Proposed Experiment in Two-Qubit Linear Optical Photonic Gates for Maximal Success Rates

Here we propose an experiment in Linear Optical Quantum Computing (LOQC) using the framework first developed by Knill, Laflamme, and Milburn. This experiment will test the ideas of the authors' previous work on imperfect LOQC gates using number-resolving photon detectors. We suggest a relatively simple physical apparatus capable of producing CZ gates with controllable fidelity less than 1 and success rates higher than the current theoretical maximum (S=2/27) for perfect fidelity. These experimental setups are within the reach of many experimental groups and would provide an interesting experiment in photonic quantum computing.Comment: 9 pages, 3 figure

Imperfect Linear Optical Photonic Gates with Number-Resolving Photodetection

We use the numerical optimization techniques of Uskov et al. [PRA 81, 012303 (2010)] to investigate the behavior of the success rates for KLM style [Nature 409, 46 (2001)] two- and three-qubit entangling gates. The methods are first demonstrated at perfect fidelity, and then extended to imperfect gates. We find that as the perfect fidelity condition is relaxed, the maximum attainable success rates increase in a predictable fashion depending on the size of the system, and we compare that rate of increase for several gates.Comment: 7 pages, 7 figure

Linear and Nonlinear Rogue Wave Statistics in the Presence of Random Currents

We review recent progress in modeling the probability distribution of wave heights in the deep ocean as a function of a small number of parameters describing the local sea state. Both linear and nonlinear mechanisms of rogue wave formation are considered. First, we show that when the average wave steepness is small and nonlinear wave effects are subleading, the wave height distribution is well explained by a single "freak index" parameter, which describes the strength of (linear) wave scattering by random currents relative to the angular spread of the incoming random sea. When the average steepness is large, the wave height distribution takes a very similar functional form, but the key variables determining the probability distribution are the steepness, and the angular and frequency spread of the incoming waves. Finally, even greater probability of extreme wave formation is predicted when linear and nonlinear effects are acting together.Comment: 25 pages, 12 figure

Systematic Study of Rogue Wave Probability Distributions in a Fourth-Order Nonlinear Schr\"odinger Equation

Nonlinear instability and refraction by ocean currents are both important mechanisms that go beyond the Rayleigh approximation and may be responsible for the formation of freak waves. In this paper, we quantitatively study nonlinear effects on the evolution of surface gravity waves on the ocean, to explore systematically the effects of various input parameters on the probability of freak wave formation. The fourth-order current-modified nonlinear Schr\"odinger equation (CNLS4) is employed to describe the wave evolution. By solving CNLS4 numerically, we are able to obtain quantitative predictions for the wave height distribution as a function of key environmental conditions such as average steepness, angular spread, and frequency spread of the local sea state. Additionally, we explore the spatial dependence of the wave height distribution, associated with the buildup of nonlinear development.Comment: 10 pages, 11 figures, to appear in Journal of Geophysical Research - Ocean

Nanoscale probing of electron-regulated structural transitions in silk proteins by near-field IR imaging and nano-spectroscopy

Silk protein fibres produced by silkworms and spiders are renowned for their unparalleled mechanical strength and extensibility arising from their high-β-sheet crystal contents as natural materials. Investigation of β-sheet-oriented conformational transitions in silk proteins at the nanoscale remains a challenge using conventional imaging techniques given their limitations in chemical sensitivity or limited spatial resolution. Here, we report on electron-regulated nanoscale polymorphic transitions in silk proteins revealed by near-field infrared imaging and nano-spectroscopy at resolutions approaching the molecular level. The ability to locally probe nanoscale protein structural transitions combined with nanometre-precision electron-beam lithography offers us the capability to finely control the structure of silk proteins in two and three dimensions. Our work paves the way for unlocking essential nanoscopic protein structures and critical conditions for electron-induced conformational transitions, offering new rules to design protein-based nanoarchitectures.National Science Foundation (U.S.) (1563422)National Science Foundation (U.S.) (1562915

Discovery of directional and nondirectional pioneer transcription factors by modeling DNase profile magnitude and shape

We describe protein interaction quantitation (PIQ), a computational method for modeling the magnitude and shape of genome-wide DNase I hypersensitivity profiles to identify transcription factor (TF) binding sites. Through the use of machine-learning techniques, PIQ identified binding sites for >700 TFs from one DNase I hypersensitivity analysis followed by sequencing (DNase-seq) experiment with accuracy comparable to that of chromatin immunoprecipitation followed by sequencing (ChIP-seq). We applied PIQ to analyze DNase-seq data from mouse embryonic stem cells differentiating into prepancreatic and intestinal endoderm. We identified 120 and experimentally validated eight 'pioneer' TF families that dynamically open chromatin. Four pioneer TF families only opened chromatin in one direction from their motifs. Furthermore, we identified 'settler' TFs whose genomic binding is principally governed by proximity to open chromatin. Our results support a model of hierarchical TF binding in which directional and nondirectional pioneer activity shapes the chromatin landscape for population by settler TFs.National Institutes of Health (U.S.) (Common Fund 5UL1DE019581)National Institutes of Health (U.S.) (Common Fund RL1DE019021)National Institutes of Health (U.S.) (Common Fund 5TL1EB008540)National Institutes of Health (U.S.) (Grant 1U01HG007037)National Institutes of Health (U.S.) (Grant 5P01NS055923

Evidence for an association of HLA-DRB1*15 and DRB1*09 with leprosy and the impact of DRB1*09 on disease onset in a Chinese Han population

<p>Abstract</p> <p>Background</p> <p>Human leukocyte antigens (HLAs) have been proposed to modulate the immune response to <it>Mycobacterium leprae</it>. The association of HLA-DRB1 with leprosy has been reported in several populations, but not in a Chinese population.</p> <p>Methods</p> <p>The polymerase chain reaction-sequence-specific oligonucleotide probe with Luminex100 (PCR-SSOP-Luminex) method was used to genotype HLA-DRB1 alleles in 305 leprosy patients and 527 healthy control individuals.</p> <p>Results</p> <p>The HLA-DRB1*15 allele was significantly more prevalent among leprosy patients than healthy controls, whereas the frequency of the HLA-DRB1*09 allele was lower among leprosy patients, especially those with early-onset disease.</p> <p>Conclusion</p> <p>HLA-DRB1 alleles are associated with leprosy susceptibility in a Chinese population. The HLA-DRB1*09 allele was found to be protective exclusively in a subset of early-onset leprosy patients.</p

Midkine is a NF-κB-inducible gene that supports prostate cancer cell survival

BackgroundMidkine is a heparin-binding growth factor that is over-expressed in various human cancers and plays important roles in cell transformation, growth, survival, migration, and angiogenesis. However, little is known about the upstream factors and signaling mechanisms that regulate midkine gene expression.MethodsTwo prostate cancer cell lines LNCaP and PC3 were studied for their expression of midkine. Induction of midkine expression in LNCaP cells by serum, growth factors and cytokines was determined by Western blot analysis and/or real-time quantitative reverse-transcription - polymerase chain reaction (RT-PCR). The cell viability was determined by the trypan blue exclusion assay when the LNCaP cells were treated with tumor necrosis factor alpha (TNFalpha) and/or recombinant midkine. When the LNCaP cells were treated with recombinant midkine, activation of intracellular signalling pathways was determined by Western blot analysis. Prostate tissue microarray slides containing 129 cases (18 normal prostate tissues, 40 early stage cancers, and 71 late stage cancers) were assessed for midkine expression by immunohistochemical staining.ResultsWe identified that fetal bovine serum, some growth factors (epidermal growth factor, androgen, insulin-like growth factor-I, and hepatocyte growth factor) and cytokines (TNFalpha and interleukin-1beta) induced midkine expression in a human prostate cancer cell line LNCaP cells. TNFalpha also induced midkine expression in PC3 cells. TNFalpha was the strongest inducer of midkine expression via nuclear factor-kappa B pathway. Midkine partially inhibited TNFalpha-induced apoptosis in LNCaP cells. Knockdown of endogenous midkine expression by small interfering RNA enhanced TNFalpha-induced apoptosis in LNCaP cells. Midkine activated extracellular signal-regulated kinase 1/2 and p38 mitogen-activated protein kinase pathways in LNCaP cells. Furthermore, midkine expression was significantly increased in late stage prostate cancer, which coincides with previously reported high serum levels of TNFalpha in advanced prostate cancer.ConclusionThese findings provide the first demonstration that midkine expression is induced by certain growth factors and cytokines, particularly TNFalpha, which offers new insight into understanding how midkine expression is increased in the late stage prostate cancer

Speech and melody recognition in binaurally combined acoustic and electric hearing

Speech recognition in noise and music perception is especially challenging for current cochlear implant users. The present study utilizes the residual acoustic hearing in the nonimplanted ear in five cochlear implant users to elucidate the role of temporal fine structure at low frequencies in auditory perception and to test the hypothesis that combined acoustic and electric hearing produces better performance than either mode alone. The first experiment measured speech recognition in the presence of competing noise. It was found that, although the residual low-frequency (&lt; 1000 Hz) acoustic hearing produced essentially no recognition for speech recognition in noise, it significantly enhanced performance when combined with the electric hearing. The second experiment measured melody recognition in the same group of subjects and found that, contrary to the speech recognition result, the low-frequency acoustic hearing produced significantly better performance than the electric hearing. It is hypothesized that listeners with combined acoustic and electric hearing might use the correlation between the salient pitch in low-frequency acoustic hearing and the weak pitch in the envelope to enhance segregation between signal and noise. The present study suggests the importance and urgency of accurately encoding the fine-structure cue in cochlear implants. (c) 2005 Acoustical Society of America