Computational Challenges in High-Resolution Cryo-Electron Microscopy

To avoid the challenges of crystallization and the size limitations of NMR, it has long been hoped that single-particle cryo-electron microscopy (cryo-EM) would eventually yield atomically interpretable reconstructions. For the most favorable class of specimens (large icosahedral viruses), two of the key obstacles are the large computational requirements of high-resolution reconstructions and the curvature of the Ewald sphere, which leads to a breakdown of the projection theorem used by conventional 3D reconstruction programs. Here, two solutions to these obstacles are presented. First, a simple distributed processing system named Peach was developed to meet the rising computational demands of modern structural biology (and other) laboratories without additional expense by using existing hardware resources more efficiently. A central server distributes jobs to idle workstations in such a way that each computer is used maximally, but without disturbing intermittent interactive users. As compared to other distributed systems, Peach is simple, easy to install, easy to administer, easy to use, scalable, and robust. While it was designed to queue and distribute large numbers of small tasks to participating computers, it can also be used to send single jobs automatically to the fastest currently available computer and/or survey the activity of an entire laboratory's computers. Tests of robustness and scalability are reported, as are three specific cryo-EM applications where Peach enabled projects that would not otherwise have been feasible without an expensive, dedicated cluster. Second, an iterative refinement reconstruction algorithm, Prec, is described that overcomes the curvature of the Ewald sphere resolution limitation by averaging information from images recorded from different points of view, as are present in typical micrographs. Prec was implemented in the popular software packages IMIRS, EMAN, and Bsoft. In preliminary tests with both simple and multi-slice simulated images, Prec overcame the curvature problem even in the presence of noise. Prec was then used to refine the three recently published, ~ 4 Å resolution, icosahedral virus reconstructions from experimental cryo-EM images, but unfortunately no significant improvements in resolution were realized. Further simulations showed that limitations other than the Ewald sphere curvature problem must still be dominant in these experimental studies.</p

Correcting for the Ewald Sphere in High-Resolution Single-Particle Reconstructions

To avoid the challenges of crystallization and the size limitations of NMR, it has long been hoped that single-particle cryo-electron microscopy (cryo-EM) would eventually yield atomically interpretable reconstructions. For the most favorable class of specimens (large icosahedral viruses), one of the key obstacles is curvature of the Ewald sphere, which leads to a breakdown of the Projection Theorem used by conventional three-dimensional (3D) reconstruction programs. Here, we review the basic problem and our implementation of the “paraboloid” reconstruction method, which overcomes the limitation by averaging information from images recorded from different points of view

Virtual Worlds - in Elementary School & College Classrooms

This paper presents case studies of an elementary school class and a graduate college course designed to provide students with the opportunity to explore the use of virtual worlds—primarily Minecraft and Second Life—for teaching and learning. Based on the findings, implications for the design of virtual world classes are provided

ICT-Enabled Community Empowerment in Crisis Response: Social Media in Thailand Flooding 2011

In this paper, we examine the emerging use of ICT in social phenomena such as natural disasters. Researchers have acknowledged that a community possesses the capacity to manage the challenges in crisis response on its own. However, extant IS studies focus predominantly on IS use from the crisis response agency’s perspective, which undermines communities’ role. By adopting an empowerment perspective, we focus on understanding how social media empowers communities during crisis response. As such, we present a qualitative case study of the 2011 Thailand flooding. Using an interpretive approach, we show how social media can empower the community from three dimensions of empowerment process (structural, psychological, and resource empowerment) to achieve collective participation, shared identification, and collaborative control in the community. We make two contributions: 1) we explore an emerging social consequence of ICT by illustrating the roles of social media in empowering communities when responding to crises, and 2) we address the literature gap in empowerment by elucidating the actualization process of empowerment that social media as a mediating structure enables

Microbial-induced carbonate precipitation using a sustainable treatment technique / Armstrong Ighodalo Omoregie… [et al.]

Biocementation is a green treatment technique which makes use of microbially induced carbonate precipitation (MICP) process to enhance the geotechnical features of substandard soils. The objective of this study was to conduct a biocement test in laboratoryscale using native urease-producing bacteria to improve the surface strength of poorly graded soil. Selected sand samples were pre-mixed with native bacterial culture and the cementation solution before being compacted into their respective columns. After completing the biocement process, all the sand columns were allowed to air-dry at room temperature (26o C) for 14 days before the treated sands were removed from their respective moulds. Unconfined compression strength (UCS) test was performed on the moulds to determine their strengths, while quick acid test and calcium carbonate (CaCO3) content measurement were conveyed to analyse the precipitated CaCO3 minerals. The results showed that the native urease-producing bacteria could bind soil particles together. The proficiency of this treatment process to improve the strength of soil samples varied among the specimen samples, leading to a non-homogeneous distribution of CaCO3 contents in the specimens. The UCS test showed that the sand treated with native isolate NB 28 had the highest strength (0.219 N/mm2 ), sustaining a force of 1.020 kN, while the control strain (Sporosarcina pasteurii DSM 33) had the lowest strength (0.143 N/mm2 ) with a sustaining force of 0.697 kN. The findings in this study suggest that the native urease-producing bacteria isolated from Sarawak limestone cave can be used as alternative MICP agents for the biocement application for sustainability in the construction industry

Microbial-induced carbonate precipitation using a sustainable treatment technique / Armstrong Ighodalo Omoregie … [et.al]

Biocementation is a green treatment technique which makes use of microbially induced carbonate precipitation (MICP) process to enhance the geotechnical features of substandard soils. The objective of this study was to conduct a biocement test in laboratoryscale using native urease-producing bacteria to improve the surface strength of poorly graded soil. Selected sand samples were pre-mixed with native bacterial culture and the cementation solution before being compacted into their respective columns. After completing the biocement process, all the sand columns were allowed to air-dry at room temperature (26o C) for 14 days before the treated sands were removed from their respective moulds. Unconfined compression strength (UCS) test was performed on the moulds to determine their strengths, while quick acid test and calcium carbonate (CaCO3) content measurement were conveyed to analyse the precipitated CaCO3 minerals. The results showed that the native urease-producing bacteria could bind soil particles together. The proficiency of this treatment process to improve the strength of soil samples varied among the specimen samples, leading to a non-homogeneous distribution of CaCO3 contents in the specimens. The UCS test showed that the sand treated with native isolate NB 28 had the highest strength (0.219 N/mm2 ), sustaining a force of 1.020 kN, while the control strain (Sporosarcina pasteurii DSM 33) had the lowest strength (0.143 N/mm2 ) with a sustaining force of 0.697 kN. The findings in this study suggest that the native urease-producing bacteria isolated from Sarawak limestone cave can be used as alternative MICP agents for the biocement application for sustainability in the construction industry

A constraints-based resource discovery model for multi-provider cloud environments

Abstract Abstract Increasingly infrastructure providers are supplying the cloud marketplace with storage and on-demand compute resources to host cloud applications. From an application user’s point of view, it is desirable to identify the most appropriate set of available resources on which to execute an application. Resource choice can be complex and may involve comparing available hardware specifications, operating systems, value-added services (such as network configuration or data replication) and operating costs (such as hosting cost and data throughput). Providers’ cost models often change and new commodity cost models (such as spot pricing) can offer significant savings. In this paper, a software abstraction layer is used to discover the most appropriate infrastructure resources for a given application, by applying a two-phase constraints-based approach to a multi-provider cloud environment. In the first phase, a set of possible infrastructure resources is identified for the application. In the second phase, a suitable heuristic is used to select the most appropriate resources from the initial set. For some applications a cost-based heuristic may be most appropriate; for others a performance-based heuristic may be of greater relevance. A financial services application and a high performance computing application are used to illustrate the execution of the proposed resource discovery mechanism. The experimental results show that the proposed model can dynamically select appropriate resouces for an application’s requirements. </jats:sec