Mn 2+ coordinates Cap-0-RNA to align substrates for efficient 2′- O -methyl transfer by SARS-CoV-2 nsp16
Efficient RNA capping by the SARS-CoV-2 methyltransferase requires metal ions and a unique four-residue insert.
Minasov, George↗
SEARCH · Engineering Papers
Results for “alignment”
Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
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When Whole-Genome Alignments Just Won't Work: kSNP v2 Software for Alignment-Free SNP Discovery and Phylogenetics of Hundreds of Microbial Genomes
Abstract not provided
59 BASIC BIOLOGICAL SCIENCES↗
Microstructure Alignment Effects from Engineered Cooling during Additive Manufacturing of Alnico Magnets from Prealloyed Powder
Alnico is a rare-earth free; permanent magnet (PM) which maintains its saturation magnetization while at temperatures up to 550°C but lacks the coercivity and energy product needed for a wide range of demanding applications. With an optimal set of processing and manufacturing techniques, Alnico could replace Dy-free Nd-Fe-B magnets in certain applications if the microstructure is textured in a $\langle$001$\rangle$ direction. Additive manufacturing (AM) of near-net-shape magnets may provide such texture. To investigate the possibility, directed-energy deposition (DED) in conjunction with an actively cooled substrate was used to build samples with a compositionally modified, gas-atomized, Alnico 8 alloy. The resulting samples were solutionized and quenched, followed by magnetic annealing and a heat treatment. Magnetic properties and microstructures are compared to previous work.
36 MATERIALS SCIENCE↗
Scanning Lidar Spatial Calibration and Alignment Method for Wind Turbine Wake Characterization.
Abstract not provided.
Herges, Thomas↗
Part 1: The Use of a Magnetic Pickup as an Alignment Indicator With a Stretched-Wire Technique Part 2: Proposed Systems and Circuits for Magnetic Alignment Pickups
Explore the source record for details and available documents.
Panofsky, W.↗
Mask alignment system for semiconductor processing
A mask alignment system for providing precise and repeatable alignment between ion implantation masks and workpieces. The system includes a mask frame having a plurality of ion implantation masks loosely connected thereto. The mask frame is provided with a plurality of frame alignment cavities, and each mask is provided with a plurality of mask alignment cavities. The system further includes a platen for holding workpieces. The platen may be provided with a plurality of mask alignment pins and frame alignment pins configured to engage the mask alignment cavities and frame alignment cavities, respectively. The mask frame can be lowered onto the platen, with the frame alignment cavities moving into registration with the frame alignment pins to provide rough alignment between the masks and workpieces. The mask alignment cavities are then moved into registration with the mask alignment pins, thereby shifting each individual mask into precise alignment with a respective workpiece.
42 ENGINEERING↗
BRIGHTEST SATELLITE GALAXY ALIGNMENT OF SLOAN DIGITAL SKY SURVEY GALAXY GROUPS
We study the alignment signal between the distribution of the brightest satellite galaxies (BSGs) and the major axes of their host groups using the Sloan Digital Sky Survey group catalog constructed by Yang et al. After correcting for the effect of group ellipticity, a statistically significant ({approx}5{sigma}) major-axis alignment is detected and the alignment angle is found to be 43. Degree-Sign 0 {+-} 0. Degree-Sign 4. More massive and richer groups show a stronger BSG alignment. The BSG alignment around blue brightest central galaxies (BCGs) is slightly stronger than that around red BCGs. Red BSGs have a much stronger major-axis alignment than blue BSGs. Unlike BSGs, other satellites do not show very significant alignment with their group's major axis. We further explore BSG alignment using the semi-analytic model (SAM) constructed by Guo et al. In general, we found good agreement of the model with observations: BSGs in the SAM show a strong major-axis alignment that depends on group mass and richness in the same way as in observations and none of the other satellites exhibit prominent alignment. However, a discrepancy also exists in that the SAM shows a BSG color dependence opposite of that in observations, which is most probably induced by a missing large-scale environment ingredient in the SAM. The combination of two popular scenarios can explain the BSG alignment we detected. First, satellites merged into the group along the surrounding filaments, which are strongly aligned with the major axis of the group. Second, BSGs entered their host group more recently than other satellites, so they have preserved more information about their assembling history and major-axis alignment. In the SAM, we found positive evidence for the second scenario in the fact that BSGs merged into groups statistically more recently than other satellites. We also found that most of the BSGs (80%) were BCGs before they merged into groups and earlier merging BSGs tend to be closer to their BCGs than other BSGs. On the other hand, although the BSG color dependence in observations is the opposite of that in the SAM, it might also indicate that the first scenario is a good explanation.
79 ASTRONOMY AND ASTROPHYSICS↗
A line-source method for aligning on-board and other pinhole SPECT systems
Purpose: In order to achieve functional and molecular imaging as patients are in position for radiation therapy, a robotic multipinhole SPECT system is being developed. Alignment of the SPECT system—to the linear accelerator (LINAC) coordinate frame and to the coordinate frames of other on-board imaging systems such as cone-beam CT (CBCT)—is essential for target localization and image reconstruction. An alignment method that utilizes line sources and one pinhole projection is proposed and investigated to achieve this goal. Potentially, this method could also be applied to the calibration of the other pinhole SPECT systems.Methods: An alignment model consisting of multiple alignment parameters was developed which maps line sources in three-dimensional (3D) space to their two-dimensional (2D) projections on the SPECT detector. In a computer-simulation study, 3D coordinates of line-sources were defined in a reference room coordinate frame, such as the LINAC coordinate frame. Corresponding 2D line-source projections were generated by computer simulation that included SPECT blurring and noise effects. The Radon transform was utilized to detect angles (α) and offsets (ρ) of the line-source projections. Alignment parameters were then estimated by a nonlinear least squares method, based on the α and ρ values and the alignment model. Alignment performance was evaluated as a function of number of line sources, Radon transform accuracy, finite line-source width, intrinsic camera resolution, Poisson noise, and acquisition geometry. Experimental evaluations were performed using a physical line-source phantom and a pinhole-collimated gamma camera attached to a robot.Results: In computer-simulation studies, when there was no error in determining angles (α) and offsets (ρ) of the measured projections, six alignment parameters (three translational and three rotational) were estimated perfectly using three line sources. When angles (α) and offsets (ρ) were provided by the Radon transform, estimation accuracy was reduced. The estimation error was associated with rounding errors of Radon transform, finite line-source width, Poisson noise, number of line sources, intrinsic camera resolution, and detector acquisition geometry. Statistically, the estimation accuracy was significantly improved by using four line sources rather than three and by thinner line-source projections (obtained by better intrinsic detector resolution). With five line sources, median errors were 0.2 mm for the detector translations, 0.7 mm for the detector radius of rotation, and less than 0.5° for detector rotation, tilt, and twist. In experimental evaluations, average errors relative to a different, independent registration technique were about 1.8 mm for detector translations, 1.1 mm for the detector radius of rotation (ROR), 0.5° and 0.4° for detector rotation and tilt, respectively, and 1.2° for detector twist.Conclusions: Alignment parameters can be estimated using one pinhole projection of line sources. Alignment errors are largely associated with limited accuracy of the Radon transform in determining angles (α) and offsets (ρ) of the line-source projections. This alignment method may be important for multipinhole SPECT, where relative pinhole alignment may vary during rotation. For pinhole and multipinhole SPECT imaging on-board radiation therapy machines, the method could provide alignment of SPECT coordinates with those of CBCT and the LINAC.
62 RADIOLOGY AND NUCLEAR MEDICINE↗
Cellular alignment and fusion: Quantifying the effect of macrophages and fibroblasts on myoblast terminal differentiation
Highlights: • We present a method for cellular alignment calculation during routine cell culture. • Application revealed that macrophages promote myoblast alignment, but delay fusion. • Furthermore, fibroblasts regulate myoblast fusion, but not alignment. • Effect of macrophages on alignment is not altered by co-culture with fibroblasts. Successful skeletal muscle wound repair requires the alignment and fusion of myoblasts to generate multinucleated myofibers. In vitro, the accurate quantification of cellular alignment remains a challenge. Here we present the application of ImageJ and ct-FIRE to quantify muscle cell orientation by means of an alignment index (AI). Our optimised method, which does not require programming skills, allows the alignment of myoblasts in vitro to be determined independently of a predefined reference point. Using this method, we demonstrate that co-culture of myoblasts with macrophages, but not fibroblasts, promotes myoblast alignment in a cell density-dependent manner. Interestingly, myoblast fusion was significantly decreased in response to co-culture with macrophages, while the effect of fibroblasts on fusion was density-dependent. At lower numbers, fibroblasts significantly increased myoblast fusion, whereas at higher numbers a significant decrease was observed. Finally, triple co-culture revealed that the effect of macrophages on myoblast alignment and fusion is unaltered by the additional presence of fibroblasts. Application of our optimised method has therefore revealed quantitative differences in the roles of macrophages versus fibroblasts during alignment and fusion: while successful myoblast alignment is promoted by increasing macrophage numbers, regenerative fusion coincides with a decreasing macrophage population and initial rise in fibroblast numbers.
60 APPLIED LIFE SCIENCES↗
INTRINSIC ALIGNMENT OF CLUSTER GALAXIES: THE REDSHIFT EVOLUTION
We present measurements of two types of cluster galaxy alignments based on a volume limited and highly pure ({>=}90%) sample of clusters from the GMBCG catalog derived from Data Release 7 of the Sloan Digital Sky Survey (SDSS DR7). We detect a clear brightest cluster galaxy (BCG) alignment (the alignment of major axis of the BCG toward the distribution of cluster satellite galaxies). We find that the BCG alignment signal becomes stronger as the redshift and BCG absolute magnitude decrease and becomes weaker as BCG stellar mass decreases. No dependence of the BCG alignment on cluster richness is found. We can detect a statistically significant ({>=}3{sigma}) satellite alignment (the alignment of the major axes of the cluster satellite galaxies toward the BCG) only when we use the isophotal fit position angles (P.A.s), and the satellite alignment depends on the apparent magnitudes rather than the absolute magnitudes of the BCGs. This suggests that the detected satellite alignment based on isophotal P.A.s from the SDSS pipeline is possibly due to the contamination from the diffuse light of nearby BCGs. We caution that this should not be simply interpreted as non-existence of the satellite alignment, but rather that we cannot detect them with our current photometric SDSS data. We perform our measurements on both SDSS r-band and i-band data, but do not observe a passband dependence of the alignments.
79 ASTRONOMY AND ASTROPHYSICS↗
SU-E-T-27: A Dosimetric Evaluation of Boney Anatomy Versus Fiducial Marker Alignment for the Treatment of Prostate Cancer Using Scanned Beam Proton Therapy
Purpose: In prostate proton radiotherapy, three fiducial markers are used for patient daily alignment. However fiducial alignment can change beamline heterogeneity in proton therapy. The purpose of this study is to determine the difference in fiducial and boney anatomy alignment for patient treatment. Methods and materials: Prostate cancer patients who received proton treatment were included in this study. 3 fiducial markers were implanted before the initial CT. All the patients were re-CT’d every 2 weeks to check the fiducial marker position reproducibility as well as dosimetric consistence of target coverage. In geometry study, re-CT were fused to the initial CT base on the boney anatomy and the average fiducial marker displacement was measured the centers of the fiducials. Dosimetrically, the initial plan was recalculated directly to re-CT image set based on the boney alignment and fiducial alignment to determine the difference from daily treatment. Prostate coverage and hotspots were evaluated using the dose to 98% of the CTV (D98) and dose to 2% (D2), respectively. Results: The shift from the initial 6 patient CT image sets resulted in an average change in the fiducial location of 5.70 +/− 3 mm. Dosimetric comparison from a single patient revealed that differences from the planned dose resulted from both boney and fiducial alignment. Planned clinical treatment volume coverage resulted in a D98 of 70.44Gy and D2 of 70.84Gy compared to a D98 of 70.13Gy and D2 70.94Gy for boney alignment and a D98 of 70.08Gy and D2 71.18Gy for fiducial alignment respectively. Conclusion: This study demonstrates that with boney anatomy alignment there is little change to CTV coverage and only slightly worse CTV coverage and hotspot production with fiducial alignment. An increase patient cohort and further investigation is necessary to determine the whether boney alignment can help better control dose heterogeneity.
60 APPLIED LIFE SCIENCES↗
Individual NSLS-II Multipole Magnet Alignment by Laser Trackers
The magnet alignment of the 90 th and final multipole girder assembly was completed January 17 th , 2013. Our procedure of “rough” pre-alignment by laser trackers and final alignment by vibrating wire & “Differential Variable Reluctance Transducers” (DVRT) has been quite successful, achieving magnet to magnet alignment well under the 30 micron specification. The pre-alignment accuracy is verified by the initial scan from the vibrating wire. The alignment residuals can be calculated from the offsets of a best fit line. The results are impressive, especially considering the environment of the Building 902 Annex (which has a large bay door that would open during pre-alignment, without fail), the sloppiness of the magnets’ fiducials, and especially the fact that the girders were pre-aligned to their mechanical centers, but the vibrating wire reports the magnetic centers which may be considerably different. This result hints at the potential feasibility of alignment with laser trackers for replacement magnets of NSLS-II and maybe even all magnets of future accelerators. But, it is difficult to predict the achievable accuracy until the main three error sources (a.k.a. Survey group excuses) are eliminated: measuring environment, bad magnet fiducials, and mechanical/magnetic center differences. The test performed on a large aperture quadrupole on girder assembly C19G4 was designed to answer the following questions with the aforementioned error sources either eliminated or simulated: 1) How accurately can a NSLS-II multipole be realigned after repair or other disturbance given the existing fiducials? 2) How accurately can a replacement NSLS-II multipole be installed in situ if its magnetic center is known relative to good fiducials? 3) If the current NSLS-II spares are never magnetically fiducialized, how well can they be installed using only mechanical data? 4) Could the magnets of a future accelerator (with similar alignment specifications as NSLS-II) be aligned using commercially available metrology instruments? This paper will answer these questions.
36 MATERIALS SCIENCE↗
Alignment of Short Reads: A Crucial Step for Application of Next-Generation Sequencing Data in Precision Medicine
Precision medicine or personalized medicine has been proposed as a modernized and promising medical strategy. Genetic variants of patients are the key information for implementation of precision medicine. Next-generation sequencing (NGS) is an emerging technology for deciphering genetic variants. Alignment of raw reads to a reference genome is one of the key steps in NGS data analysis. Many algorithms have been developed for alignment of short read sequences since 2008. Users have to make a decision on which alignment algorithm to use in their studies. Selection of the right alignment algorithm determines not only the alignment algorithm but also the set of suitable parameters to be used by the algorithm. Understanding these algorithms helps in selecting the appropriate alignment algorithm for different applications in precision medicine. Here, we review current available algorithms and their major strategies such as seed-and-extend and q-gram filter. We also discuss the challenges in current alignment algorithms, including alignment in multiple repeated regions, long reads alignment and alignment facilitated with known genetic variants.
59 BASIC BIOLOGICAL SCIENCES↗
Heavy Higgs boson decays in the alignment limit of the 2HDM
The Standard Model (SM)-like couplings of the observed Higgs boson impose strong constraints on the structure of any extended Higgs sector. We consider the theoretical properties and the phenomenological implications of a generic two Higgs doublet model (2HDM). This model constitutes a simple and attractive extension of the SM that is consistent with the observation of the SM-like Higgs boson and precision electroweak observables, while providing a potential new source of CP-violation. In this paper we focus on the so-called Higgs alignment limit of the generic 2HDM, where the neutral scalar field H 1 , with the tree-level couplings of the SM Higgs boson, is a mass eigenstate that is aligned in field space with the direction of the Higgs vacuum expectation value. Tihe properties of the two other heavier neutral Higgs scalars, H 2 and H 3 , in the alignment limit of the 2HDM are also elucidated. It is shown that the couplings of H 2 and H 3 in the alignment limit are tightly constrained and correlated. For example, in the exact alignment limit at tree level, for bosonic final states BR( H 2,3 → W + W - , ZZ, H 1 Z ) = 0 and BR( H ± → W ± H 1 ) = 0, whereas for fermionic final states Γ( H 2 → ff ¯) / Γ( H 3 → ff ¯) ~ M 2 /M 3 (where M α is the mass of H α ). In some cases, the results of the alignment limit differ depending on whether or not alignment is achieved via the decoupling of heavy scalar states. In particular, in the exact alignment limit without decoupling BR( H 2,3 → H 1 H 1 ) = 0, whereas these branching ratios are nonzero in the decoupling regime. Observables that could be used to test the alignment scenario at the LHC are defined and discussed. The couplings of the Higgs bosons away from their exact alignment values are determined to leading order, and some consequences are elucidated.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
Thermoreversible Changes in Aligned and Cross-Linked Block Copolymer Melts Studied by Two Color Depolarized Light Scattering
A procedure for creating samples that can be repeatedly cycled between weakly aligned and strongly aligned states is described. Poly(styrene-b-isoprene) block copolymer samples were first shear-aligned and then cross-linked using a high energy electron beam. Samples with more than 1.0 cross-links per chain on average showed almost complete recovery of their initial alignment state even after 20 cycles of heating above the order–disorder transition temperature of the un-cross-linked block copolymer. Samples with 1.1 cross-links per chain, which showed over 90% loss of alignment on heating and almost 100% recovery of alignment on cooling, provided the best example of a reversible aligned-to-unaligned transition. Samples with lower cross-linking densities exhibited irreversible loss of alignment upon heating, while those with higher cross-linking densities exhibited less than 90% loss of alignment upon heating. Alignment was quantified by a technique that we call two color depolarized light scattering (TCDLS), an extension of the traditional depolarized light scattering experiment used to determine the state of order in block copolymers. Qualitative confirmation of our interpretation of TCDLS data was obtained by small-angle X-ray scattering and transmission electron microscopy.
Wilbur, Jeffrey D.↗
SU-F-J-44: Development of a Room Laser Based Real-Time Alignment Monitoring System Using An Array of Photodiodes
Purpose: To develop a real-time alignment monitoring system (RAMS) to compensate for the limitations of the conventional room laser based alignment system, and to verify the feasibility of the RAMS. Methods: The RAMS was composed of a room laser sensing array (RLSA), an analog-todigital converter, and a control PC. In the RLSA, seven photodiodes (each in 1 mm width) are arranged in a pattern that the RAMS provides alignment in 1 mm resolution. It works based on detecting laser light aligned on one of photodiodes. When misaligned, the laser would match with different photodiode(s) giving signal at unexpected location. Thus, how much displaced can be determined. To verify the reproducibility of the system with respect to time as well as repeated set-ups, temporal reproducibility and repeatability test was conducted. The accuracy of the system was tested by obtaining detection signals with varying laser-match positions. Results: The signal of the RAMS was found to be stable with respect to time. The repeatability test resulted in a maximum coefficient of variance of 1.14%, suggesting that the signal of the RAMS was stable over repeated set-ups. In the accuracy test, signals between when the laser was aligned and notaligned with any of sensors could be distinguished by signal intensity. The signals of not-aligned sensors were always below 75% of the signal of the aligned sensor. It was confirmed that the system could detect 1 mm of movement by monitoring the pattern of signals, and could observe the movement of the system in real-time. Conclusion: We developed a room laser based alignment monitoring system. The feasibility test verified that the system is capable of quantitative alignment monitoring in real time. The system is relatively simple, not expensive, and considered to be easily incorporated into conventional room laser systems for real-time alignment monitoring. This research was supported by the Mid-career Researcher Program through NRF funded by the Ministry of Science, ICT & Future Planning of Korea (NRF-2014R1A2A1A10050270) and by the Radiation Technology R&D program through the National Research Foundation of Korea funded by the Ministry of Science, ICT & Future Planning (No. 2013M2A2A7038291)
46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
Alignments between Galaxies and the Cosmic Web at z ~ 1–2 in the IllustrisTNG Simulations
Galaxy formation theories predict that galaxy shapes and angular momenta have nonrandom alignments with the cosmic web. This leads to so-called intrinsic alignment between pairs of galaxies, which is important to quantify as a nuisance parameter for weak lensing. We study galaxy–cosmic web alignment in the IllustrisTNG suite of hydrodynamical simulations at redshifts 1 and 2, finding that alignment trends are consistent with previous studies. However, we find that the magnitude of the spin alignment signal is ~2.4× weaker than seen in previous studies of the Horizon-AGN simulation, suggesting that this signal may have a significant dependence on subgrid physics. Based on IllustrisTNG, we then construct mock observational spectroscopic surveys that can probe shape–cosmic web alignment at z ~ 1–2, modeled on the low-z galaxy redshift and IGM tomography surveys on the upcoming Subaru Prime Focus Spectrograph Galaxy Evolution (PFS GE) survey. However, even over box sizes of L = 205 h -1 Mpc, we find that global anisotropies induce a sample variance in the 2D projected alignment signal that depend on the projected direction; this induces significant errors in the observed alignment. We predict a 5.3σ detection of IllustrisTNG's shape alignment signal at z ~ 1 from Subaru PFS GE, although a detection would be challenging at z ~ 2. However, a rough rescaling of the relative alignment signal strengths between the TNG and Horizon-AGN simulations suggests that PFS GE should be able to more easily constrain the latter's stronger signal.
79 ASTRONOMY AND ASTROPHYSICS↗
System and method for 2D workpiece alignment
A carrier capable of holding one or more workpieces is disclosed. The carrier includes movable projections located along the sides of each cell in the carrier. This carrier, in conjunction with a separate alignment apparatus, aligns each workpiece within its respective cell against several alignment pins, using a multiple step alignment process to guarantee proper positioning of the workpiece in the cell. First, the workpieces are moved toward one side of the cell. Once the workpieces have been aligned against this side, the workpieces are then moved toward an adjacent orthogonal side such that the workpieces are aligned to two sides of the cell. Once aligned, the workpiece is held in place by the projections located along each side of each cell. In addition, the alignment pins are also used to align the associated mask, thereby guaranteeing that the mask is properly aligned to the workpiece.
42 ENGINEERING↗