"Virus hunting" using radial distance weighted discrimination

Motivated by the challenge of using DNA-seq data to identify viruses in human blood samples, we propose a novel classification algorithm called "Radial Distance Weighted Discrimination" (or Radial DWD). This classifier is designed for binary classification, assuming one class is surrounded by the other class in very diverse radial directions, which is seen to be typical for our virus detection data. This separation of the 2 classes in multiple radial directions naturally motivates the development of Radial DWD. While classical machine learning methods such as the Support Vector Machine and linear Distance Weighted Discrimination can sometimes give reasonable answers for a given data set, their generalizability is severely compromised because of the linear separating boundary. Radial DWD addresses this challenge by using a more appropriate (in this particular case) spherical separating boundary. Simulations show that for appropriate radial contexts, this gives much better generalizability than linear methods, and also much better than conventional kernel based (nonlinear) Support Vector Machines, because the latter methods essentially use much of the information in the data for determining the shape of the separating boundary. The effectiveness of Radial DWD is demonstrated for real virus detection.Comment: Published at http://dx.doi.org/10.1214/15-AOAS869 in the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

Gravitational Lensing by Dark Matter Halos with Non-universal Density Profiles

The statistics of gravitational lensing can provide us with a very powerful probe of the mass distribution of matter in the universe. By comparing predicted strong lensing probabilities with observations, we can test the mass distribution of dark matter halos, in particular, the inner density slope. In this letter, unlike previous work that directly models the density profiles of dark matter halos semi-analytically, we generalize the density profiles of dark matter halos from high-resolution N-body simulations by means of generalized Navarro-Frenk-White (GNFW) models of three populations with slopes, $\alpha$, of about -1.5, -1.3 and -1.1 for galaxies, groups and clusters, respectively. This approach is an alternative and independent way to examine the slopes of mass density profiles of halos. We present calculations of lensing probabilities using these GNFW profiles for three populations in various spatially flat cosmological models with a cosmological constant $\Lambda$. It is shown that the compound model of density profiles does not match well with the observed lensing probabilities derived from the Jodrell-Bank VLA Astrometric Survey data in combination with the Cosmic Lens All-Sky Survey data. Together with the previous work on lensing probability, our results suggest that a singular isothermal sphere mass model of less than about 10^{13}h^{-1}M_{\sun} can predict strong lensing probabilities that are consistent with observations of small splitting angles.Comment: 11 pages, 2 figures, Accepted by ApJL for publication (February 10 issue 2004

Regulating the adaptive immune response to respiratory virus infection

This article is made available for unrestricted research re-use and secondary analysis in any form or by any means with acknowledgement of the original source. These permissions are granted for the duration of the World Health Organization (WHO) declaration of COVID-19 as a global pandemic.Recent years have seen several advances in our understanding of immunity to virus infection of the lower respiratory tract, including to influenza virus infection. Here, we review the cellular targets of viruses and the features of the host immune response that are unique to the lungs. We describe the interplay between innate and adaptive immune cells in the induction, expression and control of antiviral immunity, and discuss the impact of the infected lung milieu on moulding the response of antiviral effector T cells. Recent findings on the mechanisms that underlie the increased frequency of severe pulmonary bacterial infections following respiratory virus infection are also discussed

Local vertical measurements and violation of Bell inequality

For two qubits belonging to Alice and Bob, we derive an approach to setup the bound of Bell operator in the condition that Alice and Bob continue to perform local vertical measurements. For pure states we find that if the entanglement of the two qubits is less than 0.2644 (measured with von Neumann entropy) the violation of the Bell inequality will never be realized, and only when the entanglement is equal to 1 the maximal violation ($2\sqrt{2}$) can occur. For specific form of mixed states, we prove that the bound of the Bell inequality depends on the concurrence. Only when the concurrence is greater than 0.6 the violation of the Bell inequality can occur, and the maximal violation can never be achieved. We suggest that the bound of the Bell operator in the condition of local vertical measurements may be used as a measure of the entanglement.Comment: 4 pages, 3 figure

T Cell Responses during Acute Respiratory Virus Infection

This article is made available for unrestricted research re-use and secondary analysis in any form or by any means with acknowledgement of the original source. These permissions are granted for the duration of the World Health Organization (WHO) declaration of COVID-19 as a global pandemic.The T cell response is an integral and essential part of the host immune response to acute virus infection. Each viral pathogen has unique, frequently nuanced, aspects to its replication, which affects the host response and as a consequence the capacity of the virus to produce disease. There are, however, common features to the T cell response to viruses, which produce acute limited infection. This is true whether virus replication is restricted to a single site, for example, the respiratory tract (RT), CNS etc., or replication is in multiple sites throughout the body. In describing below the acute T cell response to virus infection, we employ acute virus infection of the RT as a convenient model to explore this process of virus infection and the host response. We divide the process into three phases: the induction (initiation) of the response, the expression of antiviral effector activity resulting in virus elimination, and the resolution of inflammation with restoration of tissue homeostasis

Correlation Between the Halo Concentration (c) and the Virial Mass (Mvir) Determined from X-ray Clusters

Numerical simulations of structure formation have suggested that there exists a good correlation between the halo concentration c (or the characteristic density delta_c) and the virial mass Mvir for any virialized dark halo described by the Navarro, Frenk & White (1995) density profile. In this Letter, we present an observational determination of the c-Mvir (or delta_c-Mvir) relation in the mass range of 10^14< Mvir <10^16 (solar mass) using a sample of 63 X-ray luminous clusters. The best-fit power law relation, which is roughly independent of the values of Omega_M and Lambda, is c propto Mvir^(-0.5) or delta_c propto Mvir^(-1.2), indicating n=-0.7 for a scale-free power spectrum of the primordial density fluctuations. We discuss the possible reasons for the conflict with the predictions by typical CDM models such as SCDM, LCDM and OCDM.Comment: 13 pages, 1 figure, two tables. Accepted for publication in ApJ

Electromagnetically controlled multiferroic thermal diode

We propose an electromagnetically tunable thermal diode based on a two phase multiferroics composite. Analytical and full numerical calculations for prototypical heterojunction composed of Iron on Barium titanate in the tetragonal phase demonstrate a strong heat rectification effect that can be controlled externally by a moderate electric field. This finding is of an importance for thermally based information processing and sensing and can also be integrated in (spin)electronic circuits for heat management and recycling.Comment: Accepted in Phys. Rev.

Quantum phase transition in easy-axis antiferromagnetic Heisenberg spin-1 chain

The fidelity and entropy in an easy-axis antiferromagnetic Heisenberg spin-1 chain are studied numerically. By using the method of density-matrix renormalization group, the effects of anisotropy on fidelity and entanglement entropy are investigated. Their relations with quantum phase transition are analyzed. It is found that the quantum phase transition from the Haldane spin liquid to N\'eel spin solid can be well characterized by the fidelity. The phase transition can be hardly detected by the entropy but it can be successfully detected by the first deviation of the entropy.Comment: 3 figure

Quantum discord dynamical behaviors due to initial system-cavity correlations

We analyze the roles of initial correlations between the two-qubit system and a dissipative cavity on quantum discord dynamics of two qubits. Considering two initial system-cavity states, we show that the initial system-cavity correlations not only can initially increase the two-qubit quantum discord but also would lead to a larger long-time quantum discord asymptotic value. Moreover, quantum discord due to initial correlations is more robust than the case of the initial factorized state. Finally, we show the initial correlations' importance for dynamics behaviors of mutual information and classical correlation