Improving accuracy of protein-protein interaction prediction by considering the converse problem for sequence representation

<p>Abstract</p> <p>Background</p> <p>With the development of genome-sequencing technologies, protein sequences are readily obtained by translating the measured mRNAs. Therefore predicting protein-protein interactions from the sequences is of great demand. The reason lies in the fact that identifying protein-protein interactions is becoming a bottleneck for eventually understanding the functions of proteins, especially for those organisms barely characterized. Although a few methods have been proposed, the converse problem, if the features used extract sufficient and unbiased information from protein sequences, is almost untouched.</p> <p>Results</p> <p>In this study, we interrogate this problem theoretically by an optimization scheme. Motivated by the theoretical investigation, we find novel encoding methods for both protein sequences and protein pairs. Our new methods exploit sufficiently the information of protein sequences and reduce artificial bias and computational cost. Thus, it significantly outperforms the available methods regarding sensitivity, specificity, precision, and recall with cross-validation evaluation and reaches ~80% and ~90% accuracy in <it>Escherichia coli </it>and <it>Saccharomyces cerevisiae </it>respectively. Our findings here hold important implication for other sequence-based prediction tasks because representation of biological sequence is always the first step in computational biology.</p> <p>Conclusions</p> <p>By considering the converse problem, we propose new representation methods for both protein sequences and protein pairs. The results show that our method significantly improves the accuracy of protein-protein interaction predictions.</p

Holographic Storage of Biphoton Entanglement

Coherent and reversible storage of multi-photon entanglement with a multimode quantum memory is essential for scalable all-optical quantum information processing. Although single photon has been successfully stored in different quantum systems, storage of multi-photon entanglement remains challenging because of the critical requirement for coherent control of photonic entanglement source, multimode quantum memory, and quantum interface between them. Here we demonstrate a coherent and reversible storage of biphoton Bell-type entanglement with a holographic multimode atomic-ensemble-based quantum memory. The retrieved biphoton entanglement violates Bell's inequality for 1 microsecond storage time and a memory-process fidelity of 98% is demonstrated by quantum state tomography.Comment: 5 pages, 4 figures, accepted by Phys. Rev. Let

Laminin-coated multifilament entubulation, combined with Schwann cells and glial cell line-derived neurotrophic factor, promotes unidirectional axonal regeneration in a rat model of thoracic spinal cord hemisection

Biomaterial bridging provides physical substrates to guide axonal growth across the lesion. To achieve efficient directional guidance, combinatory strategies using permissive matrix, cells and trophic factors are necessary. In the present study, we evaluated permissive effect of poly (acrylonitrile-co-vinyl chloride) guidance channels filled by different densities of laminin-precoated unidirectional polypropylene filaments combined with Schwann cells, and glial cell line-derived neurotrophic factor for axonal regeneration through a T10 hemisected spinal cord gap in adult rats. We found that channels with filaments significantly reduced the lesion cavity, astrocytic gliosis, and inflammatory responses at the graft-host boundaries. The laminin coated low density filament provided the most favorable directional guidance for axonal regeneration which was enhanced by co-grafting of Schwann cells and glial cell line-derived neurotrophic factor. These results demonstrate that the combinatorial strategy of filament-filled guiding scaffold, adhesive molecular laminin, Schwann cells, and glial cell line-derived neurotrophic factor, provides optimal topographical cues in stimulating directional axonal regeneration following spinal cord injur