Efficiency limits for linear optical processing of single photons and single-rail qubits

We analyze the problem of increasing the efficiency of single-photon sources or single-rail photonic qubits via linear optical processing and destructive conditional measurements. In contrast to previous work we allow for the use of coherent states and do not limit to photon-counting measurements. We conjecture that it is not possible to increase the efficiency, prove this conjecture for several important special cases, and provide extensive numerical results for the general case.Comment: 10 pages, 4 figure

Wehrl information entropy and phase distributions of Schrodinger cat and cat-like states

The Wehrl information entropy and its phase density, the so-called Wehrl phase distribution, are applied to describe Schr\"odinger cat and cat-like (kitten) states. The advantages of the Wehrl phase distribution over the Wehrl entropy in a description of the superposition principle are presented. The entropic measures are compared with a conventional phase distribution from the Husimi Q-function. Compact-form formulae for the entropic measures are found for superpositions of well-separated states. Examples of Schr\"odinger cats (including even, odd and Yurke-Stoler coherent states), as well as the cat-like states generated in Kerr medium are analyzed in detail. It is shown that, in contrast to the Wehrl entropy, the Wehrl phase distribution properly distinguishes between different superpositions of unequally-weighted states in respect to their number and phase-space configuration.Comment: 10 pages, 4 figure

PFresGO: an attention mechanism-based deep-learning approach for protein annotation by integrating gene ontology inter-relationships

MOTIVATION: The rapid accumulation of high-throughput sequence data demands the development of effective and efficient data-driven computational methods to functionally annotate proteins. However, most current approaches used for functional annotation simply focus on the use of protein-level information but ignore inter-relationships among annotations. RESULTS: Here, we established PFresGO, an attention-based deep-learning approach that incorporates hierarchical structures in Gene Ontology (GO) graphs and advances in natural language processing algorithms for the functional annotation of proteins. PFresGO employs a self-attention operation to capture the inter-relationships of GO terms, updates its embedding accordingly and uses a cross-attention operation to project protein representations and GO embedding into a common latent space to identify global protein sequence patterns and local functional residues. We demonstrate that PFresGO consistently achieves superior performance across GO categories when compared with 'state-of-the-art' methods. Importantly, we show that PFresGO can identify functionally important residues in protein sequences by assessing the distribution of attention weightings. PFresGO should serve as an effective tool for the accurate functional annotation of proteins and functional domains within proteins. AVAILABILITY AND IMPLEMENTATION: PFresGO is available for academic purposes at https://github.com/BioColLab/PFresGO. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online

Quantum Cryptography with Coherent States

The safety of a quantum key distribution system relies on the fact that any eavesdropping attempt on the quantum channel creates errors in the transmission. For a given error rate, the amount of information that may have leaked to the eavesdropper depends on both the particular system and the eavesdropping strategy. In this work, we discuss quantum cryptographic protocols based on the transmission of weak coherent states and present a new system, based on a symbiosis of two existing ones, and for which the information available to the eavesdropper is significantly reduced. This system is therefore safer than the two previous ones. We also suggest a possible experimental implementation.Comment: 20 pp. Revtex, Figures available from the authors upon request, To be published in PRA (March 95

Holographic Approach to Regge Trajectory and Rotating D5 brane

We study the Regge trajectories of holographic mesons and baryons by considering rotating strings and D5 brane, which is introduced as the baryon vertex. Our model is based on the type IIB superstring theory with the background of asymptotic $AdS_5\times S^5$. This background is dual to a confining supersymmetric Yang-Mills theory (SYM) with gauge condensate, $$, which determines the tension of the linear potential between the quark and anti-quark. Then the slope of the meson trajectory ($\alpha'_{M}$) is given by this condensate as $\alpha'_{M}=1/\sqrt{\pi }$ at large spin $J$. This relation is compatible with the other theoretical results and experiments. For the baryon, we show the importance of spinning baryon vertex to obtain a Regge slope compatible with the one of $N$ and $\Delta$ series. In both cases, mesons and baryons, the trajectories are shifted to large mass side with the same slope for increasing current quark mass.Comment: 28 pages, 7 figure

Quantitative utilization of prior biological knowledge in the Bayesian network modeling of gene expression data

<p>Abstract</p> <p>Background</p> <p>Bayesian Network (BN) is a powerful approach to reconstructing genetic regulatory networks from gene expression data. However, expression data by itself suffers from high noise and lack of power. Incorporating prior biological knowledge can improve the performance. As each type of prior knowledge on its own may be incomplete or limited by quality issues, integrating multiple sources of prior knowledge to utilize their consensus is desirable.</p> <p>Results</p> <p>We introduce a new method to incorporate the quantitative information from multiple sources of prior knowledge. It first uses the Naïve Bayesian classifier to assess the likelihood of functional linkage between gene pairs based on prior knowledge. In this study we included cocitation in PubMed and schematic similarity in Gene Ontology annotation. A candidate network edge reservoir is then created in which the copy number of each edge is proportional to the estimated likelihood of linkage between the two corresponding genes. In network simulation the Markov Chain Monte Carlo sampling algorithm is adopted, and samples from this reservoir at each iteration to generate new candidate networks. We evaluated the new algorithm using both simulated and real gene expression data including that from a yeast cell cycle and a mouse pancreas development/growth study. Incorporating prior knowledge led to a ~2 fold increase in the number of known transcription regulations recovered, without significant change in false positive rate. In contrast, without the prior knowledge BN modeling is not always better than a random selection, demonstrating the necessity in network modeling to supplement the gene expression data with additional information.</p> <p>Conclusion</p> <p>our new development provides a statistical means to utilize the quantitative information in prior biological knowledge in the BN modeling of gene expression data, which significantly improves the performance.</p

Study of the Baryon-Antibaryon Low-Mass Enhancements in Charmless Three-body Baryonic B Decays

The angular distributions of the baryon-antibaryon low-mass enhancements seen in the charmless three-body baryonic B decays B+ -> p pbar K+, B0 -> p pbar Ks, and B0 -> p Lambdabar pi- are reported. A quark fragmentation interpretation is supported, while the gluonic resonance picture is disfavored. Searches for the Theta+ and Theta++ pentaquarks in the relevant decay modes and possible glueball states G with 2.2 GeV/c2 < M-ppbar < 2.4 GeV/c2 in the ppbar systems give null results. We set upper limits on the products of branching fractions, B(B0 -> Theta+ p)\times B(Theta+ -> p Ks) Theta++ pbar) \times B(Theta++ -> p K+) G K+) \times B(G -> p pbar) < 4.1 \times 10^{-7} at the 90% confidence level. The analysis is based on a 140 fb^{-1} data sample recorded on the Upsilon(4S) resonance with the Belle detector at the KEKB asymmetric-energy e+e- collider.Comment: 14 pages, 13 figure files, update of hep-ex/0409010 for journal submisssio

Optical Holonomic Quantum Computer

In this paper the idea of holonomic quantum computation is realized within quantum optics. In a non-linear Kerr medium the degenerate states of laser beams are interpreted as qubits. Displacing devices, squeezing devices and interferometers provide the classical control parameter space where the adiabatic loops are performed. This results into logical gates acting on the states of the combined degenerate subspaces of the lasers, producing any one qubit rotations and interactions between any two qubits. Issues such as universality, complexity and scalability are addressed and several steps are taken towards the physical implementation of this model.Comment: 16 pages, 3 figures, REVTE

Clinical significance of Phosphatidyl Inositol Synthase overexpression in oral cancer

<p>Abstract</p> <p>Background</p> <p>We reported increased levels of Phosphatidyl Inositol synthase (PI synthase), (enzyme that catalyses phosphatidyl inositol (PI) synthesis-implicated in intracellular signaling and regulation of cell growth) in smokeless tobacco (ST) exposed oral cell cultures by differential display. This study determined the clinical significance of PI synthase overexpression in oral squamous cell carcinoma (OSCC) and premalignant lesions (leukoplakia), and identified the downstream signaling proteins in PI synthase pathway that are perturbed by smokeless tobacco (ST) exposure.</p> <p>Methods</p> <p>Tissue microarray (TMA) Immunohistochemistry, Western blotting, Confocal laser scan microscopy, RT-PCR were performed to define the expression of PI synthase in clinical samples and in oral cell culture systems.</p> <p>Results</p> <p>Significant increase in PI synthase immunoreactivity was observed in premalignant lesions and OSCCs as compared to oral normal tissues (p = 0.000). Further, PI synthase expression was significantly associated with de-differentiation of OSCCs, (p = 0.005) and tobacco consumption (p = 0.03, OR = 9.0). Exposure of oral cell systems to smokeless tobacco (ST) in vitro confirmed increase in PI synthase, Phosphatidylinositol 3-kinase (PI3K) and cyclin D1 levels.</p> <p>Conclusion</p> <p>Collectively, increased PI synthase expression was found to be an early event in oral cancer and a target for smokeless tobacco.</p