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Comparing 2 crystal structures and 12 AlphaFold2-predicted human membrane glucose transporters and their water-soluble glutamine, threonine and tyrosine variants
- Eva Smorodina, Fei Tao, Rui Qing, David Jin, Steve Yang, Shuguang Zhang
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- Journal:
- QRB Discovery / Volume 3 / 2022
- Published online by Cambridge University Press:
- 13 June 2022, e5
- Print publication:
- 2022
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Membrane transporters including glucose transporters (GLUTs) are involved in cellular energy supplies, cell metabolism and other vital biological activities. They have also been implicated in cancer proliferation and metastasis, thus they represent an important target in combatting cancer. However, membrane transporters are very difficult to study due to their multispan transmembrane properties. The new computational tool, AlphaFold2, offers highly accurate predictions of three-dimensional protein structures. The glutamine, threonine and tyrosine (QTY) code provides a systematic method of rendering hydrophobic sequences into hydrophilic ones. Here, we present computational studies of native integral membrane GLUTs with 12 transmembrane helical segments determined by X-ray crystallography and CryoEM, comparing the AlphaFold2-predicted native structure to their water-soluble QTY variants predicted by AlphaFold2. In the native structures of the transmembrane helices, there are hydrophobic amino acids leucine (L), isoleucine (I), valine (V) and phenylalanine (F). Applying the QTY code, these hydrophobic amino acids are systematically replaced by hydrophilic amino acids, glutamine (Q), threonine (T) and tyrosine (Y) rendering them water-soluble. We present the superposed structures of native GLUTs and their water-soluble QTY variants. The superposed structures show remarkable similar residue mean square distance values between 0.47 and 3.6 Å (most about 1–2 Å) despite >44% transmembrane amino acid differences. We also show the differences of hydrophobicity patches between the native membrane transporters and their QTY variants. We explain the rationale why the membrane protein QTY variants become water-soluble. Our study provides insight into the differences between the hydrophobic helices and hydrophilic helices, and offers confirmation of the QTY method for studying multispan transmembrane proteins and other aggregated proteins through their water-soluble variants.
Comparing 2 crystal structures and 12 AlphaFold2-predicted human membrane glucose transporters and their water-soluble glutamine, threonine and tyrosine variants – CORRIGENDUM
- Eva Smorodina, Fei Tao, Rui Qing, David Jin, Steve Yang, Shuguang Zhang
-
- Journal:
- QRB Discovery / Volume 3 / 2022
- Published online by Cambridge University Press:
- 21 July 2022, e8
- Print publication:
- 2022
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Contributors
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- By Mitchell Aboulafia, Frederick Adams, Marilyn McCord Adams, Robert M. Adams, Laird Addis, James W. Allard, David Allison, William P. Alston, Karl Ameriks, C. Anthony Anderson, David Leech Anderson, Lanier Anderson, Roger Ariew, David Armstrong, Denis G. Arnold, E. J. Ashworth, Margaret Atherton, Robin Attfield, Bruce Aune, Edward Wilson Averill, Jody Azzouni, Kent Bach, Andrew Bailey, Lynne Rudder Baker, Thomas R. Baldwin, Jon Barwise, George Bealer, William Bechtel, Lawrence C. Becker, Mark A. Bedau, Ernst Behler, José A. Benardete, Ermanno Bencivenga, Jan Berg, Michael Bergmann, Robert L. Bernasconi, Sven Bernecker, Bernard Berofsky, Rod Bertolet, Charles J. Beyer, Christian Beyer, Joseph Bien, Joseph Bien, Peg Birmingham, Ivan Boh, James Bohman, Daniel Bonevac, Laurence BonJour, William J. Bouwsma, Raymond D. Bradley, Myles Brand, Richard B. Brandt, Michael E. Bratman, Stephen E. Braude, Daniel Breazeale, Angela Breitenbach, Jason Bridges, David O. Brink, Gordon G. Brittan, Justin Broackes, Dan W. Brock, Aaron Bronfman, Jeffrey E. Brower, Bartosz Brozek, Anthony Brueckner, Jeffrey Bub, Lara Buchak, Otavio Bueno, Ann E. Bumpus, Robert W. Burch, John Burgess, Arthur W. Burks, Panayot Butchvarov, Robert E. Butts, Marina Bykova, Patrick Byrne, David Carr, Noël Carroll, Edward S. Casey, Victor Caston, Victor Caston, Albert Casullo, Robert L. Causey, Alan K. L. Chan, Ruth Chang, Deen K. Chatterjee, Andrew Chignell, Roderick M. Chisholm, Kelly J. Clark, E. J. Coffman, Robin Collins, Brian P. Copenhaver, John Corcoran, John Cottingham, Roger Crisp, Frederick J. Crosson, Antonio S. Cua, Phillip D. Cummins, Martin Curd, Adam Cureton, Andrew Cutrofello, Stephen Darwall, Paul Sheldon Davies, Wayne A. Davis, Timothy Joseph Day, Claudio de Almeida, Mario De Caro, Mario De Caro, John Deigh, C. F. Delaney, Daniel C. Dennett, Michael R. DePaul, Michael Detlefsen, Daniel Trent Devereux, Philip E. Devine, John M. Dillon, Martin C. Dillon, Robert DiSalle, Mary Domski, Alan Donagan, Paul Draper, Fred Dretske, Mircea Dumitru, Wilhelm Dupré, Gerald Dworkin, John Earman, Ellery Eells, Catherine Z. Elgin, Berent Enç, Ronald P. Endicott, Edward Erwin, John Etchemendy, C. Stephen Evans, Susan L. Feagin, Solomon Feferman, Richard Feldman, Arthur Fine, Maurice A. Finocchiaro, William FitzPatrick, Richard E. Flathman, Gvozden Flego, Richard Foley, Graeme Forbes, Rainer Forst, Malcolm R. Forster, Daniel Fouke, Patrick Francken, Samuel Freeman, Elizabeth Fricker, Miranda Fricker, Michael Friedman, Michael Fuerstein, Richard A. Fumerton, Alan Gabbey, Pieranna Garavaso, Daniel Garber, Jorge L. A. Garcia, Robert K. Garcia, Don Garrett, Philip Gasper, Gerald Gaus, Berys Gaut, Bernard Gert, Roger F. Gibson, Cody Gilmore, Carl Ginet, Alan H. Goldman, Alvin I. Goldman, Alfonso Gömez-Lobo, Lenn E. Goodman, Robert M. Gordon, Stefan Gosepath, Jorge J. E. Gracia, Daniel W. Graham, George A. Graham, Peter J. Graham, Richard E. Grandy, I. Grattan-Guinness, John Greco, Philip T. Grier, Nicholas Griffin, Nicholas Griffin, David A. Griffiths, Paul J. Griffiths, Stephen R. Grimm, Charles L. Griswold, Charles B. Guignon, Pete A. Y. Gunter, Dimitri Gutas, Gary Gutting, Paul Guyer, Kwame Gyekye, Oscar A. Haac, Raul Hakli, Raul Hakli, Michael Hallett, Edward C. Halper, Jean Hampton, R. James Hankinson, K. R. Hanley, Russell Hardin, Robert M. Harnish, William Harper, David Harrah, Kevin Hart, Ali Hasan, William Hasker, John Haugeland, Roger Hausheer, William Heald, Peter Heath, Richard Heck, John F. Heil, Vincent F. Hendricks, Stephen Hetherington, Francis Heylighen, Kathleen Marie Higgins, Risto Hilpinen, Harold T. Hodes, Joshua Hoffman, Alan Holland, Robert L. Holmes, Richard Holton, Brad W. Hooker, Terence E. Horgan, Tamara Horowitz, Paul Horwich, Vittorio Hösle, Paul Hoβfeld, Daniel Howard-Snyder, Frances Howard-Snyder, Anne Hudson, Deal W. Hudson, Carl A. Huffman, David L. Hull, Patricia Huntington, Thomas Hurka, Paul Hurley, Rosalind Hursthouse, Guillermo Hurtado, Ronald E. Hustwit, Sarah Hutton, Jonathan Jenkins Ichikawa, Harry A. Ide, David Ingram, Philip J. Ivanhoe, Alfred L. Ivry, Frank Jackson, Dale Jacquette, Joseph Jedwab, Richard Jeffrey, David Alan Johnson, Edward Johnson, Mark D. Jordan, Richard Joyce, Hwa Yol Jung, Robert Hillary Kane, Tomis Kapitan, Jacquelyn Ann K. Kegley, James A. Keller, Ralph Kennedy, Sergei Khoruzhii, Jaegwon Kim, Yersu Kim, Nathan L. King, Patricia Kitcher, Peter D. Klein, E. D. Klemke, Virginia Klenk, George L. Kline, Christian Klotz, Simo Knuuttila, Joseph J. Kockelmans, Konstantin Kolenda, Sebastian Tomasz Kołodziejczyk, Isaac Kramnick, Richard Kraut, Fred Kroon, Manfred Kuehn, Steven T. Kuhn, Henry E. Kyburg, John Lachs, Jennifer Lackey, Stephen E. Lahey, Andrea Lavazza, Thomas H. Leahey, Joo Heung Lee, Keith Lehrer, Dorothy Leland, Noah M. Lemos, Ernest LePore, Sarah-Jane Leslie, Isaac Levi, Andrew Levine, Alan E. Lewis, Daniel E. Little, Shu-hsien Liu, Shu-hsien Liu, Alan K. L. Chan, Brian Loar, Lawrence B. Lombard, John Longeway, Dominic McIver Lopes, Michael J. Loux, E. J. Lowe, Steven Luper, Eugene C. Luschei, William G. Lycan, David Lyons, David Macarthur, Danielle Macbeth, Scott MacDonald, Jacob L. Mackey, Louis H. Mackey, Penelope Mackie, Edward H. Madden, Penelope Maddy, G. B. Madison, Bernd Magnus, Pekka Mäkelä, Rudolf A. Makkreel, David Manley, William E. Mann (W.E.M.), Vladimir Marchenkov, Peter Markie, Jean-Pierre Marquis, Ausonio Marras, Mike W. Martin, A. P. Martinich, William L. McBride, David McCabe, Storrs McCall, Hugh J. McCann, Robert N. McCauley, John J. McDermott, Sarah McGrath, Ralph McInerny, Daniel J. McKaughan, Thomas McKay, Michael McKinsey, Brian P. McLaughlin, Ernan McMullin, Anthonie Meijers, Jack W. Meiland, William Jason Melanson, Alfred R. Mele, Joseph R. Mendola, Christopher Menzel, Michael J. Meyer, Christian B. Miller, David W. Miller, Peter Millican, Robert N. Minor, Phillip Mitsis, James A. Montmarquet, Michael S. Moore, Tim Moore, Benjamin Morison, Donald R. Morrison, Stephen J. Morse, Paul K. Moser, Alexander P. D. Mourelatos, Ian Mueller, James Bernard Murphy, Mark C. Murphy, Steven Nadler, Jan Narveson, Alan Nelson, Jerome Neu, Samuel Newlands, Kai Nielsen, Ilkka Niiniluoto, Carlos G. Noreña, Calvin G. Normore, David Fate Norton, Nikolaj Nottelmann, Donald Nute, David S. Oderberg, Steve Odin, Michael O’Rourke, Willard G. Oxtoby, Heinz Paetzold, George S. Pappas, Anthony J. Parel, Lydia Patton, R. P. Peerenboom, Francis Jeffry Pelletier, Adriaan T. Peperzak, Derk Pereboom, Jaroslav Peregrin, Glen Pettigrove, Philip Pettit, Edmund L. Pincoffs, Andrew Pinsent, Robert B. Pippin, Alvin Plantinga, Louis P. Pojman, Richard H. Popkin, John F. Post, Carl J. Posy, William J. Prior, Richard Purtill, Michael Quante, Philip L. Quinn, Philip L. Quinn, Elizabeth S. Radcliffe, Diana Raffman, Gerard Raulet, Stephen L. Read, Andrews Reath, Andrew Reisner, Nicholas Rescher, Henry S. Richardson, Robert C. Richardson, Thomas Ricketts, Wayne D. Riggs, Mark Roberts, Robert C. Roberts, Luke Robinson, Alexander Rosenberg, Gary Rosenkranz, Bernice Glatzer Rosenthal, Adina L. Roskies, William L. Rowe, T. M. Rudavsky, Michael Ruse, Bruce Russell, Lilly-Marlene Russow, Dan Ryder, R. M. Sainsbury, Joseph Salerno, Nathan Salmon, Wesley C. Salmon, Constantine Sandis, David H. Sanford, Marco Santambrogio, David Sapire, Ruth A. Saunders, Geoffrey Sayre-McCord, Charles Sayward, James P. Scanlan, Richard Schacht, Tamar Schapiro, Frederick F. Schmitt, Jerome B. Schneewind, Calvin O. Schrag, Alan D. Schrift, George F. Schumm, Jean-Loup Seban, David N. Sedley, Kenneth Seeskin, Krister Segerberg, Charlene Haddock Seigfried, Dennis M. Senchuk, James F. Sennett, William Lad Sessions, Stewart Shapiro, Tommie Shelby, Donald W. Sherburne, Christopher Shields, Roger A. Shiner, Sydney Shoemaker, Robert K. Shope, Kwong-loi Shun, Wilfried Sieg, A. John Simmons, Robert L. Simon, Marcus G. Singer, Georgette Sinkler, Walter Sinnott-Armstrong, Matti T. Sintonen, Lawrence Sklar, Brian Skyrms, Robert C. Sleigh, Michael Anthony Slote, Hans Sluga, Barry Smith, Michael Smith, Robin Smith, Robert Sokolowski, Robert C. Solomon, Marta Soniewicka, Philip Soper, Ernest Sosa, Nicholas Southwood, Paul Vincent Spade, T. L. S. Sprigge, Eric O. Springsted, George J. Stack, Rebecca Stangl, Jason Stanley, Florian Steinberger, Sören Stenlund, Christopher Stephens, James P. Sterba, Josef Stern, Matthias Steup, M. A. Stewart, Leopold Stubenberg, Edith Dudley Sulla, Frederick Suppe, Jere Paul Surber, David George Sussman, Sigrún Svavarsdóttir, Zeno G. Swijtink, Richard Swinburne, Charles C. Taliaferro, Robert B. Talisse, John Tasioulas, Paul Teller, Larry S. Temkin, Mark Textor, H. S. Thayer, Peter Thielke, Alan Thomas, Amie L. Thomasson, Katherine Thomson-Jones, Joshua C. Thurow, Vzalerie Tiberius, Terrence N. Tice, Paul Tidman, Mark C. Timmons, William Tolhurst, James E. Tomberlin, Rosemarie Tong, Lawrence Torcello, Kelly Trogdon, J. D. Trout, Robert E. Tully, Raimo Tuomela, John Turri, Martin M. Tweedale, Thomas Uebel, Jennifer Uleman, James Van Cleve, Harry van der Linden, Peter van Inwagen, Bryan W. Van Norden, René van Woudenberg, Donald Phillip Verene, Samantha Vice, Thomas Vinci, Donald Wayne Viney, Barbara Von Eckardt, Peter B. M. Vranas, Steven J. Wagner, William J. Wainwright, Paul E. Walker, Robert E. Wall, Craig Walton, Douglas Walton, Eric Watkins, Richard A. Watson, Michael V. Wedin, Rudolph H. Weingartner, Paul Weirich, Paul J. Weithman, Carl Wellman, Howard Wettstein, Samuel C. Wheeler, Stephen A. White, Jennifer Whiting, Edward R. Wierenga, Michael Williams, Fred Wilson, W. Kent Wilson, Kenneth P. Winkler, John F. Wippel, Jan Woleński, Allan B. Wolter, Nicholas P. Wolterstorff, Rega Wood, W. Jay Wood, Paul Woodruff, Alison Wylie, Gideon Yaffe, Takashi Yagisawa, Yutaka Yamamoto, Keith E. Yandell, Xiaomei Yang, Dean Zimmerman, Günter Zoller, Catherine Zuckert, Michael Zuckert, Jack A. Zupko (J.A.Z.)
- Edited by Robert Audi, University of Notre Dame, Indiana
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- Book:
- The Cambridge Dictionary of Philosophy
- Published online:
- 05 August 2015
- Print publication:
- 27 April 2015, pp ix-xxx
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Automated Measures of Hand Hygiene Compliance among Healthcare Workers Using Ultrasound: Validation and a Randomized Controlled Trial
- Dale A. Fisher, Theresa Seetoh, Helen Oh May-Lin, Sivakumar Viswanathan, Yanling Toh, Wong Chiang Yin, Loh Siw Eng, Tan Shire Yang, Steve Schiefen, Minkyu Je, Ruey Feng Peh, Fiona Wei Ling Loke, Michael Dempsey
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- Journal:
- Infection Control & Hospital Epidemiology / Volume 34 / Issue 9 / September 2013
- Published online by Cambridge University Press:
- 02 January 2015, pp. 919-928
- Print publication:
- September 2013
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Objective.
The primary objective of this study was to validate a novel method of assessing hand hygiene compliance using ultrasound transmitters in patient zones and staff tagged with receivers. The secondary objective was to assess the impact of audio reminders and quantified individual feedback.
Design.An observational comparison against manual assessment followed by assessment using an open-label randomized control method.
Setting.Patient zones were established in 3 wards of 2 large teaching hospitals, including 88 general and 18 intensive care unit ward beds.
Participants.Consented regular ward nursing, medical, and allied health staff.
Methods.Concordance between 40 hours of manual observation using trained hand hygiene auditors and automated measures of opportunities and compliance. Subsequent measured interventions were reminder beeps and written individual feedback.
Results.When compared with manual observations, ultrasound monitoring underestimated percentage compliances by a nonsignificant mean (95% confidence interval [CI]) difference of 5.2% (−20.1% to 9.8%; P = .491). After the intervention, adjusted multivariate analysis showed mean (95% CI) overall compliance in the intervention arm was 6.8% (2.5%−11.1%; P = .002) higher than in the control arm. Results stratified by compliance at entry and exit showed that the effect of intervention was stronger for compliance at exit than at entry.
Conclusions.Our automated measure of hand hygiene compliance is valid when compared with the traditional gold standard of manual observations. As an interventional tool, ultrasound-based automated hand hygiene audits have significant benefit that can be built upon with enhancements and find increasing acceptance with time.
Advanced Functional Graphite-Coated Magnetic Nanoparticles as RF Thermal Ablation Agents for Cancer Therapies
- Yang Xu, Meena Waleed Mahmood, Zhongrui Li, Enkeleda Dervishi, Steve Trigwell, Vladimir P. Zharov, Nawab Ali, Viney Saini, Alexandru R. Biris, Dan Lupu, Alexandru S. Biris
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- Journal:
- MRS Online Proceedings Library Archive / Volume 1138 / 2008
- Published online by Cambridge University Press:
- 01 February 2011, 1138-FF06-15
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- 2008
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Graphitic shells coated ferromagnetic cobalt nanoparticles (C-Co-NPs) with diameters of around 7-9 nm cubic crystalline structures were synthesized by catalytic chemical vapor deposition (CCVD). X-ray diffraction (XRD) and X-ray photoelectron spectroscopy (XPS) analysis indicated that the Co-NPs inside the carbon shells were preserved in the metallic state. Confocal microscope images revealed effective penetrations of C-Co-NPs through plasmatic membranes into the nucleus of the cultured HeLa cancerous cells. Low RF radiation of 350 kHz triggered the cell death, process that was found to be dependent on the NPs concentration and application time. Compared to carbon nanostructures such as single wall carbon nanotubes, super paramagnetic cobalt nanoparticles demonstrated higher specificity for RF absorption and heating. This work indicates a great potential of a new technology for tumor thermal ablation.
Increased Ordering in the Amorphous SiOx due to Hyperthermal Atomic Oxygen.
- Maja Kisa, William G. Stratton, Timothy K. Minton, Klaus van Benthem, Steve J. Pennycook, Paul M. Voyles, Xidong Chen, Long Li, Judith C. Yang
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- Journal:
- MRS Online Proceedings Library Archive / Volume 851 / 2004
- Published online by Cambridge University Press:
- 01 February 2011, NN9.5
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- 2004
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We had studied the effects of hyperthermal (5.1eV) atomic oxygen (AO) on the structural characteristics of the silica layer and Si/SiOx interface formed by the oxidation of Si-single crystal by a variety of microcharacterization techniques. A laser detonation source was used to produce atomic oxygen with 5.1eV kinetic energy. High Resolution Transmission Electron Microscopy (HRTEM) and Selected Area Electron Diffraction (SAED) demonstrated that the silica layer formed on Si(100) by atomic oxygen is thicker, more homogeneous, and less amorphous, compared to the oxide layer created by molecular oxygen (MO). High spatial resolution Electron Energy Loss Spectroscopy (EELS) study confirmed that the Si/SiOx interface created by atomic oxygen is abrupt containing no suboxides as opposed to the broad interface with transitional states formed by molecular oxygen. SAED technique was used to observe sharper diffraction rings present in the diffraction pattern of Si(100) oxidized by reactive atomic oxygen as opposed to the diffused haloes present in the diffraction pattern of Si(100) oxidized by molecular oxygen. Radial Distribution Function (RDF) analyses were performed on the SAED patterns of Si(100) oxidized in atomic and molecular oxygen, indicating that a more ordered oxide is formed by atomic oxygen. Initial Fluctuation Electron Microscopy (FEM) results confirmed an increased medium range ordering in SiOx formed by atomic oxygen when compared to the non-regular arrangement present in the amorphous oxide formed by the oxidation of Si(100) in molecular oxygen.
A Generalized Characterization of Commutators of Parabolic Singular Integrals
- Steve Hofmann, Xinwei Li, Dachun Yang
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- Journal:
- Canadian Mathematical Bulletin / Volume 42 / Issue 4 / 01 December 1999
- Published online by Cambridge University Press:
- 20 November 2018, pp. 463-477
- Print publication:
- 01 December 1999
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Let $x\,=\,\left( {{x}_{1}},\,.\,.\,.\,,\,{{x}_{n}} \right)\,\in \,{{\mathbb{R}}^{n}}$ and ${{\delta }_{\text{ }\!\!\lambda\!\!\text{ }}}x\,=\,\left( {{\text{ }\!\!\lambda\!\!\text{ }}^{{{\alpha }_{1}}}}{{x}_{1}},\,.\,.\,.\,,\,{{\text{ }\!\!\lambda\!\!\text{ }}^{{{\alpha }_{n}}}}{{x}_{n}} \right)$, where $\text{ }\lambda \,>\text{0}$ and $1\,\le \,{{\alpha }_{1}}\,\le \,\cdot \,\cdot \,\cdot \,\le \,{{\alpha }_{n}}$. Denote $\left| \alpha \right|\,=\,{{\alpha }_{1}}+\,\cdot \,\cdot \,\cdot \,+{{\alpha }_{n}}$. We characterize those functions $A\left( x \right)$ for which the parabolic Calderón commutator
1
$$\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,{{T}_{A}}f\left( x \right)\equiv \text{p}\text{.v}\text{.}\int_{{{\mathbb{R}}^{n}}}{K\left( x-y \right)\left[ A\left( x \right)-A\left( y \right) \right]}f\left( y \right)dy$$is bounded on ${{L}^{2}}\left( {{\mathbb{R}}^{n}} \right)$, where $K\left( {{\delta }_{\text{ }\!\!\lambda\!\!\text{ }}}x \right)\,=\,{{\text{ }\!\!\lambda\!\!\text{ }}^{-\,\left| \alpha \right|\,-\,1}}K\left( x \right)$, $K$ is smooth away fromthe origin and satisfies a certain cancellation property.
The Detailed Variation of Boron and Fluorine Profiles with Tilt and Rotation Angles for BF2+ ION Implantation in (100) Silicon
- Puneet Gupta, Changhae Park, Kevin Klein, Shyh-horng Yang, Steve Morris, Vu Do, Al Tasch, Robert Simonton, Gayle Lux
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- Journal:
- MRS Online Proceedings Library Archive / Volume 235 / 1991
- Published online by Cambridge University Press:
- 28 February 2011, 203
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- 1991
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Over 250 boron and over 250 fluorine profiles have been obtained from BF2+ implants over a wide range of implant energies, doses, tilt angles, and rotation angles. A detailed study has been conducted on the boron and fluorine profile variations with the tilt and rotation angles over the available range of energies and doses. Channeling through a few low index axial and planar channels in (100) silicon has been found to account for the observed profile variations with implant angle. Tilt and rotation angle combinations which minimize channeling and ensure process uniformity have been deduced.