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Demaine E.D.,Cambridge Intelligence | Schulz A.,University of Hagen
Discrete and Computational Geometry | Year: 2017

A stacking operation adds a d-simplex on top of a facet of a simplicial d-polytope while maintaining the convexity of the polytope. A stacked d-polytope is a polytope that is obtained from a d-simplex and a series of stacking operations. We show that for a fixed d every stacked d-polytope with n vertices can be realized with nonnegative integer coordinates. The coordinates are bounded by (Formula presented.), except for one axis, where the coordinates are bounded by (Formula presented.). The described realization can be computed with an easy algorithm. The realization of the polytopes is obtained with a lifting technique which produces an embedding on a large grid. We establish a rounding scheme that places the vertices on a sparser grid, while maintaining the convexity of the embedding. © 2017 Springer Science+Business Media New York


Bryan Jr. A.W.,Harvard Massachusetts Institute of Technology Division of Health Sciences and Technology | Bryan Jr. A.W.,Whitehead Institute For Biomedical Research | Bryan Jr. A.W.,Cambridge Intelligence | Starner-Kreinbrink J.L.,University of Notre Dame | And 4 more authors.
Proceedings of the National Academy of Sciences of the United States of America | Year: 2011

The parallel β-helix is a geometrically regular fold commonly found in the proteomes of bacteria, viruses, fungi, archaea, and some vertebrates. β-helix structure has been observed in monomeric units of some aggregated amyloid fibers. In contrast, soluble β-helices, both right- and left-handed, are usually "capped" on each end by one or more secondary structures. Here, an in-depth classification of the diverse range of β-helix cap structures reveals subtle commonalities in structural components and in interactions with the β-helix core. Based on these uncovered commonalities, a toolkit of automated predictors was developed for the two distinct types of cap structures. In vitro deletion of the toolkit-predicted C-terminal cap from the pertactin β-helix resulted in increased aggregation and the formation of soluble oligomeric species. These results suggest that β-helix cap motifs can prevent specific, β-sheet-mediated oligomeric interactions, similar to those observed in amyloid formation.


Shevlin H.,Cambridge Intelligence
Journal of Consciousness Studies | Year: 2017

In debates in philosophy and cognitive science concerning short-term memory mechanisms and perceptual experience, most discussion has focused on the working memory and the various forms of sensory memory such as iconic memory. In this paper, I present a summary of some evidence for a proposed further form of memory termed conceptual short-term memory. I go on to outline some of the ways in which this additional distinctive sort of short-term memory might be of relevance to ongoing philosophical debates, specifically in relation to questions about high-level perceptual phenomenology, the relationship between consciousness and reportability, and the boundary between cognition and perception. I conclude that conceptual short-term memory offers a promising new direction of research and philosophical investigation. © Imprint Academic 2016.


Popa R.A.,Cambridge Intelligence | Redfield C.M.S.,Cambridge Intelligence | Zeldovich N.,Cambridge Intelligence | Balakrishnan H.,Cambridge Intelligence
Communications of the ACM | Year: 2012

CryptDB is a practical system that explores an intermediate design point to provide confidentiality for applications that use database management systems (DBMSes). CryptDB is the first practical system that can execute a wide range of SQL queries over encrypted data. CryptDB requires no changes to the internals of the DBMS server, and should work with most standard SQL DBMSes. CryptDB's architecture consisting of two parts, a proxy and an unmodified DBMS. It uses user-defined functions (UDFs) to perform cryptographic operations in the DBMS. The only information that CryptDB reveals to the DBMS server is relationships among data items corresponding to classes of computation that queries perform on the database, such as comparing items for equality, sorting, or performing word search. RND provides the maximum security in CryptDB, indistinguishability under an adaptive chosen plain text attack (IND-CPA).


Benczur A.A.,Hungarian Academy of Sciences | Karger D.R.,Cambridge Intelligence
SIAM Journal on Computing | Year: 2015

We describe random sampling techniques for approximately solving problems that involve cuts and flows in graphs. We give a near-linear-time randomized combinatorial construction that transforms any graph on n vertices into an O(n log n)-edge graph on the same vertices whose cuts have approximately the same value as the original graph's. In this new graph, for example, we can run the Õ (m3/2)-time maximum flow algorithm of Goldberg and Rao to find an s-t minimum cut in Õ(n3/2) time. This corresponds to a (1 + ε)-times minimum s-t cut in the original graph. A related approach leads to a randomized divide-and-conquer algorithm producing an approximately maximum flow in Õ(m √n) time. Our algorithm can also be used to improve the running time of sparsest cut approximation algorithms from Õ(mn) to Õ (n2) and to accelerate several other recent cut and flow algorithms. Our algorithms are based on a general theorem analyzing the concentration of random graphs' cut values near their expectations. Our work draws only on elementary probability and graph theory. © 2015 Andras Benczúr and David R. Karger.


Che A.J.,Cambridge Intelligence | Che A.J.,Ginkgo BioWorks, Inc. | Knight Jr. T.F.,Cambridge Intelligence | Knight Jr. T.F.,Ginkgo BioWorks, Inc.
Nucleic Acids Research | Year: 2010

Controlling RNA splicing opens up possibilities for the synthetic biologist. The Tetrahymena ribozyme is a model group I self-splicing ribozyme that has been shown to be useful in synthetic circuits. To create additional splicing ribozymes that can function in synthetic circuits, we generated synthetic ribozyme variants by rationally mutating the Tetrahymena ribozyme. We present an alignment visualization for the ribozyme termed as structure information diagram that is similar to a sequence logo but with alignment data mapped on to secondary structure information. Using the alignment data and known biochemical information about the Tetrahymena ribozyme, we designed synthetic ribozymes with different primary sequences without altering the secondary structure. One synthetic ribozyme with 110 nt mutated retained 12% splicing efficiency in vivo. The results indicate that our biochemical understanding of the ribozyme is accurate enough to engineer a family of active splicing ribozymes with similar secondary structure but different primary sequences. © The Author(s) 2010. Published by Oxford University Press.


Grant
Agency: GTR | Branch: Innovate UK | Program: | Phase: Innovation Voucher | Award Amount: 5.00K | Year: 2015

We are looking for cyber security expertise to review and improve our current procedures.


News Article | March 20, 2014
Site: keylines.com

KeyLines is a toolkit for building your own data visualization capability and integrating it into your own web applications with very little effort. KeyLines is compatible with any data store, so How you collect and store the data is entirely up to you. The application you build will also run on any device and in any web browser, meaning it can be deployed to anyone who needs to use it. Your data stays in your control at all times: KeyLines is self-contained and needs no external connections.


News Article | July 23, 2014
Site: cambridge-intelligence.com

Cambridge Intelligence, today announced the release of KeyLines 2.0 – the next generation of network visualisation software. This latest release of their web software development kit (or SDK) makes it the first in the world to offer full support for dynamic graphs and temporal visualisation – meaning users can now watch their networks evolving through time in any web browser. This new dimension to data analysis is provided via the KeyLines Time Bar. Using the time bar, data analysts can instantly understand network trends and focus on the points in time that matter most. It is expected to reduce data processing and investigation time significantly, helping analysts to follow trends and predict future events with even greater accuracy. Global organisations, including government agencies, police forces, and companies already rely upon KeyLines to uncover relationships and patterns in large and complex datasets. Many of Cambridge Intelligence’s existing customers are planning to stay ahead of the innovation curve by deploying the time bar to their users this year. Cambridge Intelligence CEO, Joe Parry, said of the new release, “The ability to view networks change through time ensures that KeyLines remains at the forefront of the industry. These new capabilities have generated a significant buzz among current customers and are sure to drive our growth into 2015.” This release comes after a busy six months of success for the three-year-old Cambridge company. In March they celebrated moving into modern new park-side offices on Regent Street, and have enjoyed recognition in innovation and technology awards – most recently being shortlisted for PwC’s Private Business of the Year.

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