BORIS/CTCFL is an RNA-binding protein that associates with polysomes

© 2013 Ogunkolade et al.; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited

On the dynamic response of an instrumented headform for alternative mounting stiffnesses when subjected to ballistic impacts

© 2017, © IMechE 2017. The current British Standard for head protectors for cricketers has been recently revised to include a projectile-based battery of tests, the intention being to ensure that a certified helmet will also prevent contact of the ball or grille with the specified headform facial region. The purpose of this study was to characterise the dynamic response of the headform to direct ballistic impacts for alternative headform mounting arrangements. On one hand, and in accordance with the relevant sections of the Standard, what might be described as a ‘Constrained’ setup was evaluated while, on the other hand, an arrangement with significantly reduced stiffness, in line with that previously reported for the passive human neck, was subject to equivalent appraisal. For each mounting scenario, an air cannon was used to project a cricket training ball at three speeds towards the instrumented headform at three locations with five repeats per speed/location combination. High-rate/resolution video and piezoelectric accelerometer data were collected and processed to determine the headform response. While differences between specific ball impact speed and location scenarios are set out in detail later in the article, overall observations are summarised as follows. From a ball/headform contact duration standpoint, video derived results showed ranges of 1.30–1.45 ms (Constrained) versus 1.26–1.41 ms. Maximum ball deformations, the timing of which enabling the event to be subdivided into ‘loading’ and ‘unloading’ phases, were found to be 82.5%–86.2% (Constrained) versus 82.8%–86.4% of original ball diameter; mean peak headform accelerations during loading were found to be 860–1615 m/s2 (Constrained) versus 967–1638 m/s2; and headform speeds at the end of the loading phase were found to be 0.5–0.92 m/s (Constrained) versus 0.54–0.93 m/s. Differences between headform response for the two mounting arrangements were observed to be more substantial during the loading rather than unloading phase

Applying Grover's algorithm to AES: quantum resource estimates

We present quantum circuits to implement an exhaustive key search for the Advanced Encryption Standard (AES) and analyze the quantum resources required to carry out such an attack. We consider the overall circuit size, the number of qubits, and the circuit depth as measures for the cost of the presented quantum algorithms. Throughout, we focus on Clifford$+T$ gates as the underlying fault-tolerant logical quantum gate set. In particular, for all three variants of AES (key size 128, 192, and 256 bit) that are standardized in FIPS-PUB 197, we establish precise bounds for the number of qubits and the number of elementary logical quantum gates that are needed to implement Grover's quantum algorithm to extract the key from a small number of AES plaintext-ciphertext pairs.Comment: 13 pages, 3 figures, 5 tables; to appear in: Proceedings of the 7th International Conference on Post-Quantum Cryptography (PQCrypto 2016

Experimental magic state distillation for fault-tolerant quantum computing

Any physical quantum device for quantum information processing is subject to errors in implementation. In order to be reliable and efficient, quantum computers will need error correcting or error avoiding methods. Fault-tolerance achieved through quantum error correction will be an integral part of quantum computers. Of the many methods that have been discovered to implement it, a highly successful approach has been to use transversal gates and specific initial states. A critical element for its implementation is the availability of high-fidelity initial states such as |0> and the Magic State. Here we report an experiment, performed in a nuclear magnetic resonance (NMR) quantum processor, showing sufficient quantum control to improve the fidelity of imperfect initial magic states by distilling five of them into one with higher fidelity

Complete quantum teleportation using nuclear magnetic resonance

Quantum mechanics provides spectacular new information processing abilities (Bennett 1995, Preskill 1998). One of the most unexpected is a procedure called quantum teleportation (Bennett et al 1993) that allows the quantum state of a system to be transported from one location to another, without moving through the intervening space. Partial implementations of teleportation (Bouwmeester et al 1997, Boschi et al 1998) over macroscopic distances have been achieved using optical systems, but omit the final stage of the teleportation procedure. Here we report an experimental implementation of the full quantum teleportation operation over inter-atomic distances using liquid state nuclear magnetic resonance (NMR). The inclusion of the final stage enables for the first time a teleportation implementation which may be used as a subroutine in larger quantum computations, or for quantum communication. Our experiment also demonstrates the use of quantum process tomography, a procedure to completely characterize the dynamics of a quantum system. Finally, we demonstrate a controlled exploitation of decoherence as a tool to assist in the performance of an experiment.Comment: 15 pages, 2 figures. Minor differences between this and the published versio

Bayesian Optimization Approaches for Massively Multi-modal Problems

The optimization of massively multi-modal functions is a challenging task, particularly for problems where the search space can lead the op- timization process to local optima. While evolutionary algorithms have been extensively investigated for these optimization problems, Bayesian Optimization algorithms have not been explored to the same extent. In this paper, we study the behavior of Bayesian Optimization as part of a hybrid approach for solving several massively multi-modal functions. We use well-known benchmarks and metrics to evaluate how different variants of Bayesian Optimization deal with multi-modality.TIN2016-78365-

The Viking viewer for connectomics: scalable multi-user annotation and summarization of large volume data sets

Modern microscope automation permits the collection of vast amounts of continuous anatomical imagery in both two and three dimensions. These large data sets present significant challenges for data storage, access, viewing, annotation and analysis. The cost and overhead of collecting and storing the data can be extremely high. Large data sets quickly exceed an individual's capability for timely analysis and present challenges in efficiently applying transforms, if needed. Finally annotated anatomical data sets can represent a significant investment of resources and should be easily accessible to the scientific community. The Viking application was our solution created to view and annotate a 16.5 TB ultrastructural retinal connectome volume and we demonstrate its utility in reconstructing neural networks for a distinctive retinal amacrine cell class. Viking has several key features. (1) It works over the internet using HTTP and supports many concurrent users limited only by hardware. (2) It supports a multi-user, collaborative annotation strategy. (3) It cleanly demarcates viewing and analysis from data collection and hosting. (4) It is capable of applying transformations in real-time. (5) It has an easily extensible user interface, allowing addition of specialized modules without rewriting the viewer

Distances and ages of globular clusters using Hipparcos parallaxes of local subdwarfs

We discuss the impact of Population II and Globular Cluster (GCs) stars on the derivation of the age of the Universe, and on the study of the formation and early evolution of galaxies, our own in particular. The long-standing problem of the actual distance scale to Population II stars and GCs is addressed, and a variety of different methods commonly used to derive distances to Population II stars are briefly reviewed. Emphasis is given to the discussion of distances and ages for GCs derived using Hipparcos parallaxes of local subdwarfs. Results obtained by different authors are slightly different, depending on different assumptions about metallicity scale, reddenings, and corrections for undetected binaries. These and other uncertainties present in the method are discussed. Finally, we outline progress expected in the near future.Comment: Invited review article to appear in: `Post-Hipparcos Cosmic Candles', A. Heck & F. Caputo (Eds), Kluwer Academic Publ., Dordrecht, in press. 22 pages including 3 tables and 2 postscript figures, uses Kluwer's crckapb.sty LaTeX style file, enclose

From Nonspecific DNA–Protein Encounter Complexes to the Prediction of DNA–Protein Interactions

©2009 Gao, Skolnick. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.doi:10.1371/journal.pcbi.1000341DNA–protein interactions are involved in many essential biological activities. Because there is no simple mapping code between DNA base pairs and protein amino acids, the prediction of DNA–protein interactions is a challenging problem. Here, we present a novel computational approach for predicting DNA-binding protein residues and DNA–protein interaction modes without knowing its specific DNA target sequence. Given the structure of a DNA-binding protein, the method first generates an ensemble of complex structures obtained by rigid-body docking with a nonspecific canonical B-DNA. Representative models are subsequently selected through clustering and ranking by their DNA–protein interfacial energy. Analysis of these encounter complex models suggests that the recognition sites for specific DNA binding are usually favorable interaction sites for the nonspecific DNA probe and that nonspecific DNA–protein interaction modes exhibit some similarity to specific DNA–protein binding modes. Although the method requires as input the knowledge that the protein binds DNA, in benchmark tests, it achieves better performance in identifying DNA-binding sites than three previously established methods, which are based on sophisticated machine-learning techniques. We further apply our method to protein structures predicted through modeling and demonstrate that our method performs satisfactorily on protein models whose root-mean-square Ca deviation from native is up to 5 Å from their native structures. This study provides valuable structural insights into how a specific DNA-binding protein interacts with a nonspecific DNA sequence. The similarity between the specific DNA–protein interaction mode and nonspecific interaction modes may reflect an important sampling step in search of its specific DNA targets by a DNA-binding protein