Journal articles: 'Phasing-in'

1

J. H. "Phasing In." Scientific American 258, no. 1 (January 1988): 18–20. http://dx.doi.org/10.1038/scientificamerican0188-18.

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Flegel, Willy A., Susan D. Roseff, and Ashok Tholpady. "Phasing-In RHD Genotyping." Archives of Pathology & Laboratory Medicine 138, no. 5 (May 1, 2014): 585–88. http://dx.doi.org/10.5858/2013-0509-ed.

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Matz, Robert. "Phasing in SI units." Journal of General Internal Medicine 3, no. 3 (May 1988): 304–5. http://dx.doi.org/10.1007/bf02596356.

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4

Shorter, James. "Phasing in and out." Nature Chemistry 8, no. 6 (May 24, 2016): 528–30. http://dx.doi.org/10.1038/nchem.2534.

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Martin, Kenneth, and James Carroll. "Phasing in the Technology." IEEE Power and Energy Magazine 6, no. 5 (2008): 24–33. http://dx.doi.org/10.1109/mpe.2008.927474.

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McCoy, Airlie J., and Thomas Schneider. "Advances in experimental phasing." Acta Crystallographica Section D Structural Biology 72, no. 3 (March 1, 2016): 291–92. http://dx.doi.org/10.1107/s2059798316003375.

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Stone, Louise. "Phasing in new treatment." Nature Reviews Urology 11, no. 8 (August 2014): 423. http://dx.doi.org/10.1038/nrurol.2014.173.

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Chakrabartty, Aparajita, and Sudakshina Gupta. "Vehicular Pollution in Kolkata in the Pre Phasing-Out, Phasing-Out and Post Phasing-Out Periods: A Case Study." Journal of Intelligent Transportation and Urban Planning 4, no. 1 (December 30, 2016): 22–34. http://dx.doi.org/10.18005/itup0401003.

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9

Karp, Larry, and Thierry Paul. "Phasing in and Phasing Out Protectionism with Costly Adjustment of Labour." Economic Journal 104, no. 427 (November 1994): 1379. http://dx.doi.org/10.2307/2235454.

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Chuang-ge, WANG, XU Gen, CHEN Dan-he, and LIAO Wen-he. "Micro-nano Satellite Phasing Maneuver Method under Microthrust Constraint." Journal of Physics: Conference Series 2235, no. 1 (May 1, 2022): 012106. http://dx.doi.org/10.1088/1742-6596/2235/1/012106.

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Abstract The micro-thruster of micro-nano satellite cannot provide a large impulse for a single time to satisfy the requirements of the general phasing maneuver because of the constraints of thrust and the stability of attitude control system. A multi impulses phasing method is proposed based on the four impulses phasing maneuver, which satisfies the constraint of the working time of the micro thruster. In this method, a large impulse is divided into multiple small impulses, and the impulses can be re-optimized under the constraint of phasing time, which can realize the phasing maneuver of micro-nano satellites using microthrusters. The simulation results show that the error of phasing time is less than 30 s, and the phasing accuracy in two-body orbit dynamic is less than 0.2 km. Considering the perturbation and the error of the micro thruster, the phasing accuracy is less than 5 km, which meets the time limit and fuel consumption limit in phasing maneuver of the micro-nano satellite.

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Tyrrell, R., J. D. Ferrara, C. Yang, R. Bolotovsky, and J. W. Pflugrath. "Phasing in the home laboratory." Acta Crystallographica Section A Foundations of Crystallography 62, a1 (August 6, 2006): s35. http://dx.doi.org/10.1107/s0108767306099296.

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Tyrrell, R., J. D. Ferrara, C. Yang, R. Bolotovsky, and J. W. Pflugrath. "Phasing in the home laboratory." Acta Crystallographica Section A Foundations of Crystallography 63, a1 (August 22, 2007): s88. http://dx.doi.org/10.1107/s0108767307098066.

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13

Berkovitch-Yellin, Z., I. Agmon, K. Anagnostopoulos, H. Bartels, A. Bashan, W. S. Bennett, A. Dribin, et al. "Initial phasing in ribosomal crystallography." Acta Crystallographica Section A Foundations of Crystallography 52, a1 (August 8, 1996): C175. http://dx.doi.org/10.1107/s0108767396092288.

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Brossaud, Julie, Philippe Gosse, Blandine Gatta, Antoine Tabarin, Guy Simonnet, and Jean-Benoît Corcuff. "Phasing-in plasma metanephrines determination." European Journal of Endocrinology 169, no. 2 (August 2013): 163–70. http://dx.doi.org/10.1530/eje-13-0044.

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ObjectivesWe set up plasma normetanephrine (pNMA) and metanephrine (pMA) assays as they demonstrated their usefulness for diagnosing phaeochromocytomas. Our scope is to describe some practical laboratory aspects and the clinical relevance of these assays in our endocrinological or cardiological departments.MethodsWe retrospectively reviewed the results of MA from a population of in- and outpatients over a 7-year period. Subjects (n=2536) from endocrinological or cardiological departments were investigated (66 phaeochromocytomas). Urinary NMA (uNMA) and pNMA, and urinary MA (uMA) and pMA were assayed by HPLC with electrochemical detection.ResultspNMA and pMA assays are now more frequently requested than uNMA and uMA. This changed our laboratory work load with improved delivery, sensitivity and reliability of plasma assays as well as reduced apparatus maintenance time.The pNMA and pMA upper reference limits (URLs) of subjects with no phaeochromocytoma were 1040 and 430 pmol/l respectively. Sensitivity and specificity based on receiver operating characteristic curves optimal points were 83 and 93% for pNMA at 972 pmol/l and 67 and 98% for pMA at 638 pmol/l. Sensitivity and specificity of paired tests of pMA (positive test: at least one analyte above its URLs) were 100 and 91% respectively.ConclusionThe very low concentration of analytes requires a sustained very good apparatus analytical sensitivity. This can be obtained in an up-to-date laboratory. In terms of clinical performances, assays in plasma or urine are equivalent. Depending on local preferences, populations, strategies or departments, requests for one or the other assay may sustain the need for specifically defined reference ranges.

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Ferrara, J. D., P. L. Magueres, M. Murray, J. W. Pflugrath, and C. Yang. "Phasing in the home laboratory." Acta Crystallographica Section A Foundations of Crystallography 67, a1 (August 22, 2011): C352. http://dx.doi.org/10.1107/s0108767311091124.

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16

Yeates, T. O., and K. Y. J. Zhang. "Ambiguities in Ab Initio Phasing." Science 259, no. 5102 (March 19, 1993): 1771–72. http://dx.doi.org/10.1126/science.259.5102.1771.

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Dorset, D. L., and M. P. McCourt. "Direct phasing in electron crystallography." Acta Crystallographica Section A Foundations of Crystallography 49, s1 (August 21, 1993): c39—c40. http://dx.doi.org/10.1107/s0108767378098918.

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Armstrong, Robin L., and Robert J. Duronio. "Phasing in heterochromatin during development." Genes & Development 33, no. 7-8 (April 1, 2019): 379–81. http://dx.doi.org/10.1101/gad.324731.119.

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19

Terwilliger, Thomas C., Gábor Bunkóczi, Li-Wei Hung, Peter H. Zwart, Janet L. Smith, David L. Akey, and Paul D. Adams. "Can I solve my structure by SAD phasing? Anomalous signal in SAD phasing." Acta Crystallographica Section D Structural Biology 72, no. 3 (March 1, 2016): 346–58. http://dx.doi.org/10.1107/s2059798315019269.

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A key challenge in the SAD phasing method is solving a structure when the anomalous signal-to-noise ratio is low. A simple theoretical framework for describing measurements of anomalous differences and the resulting useful anomalous correlation and anomalous signal in a SAD experiment is presented. Here, the useful anomalous correlation is defined as the correlation of anomalous differences with ideal anomalous differences from the anomalous substructure. The useful anomalous correlation reflects the accuracy of the data and the absence of minor sites. The useful anomalous correlation also reflects the information available for estimating crystallographic phases once the substructure has been determined. In contrast, the anomalous signal (the peak height in a model-phased anomalous difference Fourier at the coordinates of atoms in the anomalous substructure) reflects the information available about each site in the substructure and is related to the ability to find the substructure. A theoretical analysis shows that the expected value of the anomalous signal is the product of the useful anomalous correlation, the square root of the ratio of the number of unique reflections in the data set to the number of sites in the substructure, and a function that decreases with increasing values of the atomic displacement factor for the atoms in the substructure. This means that the ability to find the substructure in a SAD experiment is increased by high data quality and by a high ratio of reflections to sites in the substructure, and is decreased by high atomic displacement factors for the substructure.

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20

Schindler-Ivens, Sheila, David A. Brown, and John D. Brooke. "Direction-Dependent Phasing of Locomotor Muscle Activity Is Altered Post-Stroke." Journal of Neurophysiology 92, no. 4 (October 2004): 2207–16. http://dx.doi.org/10.1152/jn.01207.2003.

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A major contributor to impaired locomotion post-stroke is abnormal phasing of muscle activity. While inappropriate paretic muscle phasing adapts to changing body orientation, load, and speed, it remains unclear whether paretic muscle phasing adapts to reversal of locomotor direction. We examined muscle phasing in backward pedaling, a task that requires shifts in biarticular but not uniarticular muscle phasing relative to forward pedaling. We hypothesized that if paretic and neurologically intact muscle phasing adapt similarly, then paretic biarticular but not paretic uniarticular muscles would shift phasing in backward pedaling. Paretic and neurologically intact individuals pedaled forward and backward while recording electromyograms (EMGs) from vastus medialis (VM), soleus (SOL), rectus femoris (RF), semimembranosus (SM), and biceps femoris (BF). Changes in muscle phasing were assessed by comparing the probability of muscle activity in forward and backward pedaling throughout 18 pedaling cycles. Paretic uniarticular muscles (VM and SOL) showed phase-advanced activity in backward versus forward pedaling, whereas the corresponding neurologically intact muscles showed little to no phasing change. Paretic biarticular muscles were less likely than neurologically intact biarticular muscles to display phasing changes in backward pedaling. Paretic RF displayed no phase change during backward pedaling, and paretic BF displayed no consistent adaptation to backward pedaling. Paretic SM was the only muscle to display backward/forward phase changes that were similar to the neurologically intact group. We conclude that paretic uniarticular muscles are more susceptible and paretic biarticular muscles are less susceptible to direction-dependent phase shifts, consistent with altered sensory integration and impaired cortical control of locomotion.

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21

Gilmore, C. J. "Maximum Entropy and Bayesian Methods of Solving the Phase Problem in Electron Diffraction." Microscopy and Microanalysis 3, S2 (August 1997): 1021–22. http://dx.doi.org/10.1017/s1431927600011995.

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The phasing of electron diffraction data poses considerable problems for traditional direct or heavy atom crystallographic methods since the data are incomplete or at less than atomic resolution (i.e. 1.1Å), and subject to errors arising from dynamical scattering effects. The Bricogne formalism for phasing diffraction data using maximum entropy (ME) and Bayesian methods has proved especially useful in these situations1 since this formalism is stable irrespective of data resolution and completeness, and is robust with respect to errors on the measured diffraction intensities.Successes with this formalism this include a wide range of structures: (1)The ab initio phasing of diketopiperazine C4H6N2O2 (Fig 1).(2)The structure solution of CuCl2.3Cu(OH)2 (Fig 2).(3)The ab initio phasing of two 2-D membrane data sets at ca. 6Å resolution without the use of image phases (Halorhodopsin and Omp F Porin4 - Figs 3 and 4). In addition, we have had some success in phasing the 3-D data of bacteriorhodopsin at 6Å.

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22

Liaudanski, A. D., R. S. Shulinski, Y. A. Mishuk, and L. N. Sivitskaya. "COMPARISON OF GENOTYPE PHASING METODS FOR THE HIGH THROUGHPUT SEQUENCING DATA OF CLINICAL EXOMES." Молекулярная и прикладная генетика 31 (December 8, 2021): 114–23. http://dx.doi.org/10.47612/1999-9127-2021-31-114-123.

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The aim of this investigation was to search for an algorithm for phasing of exome NGS data that would be optimal for analyzing the cis-/transposition of closely located polymorphic loci in patients with hereditary diseases. The NGS data on clinical exome sequences from 149 patients was collected and analyzed, and its primary processing was carried out. A combined reference panel for phasing and genotype imputation “Belref1000G” was created by adding 131 samples of Belarusian patients to the panel from the “1000 Genomes” project. The most effective methods of phasing have been determined: the Michigan Imputation Server (online service) allows achieving the highest accuracy of phasing data from clinical exomes in Belarus. In cases where an online format of phasing is not appropriate for whatever reason, Beagle software with the combined reference panel “Belref1000G” is recommended for use. Beagle software with the “1000G” reference panel should be used to obtain the longest phasing blocks.

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Panjikar, Santosh, and Daniele de Sanctis. "Alternative phasing method in macromolecular crystallography." Acta Crystallographica Section A Foundations and Advances 70, a1 (August 5, 2014): C342. http://dx.doi.org/10.1107/s2053273314096570.

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Selenium is the most widely used heavy atom for experimental phasing, either by single anomalous scattering (SAD) or multiple-wavelength anomalous diffraction (MAD) procedures. The use of the single isomorphous replacement (SIR) or single isomorphous replacement with anomalous scattering (SIRAS) phasing procedure with selenomethionine (Mse) containing proteins is not so commonly used, as it requires isomorphous native data. Several non-redundant X-ray diffraction data sets from various Mse derivatised protein crystals were collected at energies far below the absorption edge before and after exposing the crystal to ultraviolet (UV) radiation with 266 nm lasers. A detailed analysis revealed that significant changes in diffracted intensities were induced by ultraviolet irradiation whilst retaining crystal isomorphism. These intensity changes allowed the crystal structures to be solved by the radiation damage-induced phasing (RIP) technique [1]. These can be coupled with the anomalous signal from the dataset collected at the selenium absorption edge to obtain SIRAS phases in a UV-RIPAS phasing experiment [2]. Inspection of the crystal structures and electron-density maps demonstrated that covalent bonds between selenium and carbon at all sites located in the core of the proteins or in a hydrophobic environment were much more susceptible to UV radiation-induced cleavage than other bonds typically present in Mse proteins. The rapid UV radiation-induced bond cleavage opens a reliable new paradigm for phasing at synchrotron [1,2] and at in-house X-ray source [3].

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McCoy, Airlie J., and Randy J. Read. "Experimental phasing: best practice and pitfalls." Acta Crystallographica Section D Biological Crystallography 66, no. 4 (March 24, 2010): 458–69. http://dx.doi.org/10.1107/s0907444910006335.

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Developments in protein crystal structure determination by experimental phasing are reviewed, emphasizing the theoretical continuum between experimental phasing, density modification, model building and refinement. Traditional notions of the composition of the substructure and the best coefficients for map generation are discussed. Pitfalls such as determining the enantiomorph, identifying centrosymmetry (or pseudo-symmetry) in the substructure and crystal twinning are discussed in detail. An appendix introduces combined real–imaginary log-likelihood gradient map coefficients for SAD phasing and their use for substructure completion as implemented in the softwarePhaser. Supplementary material includes animated probabilistic Harker diagrams showing how maximum-likelihood-based phasing methods can be used to refine parameters in the case of SIR and MIR; it is hoped that these will be useful for those teaching best practice in experimental phasing methods.

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Hattne, Johan, Michael W. Martynowycz, Max T. B. Clabbers, and Tamir Gonen. "Electron Counting and Phasing in MicroED." Microscopy and Microanalysis 28, S1 (July 22, 2022): 1076–78. http://dx.doi.org/10.1017/s1431927622004561.

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Brown, Gregory. "Phasing Risk in Aircraft Development Programs." Risk In Business 29, no. 102 (October 1, 2022): 388–421. http://dx.doi.org/10.22594/dau.21-885.29.04.

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This article analyzes the timing of cumulative cost growth over the planned development schedule, with the goal of utilizing the pattern of historic cost growth to phase the risk dollars for new aircraft development programs. Using data from Selected Acquisition Reports for 21 completed programs, a polynomial regression model is fit to cost growth. The polynomial indicates that 85% of cost growth occurs in the second half of the planned development schedule, on average. These results suggest that risk dollars for new programs should be “backloaded,” or phased later in the program schedule. Backloading risk dollars could improve early program execution and provide greater budget flexibility in the event of schedule delays or schedule growth.

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27

Rius, Jordi. "Phasing in crystallography: a modern perspective." Crystallography Reviews 20, no. 3 (February 28, 2014): 236–38. http://dx.doi.org/10.1080/0889311x.2014.894032.

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Rüdig, Wolfgang. "Phasing out nuclear energy in Germany." German Politics 9, no. 3 (December 2000): 43–80. http://dx.doi.org/10.1080/09644000008404607.

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Sokova, Elena K. "PHASING OUT CIVILIAN HEU IN RUSSIA." Nonproliferation Review 15, no. 2 (July 2008): 209–36. http://dx.doi.org/10.1080/10736700802117288.

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Bunkoczi, G., J. E. Debreczeni, J. Kaercher, and G. M. Sheldrick. "In-house phasing with iodide soaks." Acta Crystallographica Section A Foundations of Crystallography 58, s1 (August 6, 2002): c82. http://dx.doi.org/10.1107/s010876730208830x.

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31

Lawrence, Joshua M., Julien Orlans, Gwyndaf Evans, Allen M. Orville, James Foadi, and Pierre Aller. "High-throughput in situ experimental phasing." Acta Crystallographica Section D Structural Biology 76, no. 8 (July 28, 2020): 790–801. http://dx.doi.org/10.1107/s2059798320009109.

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In this article, a new approach to experimental phasing for macromolecular crystallography (MX) at synchrotrons is introduced and described for the first time. It makes use of automated robotics applied to a multi-crystal framework in which human intervention is reduced to a minimum. Hundreds of samples are automatically soaked in heavy-atom solutions, using a Labcyte Inc. Echo 550 Liquid Handler, in a highly controlled and optimized fashion in order to generate derivatized and isomorphous crystals. Partial data sets obtained on MX beamlines using an in situ setup for data collection are processed with the aim of producing good-quality anomalous signal leading to successful experimental phasing.

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32

Dauter, Zbigniew. "Phasing in iodine for structure determination." Nature Biotechnology 22, no. 10 (October 2004): 1239–40. http://dx.doi.org/10.1038/nbt1004-1239.

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Jiang, Junlun, and Weirui Zhao. "Phasing piston error in segmented telescopes." Optics Express 24, no. 17 (August 10, 2016): 19123. http://dx.doi.org/10.1364/oe.24.019123.

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34

Giacovazzo, Carmelo. "Phasing in crystallography: a modern perspective." Rendiconti Lincei 24, S1 (October 18, 2012): 71–76. http://dx.doi.org/10.1007/s12210-012-0209-x.

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35

Gilmore, Christopher J. "Novel phasing techniques in macromolecular crystallography." Current Opinion in Structural Biology 2, no. 6 (January 1992): 806–10. http://dx.doi.org/10.1016/0959-440x(92)90102-d.

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36

Edberg, Karin, and Ekaterina Tarasova. "Phasing out or phasing in: Framing the role of nuclear power in the Swedish energy transition." Energy Research & Social Science 13 (March 2016): 170–79. http://dx.doi.org/10.1016/j.erss.2015.12.008.

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McCoy, Airlie J., Duncan H. Stockwell, Massimo D. Sammito, Robert D. Oeffner, Kaushik S. Hatti, Tristan I. Croll, and Randy J. Read. "Phasertng: directed acyclic graphs for crystallographic phasing." Acta Crystallographica Section D Structural Biology 77, no. 1 (January 1, 2021): 1–10. http://dx.doi.org/10.1107/s2059798320014746.

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Crystallographic phasing strategies increasingly require the exploration and ranking of many hypotheses about the number, types and positions of atoms, molecules and/or molecular fragments in the unit cell, each with only a small chance of being correct. Accelerating this move has been improvements in phasing methods, which are now able to extract phase information from the placement of very small fragments of structure, from weak experimental phasing signal or from combinations of molecular replacement and experimental phasing information. Describing phasing in terms of a directed acyclic graph allows graph-management software to track and manage the path to structure solution. The crystallographic software supporting the graph data structure must be strictly modular so that nodes in the graph are efficiently generated by the encapsulated functionality. To this end, the development of new software, Phasertng, which uses directed acyclic graphs natively for input/output, has been initiated. In Phasertng, the codebase of Phaser has been rebuilt, with an emphasis on modularity, on scripting, on speed and on continuing algorithm development. As a first application of phasertng, its advantages are demonstrated in the context of phasertng.xtricorder, a tool to analyse and triage merged data in preparation for molecular replacement or experimental phasing. The description of the phasing strategy with directed acyclic graphs is a generalization that extends beyond the functionality of Phasertng, as it can incorporate results from bioinformatics and other crystallographic tools, and will facilitate multifaceted search strategies, dynamic ranking of alternative search pathways and the exploitation of machine learning to further improve phasing strategies.

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Srikanth, Krishnamoorthy, Jong-Eun Park, Dajeong Lim, Jihye Cha, Sang-Rae Cho, In-Cheol Cho, and Woncheoul Park. "A Comparison between Hi-C and 10X Genomics Linked Read Sequencing for Whole Genome Phasing in Hanwoo Cattle." Genes 11, no. 3 (March 20, 2020): 332. http://dx.doi.org/10.3390/genes11030332.

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Until recently, genome-scale phasing was limited due to the short read sizes of sequence data. Though the use of long-read sequencing can overcome this limitation, they require extensive error correction. The emergence of technologies such as 10X genomics linked read sequencing and Hi-C which uses short-read sequencers along with library preparation protocols that facilitates long-read assemblies have greatly reduced the complexities of genome scale phasing. Moreover, it is possible to accurately assemble phased genome of individual samples using these methods. Therefore, in this study, we compared three phasing strategies which included two sample preparation methods along with the Long Ranger pipeline of 10X genomics and HapCut2 software, namely 10X-LG, 10X-HapCut2, and HiC-HapCut2 and assessed their performance and accuracy. We found that the 10X-LG had the best phasing performance amongst the method analyzed. They had the highest phasing rate (89.6%), longest adjusted N50 (1.24 Mb), and lowest switch error rate (0.07%). Moreover, the phasing accuracy and yield of the 10X-LG stayed over 90% for distances up to 4 Mb and 550 Kb respectively, which were considerably higher than 10X-HapCut2 and Hi-C Hapcut2. The results of this study will serve as a good reference for future benchmarking studies and also for reference-based imputation in Hanwoo.

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Gawande, S. H., and S. N. Shaikh. "Experimental Investigations of Noise Control in Planetary Gear Set by Phasing." Journal of Engineering 2014 (2014): 1–11. http://dx.doi.org/10.1155/2014/857462.

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Now a days reduction of gear noise and resulting vibrations has received much attention of the researchers. The internal excitation caused by the variation in tooth mesh stiffness is a key factor in causing vibration. Therefore to reduce gear noise and vibrations several techniques have been proposed in recent years. In this research the experimental work is carried out to study the effect of planet phasing on noise and subsequent resulting vibrations of Nylon-6 planetary gear drive. For this purpose experimental set-up was built and trials were conducted for two different arrangements (i.e., with phasing and without phasing) and it is observed that the noise level and resulting vibrations were reduced by planet phasing arrangement. So from the experimental results it is observed that by applying the meshing phase difference one can reduce planetary gear set noise and vibrations.

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Adamson, Michael, Grant G. Schultz, Mitsuru Saito, and Michael D. Stevens. "Developing Decision Boundaries for Left-Turn Treatments." Transportation Research Record: Journal of the Transportation Research Board 2674, no. 5 (April 23, 2020): 315–26. http://dx.doi.org/10.1177/0361198120915470.

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The purpose of this research was to evaluate the interaction of left-turn and opposing through traffic volumes for permitted and protected left-turn phasing at intersections and develop boundaries that help identify when to switch from permitted to protected phasing at signalized intersections. Permitted phasing allows vehicles to turn left after yielding to opposing vehicles; protected phasing provides an exclusive phase for vehicles to turn left without opposition; and protected-permitted phasing combines these phasing alternatives, allowing both permitted and protected turning movements. Intersections with 1, 2, and 3 opposing-lane configurations with permitted and protected-permitted models (split into green times of 10, 15, and 20 s) were analyzed for a total of 12 simulation models. Each model was divided into 100–225 different volume scenarios, with incremental increases in left-turn and opposing volumes. By exporting trajectory files from VISSIM and importing these into the Surrogate Safety Assessment Model, crossing conflicts for each volume combination in each model were extracted. MATLAB was then used to create contour maps representing the number of crossing conflicts per hour associated with different combinations of left-turn and opposing volume. Basic decision boundaries were examined in each contour map. Statistical analysis software was used to perform a linear regression analysis on transformed data and to develop natural log-based equations that form the decision boundaries for each configuration and phase alternative. These equations were graphed and final decision boundaries developed for the 1-, 2-, and 3-lane configurations between permitted and protected-permitted phasing as well as between protected-permitted and protected phasing.

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Lindholt, Lars, and Solveig Glomsrød. "Phasing out coal and phasing in renewables – Good or bad news for arctic gas producers?" Energy Economics 70 (February 2018): 1–11. http://dx.doi.org/10.1016/j.eneco.2017.12.015.

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42

Beck, Tobias, Tim Gruene, and George M. Sheldrick. "The magic triangle goes MAD: experimental phasing with a bromine derivative." Acta Crystallographica Section D Biological Crystallography 66, no. 4 (March 24, 2010): 374–80. http://dx.doi.org/10.1107/s0907444909051609.

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Experimental phasing is an essential technique for the solution of macromolecular structures. Since many heavy-atom ion soaks suffer from nonspecific binding, a novel class of compounds has been developed that combines heavy atoms with functional groups for binding to proteins. The phasing tool 5-amino-2,4,6-tribromoisophthalic acid (B3C) contains three functional groups (two carboxylate groups and one amino group) that interact with proteinsviahydrogen bonds. Three Br atoms suitable for anomalous dispersion phasing are arranged in an equilateral triangle and are thus readily identified in the heavy-atom substructure. B3C was incorporated into proteinase K and a multiwavelength anomalous dispersion (MAD) experiment at the Br Kedge was successfully carried out. Radiation damage to the bromine–carbon bond was investigated. A comparison with the phasing tool I3C that contains three I atoms for single-wavelength anomalous dispersion (SAD) phasing was also carried out.

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43

Ickes, A. M., S. V. Bohac, and D. N. Assanis. "Effect of fuel cetane number on a premixed diesel combustion mode." International Journal of Engine Research 10, no. 4 (June 26, 2009): 251–63. http://dx.doi.org/10.1243/14680874jer03809.

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The ability of premixed low-temperature diesel combustion to deliver low particulate matter (PM) and NO x emissions is dependent on achieving optimal combustion phasing. Small deviations in combustion phasing can shift the combustion to less optimal modes, yielding increased emissions, increased noise, and poor stability. This paper demonstrates how variations in fuel cetane number affect the detailed combustion behaviour of a direct-injection, diesel-fuelled, premixed combustion mode. Testing was conducted under light load conditions on a modern single-cylinder engine, fuelled with a range of ultra-low sulphur fuels with cetane numbers ranging from 42 to 53. Fuel cetane number is found to affect ignition delay and, accordingly, combustion phasing. Gaseous emissions are a function of combustion phasing and exhaust gas recirculation (EGR) quantity, but are not directly tied to fuel cetane number. Fuel cetane number is merely one of many different engine parameters that shift combustion phasing. Furthermore, the operating range is constrained by the changes in cetane number: no injection timings yield acceptable combustion across the whole spread of tested cetane numbers. However, in terms of combustion phasing, the operating range is consistent, independent of fuel cetane number.

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Marnell, Patrick, Paul Zebell, Peter Koonce, and Shaun Quayle. "Evaluating Transit Priority Signal Phasing at Most Multimodal Intersection in Portland, Oregon." Transportation Research Record: Journal of the Transportation Research Board 2619, no. 1 (January 2017): 44–54. http://dx.doi.org/10.3141/2619-05.

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This research documents the operational benefits of additional phases, barrier bars, and a call-based transit priority signal-phasing strategy over a more traditional eight-phase, two-barrier preemption-based transit signal–phasing strategy. The call-based timing strategy, with a more flexible ring-and-barrier structure, takes advantage of additional phases to run less-impactful transit prioritization for light-rail trains. These two strategies have been field implemented in Portland, Oregon, at the signalized intersection of Southwest Porter Street and Southwest Moody Avenue, an intersection that has distinct signalized movements for the private-automobile, streetcar, light-rail train, bus, pedestrian, and bicycle modes. The operations of the two-intersection signal-phasing strategies were evaluated and tested by using hardware and software-in-the-loop microsimulation (in Vissim) to isolate the expected change in operational efficiency in modal delay. The two-barrier preemption-based transit signal-phasing strategy showed high variability in delay for certain movements, in particular, pedestrians. The call-based phasing strategy with flexible ring-and-barrier structure reduced total and average intersection delay. This research shows that the call-based phasing strategy with flexible ring-and-barrier structure can provide a less disruptive transit prioritization. Agencies should consider the call-phased transit priority strategy over the more traditional preemption-based strategy at a signalized intersection when ( a) delaying potential preemptive movements mode will not have large safety effects, ( b) pedestrian demand is high, ( c) preemption service will be frequent, or ( d) the intersection is operating at or over capacity.

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Hurtley, Stella M. "Phasing-in quality control in the nucleus." Science 365, no. 6451 (July 25, 2019): 337.1–337. http://dx.doi.org/10.1126/science.365.6451.337-a.

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McCoy, Airlie J., Ralf W. Grosse-Kunstleve, Paul D. Adams, Martyn D. Winn, Laurent C. Storoni, and Randy J. Read. "Phasercrystallographic software." Journal of Applied Crystallography 40, no. 4 (July 13, 2007): 658–74. http://dx.doi.org/10.1107/s0021889807021206.

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Phaseris a program for phasing macromolecular crystal structures by both molecular replacement and experimental phasing methods. The novel phasing algorithms implemented inPhaserhave been developed using maximum likelihood and multivariate statistics. For molecular replacement, the new algorithms have proved to be significantly better than traditional methods in discriminating correct solutions from noise, and for single-wavelength anomalous dispersion experimental phasing, the new algorithms, which account for correlations betweenF+andF−, give better phases (lower mean phase error with respect to the phases given by the refined structure) than those that use meanFand anomalous differences ΔF. One of the design concepts ofPhaserwas that it be capable of a high degree of automation. To this end,Phaser(written in C++) can be called directly from Python, although it can also be called using traditionalCCP4keyword-style input.Phaseris a platform for future development of improved phasing methods and their release, including source code, to the crystallographic community.

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Doutch, James, Michael A. Hough, S. Samar Hasnain, and Richard W. Strange. "Challenges of sulfur SAD phasing as a routine method in macromolecular crystallography." Journal of Synchrotron Radiation 19, no. 1 (November 29, 2011): 19–29. http://dx.doi.org/10.1107/s0909049511049004.

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The sulfur SAD phasing method allows the determination of protein structuresde novowithout reference to derivatives such as Se-methionine. The feasibility for routine automated sulfur SAD phasing using a number of current protein crystallography beamlines at several synchrotrons was examined using crystals of trimericAchromobacter cycloclastesnitrite reductase (AcNiR), which contains a near average proportion of sulfur-containing residues and two Cu atoms per subunit. Experiments using X-ray wavelengths in the range 1.9–2.4 Å show that we are not yet at the level where sulfur SAD is routinely successful forautomatedstructure solution and model building using existing beamlines and current software tools. On the other hand, experiments using the shortest X-ray wavelengths available on existing beamlines could be routinely exploited to solve and produce unbiased structural models using the similarly weak anomalous scattering signals from the intrinsic metal atoms in proteins. The comparison of long-wavelength phasing (the Bijvoet ratio for nine S atoms and two Cu atoms is ∼1.25% at ∼2 Å) and copper phasing (the Bijvoet ratio for two Cu atoms is 0.81% at ∼0.75 Å) forAcNiR suggests that lower data multiplicity than is currently required for success should in general be possible for sulfur phasing if appropriate improvements to beamlines and data collection strategies can be implemented.

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Panneerselvam, Saravanan, Esa-Pekka Kumpula, Inari Kursula, Anja Burkhardt, and Alke Meents. "Rapid cadmium SAD phasing at the standard wavelength (1 Å)." Acta Crystallographica Section D Structural Biology 73, no. 7 (June 30, 2017): 581–90. http://dx.doi.org/10.1107/s2059798317006970.

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Cadmium ions can be effectively used to promote crystal growth and for experimental phasing. Here, the use of cadmium ions as a suitable anomalous scatterer at the standard wavelength of 1 Å is demonstrated. The structures of three different proteins were determined using cadmium single-wavelength anomalous dispersion (SAD) phasing. Owing to the strong anomalous signal, the structure of lysozyme could be automatically phased and built using a very low anomalous multiplicity (1.1) and low-completeness (77%) data set. Additionally, it is shown that cadmium ions can easily substitute divalent ions in ATP–divalent cation complexes. This property could be generally applied for phasing experiments of a wide range of nucleotide-binding proteins. Improvements in crystal growth and quality, good anomalous signal at standard wavelengths (i.e.no need to change photon energy) and rapid phasing and refinement using a single data set are benefits that should allow cadmium ions to be widely used for experimental phasing.

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Sui, Wenbo, and Carrie M. Hall. "Combustion phasing modeling and control for compression ignition engines with high dilution and boost levels." Proceedings of the Institution of Mechanical Engineers, Part D: Journal of Automobile Engineering 233, no. 7 (August 1, 2018): 1834–50. http://dx.doi.org/10.1177/0954407018790176.

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Because fuel efficiency is significantly affected by the timing of combustion in internal combustion engines, accurate control of combustion phasing is critical. In this paper, a nonlinear combustion phasing model is introduced and calibrated, and both a feedforward model–based control strategy and an adaptive model–based control strategy are investigated for combustion phasing control. The combustion phasing model combines a knock integral model, burn duration model, and a Wiebe function to predict the combustion phasing of a diesel engine. This model is simplified to be more suitable for combustion phasing control and is calibrated and validated using simulations and experimental data that include conditions with high exhaust gas recirculation fractions and high boost levels. Based on this model, an adaptive nonlinear model–based controller is designed for closed-loop control, and a feedforward model–based controller is designed for open-loop control. These two control approaches were tested in simulations. The simulation results show that during transient changes, the CA50 (the crank angle at which 50% of the mass of fuel has burned) can reach steady state in no more than five cycles and the steady-state errors are less than ±0.1 crank angle degree for adaptive control and less than ±0.5 crank angle degree for feedforward model–based control.

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Chai, Lawrence, Ping Zhu, Jin Chai, Changxu Pang, Babak Andi, Sean McSweeney, John Shanklin, and Qun Liu. "AlphaFold Protein Structure Database for Sequence-Independent Molecular Replacement." Crystals 11, no. 10 (October 12, 2021): 1227. http://dx.doi.org/10.3390/cryst11101227.

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Crystallographic phasing recovers the phase information that is lost during a diffraction experiment. Molecular replacement is a commonly used phasing method for crystal structures in the protein data bank. In one form it uses a protein sequence to search a structure database to find suitable templates for phasing. However, sequence information is not always available, such as when proteins are crystallized with unknown binding partner proteins or when the crystal is of a contaminant. The recent development of AlphaFold published the predicted protein structures for every protein from twenty distinct species. In this work, we tested whether AlphaFold-predicted E. coli protein structures were accurate enough to enable sequence-independent phasing of diffraction data from two crystallization contaminants of unknown sequence. Using each of more than 4000 predicted structures as a search model, robust molecular replacement solutions were obtained, which allowed the identification and structure determination of YncE and YadF. Our results demonstrate the general utility of the AlphaFold-predicted structure database with respect to sequence-independent crystallographic phasing.

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Journal articles on the topic 'Phasing-in'

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