T Oligo-Primed Polymerase Chain Reaction (TOP-PCR): A Robust Method for the Amplification of Minute DNA Fragments in Body Fluids.

Body fluid DNA sequencing is a powerful noninvasive approach for the diagnosis of genetic defects, infectious agents and diseases. The success relies on the quantity and quality of the DNA samples. However, numerous clinical samples are either at low quantity or of poor quality due to various reasons. To overcome these problems, we have developed T oligo-primed polymerase chain reaction (TOP-PCR) for full-length nonselective amplification of minute quantity of DNA fragments. TOP-PCR adopts homogeneous "half adaptor" (HA), generated by annealing P oligo (carrying a phosphate group at the 5' end) and T oligo (carrying a T-tail at the 3' end), for efficient ligation to target DNA and subsequent PCR amplification primed by the T oligo alone. Using DNA samples from body fluids, we demonstrate that TOP-PCR recovers minute DNA fragments and maintains the DNA size profile, while enhancing the major molecular populations. Our results also showed that TOP-PCR is a superior method for detecting apoptosis and outperforms the method adopted by Illumina for DNA amplification

A proposal for implementing an n-qubit controlled-rotation gate with three-level superconducting qubit systems in cavity QED

We present a way for implementing an n-qubit controlled-rotation gate with three-level superconducting qubit systems in cavity QED. The two logical states of a qubit are represented by the two lowest levels of each system while a higher-energy level is used for the gate implementation. The method operates essentially by preparing a $W$ state conditioned on the states of the control qubits, creating a single photon in the cavity mode, and then performing an arbitrary rotation on the states of the target qubit with assistance of the cavity photon. It is interesting to note that the basic operational steps for implementing the proposed gate do not increase with the number $n$ of qubits, and the gate operation time decreases as the number of qubits increases. This proposal is quite general, which can be applied to various types of superconducting devices in a cavity or coupled to a resonator.Comment: Six figures, accepted by Journal of Physics: Condensed Matte

Apparent source levels and active communication space of whistles of free-ranging Indo-Pacific humpback dolphins (Sousa chinensis) in the Pearl River Estuary and Beibu Gulf, China

Grants for this study was provided by the National Natural Science Foundation (NNSF) of China (Grant No.31070347), the Ministry of Science and Technology of China (Grant No. 2011BAG07B05-3), the Knowledge Innovation Program of the Chinese Academy of Sciences (Grant No. KSCX2-EW-Z-4) and the Special Fund for Agro-scientific Research in the Public Interest of the Ministry of Agriculture of China (Grant No. 201203086) to DW, the State Oceanic Administration of China (Grant No. 201105011-3) and NNSF of China (Grant No. 31170501) to KXW and the China Scholarship Council (Grant No. (2014)3026) to ZTW.Background . Knowledge of species-specific vocalization characteristics and their associated active communication space, the effective range over which a communication signal can be detected by a conspecific, is critical for understanding the impacts of underwater acoustic pollution, as well as other threats. Methods. We used a two-dimensional cross-shaped hydrophone array system to record the whistles of free-ranging Indo-Pacific humpback dolphins (Sousa chinensis) in shallow-water environments of the Pearl River Estuary (PRE) and Beibu Gulf (BG), China. Using hyperbolic position fixing, which exploits time differences of arrival of a signal between pairs of hydrophone receivers, we obtained source location estimates for whistles with good signal-to-noise ratio (SNR  ≥ 10 dB) and not polluted by other sounds and back-calculated their apparent source levels (ASL). Combining with the masking levels (including simultaneous noise levels, masking tonal threshold, and the Sousa auditory threshold) and the custom made site-specific sound propagation models, we further estimated their active communication space (ACS). Results. Humpback dolphins produced whistles with average root-mean-square ASL of 138.5 ± 6.8 (mean ± standard deviation) and 137.2 ± 7.0 dB re 1 µPa in PRE (N = 33) and BG (N = 209), respectively. We found statistically significant differences in ASLs among different whistle contour types. The mean and maximum ACS of whistles were estimated to be 14.7 ± 2.6 (median ± quartile deviation) and 17.1 ± 3.5 m in PRE, and 34.2 ± 9.5 and 43.5 ±12.2 m in BG. Using just the auditory threshold as the masking level produced the mean and maximum ACSat of 24.3 ± 4.8 and 35.7 ± 4.6 m for PRE, and 60.7 ± 18.1 and 74.3 ± 25.3 m for BG. The small ACSs were due to the high ambient noise level. Significant differences in ACSs were also observed among different whistle contour types. Discussion. Besides shedding some light for evaluating appropriate noise exposure levels and information for the regulation of underwater acoustic pollution, these baseline data can also be used for aiding the passive acoustic monitoring of dolphin populations, defining the boundaries of separate groups in a more biologically meaningful way during field surveys, and guiding the appropriate approach distance for local dolphin-watching boats and research boat during focal group following.Publisher PDFPeer reviewe

Efficient symmetric multiparty quantum state sharing of an arbitrary m-qubit state

We present a scheme for symmetric multiparty quantum state sharing of an arbitrary $m$-qubit state with $m$ Greenberger-Horne-Zeilinger states following some ideas from the controlled teleportation [Phys. Rev. A \textbf{72}, 02338 (2005)]. The sender Alice performs $m$ Bell-state measurements on her $2m$ particles and the controllers need only to take some single-photon product measurements on their photons independently, not Bell-state measurements, which makes this scheme more convenient than the latter. Also it does not require the parties to perform a controlled-NOT gate on the photons for reconstructing the unknown $m$-qubit state and it is an optimal one as its efficiency for qubits approaches the maximal value.Comment: 6 pages, no figures; It simplifies the process for sharing an arbitrary m-qubit state in Phys. Rev. A 72, 022338 (2005) (quant-ph/0501129

A Novel Clustering Algorithm Based on Quantum Games

Enormous successes have been made by quantum algorithms during the last decade. In this paper, we combine the quantum game with the problem of data clustering, and then develop a quantum-game-based clustering algorithm, in which data points in a dataset are considered as players who can make decisions and implement quantum strategies in quantum games. After each round of a quantum game, each player's expected payoff is calculated. Later, he uses a link-removing-and-rewiring (LRR) function to change his neighbors and adjust the strength of links connecting to them in order to maximize his payoff. Further, algorithms are discussed and analyzed in two cases of strategies, two payoff matrixes and two LRR functions. Consequently, the simulation results have demonstrated that data points in datasets are clustered reasonably and efficiently, and the clustering algorithms have fast rates of convergence. Moreover, the comparison with other algorithms also provides an indication of the effectiveness of the proposed approach.Comment: 19 pages, 5 figures, 5 table

Improving the coverage and accuracy of syphilis testing: The development of a novel rapid, point-of-care test for confirmatory testing of active syphilis infection and its early evaluation in China and South Africa

Background: Current point-of-care tests (POCT) for syphilis, based on the detection of Treponema pallidum (TP) total antibodies, have limited capacity in distinguishing between active and past/treated syphilis. We report the development and early evaluation of a new prototype POCT based on the detection of TP-IgA antibodies, a novel biomarker for active syphilis. Methods: The TP-IgA POCT (index test) was developed in response to the World Health Organisation (WHO) target product profile (TPP) for a POCT for confirmatory syphilis testing. Two sub-studies were conducted consecutively using 458 pre-characterised stored plasma samples in China (sub-study one, addressing the criteria for the WHO TPP), and 503 venous blood samples collected from pregnant/postpartum women in South Africa (sub-study two, addressing potential clinical utility). Performance of the index test was assessed against standard laboratory-based serology using a combination of treponemal (TPHA) and non-treponemal (rapid plasma reagin [RPR]) tests. Findings: In sub-study one, the index test demonstrated 96·1% (95%CI=91·7%-98·5%) sensitivity and 84·7% (95%CI=80·15–88·6%) specificity for identification of active syphilis (TPHA positive, RPR positive). It correctly identified 71% (107/150) samples of past-treated syphilis (TPHA positive, RPR negative). In sub-study two, the index test achieved 100% (95%CI=59%-100%) sensitivity for active syphilis and correctly identified all nine women with past syphilis. Interpretation: The TP-IgA POCT has met the WHO TPP for a POCT for diagnosis of active syphilis and demonstrated its potential utility in a clinical setting. Future studies are warranted to evaluate field performance of the final manufactured test. Funding: Saving Lives at Birth: Grand Challenge for Development, Thrasher Research Fund, and the Victorian Government Operational Infrastructure Scheme

Multiparty Quantum Secret Report

A multiparty quantum secret report scheme is proposed with quantum encryption. The boss Alice and her $M$ agents first share a sequence of ($M$+1)-particle Greenberger--Horne--Zeilinger (GHZ) states that only Alice knows which state each ($M$+1)-particle quantum system is in. Each agent exploits a controlled-not (CNot) gate to encrypt the travelling particle by using the particle in the GHZ state as the control qubit. The boss Alice decrypts the travelling particle with a CNot gate after performing a $\sigma_x$ operation on her particle in the GHZ state or not. After the GHZ states (the quantum key) are used up, the parties check whether there is a vicious eavesdropper, say Eve, monitoring the quantum line, by picking out some samples from the GHZ states shared and measure them with two measuring bases. After confirming the security of the quantum key, they use the GHZ states remained repeatedly for next round of quantum communication. This scheme has the advantage of high intrinsic efficiency for qubits and the total efficiency.Comment: 4 pages, no figure

Disruption of estrogen receptor DNA-binding domain and related intramolecular communication restores tamoxifen sensitivity in resistant breast cancer

SummaryA serious obstacle to successful treatment of estrogen receptor (ER)-positive human breast cancer is cell resistance to tamoxifen (TAM) therapy. Here we show that the electrophile disulfide benzamide (DIBA), an ER zinc finger inhibitor, blocks ligand-dependent and -independent cell growth of TAM-resistant breast cancer in vitro and in vivo. Such inhibition depends on targeting disruption of the ER DNA-binding domain and its communication with neighboring functional domains, facilitating ERα dissociation from its coactivator AIB1 and concomitant association with its corepressor NCoR bound to chromatin. DIBA does not affect phosphorylation of HER2, MAPK, AKT, and AIB1, suggesting that DIBA-modified ERα may induce a switch from agonistic to antagonistic effects of TAM on resistant breast cancer cells

Adaptation of a visualized loop-mediated isothermal amplification technique for field detection of Plasmodium vivax infection

<p>Abstract</p> <p>Background</p> <p>Loop-mediated isothermal amplification (LAMP) is a high performance method for detecting DNA and holds promise for use in the molecular detection of infectious pathogens, including <it>Plasmodium </it>spp. However, in most malaria-endemic areas, which are often resource-limited, current LAMP methods are not feasible for diagnosis due to difficulties in accurately interpreting results with problems of sensitive visualization of amplified products, and the risk of contamination resulting from the high quantity of amplified DNA produced. In this study, we establish a novel visualized LAMP method in a closed-tube system, and validate it for the diagnosis of malaria under simulated field conditions.</p> <p>Methods</p> <p>A visualized LAMP method was established by the addition of a microcrystalline wax-dye capsule containing the highly sensitive DNA fluorescence dye SYBR Green I to a normal LAMP reaction prior to the initiation of the reaction. A total of 89 blood samples were collected on filter paper and processed using a simple boiling method for DNA extraction, and then tested by the visualized LAMP method for <it>Plasmodium vivax </it>infection.</p> <p>Results</p> <p>The wax capsule remained intact during isothermal amplification, and released the DNA dye to the reaction mixture only when the temperature was raised to the melting point following amplification. Soon after cooling down, the solidified wax sealed the reaction mix at the bottom of the tube, thus minimizing the risk of aerosol contamination. Compared to microscopy, the sensitivity and specificity of LAMP were 98.3% (95% confidence interval (CI): 91.1-99.7%) and 100% (95% CI: 88.3-100%), and were in close agreement with a nested polymerase chain reaction method.</p> <p>Conclusions</p> <p>This novel, cheap and quick visualized LAMP method is feasible for malaria diagnosis in resource-limited field settings.</p

Magnetic Behavior of a Mixed Ising Ferrimagnetic Model in an Oscillating Magnetic Field

The magnetic behavior of a mixed Ising ferrimagnetic system on a square lattice, in which the two interpenetrating square sublattices have spins +- 1/2 and spins +-1,0, in the presence of an oscillating magnetic field has been studied with Monte Carlo techniques. The model includes nearest and next-nearest neighbor interactions, a crystal field and the oscillating external field. By studying the hysteretic response of this model to an oscillating field we found that it qualitatively reproduces the increasing of the coercive field at the compensation temperature observed in real ferrimagnets, a crucial feature for magneto-optical applications. This behavior is basically independent of the frequency of the field and the size of the system. The magnetic response of the system is related to a dynamical transition from a paramagnetic to a ferromagnetic phase and to the different temperature dependence of the relaxation times of both sublattices.Comment: 10 figures. To be published in Phys.Rev