together with determining the associated mechanical properties. Cavity preparations were made on the occlusal surfaces of premolars. Three HV-GICs (Fuji IX GP, GlasIonomer FX-II and Ketac Molar) and one conventional glass-ionomer cement (C-GIC, Fuji II, as a control) were studied, with specimen subgroups (n=10) for each property measured. After polishing, either immediately (six minutes) after setting or after 24 hours storage, the restored teeth were sectioned in a mesiodistal direction through the center of the model Class I restorations. The presence or absence of interfacial-gaps was measured at 1000× magnification at 14 points (each 0.5-mm apart) along the cavity restoration interface (n=10; total points measured per group = 140). Marginal gaps were similarly measured in Teflon molds as swelling data, together with shear-bond-strength to enamel and dentin, flexural strength and moduli. For three HV-GICs and one C-GIC, significant differences (p<0.05) in gap-incidence were observed between polishing immediately and after one-day storage. In the former case, 80–100 gaps were found. In the latter case, only 9–21 gaps were observed. For all materials, their shear-bond-strengths, flexural strength and moduli increased significantly after 24-hour storage.</p

Class I Gap-formation in Highly-viscous Glass-ionomer Restorations: Delayed vs Immediate Polishing

This in vitro study evaluated the effects of delayed versus immediate polishing to permit maturation of interfacial gap-formation around highly viscous conventional glass-ionomer cement (HV-GIC) in Class I restorations, together with determining the associated mechanical properties. Cavity preparations were made on the occlusal surfaces of premolars. Three HV-GICs (Fuji IX GP, GlasIonomer FX-II and Ketac Molar) and one conventional glass-ionomer cement (C-GIC, Fuji II, as a control) were studied, with specimen subgroups (n=10) for each property measured. After polishing, either immediately (six minutes) after setting or after 24 hours storage, the restored teeth were sectioned in a mesiodistal direction through the center of the model Class I restorations. The presence or absence of interfacial-gaps was measured at 1000× magnification at 14 points (each 0.5-mm apart) along the cavity restoration interface (n=10; total points measured per group = 140). Marginal gaps were similarly measured in Teflon molds as swelling data, together with shear-bond-strength to enamel and dentin, flexural strength and moduli. For three HV-GICs and one C-GIC, significant differences (p<0.05) in gap-incidence were observed between polishing immediately and after one-day storage. In the former case, 80–100 gaps were found. In the latter case, only 9–21 gaps were observed. For all materials, their shear-bond-strengths, flexural strength and moduli increased significantly after 24-hour storage.</p

Yanagi: Fast and interpretable segment-based alternative splicing and gene expression analysis

Ultra-fast pseudo-alignment approaches are the tool of choice in transcript-level RNA sequencing (RNA-seq) analyses. Unfortunately, these methods couple the tasks of pseudo-alignment and transcript quantification. This coupling precludes the direct usage of pseudo-alignment to other expression analyses, including alternative splicing or differential gene expression analysis, without including a non-essential transcript quantification step.https://doi.org/10.1186/s12859-019-2947-

Fruit and vegetable processing and food technology: a summary of research

Evaluation of tomato cultivars for processing / W. A. Gould and R. Stillabower -- Physical and subjective color evaluation of tomato juice / Kenneth L. Beck and W. A. Gould -- Flavor evaluation of tomato juice fortified with sugar and citric acid / J. A. Gould and W. A. Gould -- Effects of citric acid and sugar ratios on thermal resistance of Bacillus coagulans var. thermoacidurans in tomato juice / Dennis L. Gierhart and W. A. Gould -- Protein bodies of the germinating tomato seed cotyledon / L. K. Eggers and J. R. Geisman -- Studies concerning the protein of tomato seeds recovered from tomato cannery waste / L. K. Eggers and J. R. Geisman -- Lipid composition of cucumber / A. C. Peng -- Fatty acids in fresh and recycled brines / A. C. Peng and J. R. Geisman -- Repeated recycling of spent pickle brine affects pickle quality / J. R. Geisman and M. Lazear -- Evaluation of snap bean cultivars for processing / W. Gould, J. Gould, J. Mount, M. Skoog and R. Stillabower -- Evaluating strawberries for freezing / J. F. Gallander and J. F. Stetson -- Grapes for Ohio wines / J. F. Gallander and J. F. Stetso

Measurement of the proton and deuteron structure functions, F2p and F2d, and of the ratio sigma(L)/sigma(T)

The muon-proton and muon-deuteron inclusive deep inelastic scattering cross sections were measured in the kinematic range 0.002 < x < 0.60 and 0.5 < Q2 < 75 GeV2 at incident muon energies of 90, 120, 200 and 280 GeV. These results are based on the full data set collected by the New Muon Collaboration, including the data taken with a small angle trigger. The extracted values of the structure functions F2p and F2d are in good agreement with those from other experiments. The data cover a sufficient range of y to allow the determination of the ratio of the longitudinally to transversely polarised virtual photon absorption cross sections, R= sigma(L)/sigma(T), for 0.002 < x < 0.12 . The values of R are compatible with a perturbative QCD prediction; they agree with earlier measurements and extend to smaller x.Comment: In this replacement the erroneously quoted R values in tables 3-6 for x>0.12, and R1990 values in tables 5-6 for all x, have been corrected, and the cross sections in tables 3-4 have been adapted. Everything else, including the structure functions F2, remained unchanged. 22 pages, LateX, including figures, with two .sty files, and three separate f2tab.tex files for the F2-tables. Accepted for publication in Nucl.Phys.B 199

Identification of Radiopure Titanium for the LZ Dark Matter Experiment and Future Rare Event Searches

The LUX-ZEPLIN (LZ) experiment will search for dark matter particle interactions with a detector containing a total of 10 tonnes of liquid xenon within a double-vessel cryostat. The large mass and proximity of the cryostat to the active detector volume demand the use of material with extremely low intrinsic radioactivity. We report on the radioassay campaign conducted to identify suitable metals, the determination of factors limiting radiopure production, and the selection of titanium for construction of the LZ cryostat and other detector components. This titanium has been measured with activities of $^{238}$U$_{e}$~$<$1.6~mBq/kg, $^{238}$U$_{l}$~$<$0.09~mBq/kg, $^{232}$Th$_{e}$~$=0.28\pm 0.03$~mBq/kg, $^{232}$Th$_{l}$~$=0.25\pm 0.02$~mBq/kg, $^{40}$K~$<$0.54~mBq/kg, and $^{60}$Co~$<$0.02~mBq/kg (68\% CL). Such low intrinsic activities, which are some of the lowest ever reported for titanium, enable its use for future dark matter and other rare event searches. Monte Carlo simulations have been performed to assess the expected background contribution from the LZ cryostat with this radioactivity. In 1,000 days of WIMP search exposure of a 5.6-tonne fiducial mass, the cryostat will contribute only a mean background of $0.160\pm0.001$(stat)$\pm0.030$(sys) counts.Comment: 13 pages, 3 figures, accepted for publication in Astroparticle Physic