Matching Items (67)
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In July 2012, the Indonesian Minister of Communication and Information, Tifatul Sembiring, declared that the government had shut down one million websites in view of the Islamic holy month of Ramadhan. This was in addition to another one million sites the ministry claimed to have blocked back in February 2012.

In July 2012, the Indonesian Minister of Communication and Information, Tifatul Sembiring, declared that the government had shut down one million websites in view of the Islamic holy month of Ramadhan. This was in addition to another one million sites the ministry claimed to have blocked back in February 2012. Minister Sembiring, a politician from the Islamic-based Partai Keadilan Sejahtera (Prosperous Justice Party, PKS), said that his staff would continue blocking access to online pornography beyond the holy month.

Created2013
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The similarity attraction hypothesis posits that humans are drawn toward others who behave and appear similar to themselves. Two experiments examined this hypothesis with middle-school students learning electrical circuit analysis in a computer-based environment with an Animated Pedagogical Agent (APA). Experiment 1 was designed to determine whether matching the gender

The similarity attraction hypothesis posits that humans are drawn toward others who behave and appear similar to themselves. Two experiments examined this hypothesis with middle-school students learning electrical circuit analysis in a computer-based environment with an Animated Pedagogical Agent (APA). Experiment 1 was designed to determine whether matching the gender of the APA to the student has a positive impact on learning outcomes or student perceptions. One hundred ninety-seven middle-school students learned with the computer-based environment using an APA that matched their gender or one which was opposite in gender. Female students reported higher program ratings when the APA matched their gender. Male students, on the other hand, reported higher program ratings than females when the APA did not match their gender. Experiment 2 systematically tested the impact of providing learners the choice among four APAs on learning outcomes and student perceptions. Three hundred thirty-four middle-school students received either a pre-assigned random APA or were free to choose from four APA options: young male agent, older male agent, young female agent, or older female agent. Learners had higher far transfer scores when provided a choice of animated agent, but student perceptions were not impacted by having the ability to make this choice. We suggest that offering students learner control positively impacts student motivation and learning by increasing student perceptions of autonomy, responsibility for the success of the instructional materials, and global satisfaction with the design of materials.

ContributorsOzogul, Gamze (Author) / Johnson, Amy (Author) / Atkinson, Robert (Author) / Reisslein, Martin (Author) / ASU-SFI Center for Biosocial Complex Systems (Contributor)
Created2013-09-12
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As part of a larger trend across industrialized nations, European research policy discourse has placed increasing emphasis on socio-technical integration: the explicit incorporation of activities devoted to broader social aspects into scientific activities. In order to compare these high-level integration discourses against patterns at the level of resource allocation, we

As part of a larger trend across industrialized nations, European research policy discourse has placed increasing emphasis on socio-technical integration: the explicit incorporation of activities devoted to broader social aspects into scientific activities. In order to compare these high-level integration discourses against patterns at the level of resource allocation, we analyze nearly 2500 research solicitations from the three European Framework Programmes for R&D during the period 1998-2010. We identify four distinct types of integration (socio-ethical, stakeholder, socio-economic and industrial) that occur either as core or parallel components of R&D solicitations. Quantitative analysis reveals an overall trend towards increasing integration, with requests integrating industrial and socio-economic aspects substantially outnumbering those integrating socio-ethical and stakeholder aspects-by a 2 to 1 margin. Meanwhile, calls for socio-technical integration have become slightly more extensive (ranging across a broader range of research areas addressed), significantly more pervasive (shifting from the periphery to the core of R&D practices), and arguably less diverse (involving a wider variety of integration types) over time. The relative lack of attention to socio-ethical aspects and stakeholder participation in European research is particularly notable given that we focus on potentially controversial areas (life sciences, energy, and nanotechnology), which likely overemphasizes the prevalence of integration throughout the Framework Programmes.

Created2013-08-15
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Description
Single-particle diffraction from X-ray Free Electron Lasers offers the potential for molecular structure determination without the need for crystallization. In an effort to further develop the technique, we present a dataset of coherent soft X-ray diffraction images of Coliphage PR772 virus, collected at the Atomic Molecular Optics (AMO) beamline with

Single-particle diffraction from X-ray Free Electron Lasers offers the potential for molecular structure determination without the need for crystallization. In an effort to further develop the technique, we present a dataset of coherent soft X-ray diffraction images of Coliphage PR772 virus, collected at the Atomic Molecular Optics (AMO) beamline with pnCCD detectors in the LAMP instrument at the Linac Coherent Light Source. The diameter of PR772 ranges from 65–70 nm, which is considerably smaller than the previously reported ~600 nm diameter Mimivirus. This reflects continued progress in XFEL-based single-particle imaging towards the single molecular imaging regime. The data set contains significantly more single particle hits than collected in previous experiments, enabling the development of improved statistical analysis, reconstruction algorithms, and quantitative metrics to determine resolution and self-consistency.
ContributorsReddy, Hemanth K. N. (Author) / Yoon, Chun Hong (Author) / Aquila, Andrew (Author) / Awel, Salah (Author) / Ayyer, Kartik (Author) / Barty, Anton (Author) / Berntsen, Peter (Author) / Bielecki, Johan (Author) / Bobkov, Sergey (Author) / Bucher, Maximilian (Author) / Carini, Gabriella A. (Author) / Carron, Sebastian (Author) / Chapman, Henry (Author) / Daurer, Benedikt (Author) / DeMirci, Hasan (Author) / Ekeberg, Tomas (Author) / Fromme, Petra (Author) / Hajdu, Janos (Author) / Hanke, Max Felix (Author) / Hart, Philip (Author) / Hogue, Brenda (Author) / Hasseinizadeh, Ahmad (Author) / Kim, Yoonhee (Author) / Kirian, Richard (Author) / Kurta, Ruslan P. (Author) / Larsson, Daniel S. D. (Author) / Loh, N. Duane (Author) / Maia, Filipe R. N. C. (Author) / Mancuso, Adrian P. (Author) / Muhlig, Kerstin (Author) / Munke, Anna (Author) / Nam, Daewoong (Author) / Nettelblad, Carl (Author) / Ourmazd, Abbas (Author) / Rose, Max (Author) / Schwander, Peter (Author) / Seibert, Marvin (Author) / Sellberg, Jonas A. (Author) / Song, Changyong (Author) / Spence, John (Author) / Svenda, Martin (Author) / van der Schot, Gijs (Author) / Vartanyants, Ivan A. (Author) / Williams, Garth J. (Author) / Xavier, P. Lourdu (Author) / ASU Biodesign Center Immunotherapy, Vaccines and Virotherapy (Contributor) / Biodesign Institute (Contributor) / Applied Structural Discovery (Contributor) / College of Liberal Arts and Sciences (Contributor) / School of Molecular Sciences (Contributor) / School of Life Sciences (Contributor) / Department of Physics (Contributor)
Created2017-06-27
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Description
Crystal structure determination of biological macromolecules using the novel technique of serial femtosecond crystallography (SFX) is severely limited by the scarcity of X-ray free-electron laser (XFEL) sources. However, recent and future upgrades render microfocus beamlines at synchrotron-radiation sources suitable for room-temperature serial crystallography data collection also. Owing to the longer

Crystal structure determination of biological macromolecules using the novel technique of serial femtosecond crystallography (SFX) is severely limited by the scarcity of X-ray free-electron laser (XFEL) sources. However, recent and future upgrades render microfocus beamlines at synchrotron-radiation sources suitable for room-temperature serial crystallography data collection also. Owing to the longer exposure times that are needed at synchrotrons, serial data collection is termed serial millisecond crystallography (SMX). As a result, the number of SMX experiments is growing rapidly, with a dozen experiments reported so far. Here, the first high-viscosity injector-based SMX experiments carried out at a US synchrotron source, the Advanced Photon Source (APS), are reported. Microcrystals (5–20 µm) of a wide variety of proteins, including lysozyme, thaumatin, phycocyanin, the human A[subscript 2A] adenosine receptor (A[subscript 2A]AR), the soluble fragment of the membrane lipoprotein Flpp3 and proteinase K, were screened. Crystals suspended in lipidic cubic phase (LCP) or a high-molecular-weight poly(ethylene oxide) (PEO; molecular weight 8 000 000) were delivered to the beam using a high-viscosity injector. In-house data-reduction (hit-finding) software developed at APS as well as the SFX data-reduction and analysis software suites Cheetah and CrystFEL enabled efficient on-site SMX data monitoring, reduction and processing. Complete data sets were collected for A[subscript 2A]AR, phycocyanin, Flpp3, proteinase K and lysozyme, and the structures of A[subscript 2A]AR, phycocyanin, proteinase K and lysozyme were determined at 3.2, 3.1, 2.65 and 2.05 Å resolution, respectively. The data demonstrate the feasibility of serial millisecond crystallography from 5–20 µm crystals using a high-viscosity injector at APS. The resolution of the crystal structures obtained in this study was dictated by the current flux density and crystal size, but upcoming developments in beamline optics and the planned APS-U upgrade will increase the intensity by two orders of magnitude. These developments will enable structure determination from smaller and/or weakly diffracting microcrystals.
ContributorsMartin Garcia, Jose Manuel (Author) / Conrad, Chelsie (Author) / Nelson, Garrett (Author) / Stander, Natasha (Author) / Zatsepin, Nadia (Author) / Zook, James (Author) / Zhu, Lan (Author) / Geiger, James (Author) / Chun, Eugene (Author) / Kissick, David (Author) / Hilgart, Mark C. (Author) / Ogata, Craig (Author) / Ishchenko, Andrii (Author) / Nagaratnam, Nirupa (Author) / Roy Chowdhury, Shatabdi (Author) / Coe, Jesse (Author) / Subramanian, Ganesh (Author) / Schaffer, Alexander (Author) / James, Daniel (Author) / Ketwala, Gihan (Author) / Venugopalan, Nagarajan (Author) / Xu, Shenglan (Author) / Corcoran, Stephen (Author) / Ferguson, Dale (Author) / Weierstall, Uwe (Author) / Spence, John (Author) / Cherezov, Vadim (Author) / Fromme, Petra (Author) / Fischetti, Robert F. (Author) / Liu, Wei (Author) / College of Liberal Arts and Sciences (Contributor) / School of Molecular Sciences (Contributor) / Biodesign Institute (Contributor) / Applied Structural Discovery (Contributor) / Department of Physics (Contributor)
Created2017-05-24
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Description
CTB-MPR is a fusion protein between the B subunit of cholera toxin (CTB) and the membrane-proximal region of gp41 (MPR), the transmembrane envelope protein of Human immunodeficiency virus 1 (HIV-1), and has previously been shown to induce the production of anti-HIV-1 antibodies with antiviral functions. To further improve the design

CTB-MPR is a fusion protein between the B subunit of cholera toxin (CTB) and the membrane-proximal region of gp41 (MPR), the transmembrane envelope protein of Human immunodeficiency virus 1 (HIV-1), and has previously been shown to induce the production of anti-HIV-1 antibodies with antiviral functions. To further improve the design of this candidate vaccine, X-ray crystallography experiments were performed to obtain structural information about this fusion protein. Several variants of CTB-MPR were designed, constructed and recombinantly expressed in Escherichia coli. The first variant contained a flexible GPGP linker between CTB and MPR, and yielded crystals that diffracted to a resolution of 2.3 Å, but only the CTB region was detected in the electron-density map. A second variant, in which the CTB was directly attached to MPR, was shown to destabilize pentamer formation. A third construct containing a polyalanine linker between CTB and MPR proved to stabilize the pentameric form of the protein during purification. The purification procedure was shown to produce a homogeneously pure and monodisperse sample for crystallization. Initial crystallization experiments led to pseudo-crystals which were ordered in only two dimensions and were disordered in the third dimension. Nanocrystals obtained using the same precipitant showed promising X-ray diffraction to 5 Å resolution in femtosecond nanocrystallography experiments at the Linac Coherent Light Source at the SLAC National Accelerator Laboratory. The results demonstrate the utility of femtosecond X-ray crystallography to enable structural analysis based on nano/microcrystals of a protein for which no macroscopic crystals ordered in three dimensions have been observed before.
ContributorsLee, Ho-Hsien (Author) / Cherni, Irene (Author) / Yu, HongQi (Author) / Fromme, Raimund (Author) / Doran, Jeffrey (Author) / Grotjohann, Ingo (Author) / Mittman, Michele (Author) / Basu, Shibom (Author) / Deb, Arpan (Author) / Dorner, Katerina (Author) / Aquila, Andrew (Author) / Barty, Anton (Author) / Boutet, Sebastien (Author) / Chapman, Henry N. (Author) / Doak, R. Bruce (Author) / Hunter, Mark (Author) / James, Daniel (Author) / Kirian, Richard (Author) / Kupitz, Christopher (Author) / Lawrence, Robert (Author) / Liu, Haiguang (Author) / Nass, Karol (Author) / Schlichting, Ilme (Author) / Schmidt, Kevin (Author) / Seibert, M. Marvin (Author) / Shoeman, Robert L. (Author) / Spence, John (Author) / Stellato, Francesco (Author) / Weierstall, Uwe (Author) / Williams, Garth J. (Author) / Yoon, Chun Hong (Author) / Wang, Dingjie (Author) / Zatsepin, Nadia (Author) / Hogue, Brenda (Author) / Matoba, Nobuyuki (Author) / Fromme, Petra (Author) / Mor, Tsafrir (Author) / ASU Biodesign Center Immunotherapy, Vaccines and Virotherapy (Contributor) / Department of Chemistry and Biochemistry (Contributor) / College of Liberal Arts and Sciences (Contributor) / School of Life Sciences (Contributor) / Biodesign Institute (Contributor) / Infectious Diseases and Vaccinology (Contributor) / Department of Physics (Contributor)
Created2014-08-20
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Open-ended evolution (OEE) is relevant to a variety of biological, artificial and technological systems, but has been challenging to reproduce in silico. Most theoretical efforts focus on key aspects of open-ended evolution as it appears in biology. We recast the problem as a more general one in dynamical systems theory,

Open-ended evolution (OEE) is relevant to a variety of biological, artificial and technological systems, but has been challenging to reproduce in silico. Most theoretical efforts focus on key aspects of open-ended evolution as it appears in biology. We recast the problem as a more general one in dynamical systems theory, providing simple criteria for open-ended evolution based on two hallmark features: unbounded evolution and innovation. We define unbounded evolution as patterns that are non-repeating within the expected Poincare recurrence time of an isolated system, and innovation as trajectories not observed in isolated systems. As a case study, we implement novel variants of cellular automata (CA) where the update rules are allowed to vary with time in three alternative ways. Each is capable of generating conditions for open-ended evolution, but vary in their ability to do so. We find that state-dependent dynamics, regarded as a hallmark of life, statistically out-performs other candidate mechanisms, and is the only mechanism to produce open-ended evolution in a scalable manner, essential to the notion of ongoing evolution. This analysis suggests a new framework for unifying mechanisms for generating OEE with features distinctive to life and its artifacts, with broad applicability to biological and artificial systems.
Created2017-04-20
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The advent and application of the X-ray free-electron laser (XFEL) has uncovered the structures of proteins that could not previously be solved using traditional crystallography. While this new technology is powerful, optimization of the process is still needed to improve data quality and analysis efficiency. One area is sample heterogeneity,

The advent and application of the X-ray free-electron laser (XFEL) has uncovered the structures of proteins that could not previously be solved using traditional crystallography. While this new technology is powerful, optimization of the process is still needed to improve data quality and analysis efficiency. One area is sample heterogeneity, where variations in crystal size (among other factors) lead to the requirement of large data sets (and thus 10–100 mg of protein) for determining accurate structure factors. To decrease sample dispersity, we developed a high-throughput microfluidic sorter operating on the principle of dielectrophoresis, whereby polydisperse particles can be transported into various fluid streams for size fractionation. Using this microsorter, we isolated several milliliters of photosystem I nanocrystal fractions ranging from 200 to 600 nm in size as characterized by dynamic light scattering, nanoparticle tracking, and electron microscopy. Sorted nanocrystals were delivered in a liquid jet via the gas dynamic virtual nozzle into the path of the XFEL at the Linac Coherent Light Source. We obtained diffraction to ∼4 Å resolution, indicating that the small crystals were not damaged by the sorting process. We also observed the shape transforms of photosystem I nanocrystals, demonstrating that our device can optimize data collection for the shape transform-based phasing method. Using simulations, we show that narrow crystal size distributions can significantly improve merged data quality in serial crystallography. From this proof-of-concept work, we expect that the automated size-sorting of protein crystals will become an important step for sample production by reducing the amount of protein needed for a high quality final structure and the development of novel phasing methods that exploit inter-Bragg reflection intensities or use variations in beam intensity for radiation damage-induced phasing. This method will also permit an analysis of the dependence of crystal quality on crystal size.
ContributorsAbdallah, Bahige (Author) / Zatsepin, Nadia (Author) / Roy Chowdhury, Shatabdi (Author) / Coe, Jesse (Author) / Conrad, Chelsie (Author) / Dorner, Katerina (Author) / Sierra, Raymond G. (Author) / Stevenson, Hilary P. (Author) / Camacho Alanis, Fernanda (Author) / Grant, Thomas D. (Author) / Nelson, Garrett (Author) / James, Daniel (Author) / Calero, Guillermo (Author) / Wachter, Rebekka (Author) / Spence, John (Author) / Weierstall, Uwe (Author) / Fromme, Petra (Author) / Ros, Alexandra (Author) / Department of Chemistry and Biochemistry (Contributor) / College of Liberal Arts and Sciences (Contributor) / School of Molecular Sciences (Contributor) / Biodesign Institute (Contributor) / Applied Structural Discovery (Contributor) / Department of Physics (Contributor)
Created2015-08-19
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Description
Serial femtosecond crystallography (SFX) takes advantage of extremely bright and ultrashort pulses produced by x-ray free-electron lasers (XFELs), allowing for the collection of high-resolution diffraction intensities from micrometer-sized crystals at room temperature with minimal radiation damage, using the principle of “diffraction-before-destruction.” However, de novo structure factor phase determination using XFELs

Serial femtosecond crystallography (SFX) takes advantage of extremely bright and ultrashort pulses produced by x-ray free-electron lasers (XFELs), allowing for the collection of high-resolution diffraction intensities from micrometer-sized crystals at room temperature with minimal radiation damage, using the principle of “diffraction-before-destruction.” However, de novo structure factor phase determination using XFELs has been difficult so far. We demonstrate the ability to solve the crystallographic phase problem for SFX data collected with an XFEL using the anomalous signal from native sulfur atoms, leading to a bias-free room temperature structure of the human A[subscript 2A] adenosine receptor at 1.9 Å resolution. The advancement was made possible by recent improvements in SFX data analysis and the design of injectors and delivery media for streaming hydrated microcrystals. This general method should accelerate structural studies of novel difficult-to-crystallize macromolecules and their complexes.
ContributorsBatyuk, Alexander (Author) / Galli, Lorenzo (Author) / Ishchenko, Andrii (Author) / Han, Gye Won (Author) / Gati, Cornelius (Author) / Popov, Petr A. (Author) / Lee, Ming-Yue (Author) / Stauch, Benjamin (Author) / White, Thomas A. (Author) / Barty, Anton (Author) / Aquila, Andrew (Author) / Hunter, Mark S. (Author) / Liang, Mengning (Author) / Boutet, Sebastien (Author) / Pu, Mengchen (Author) / Liu, Zhi-jie (Author) / Nelson, Garrett (Author) / James, Daniel (Author) / Li, Chufeng (Author) / Zhao, Yun (Author) / Spence, John (Author) / Liu, Wei (Author) / Fromme, Petra (Author) / Katritch, Vsevolod (Author) / Weierstall, Uwe (Author) / Stevens, Raymond C. (Author) / Cherezov, Vadim (Author) / College of Liberal Arts and Sciences (Contributor) / Department of Physics (Contributor) / Biodesign Institute (Contributor) / Applied Structural Discovery (Contributor) / School of Molecular Sciences (Contributor)
Created2016-09-23
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Description
Mix-and-inject serial crystallography (MISC) is a technique designed to image enzyme catalyzed reactions in which small protein crystals are mixed with a substrate just prior to being probed by an X-ray pulse. This approach offers several advantages over flow cell studies. It provides (i) room temperature structures at near atomic

Mix-and-inject serial crystallography (MISC) is a technique designed to image enzyme catalyzed reactions in which small protein crystals are mixed with a substrate just prior to being probed by an X-ray pulse. This approach offers several advantages over flow cell studies. It provides (i) room temperature structures at near atomic resolution, (ii) time resolution ranging from microseconds to seconds, and (iii) convenient reaction initiation. It outruns radiation damage by using femtosecond X-ray pulses allowing damage and chemistry to be separated. Here, we demonstrate that MISC is feasible at an X-ray free electron laser by studying the reaction of M. tuberculosis ß-lactamase microcrystals with ceftriaxone antibiotic solution. Electron density maps of the apo-ß-lactamase and of the ceftriaxone bound form were obtained at 2.8 Å and 2.4 Å resolution, respectively. These results pave the way to study cyclic and non-cyclic reactions and represent a new field of time-resolved structural dynamics for numerous substrate-triggered biological reactions.
ContributorsKupitz, Christopher (Author) / Olmos, Jose L. (Author) / Holl, Mark (Author) / Tremblay, Lee (Author) / Pande, Kanupriya (Author) / Pandey, Suraj (Author) / Oberthur, Dominik (Author) / Hunter, Mark (Author) / Liang, Mengning (Author) / Aquila, Andrew (Author) / Tenboer, Jason (Author) / Calvey, George (Author) / Katz, Andrea (Author) / Chen, Yujie (Author) / Wiedorn, Max O. (Author) / Knoska, Juraj (Author) / Meents, Alke (Author) / Majriani, Valerio (Author) / Norwood, Tyler (Author) / Poudyal, Ishwor (Author) / Grant, Thomas (Author) / Miller, Mitchell D. (Author) / Xu, Weijun (Author) / Tolstikova, Aleksandra (Author) / Morgan, Andrew (Author) / Metz, Markus (Author) / Martin Garcia, Jose Manuel (Author) / Zook, James (Author) / Roy Chowdhury, Shatabdi (Author) / Coe, Jesse (Author) / Nagaratnam, Nirupa (Author) / Meza-Aguilar, Domingo (Author) / Fromme, Raimund (Author) / Basu, Shibom (Author) / Frank, Matthias (Author) / White, Thomas (Author) / Barty, Anton (Author) / Bajt, Sasa (Author) / Yefanov, Oleksandr (Author) / Chapman, Henry N. (Author) / Zatsepin, Nadia (Author) / Nelson, Garrett (Author) / Weierstall, Uwe (Author) / Spence, John (Author) / Schwander, Peter (Author) / Pollack, Lois (Author) / Fromme, Petra (Author) / Ourmazd, Abbas (Author) / Phillips, George N. (Author) / Schmidt, Marius (Author) / College of Liberal Arts and Sciences (Contributor) / Department of Physics (Contributor) / School of Molecular Sciences (Contributor) / Biodesign Institute (Contributor) / Applied Structural Discovery (Contributor)
Created2016-12-15