A unified approach to realize universal quantum gates in a coupled two-qubit system with fixed always-on coupling

We demonstrate that in a coupled two-qubit system any single-qubit gate can be decomposed into two conditional two-qubit gates and that any conditional two-qubit gate can be implemented by a manipulation analogous to that used for a controlled two-qubit gate. Based on this we present a unified approach to implement universal single-qubit and two-qubit gates in a coupled two-qubit system with fixed always-on coupling. This approach requires neither supplementary circuit or additional physical qubits to control the coupling nor extra hardware to adjust the energy level structure. The feasibility of this approach is demonstrated by numerical simulation of single-qubit gates and creation of two-qubit Bell states in rf-driven inductively coupled two SQUID flux qubits with realistic device parameters and constant always-on coupling.Comment: 4 pages, 3 figure

Quantifying differential gene connectivity between disease states for objective identification of disease-relevant genes

<p>Abstract</p> <p>Background</p> <p>Network modeling of whole transcriptome expression data enables characterization of complex epistatic (gene-gene) interactions that underlie cellular functions. Though numerous methods have been proposed and successfully implemented to develop these networks, there are no formal methods for comparing differences in network connectivity patterns as a function of phenotypic trait.</p> <p>Results</p> <p>Here we describe a novel approach for quantifying the differences in gene-gene connectivity patterns across disease states based on Graphical Gaussian Models (GGMs). We compare the posterior probabilities of connectivity for each gene pair across two disease states, expressed as a posterior odds-ratio (postOR) for each pair, which can be used to identify network components most relevant to disease status. The method can also be generalized to model differential gene connectivity patterns within previously defined gene sets, gene networks and pathways. We demonstrate that the GGM method reliably detects differences in network connectivity patterns in datasets of varying sample size. Applying this method to two independent breast cancer expression data sets, we identified numerous reproducible differences in network connectivity across histological grades of breast cancer, including several published gene sets and pathways. Most notably, our model identified two gene hubs (MMP12 and CXCL13) that each exhibited differential connectivity to more than 30 transcripts in both datasets. Both genes have been previously implicated in breast cancer pathobiology, but themselves are not differentially expressed by histologic grade in either dataset, and would thus have not been identified using traditional differential gene expression testing approaches. In addition, 16 curated gene sets demonstrated significant differential connectivity in both data sets, including the matrix metalloproteinases, PPAR alpha sequence targets, and the PUFA synthesis pathway.</p> <p>Conclusions</p> <p>Our results suggest that GGM can be used to formally evaluate differences in global interactome connectivity across disease states, and can serve as a powerful tool for exploring the molecular events that contribute to disease at a systems level.</p

A Passively Mode-locked Nanosecond Laser with an Ultra-narrow Spectral Width

Many different mode-locking techniques have been realized in the past [1, 2], but mainly focused on increasing the spectral bandwidth to achieve ultra-short coherent light pulses with well below picosecond duration. In contrast, no mode-locked laser scheme has managed to generate Fourier-limited nanosecond long pulses, which feature narrow spectral bandwidths (~MHz regime) instrumental to applications in spectroscopy, efficient excitation of molecules, sensing, and quantum optics. The related limitations are mainly caused by the adverse operation timescales of saturable absorbers, as well as by the low strength of the nonlinear effects typically reachable through nanosecond pulses with manageable energies

Copy number variation genotyping using family information

BACKGROUND: In recent years there has been a growing interest in the role of copy number variations (CNV) in genetic diseases. Though there has been rapid development of technologies and statistical methods devoted to detection in CNVs from array data, the inherent challenges in data quality associated with most hybridization techniques remains a challenging problem in CNV association studies. RESULTS: To help address these data quality issues in the context of family-based association studies, we introduce a statistical framework for the intensity-based array data that takes into account the family information for copy-number assignment. The method is an adaptation of traditional methods for modeling SNP genotype data that assume Gaussian mixture model, whereby CNV calling is performed for all family members simultaneously and leveraging within family-data to reduce CNV calls that are incompatible with Mendelian inheritance while still allowing de-novo CNVs. Applying this method to simulation studies and a genome-wide association study in asthma, we find that our approach significantly improves CNV calls accuracy, and reduces the Mendelian inconsistency rates and false positive genotype calls. The results were validated using qPCR experiments. CONCLUSIONS: In conclusion, we have demonstrated that the use of family information can improve the quality of CNV calling and hopefully give more powerful association test of CNVs

Copy number variation genotyping using family information

Abstract Background In recent years there has been a growing interest in the role of copy number variations (CNV) in genetic diseases. Though there has been rapid development of technologies and statistical methods devoted to detection in CNVs from array data, the inherent challenges in data quality associated with most hybridization techniques remains a challenging problem in CNV association studies. Results To help address these data quality issues in the context of family-based association studies, we introduce a statistical framework for the intensity-based array data that takes into account the family information for copy-number assignment. The method is an adaptation of traditional methods for modeling SNP genotype data that assume Gaussian mixture model, whereby CNV calling is performed for all family members simultaneously and leveraging within family-data to reduce CNV calls that are incompatible with Mendelian inheritance while still allowing de-novo CNVs. Applying this method to simulation studies and a genome-wide association study in asthma, we find that our approach significantly improves CNV calls accuracy, and reduces the Mendelian inconsistency rates and false positive genotype calls. The results were validated using qPCR experiments. Conclusions In conclusion, we have demonstrated that the use of family information can improve the quality of CNV calling and hopefully give more powerful association test of CNVs.http://deepblue.lib.umich.edu/bitstream/2027.42/112374/1/12859_2012_Article_5896.pd

High aldehyde dehydrogenase and expression of cancer stem cell markers selects for breast cancer cells with enhanced malignant and metastatic ability

Cancer stem cells (CSCs) have recently been identified in leukaemia and solid tumours; however, the role of CSCs in metastasis remains poorly understood. This dearth of knowledge about CSCs and metastasis is due largely to technical challenges associated with the use of primary human cancer cells in pre-clinical models of metastasis. Therefore, the objective of this study was to develop suitable pre-clinical model systems for studying stem-like cells in breast cancer metastasis, and to test the hypothesis that stem-like cells play a key role in metastatic behaviour. We assessed four different human breast cancer cell lines (MDA-MB-435, MDA-MB-231, MDA-MB-468, MCF-7) for expression of prospective CSC markers CD44/CD24 and CD133, and for functional activity of aldehyde dehydrogenase (ALDH), an enzyme involved in stem cell self-protection. We then used fluorescence-activated cell sorting and functional assays to characterize differences in malignant/metastatic behaviour in vitro (proliferation, colony-forming ability, adhesion, migration, invasion) and in vivo (tumorigenicity and metastasis). Sub-populations of cells demonstrating stem-cell-like characteristics (high expression of CSC markers and/or high ALDH) were identified in all cell lines except MCF-7. When isolated and compared to ALDHlowCD44low/- cells, ALDHhiCD44+CD24- (MDA-MB-231) and ALDHhiCD44+CD133+ (MDA-MB-468) cells demonstrated increased growth (P \u3c 0.05), colony formation (P \u3c 0.05), adhesion (P \u3c 0.001), migration (P \u3c 0.001) and invasion (P \u3c 0.001). Furthermore, following tail vein or mammary fat pad injection of NOD/SCID/IL2 gamma receptor null mice, ALDHhiCD44+CD24- and ALDHhiCD44+CD133+ cells showed enhanced tumorigenicity and metastasis relative to ALDHlowCD44low/- cells (P \u3c 0.05). These novel results suggest that stem-like ALDHhiCD44+CD24- and ALDHhiCD44+CD133+ cells may be important mediators of breast cancer metastasis

Comparisons among ten models of acoustic backscattering used in aquatic ecosystem research

Author Posting. © Acoustical Society of America, 2015. This article is posted here by permission of Acoustical Society of America for personal use, not for redistribution. The definitive version was published in Journal of the Acoustical Society of America 138 (2015); 3742, doi:10.1121/1.4937607.Analytical and numerical scatteringmodels with accompanying digital representations are used increasingly to predict acoustic backscatter by fish and zooplankton in research and ecosystem monitoring applications. Ten such models were applied to targets with simple geometric shapes and parameterized (e.g., size and material properties) to represent biological organisms such as zooplankton and fish, and their predictions of acoustic backscatter were compared to those from exact or approximate analytical models, i.e., benchmarks. These comparisons were made for a sphere, spherical shell, prolate spheroid, and finite cylinder, each with homogeneous composition. For each shape, four target boundary conditions were considered: rigid-fixed, pressure-release, gas-filled, and weakly scattering. Target strength (dB re 1 m2) was calculated as a function of insonifying frequency (f = 12 to 400 kHz) and angle of incidence (θ = 0° to 90°). In general, the numerical models (i.e., boundary- and finite-element) matched the benchmarks over the full range of simulation parameters. While inherent errors associated with the approximate analytical models were illustrated, so were the advantages as they are computationally efficient and in certain cases, outperformed the numerical models under conditions where the numerical models did not convergeThis work was supported by the NOAA Fisheries Advanced Sampling Technologies Working Group, the Office of Naval Research, and the National Oceanic Partnership Program. Josiah S. Renfree

Uniformity in the Wiener-Wintner theorem for nilsequences

We prove a uniform extension of the Wiener-Wintner theorem for nilsequences due to Host and Kra and a nilsequence extension of the topological Wiener-Wintner theorem due to Assani. Our argument is based on (vertical) Fourier analysis and a Sobolev embedding theorem.Comment: v3: 18 p., proof that the cube construction produces compact homogeneous spaces added, measurability issues in the proof of Theorem 1.5 addressed. We thank the anonymous referees for pointing out these gaps in v

Unveiling the molecular environment of the ring nebula RCW 78

We present a study of the ionized, neutral atomic, and molecular gas associated with the ring nebula RCW 78 around the WR star HD 117688 (= WR 55). We based our study on CO observations carried out with the SEST and NANTEN telescopes. We report the detection of molecular gas with velocities in the range -56 to -33 km/s. The CO emission is mainly connected to the western section, with a total molecular mass of 1.3 x 10^5 solar masses. The analysis of the HI gas distribution reveals the HI envelope of the molecular cloud, while the radio continuum emission shows a ring-like structure, which is the radio counterpart of the optical nebula. The gas distribution is compatible with the western section of RCW 78 having originated in the photodissociation and ionization of the molecular gas by HD 117688, and with the action of the stellar winds of the WR star. A number of infrared point sources classified as YSO candidates showed that stellar formation activity is present in the molecular gas linked to the nebula. The fact that the expansion of the bubble have triggered star formation in this region can not be discarded.Comment: 15 pages, 11 Postscript figures, to be published in A&