Results 21 - 30
of
313
Scalable Grid Application Scheduling via Decoupled Resource Selection and Scheduling
- In Sixth IEEE International Symposium on Cluster Computing and the Grid (CCGrid 2006) (2006
, 2006
"... Abstract — Over the past years grid infrastructures have been deployed at larger and larger scales, with envisioned deployments incorporating tens of thousands of resources. Therefore, application scheduling algorithms can become unscalable (albeit polynomial) and thus unusable in large-scale enviro ..."
Abstract
-
Cited by 8 (2 self)
- Add to MetaCart
(Show Context)
Abstract — Over the past years grid infrastructures have been deployed at larger and larger scales, with envisioned deployments incorporating tens of thousands of resources. Therefore, application scheduling algorithms can become unscalable (albeit polynomial) and thus unusable in large-scale environments. One reason for unscalability is that these algorithms perform implicit resource selection. One can achieve better scalability by performing explicit resource selection independently from scheduling in a ”decoupled” approach. Furthermore, we hypothesize that one can achieve similar or even better performance as with the non-decoupled approach, which we call the ”one step” approach, by selecting resources judiciously. Leveraging the Virtual Grid abstraction, we demonstrate that the decoupled approach is indeed both scalable and effective in large-scale and highly heterogeneous resource environments. I.
Detecting particles in cryo-em micrographs using learned features
- Journal of Structural Biology
, 2004
"... A new learning-based approach is presented for particle detection in cryo-electron micrographs using the Adaboost learning algorithm. The approach builds directly on the successful detectors developed for the domain of face detection. It is a discriminative algorithm which learns important features ..."
Abstract
-
Cited by 8 (1 self)
- Add to MetaCart
(Show Context)
A new learning-based approach is presented for particle detection in cryo-electron micrographs using the Adaboost learning algorithm. The approach builds directly on the successful detectors developed for the domain of face detection. It is a discriminative algorithm which learns important features of the particle’s appearance using a set of training examples of the particles and a set of images that do not contain particles. The algorithm is fast (10 seconds on a 1.3 GHz Pentium M processor), is generic, and is not limited to any particular shape or size of the particle to be detected. The method has been evaluated on a publicly available dataset of 82 cryo-EM images of keyhole lympet hemocyanin (KLH). From 998 automatically extracted particle images, the 3-D structure of KLH has been reconstructed at a resolution of 23.2 ˚A which is the same resolution as obtained using particles manually selected by a trained user.
Cryoelectron microscopy structures of rotavirus NSP2-NSP5 and NSP2-RNA complexes: implications for genome replication
- J
, 2006
"... The replication and packaging of the rotavirus genome, comprising 11 segments of double-stranded RNA, take place in specialized compartments called viroplasms, which are formed during infection and involve a coordinated interplay of multiple components. Two rotavirus nonstructural proteins, NSP2 (wi ..."
Abstract
-
Cited by 7 (0 self)
- Add to MetaCart
(Show Context)
The replication and packaging of the rotavirus genome, comprising 11 segments of double-stranded RNA, take place in specialized compartments called viroplasms, which are formed during infection and involve a coordinated interplay of multiple components. Two rotavirus nonstructural proteins, NSP2 (with nucleoside triphosphatase, single-stranded RNA [ssRNA] binding and helix-destabilizing activities) and NSP5, are essential in these events. Previous structural analysis of NSP2 showed that it is an octamer in crystals, obeying 4-2–2 crystal symmetry, with a large 35-Å central hole along the fourfold axis and deep grooves at one of the twofold axes. To ascertain that the solution structure of NSP2 is the same as that in the crystals and investigate how NSP2 interacts with NSP5 and RNA, we carried out single-particle cryoelectron microscopy (cryo-EM) analysis of NSP2 alone and in complexes with NSP5 and ssRNA at subnanometer resolution. Because full-length NSP5 caused severe aggregation upon mixing with NSP2, the deletion construct NSP5 66-188 was used in these studies. Our studies show that the solution structure of NSP2 is same as the crystallographic octamer and that both NSP5 66-188 and ssRNA bind to the grooves in the octamer, which are lined by positively charged residues. The fitting of the NSP2 crystal structure to cryo-EM reconstructions of the complexes indicates that, in contrast to the binding of NSP5 66-188, the binding of RNA induces noticeable conformational changes in the NSP2 octamer. Consistent with the observation that both NSP5 and RNA share the same
Transfer function restoration in 3D electron microscopy via . . .
, 2004
"... Three-dimensional electron microscopy (3D-EM) is a powerful tool for visualizing complex biological systems. As with any other imaging device, the electron microscope introduces a transfer function (called in this field the contrast transfer function, CTF) into the image acquisition process that mod ..."
Abstract
-
Cited by 7 (3 self)
- Add to MetaCart
Three-dimensional electron microscopy (3D-EM) is a powerful tool for visualizing complex biological systems. As with any other imaging device, the electron microscope introduces a transfer function (called in this field the contrast transfer function, CTF) into the image acquisition process that modulates the various frequencies of the signal. Thus, the 3D reconstructions performed with these CTF-affected projections are also affected by an implicit 3D transfer function. For high-resolution electron microscopy, the effect of the CTF is quite dramatic and limits severely the achievable resolution. In this work we make use of the iterative data refinement (IDR) technique to ameliorate the effect of the CTF. It is demonstrated that the approach can be successfully applied to noisy data.
Mapping heavy communication workflows onto grid resources within sla context
- HPCC 2006. LNCS
, 2006
"... Abstract. Service Level Agreements (SLAs) are currently one of the major research topics in Grid Computing. Among many system components for supporting SLA-aware Grid jobs, the SLA mapping mechanism receives an important position. It is responsible for assigning sub-jobs of the workflow to Grid reso ..."
Abstract
-
Cited by 7 (5 self)
- Add to MetaCart
Abstract. Service Level Agreements (SLAs) are currently one of the major research topics in Grid Computing. Among many system components for supporting SLA-aware Grid jobs, the SLA mapping mechanism receives an important position. It is responsible for assigning sub-jobs of the workflow to Grid resources in a way that meets the user’s deadline and as cheap as possible. With the distinguished workload and resource characteristics, mapping a heavy communication workflow within SLA context defines new problem and needs new method to be solved. This paper presents the mapping algorithm, which can cope with the problem. Performance measurements deliver evaluation results on the quality and efficiency of the method. 1
Three-dimensional organization of Rift Valley fever virus revealed by cryo-electron tomography
- J
, 2008
"... Rift Valley fever virus (RVFV) is a member of the Bunyaviridae virus family (genus Phlebovirus) and is considered to be one of the most important pathogens in Africa, causing viral zoonoses in livestock and humans. Here, we report the characterization of the three-dimensional structural organization ..."
Abstract
-
Cited by 7 (1 self)
- Add to MetaCart
(Show Context)
Rift Valley fever virus (RVFV) is a member of the Bunyaviridae virus family (genus Phlebovirus) and is considered to be one of the most important pathogens in Africa, causing viral zoonoses in livestock and humans. Here, we report the characterization of the three-dimensional structural organization of RVFV vaccine strain MP-12 by cryoelectron tomography. Vitrified-hydrated virions were found to be spherical, with an average diameter of 100 nm. The virus glycoproteins formed cylindrical hollow spikes that clustered into distinct capsomeres. In contrast to previous assertions that RVFV is pleomorphic, the structure of RVFV MP-12 was found to be highly ordered. The three-dimensional map was resolved to a resolution of 6.1 nm, and capsomeres were observed to be arranged on the virus surface in an icosahedral lattice with clear T12 quasisymmetry. All icosahedral symmetry axes were visible in self-rotation functions calculated using the Fourier transform of the RVFV MP-12 tomogram. To the best of our knowledge, a triangulation number of 12 had previously been reported only for Uukuniemi virus, a bunyavirus also within the Phlebovirus genus. The results presented in this study demonstrate that RVFV MP-12 possesses T12 icosahedral symmetry and suggest that other members of the Phlebovirus genus, as well as of the Bunyaviridae family, may adopt icosahedral symmetry. Knowledge of the virus architecture may provide a structural template to develop vaccines and diagnostics, since no effective anti-RVFV treatments are available for human use.
The structure of CCT-Hsc70 NBD suggests a mechanism for Hsp70 delivery of substrates to the chaperonin. Nat Struct Mol Biol 15: 858–864
, 2008
"... ..."
Molecular surface representation using 3D Zernike descriptors for protein shape comparison and docking. Curr. Protein Peptide Sci.
, 2011
"... Abstract: The tertiary structures of proteins have been solved in an increasing pace in recent years. To capitalize the enormous efforts paid for accumulating the structure data, efficient and effective computational methods need to be developed for comparing, searching, and investigating interacti ..."
Abstract
-
Cited by 7 (7 self)
- Add to MetaCart
(Show Context)
Abstract: The tertiary structures of proteins have been solved in an increasing pace in recent years. To capitalize the enormous efforts paid for accumulating the structure data, efficient and effective computational methods need to be developed for comparing, searching, and investigating interactions of protein structures. We introduce the 3D Zernike descriptor (3DZD), an emerging technique to describe molecular surfaces. The 3DZD is a series expansion of mathematical three-dimensional function, and thus a tertiary structure is represented compactly by a vector of coefficients of terms in the series. A strong advantage of the 3DZD is that it is invariant to rotation of target object to be represented. These two characteristics of the 3DZD allow rapid comparison of surface shapes, which is sufficient for real-time structure database screening. In this article, we review various applications of the 3DZD, which have been recently proposed.
Three-dimensional model for the isolated recombinant
, 2007
"... influenza virus polymerase heterotrimer ..."
(Show Context)
Reconstruction principles of icosahedral virus structure determination using electron cryomicroscopy
, 2000
"... Electron cryomicroscopy is a useful tool for studying the three-dimensional structure of icosahedral viruses. This review is intended to provide beginners with an understanding of icosahedral virus structure determination focusing on the data processing aspects. We begin with an overview of the enti ..."
Abstract
-
Cited by 6 (0 self)
- Add to MetaCart
Electron cryomicroscopy is a useful tool for studying the three-dimensional structure of icosahedral viruses. This review is intended to provide beginners with an understanding of icosahedral virus structure determination focusing on the data processing aspects. We begin with an overview of the entire structure determination process and a brief summary of the sample preparation and imaging aspects. Next, we provide detailed descriptions of each data processing step leading to three-dimensional reconstruction, including application of image corrections, resolution assessment, and structure visualization. To aid in understanding this reconstruction process we provide a variety
