Open Access. Powered by Scholars. Published by Universities.®
Physical Sciences and Mathematics Commons™
Open Access. Powered by Scholars. Published by Universities.®
- Keyword
-
- Cryo-electron microscopy (3)
- Fidelity (2)
- Homeomorphism (2)
- Image (2)
- Protein structure (2)
-
- Secondary structure (2)
- Tetrahedralization (2)
- Web archiving (2)
- Access (1)
- Ad blocker (1)
- Affordable Care Act (1)
- Archives Canada (1)
- Axis (1)
- Canonicalization patterns (1)
- Core utilization (1)
- Cryoelectron (1)
- Data patterns (1)
- Digital libraries (1)
- Digital preservation (1)
- Dynamic programming (1)
- Electron microscopy maps (1)
- Fitting (1)
- Government information (1)
- Graph (1)
- Grounded theory (1)
- Guaranteed quality (1)
- Helix (1)
- High accuracy (1)
- Hybrid programming (1)
- LOCKSS (1)
Articles 1 - 10 of 10
Full-Text Articles in Physical Sciences and Mathematics
Ansi/Niso Z39.99-2017 Resourcesync Framework Specification, Kevin Ruthen, Jill Emery, Mark Doyle, Mark Needleman, Sue Baughman, Evan Owens, Oliver Pesch, Mike Dicus, Nassib Nassar, Tim Auger, Amy Kirchhoff, Sally Mccallum, Diana Magnoni, Paul Swanson, Gregory Grazevich, Nara Newcomer, Gregory Grazevich, Juha Hakala, Barbara Rapp, Beverly Geckle, Carol Brent, Gary Van Overborg, Rick Burke, Kristin Antelman, Scott Bernier, Pascal Calarco, John Dove, Lucy Harrison, Peter Murray, Christine Stohn, Julie Zhu, Todd Carpenter, Bernhard Haslhofer, Richard Jones, Martin Klein, Graham Klyne, Carl Lagoze, Stuart Lewis, Peter Murray, Michael Nelson, Shlomo Sanders, Robert Sanderson, Herbert Van De Sompel, Paul Walk, Simeon Warner, Zhiwu Xie, Jeff Young
Ansi/Niso Z39.99-2017 Resourcesync Framework Specification, Kevin Ruthen, Jill Emery, Mark Doyle, Mark Needleman, Sue Baughman, Evan Owens, Oliver Pesch, Mike Dicus, Nassib Nassar, Tim Auger, Amy Kirchhoff, Sally Mccallum, Diana Magnoni, Paul Swanson, Gregory Grazevich, Nara Newcomer, Gregory Grazevich, Juha Hakala, Barbara Rapp, Beverly Geckle, Carol Brent, Gary Van Overborg, Rick Burke, Kristin Antelman, Scott Bernier, Pascal Calarco, John Dove, Lucy Harrison, Peter Murray, Christine Stohn, Julie Zhu, Todd Carpenter, Bernhard Haslhofer, Richard Jones, Martin Klein, Graham Klyne, Carl Lagoze, Stuart Lewis, Peter Murray, Michael Nelson, Shlomo Sanders, Robert Sanderson, Herbert Van De Sompel, Paul Walk, Simeon Warner, Zhiwu Xie, Jeff Young
Computer Science Faculty Publications
This ResourceSync specification describes a synchronization framework for the web consisting of various capabilities that allow third-party systems to remain synchronized with a server’s evolving resources. The capabilities may be combined in a modular manner to meet local or community requirements. This specification also describes how a server should advertise the synchronization capabilities it supports and how third-party systems may discover this information. The specification repurposes the document formats defined by the Sitemap protocol and introduces extensions for them.
Modeling Beta-Traces For Beta-Barrels From Cryo-Em Density Maps, Dong Si, Jing He
Modeling Beta-Traces For Beta-Barrels From Cryo-Em Density Maps, Dong Si, Jing He
Computer Science Faculty Publications
Cryo-electron microscopy (cryo-EM) has produced density maps of various resolutions. Although ά-helices can be detected from density maps at 5-8 angstrom resolutions, β-strands are challenging to detect at such density maps due to close-spacing of β-strands. The variety of shapes of β-sheets adds the complexity of β-strands detection from density maps. We propose a new approach to model traces of β-strands for β-barrel density regions that are extracted from cryo-EM density maps. In the test containing eight β-barrels extracted from experimental cryo-EM density maps at 5.5 angstrom-8.25 angstrom resolution, StrandRoller detected about 74.26% of the amino acids in the β-strands …
Impact Of Uri Canonicalization On Memento Count, Mat Kelly, Lulwah M. Alkwai, Michael L. Nelson, Michele C. Weigle, Herbert Van De Sompel
Impact Of Uri Canonicalization On Memento Count, Mat Kelly, Lulwah M. Alkwai, Michael L. Nelson, Michele C. Weigle, Herbert Van De Sompel
Computer Science Faculty Publications
Quantifying the captures of a URI over time is useful for researchers to identify the extent to which a Web page has been archived. Memento TimeMaps provide a format to list mementos (URI-Ms) for captures along with brief metadata, like Memento-Datetime, for each URI-M. However, when some URI-Ms are dereferenced, they simply provide a redirect to a different URI-M (instead of a unique representation at the datetime), often also present in the TimeMap. This infers that confidently obtaining an accurate count quantifying the number of non-forwarding captures for a URI-R is not possible using a TimeMap alone and that the …
Homeomorphic Tetrahedralization Of Multi-Material Images With Quality And Fidelity Guarantees, Jing Xu, Andrey N. Chernikov
Homeomorphic Tetrahedralization Of Multi-Material Images With Quality And Fidelity Guarantees, Jing Xu, Andrey N. Chernikov
Computer Science Faculty Publications
We present a novel algorithm for generating three-dimensional unstructured tetrahedral meshes of multi-material images. The algorithm produces meshes with high quality since it provides a guaranteed dihedral angle bound of up to 19.47° for the output tetrahedra. In addition, it allows for user-specified guaranteed bounds on the two-sided Hausdorff distance between the boundaries of the mesh and the boundaries of the materials. Moreover, the mesh boundary is proved to be homeomorphic to the object surface. The algorithm is fast and robust, it produces a sufficiently small number of mesh elements that comply with these guarantees, as compared to other software. …
Comparing An Atomic Model Or Structure To A Corresponding Cryo-Electron Microscopy Image At The Central Axis Of A Helix, Stephanie Zeil, Julio Kovacs, Willy Wriggers, Jing He
Comparing An Atomic Model Or Structure To A Corresponding Cryo-Electron Microscopy Image At The Central Axis Of A Helix, Stephanie Zeil, Julio Kovacs, Willy Wriggers, Jing He
Computer Science Faculty Publications
Three-dimensional density maps of biological specimens from cryo-electron microscopy (cryo-EM) can be interpreted in the form of atomic models that are modeled into the density, or they can be compared to known atomic structures. When the central axis of a helix is detectable in a cryo-EM density map, it is possible to quantify the agreement between this central axis and a central axis calculated from the atomic model or structure. We propose a novel arc-length association method to compare the two axes reliably. This method was applied to 79 helices in simulated density maps and six case studies using cryo-EM …
An Effective Computational Method Incorporating Multiple Secondary Structure Predictions In Topology Determination For Cryo-Em Images, Abhishek Biswas, Desh Ranjan, Mohammad Zubair, Stephanie Zeil, Kamal Al Nasr, Jing He
An Effective Computational Method Incorporating Multiple Secondary Structure Predictions In Topology Determination For Cryo-Em Images, Abhishek Biswas, Desh Ranjan, Mohammad Zubair, Stephanie Zeil, Kamal Al Nasr, Jing He
Computer Science Faculty Publications
A key idea in de novo modeling of a medium-resolution density image obtained from cryo-electron microscopy is to compute the optimal mapping between the secondary structure traces observed in the density image and those predicted on the protein sequence. When secondary structures are not determined precisely, either from the image or from the amino acid sequence of the protein, the computational problem becomes more complex. We present an efficient method that addresses the secondary structure placement problem in presence of multiple secondary structure predictions and computes the optimal mapping. We tested the method using 12 simulated images from alpha-proteins and …
Efficient Core Utilization In A Hybrid Parallel Delaunay Meshing Algorithm On Distributed-Memory Cluster, Daming Feng, Andrey N. Chernikov, Nikos P. Chrisochoides
Efficient Core Utilization In A Hybrid Parallel Delaunay Meshing Algorithm On Distributed-Memory Cluster, Daming Feng, Andrey N. Chernikov, Nikos P. Chrisochoides
Computer Science Faculty Publications
Most of the current supercomputer architectures consist of clusters of nodes that are used by many clients (users). A user wants his/her job submitted in the job queue to be scheduled promptly. However, the resource sharing and job scheduling policies that are used in the scheduling system to manage the jobs are usually beyond the control of users. Therefore, in order to reduce the waiting time of their jobs, it is becoming more and more crucial for the users to consider how to implement the algorithms that are suitable to the system scheduling policies and are able to effectively and …
Homeomorphic Tetrahedral Tessellation For Biomedical Images, Jing Xu, Andrey N. Chernikov
Homeomorphic Tetrahedral Tessellation For Biomedical Images, Jing Xu, Andrey N. Chernikov
Computer Science Faculty Publications
We present a novel algorithm for generating three-dimensional unstructured tetrahedral meshes for biomedical images. The method uses an octree as the background grid from which to build the final graded conforming meshes. The algorithm is fast and robust. It produces meshes with high quality since it provides dihedral angle lower bound for the output tetrahedra. Moreover, the mesh boundary is a geometrically and topologically accurate approximation of the object surface in the sense that it allows for guaranteed bounds on the two-sided Hausdorff distance and the homeomorphism between the boundaries of the mesh and the boundaries of the materials. The …
An Iterative Bézier Method For Fitting Beta-Sheet Component Of A Cryo-Em Density Map, Michael Poteat, Jing He
An Iterative Bézier Method For Fitting Beta-Sheet Component Of A Cryo-Em Density Map, Michael Poteat, Jing He
Computer Science Faculty Publications
Cryo-electron microscopy (Cryo-EM) is a powerful technique to produce 3-dimensional density maps for large molecular complexes. Although many atomic structures have been solved from cryo-EM density maps, it is challenging to derive atomic structures when the resolution of density maps is not sufficiently high. Geometrical shape representation of secondary structural components in a medium-resolution density map enhances modeling of atomic structures. We compare two methods in producing surface representation of the β-sheet component of a density map. Given a 3-dimensional volume of β-sheet that is segmented from a density map, the performance of a polynomial fitting was compared with that …
Avoiding Zombies In Archival Replay Using Serviceworker, Sawood Alam, Mat Kelly, Michele C. Weigle, Michael L. Nelson
Avoiding Zombies In Archival Replay Using Serviceworker, Sawood Alam, Mat Kelly, Michele C. Weigle, Michael L. Nelson
Computer Science Faculty Publications
[First paragraph] A Composite Memento is an archived representation of a web page with all the page requisites such as images and stylesheets. All embedded resources have their own URIs, hence, they are archived independently. For a meaningful archival replay, it is important to load all the page requisites from the archive within the temporal neighborhood of the base HTML page. To achieve this goal, archival replay systems try to rewrite all the resource references to appropriate archived versions before serving HTML, CSS, or JS. However, an effective server-side URL rewriting is difficult when URLs are generated dynamically using JavaScript. …