Free energy calculations of the interactions of c-Jun-based synthetic peptides with the c-Fos protein

The c-Fos–c-Jun complex forms the activator protein 1 transcription factor, a therapeutic target in the treatment of cancer. Various synthetic peptides have been designed to try to selectively disrupt the interaction between c-Fos and c-Jun at its leucine zipper domain. To evaluate the binding affinity between these synthetic peptides and c-Fos, polarizable and nonpolarizable molecular dynamics (MD) simulations were conducted, and the resulting conformations were analyzed using the molecular mechanics generalized Born surface area (MM/GBSA) method to compute free energies of binding. In contrast to empirical and semiempirical approaches, the estimation of free energies of binding using a combination of MD simulations and the MM/GBSA approach takes into account dynamical properties such as conformational changes, as well as solvation effects and hydrophobic and hydrophilic interactions. The predicted binding affinities of the series of c-Jun-based peptides targeting the c-Fos peptide show good correlation with experimental melting temperatures. This provides the basis for the rational design of peptides based on internal, van der Waals, and electrostatic interactions.

Calculations of the free energy of interaction of the c-Fos−c-Jun coiled coil: Effects of the solvation model and the inclusion of polarization effects

The leucine zipper region of activator protein-1 (AP-1) comprises the c-Jun and c-Fos proteins and constitutes a well-known coiled coil protein−protein interaction motif. We have used molecular dynamics (MD) simulations in conjunction with the molecular mechanics/Poisson−Boltzmann generalized-Born surface area [MM/PB(GB)SA] methods to predict the free energy of interaction of these proteins. In particular, the influence of the choice of solvation model, protein force field, and water potential on the stability and dynamic properties of the c-Fos−c-Jun complex were investigated. Use of the AMBER polarizable force field ff02 in combination with the polarizable POL3 water potential was found to result in increased stability of the c-Fos−c-Jun complex. MM/PB(GB)SA calculations revealed that MD simulations using the POL3 water potential give the lowest predicted free energies of interaction compared to other nonpolarizable water potentials. In addition, the calculated absolute free energy of binding was predicted to be closest to the experimental value using the MM/GBSA method with independent MD simulation trajectories using the POL3 water potential and the polarizable ff02 force field, while all other binding affinities were overestimated.

A hybrid agent architecture for modeling autonomous agents in SAGE

This paper highlights the Hybrid agent construction model being developed that allows the description and development of autonomous agents in SAGE (Scalable, fault Tolerant Agent Grooming Environment) - a second generation FIPA-Compliant Multi-Agent system. We aim to provide the programmer with a generic and well defined agent architecture enabling the development of sophisticated agents on SAGE, possessing the desired properties of autonomous agents - reactivity, pro-activity, social ability and knowledge based reasoning. © Springer-Verlag Berlin Heidelberg 2005.

A germanium/single-walled carbon nanotube composite paper as a free-standing anode for lithium-ion batteries

Paper-like free-standing germanium (Ge) and single-walled carbon nanotube (SWCNT) composite anodes were synthesized by the vacuum filtration of Ge/SWCNT composites, which were prepared by a facile aqueous-based method. The samples were characterized by X-ray diffraction, field emission scanning electron microscopy, and transmission electron microscopy. Electrochemical measurements demonstrate that the Ge/SWCNT composite paper anode with the weight percentage of 32% Ge delivered a specific discharge capacity of 417 mA h g-1 after 40 cycles at a current density of 25 mA g-1, 117% higher than the pure SWCNT paper anode. The SWCNTs not only function as a flexible mechanical support for strain release, but also provide excellent electrically conducting channels, while the nanosized Ge particles contribute to improving the discharge capacity of the paper anode.

3D hierarchical rutile TiO2 and metal-free organic sensitizer producing dye-sensitized solar cells 8.6% conversion efficiency

Three-dimensional (3D) hierarchical nanoscale architectures comprised of building blocks, with specifically engineered morphologies, are expected to play important roles in the fabrication of 'next generation' microelectronic and optoelectronic devices due to their high surface-to-volume ratio as well as opto-electronic properties. Herein, a series of well-defined 3D hierarchical rutile TiO2 architectures (HRT) were successfully prepared using a facile hydrothermal method without any surfactant or template, simply by changing the concentration of hydrochloric acid used in the synthesis. The production of these materials provides, to the best of our knowledge, the first identified example of a ledgewise growth mechanism in a rutile TiO2 structure. Also for the first time, a Dye-sensitized Solar Cell (DSC) combining a HRT is reported in conjunction with a high-extinction-coefficient metal-free organic sensitizer (D149), achieving a conversion efficiency of 5.5%, which is superior to ones employing P25 (4.5%), comparable to state-of-the-art commercial transparent titania anatase paste (5.8%). Further to this, an overall conversion efficiency 8.6% was achieved when HRT was used as the light scattering layer, a considerable improvement over the commercial transparent/reflector titania anatase paste (7.6%), a significantly smaller gap in performance than has been seen previously.

Architecture designed ZnO hollow microspheres with wide-range visible-light photoresponses

It is a challenge to increase the visible-light photoresponses of wide-gap metal oxides. In this study, we proposed a new strategy to enhance the visible-light photoresponses of wide-gap semiconductors by deliberately designing a multi-scale nanostructure with controlled architecture. Hollow ZnO microspheres with constituent units in the shape of one-dimensional (1D) nanowire networks, 2D nanosheet stacks, and 3D mesoporous nanoball blocks are synthesized via an approach of two-step assembly, where the oligomers or the constituent nanostructures with specially designed structures are first formed, and then further assembled into complex morphologies. Through deliberate designing of constituent architectures allowing multiple visible-light scattering, reflections, and dispersion inside the multiscale nanostructures, enhanced wide range visible-light photoresponses of the ZnO hollow microspheres were successfully achieved. Compared to the one-step synthesized ZnO hollow microspheres, where no nanostructured constituents were produced, the ZnO hollow microspheres with 2D nanosheet stacks presented a 50 times higher photocurrent in the visible-light range (λ > 420 nm). The nanostructure induced visible-light photoresponse enhancement gives a direction to the development of novel photosensitive materials.

Organic–inorganic bismuth (III)-based material: A lead-free, air-stable and solution-processable light-absorber beyond organolead perovskites

Methylammonium bismuth (III) iodide single crystals and films have been developed and investigated. We have further presented the first demonstration of using this organic–inorganic bismuth-based material to replace lead/tin-based perovskite materials in solution-processable solar cells. The organic–inorganic bismuth-based material has advantages of non-toxicity, ambient stability, and low-temperature solution-processability, which provides a promising solution to address the toxicity and stability challenges in organolead- and organotin-based perovskite solar cells. We also demonstrated that trivalent metal cation-based organic–inorganic hybrid materials can exhibit photovoltaic effect, which may inspire more research work on developing and applying organic-inorganic hybrid materials beyond divalent metal cations (Pb (II) and Sn (II)) for solar energy applications.

Geometry-free stochastic analysis of BDS triple frequency signals

The paper presents a geometry-free approach to assess the variation of covariance matrices of undifferenced triple frequency GNSS measurements and its impact on positioning solutions. Four independent geometryfree/ ionosphere-free (GFIF) models formed from original triple-frequency code and phase signals allow for effective computation of variance-covariance matrices using real data. Variance Component Estimation (VCE) algorithms are implemented to obtain the covariance matrices for three pseudorange and three carrier-phase signals epoch-by-epoch. Covariance results from the triple frequency Beidou System (BDS) and GPS data sets demonstrate that the estimated standard deviation varies in consistence with the amplitude of actual GFIF error time series. The single point positioning (SPP) results from BDS ionosphere-free measurements at four MGEX stations demonstrate an improvement of up to about 50% in Up direction relative to the results based on a mean square statistics. Additionally, a more extensive SPP analysis at 95 global MGEX stations based on GPS ionosphere-free measurements shows an average improvement of about 10% relative to the traditional results. This finding provides a preliminary confirmation that adequate consideration of the variation of covariance leads to the improvement of GNSS state solutions.

DIY/DIWO media architecture: The InstaBooth

Building on previous discourse regarding the ability of media architecture to be more open and accessible for the purposes of community engagement (Caldwell & Foth, 2014), this chapter explores a particular case study that was designed, constructed and implemented with the intention of allowing city users to participate in the development and creation of media architecture, the InstaBooth. In this chapter, we first explore DIY (do it yourself) and DIWO (do it with others) phenomena to examine what motivates the DIY cultures, communities, and practices. Secondly, in this chapter, we define and discuss our implementation of a DIY / DIWO media architecture example, the InstaBooth. The InstaBooth project pro-vides an opportunity to question the effectiveness of a DIY driven media architec-ture artefact to see to what extent it impacts on the experience of its users and for what benefit.

Scopophobia/Scopophilia: electric light and the anxiety of the gaze in postwar American architecture

In the years of reconstruction and economic boom that followed the Second World War, the domestic sphere encountered new expectations regarding social behaviour, modes of living, and forms of dwelling. This book brings together an international group of scholars from architecture, design, urban planning, and interior design to reappraise mid-twentieth century modern life, offering a timely reassessment of culture and the economic and political effects on civilian life. This collection contains essays that examine the material of art, objects, and spaces in the context of practices of dwelling over the long span of the postwar period. It asks what role material objects, interior spaces, and architecture played in quelling or fanning the anxieties of modernism’s ordinary denizens, and how this role informs their legacy today. Table of Contents [Book] Introduction Robin Schuldenfrei Part 1: Psychological Constructions: Anxiety of Isolation and Exposure 1. Taking Comfort in the Age of Anxiety: Eero Saarinen’s Womb Chair Cammie McAtee 2. The Future is Possibly Past: The Anxious Spaces of Gaetano Pesce Jane Pavitt 3. Scopophobia/Scopophilia: Electric Light and the Anxiety of the Gaze in American Postwar Domestic Architecture Margaret Petty Part 2: Ideological Objects: Design and Representation 4. The Allegory of the Socialist Lifestyle: The Czechoslovak Pavilion at the Brussels Expo, its Gold Medal and the Politburo Ana Miljacki 5. Assimilating Unease: Moholy-Nagy and the Wartime-Postwar Bauhaus in Chicago Robin Schuldenfrei 6. The Anxieties of Autonomy: Peter Eisenman from Cambridge to House VI Sean Keller Part 3: Societies of Consumers: Materialist Ideologies and Postwar Goods 7. "But a home is not a laboratory": The Anxieties of Designing for the Socialist Home in the German Democratic Republic 1950—1965 Katharina Pfützner 8. Architect-designed Interiors for a Culturally Progressive Upper-Middle Class: The Implicit Political Presence of Knoll International in Belgium Fredie Floré 9. Domestic Environment: Italian Neo-Avant-Garde Design and the Politics of Post-Materialism Mary Louise Lobsinger Part 4: Class Concerns and Conflict: Dwelling and Politics 10. Dirt and Disorder: Taste and Anxiety in the Working Class Home Christine Atha 11. Upper West Side Stories: Race, Liberalism, and Narratives of Urban Renewal in Postwar New York Jennifer Hock 12. Pawns or Prophets? Postwar Architects and Utopian Designs for Southern Italy Anne Parmly Toxey. Coda: From Homelessness to Homelessness David Crowley

Heritability of the network architecture of intrinsic brain functional connectivity

The brain's functional network exhibits many features facilitating functional specialization, integration, and robustness to attack. Using graph theory to characterize brain networks, studies demonstrate their small-world, modular, and "rich-club" properties, with deviations reported in many common neuropathological conditions. Here we estimate the heritability of five widely used graph theoretical metrics (mean clustering coefficient (γ), modularity (Q), rich-club coefficient (ϕnorm), global efficiency (λ), small-worldness (σ)) over a range of connection densities (k=5-25%) in a large cohort of twins (N=592, 84 MZ and 89 DZ twin pairs, 246 single twins, age 23±2.5). We also considered the effects of global signal regression (GSR). We found that the graph metrics were moderately influenced by genetic factors h2 (γ=47-59%, Q=38-59%, ϕnorm=0-29%, λ=52-64%, σ=51-59%) at lower connection densities (≤15%), and when global signal regression was implemented, heritability estimates decreased substantially h2 (γ=0-26%, Q=0-28%, ϕnorm=0%, λ=23-30%, σ=0-27%). Distinct network features were phenotypically correlated (|r|=0.15-0.81), and γ, Q, and λ were found to be influenced by overlapping genetic factors. Our findings suggest that these metrics may be potential endophenotypes for psychiatric disease and suitable for genetic association studies, but that genetic effects must be interpreted with respect to methodological choices.

Free software and the law. Out of the frying pan and into the fire: How shaking up intellectual property suits competition law just fine

Free software is viewed as a revolutionary and subversive practice, and in particular has dealt a strong blow to the traditional conception of intellectual property law (although in its current form could be considered a 'hack' of IP rights). However, other (capitalist) areas of law have been swift to embrace free software, or at least incorporate it into its own tenets. One area in particular is that of competition (antitrust) law, which itself has long been in theoretical conflict with intellectual property, due to the restriction on competition inherent in the grant of ‘monopoly’ rights by copyrights, patents and trademarks. This contribution will examine how competition law has approached free software by examining instances in which courts have had to deal with such initiatives, for instance in the Oracle Sun Systems merger, and the implications that these decisions have on free software initiatives. The presence or absence of corporate involvement in initiatives will be an important factor in this investigation, with it being posited that true instances of ‘commons-based peer production’ can still subvert the capitalist system, including perplexing its laws beyond intellectual property.

Internet privatization, WikiLeaks, and free expression

In late 2010, the online nonprofit media organization WikiLeaks published classified documents detailing correspondence between the U.S. State Department and its diplomatic missions around the world, numbering around 250,000 cables. These diplomatic cables contained classified information with comments on world leaders, foreign states, and various international and domestic issues. Negative reactions to the publication of these cables came from both the U.S. political class (which was generally condemnatory of WikiLeaks, invoking national security concerns and the jeopardizing of U.S. interests abroad) and the corporate world, with various companies ceasing to continue to provide services to WikiLeaks despite no legal measure (e.g., a court injunction) forcing them to do so. This article focuses on the legal remedies available to WikiLeaks against this corporate suppression of its speech in the U.S. and Europe since these are the two principle arenas in which the actors concerned are operating. The transatlantic legal protection of free expression will be considered, yet, as will be explained in greater detail, the legal conception of this constitutional and fundamental right comes from a time when the state posed the greater threat to freedom. As a result, it is not generally enforceable against private, non-state entities interfering with speech and expression which is the case here. Other areas of law, namely antitrust/competition, contract and tort will then be examined to determine whether WikiLeaks and its partners can attempt to enforce their right indirectly through these other means. Finally, there will be some concluding thoughts about the implications of the corporate response to the WikiLeaks embassy cables leak for freedom of expression online.

Blurring the physical boundaries of the city: Media architecture and urban informatics for community engagement

Architecture focuses on designing built environments in response to society’s needs, reflecting culture through materials and forms. The physical boundaries of the city have become blurred through the integration of digital media, connecting the physical environment with the digital. In the recent past the future was imagined as highly technological; 1982 Ridley Scott’s Blade Runner is set in 2019 and introduces a world where supersized screens inject advertisements in the cluttered urban space. Now, in 2015 screens are central to everyday life, but in a completely different way in respect to what had been imagined. Through ubiquitous computing and social media, information is abundant. Digital technologies have changed the way people relate to cities supporting discussion on multiple levels, allowing citizens to be more vocal than ever before. We question how architects can use the affordances of urban informatics to obtain and navigate useful social information to inform design. This chapter investigates different approaches to engage communities in the debate on cities, in particular it aims to capture citizens’ opinions on the use and design of public places. Physical and digital discussions have been initiated to capture citizens’ opinions on the use and design of public places. In addition to traditional consultation methods, Web 2.0 platforms, urban screens, and mobile apps are used in the context of Brisbane, Australia to explore contemporary strategies of engagement (Gray 2014).