A Comparison of Methods to Concentrate Viruses from Environmental Waters Using MS2 as a Model

Viruses such as Rotavirus, Adenovirus and Norovirus are important etiological agents of gastroenteritis worldwide. With the high sensitivity and specificity of PCR, it is now possible to develop PCR-based methods to detect and quantify pathogenic viruses in environmental water samples. To develop reliable methods however, an effective procedure to concentrate viruses from large volumes of water is required. Because of the scale of concentration required, the procedure often requires two steps. The first to reduce tens of liters of water to less than half a liter and then a second to concentrate the sample to a final volume of less than 10 mL for RNA/DNA extraction. The objectives of the study were to compare the efficacy of hollow fiber ultrafiltration (HFUF) using F200B to that of an adsorption/elution method (AEM) using positively charged filters for concentrating viruses for the first step and to compare polyethylene glycol (PEG) precipitation to centrifugal ultrafiltration for the second step. A third objective was to determine the viral detection limit using real-time RT-PCR. Using beach water spiked with a singlestranded RNA bacteriophage (MS2) as a model, our results show a virus recovery rate of 84±6% and 18±8% for the HFUF method and AEM, respectively. For the second concentration step, we obtained a recovery rate of 49±5 % and 87±7% using PEG precipitation and centrifugal ultrafiltration, respectively. A potential limiting factor to more widespread using of HFUF is the higher cost and we found that cost can be reduced by using reusable filters. We were able to sanitize and reuse the same filter at least six times without affecting the virus recovery rate or the processing time

Development of a Probe Hybridization Method to Facilitate Detection of Noroviruses in Oysters

Centers for Disease Control (CDC) reports that at least 50% of all foodborne outbreaks of gastroenteritis are due to noroviruses (NoV). Since NoV is mainly transmitted through the fecal-oral route and the infectious dose may be as low as 10 viral particles, the risk of infection after consumption of raw or improperly cooked seafood or after exposure to contaminated water is considered high. Although highly sensitive methods to detect NoV using RT-PCR are already available, isolation of either NoV RNA or virions from shellfish remains a cumbersome process. We developed a new hybridization method to extract NoV RNA from contaminated shellfish that is much faster compared to existing methods. Using the new method, NoV detection includes three basic steps: an initial extraction of total RNA using TRIZol, followed by isolation of NoV RNA using biotinylated DNA probe hybridization and then NoV detection by TaqMan RT-PCR. With oyster (Crassostrea virginica) homogenate spiked with 100 PCR detection units (PDU) of NoV, the virus can be detected with CT values at about 30. Compared to published methods that require an initial virus purification step, the new method is much faster, requiring approximately 3 hr compared to at least 8 hr using conventional methods. Coupled with TaqMan RT-PCR, the new method can be used to detect NoV in contaminated oysters and clams (Corbicula fluminea) within 8 hr. The detection limit was 100 PDU of NoV in spiked oyster tissue samples. The method has been successfully used to detect NoV in oysters artificially contaminated in the laboratory and in rare cases, oysters collected from the field

A new method for the estimation of variance matrix with prescribed zeros in nonlinear mixed effects models

We propose a new method for the Maximum Likelihood Estimator (MLE) of nonlinear mixed effects models when the variance matrix of Gaussian random effects has a prescribed pattern of zeros (PPZ). The method consists in coupling the recently developed Iterative Conditional Fitting (ICF) algorithm with the Expectation Maximization (EM) algorithm. It provides positive definite estimates for any sample size, and does not rely on any structural assumption on the PPZ. It can be easily adapted to many versions of EM.Comment: Accepted for publication in Statistics and Computin

Social media landscape of the tertiary referral hospitals in China: Observational descriptive study

Originally published in the Journal of Medical Internet Research (http://www.jmir.org), 09.08.2018. This is an open-access article distributed under the terms of the Creative Commons Attribution License. Background: Social media has penetrated all walks of life. Chinese health care institutions are increasingly utilizing social media to connect with their patients for better health service delivery. Current research has focused heavily on the use of social media in developed countries, with few studies exploring its usage in the context of developing countries, such as China. Tertiary hospitals in China are usually located in city centers, and they serve as medical hubs for multiple regions, with comprehensive and specialized medical care being provided. These hospitals are assumed to be the pioneers in creating official social media accounts to connect with their patients due to the fact that they appear to have more resources to support this innovative approach to communication and health care education. Objective: The objective of our study was to examine China's best tertiary hospitals, as recognized by The National Health Commission of the People's Republic of China (NHCPRC), and to map out the landscape of current social media usage by hospitals when engaging with patients. Methods: We examined the best 705 tertiary hospitals in China by collecting and analyzing data regarding their usage of popular Chinese social media apps Sina Weibo and WeChat. The specific data included (1) hospital characteristics (ie, time since established, number of beds, hospital type, and regions or localities) and (2) status of social media usage regarding two of the most popular local social media platforms in China (ie, time of initiation, number of followers, and number of tweets or posts). We further used a logistic regression model to test the association between hospital characteristics and social media adoption. Results: Of all, 76.2% (537/705) tertiary referral hospitals have created official accounts on either Sina Weibo or WeChat, with the latter being more popular among the two. In addition, our study suggests that larger and newer hospitals with greater resources are more likely to adopt social media, while hospital type and affiliation with universities are not significant predictors of social media adoption among hospitals. Conclusions: Our study demonstrated that hospitals are more inclined to use WeChat. The move by hospitals from Sina Weibo to WeChat indicates that patients are not satisfied by mere communication and that they now place more value on health service delivery. Meanwhile, utilizing social media requires comprehensive thinking from the hospital side. Once adopted, hospitals are encouraged to implement specific rules regarding social media usage. In the future, a long journey still lies ahead for hospitals in terms of operating their official social media accounts

Green’s function method to the ground state properties of a two-component Bose–Einstein condensate

The elementary excitation spectrum of a two-component Bose–Einstein condensate is obtained by Green’s function method. It is found to have two branches. In the long-wave limit, the two branches of the excitation spectrum are reduced to one phonon excitation and one single-particle excitation. With the obtained excitation spectrum and the Green’s functions, the depletion of the condensate and the ground state energy have also been calculated in this paper

Guiding center picture of magnetoresistance oscillations in rectangular superlattices

We calculate the magneto-resistivities of a two-dimensional electron gas subjected to a lateral superlattice (LSL) of rectangular symmetry within the guiding-center picture, which approximates the classical electron motion as a rapid cyclotron motion around a slowly drifting guiding center. We explicitly evaluate the velocity auto-correlation function along the trajectories of the guiding centers, which are equipotentials of a magnetic-field dependent effective LSL potential. The existence of closed equipotentials may lead to a suppression of the commensurability oscillations, if the mean free path and the LSL modulation potential are large enough. We present numerical and analytical results for this suppression, which allow, in contrast to previous quantum arguments, a classical explanation of similar suppression effects observed experimentally on square-symmetric LSL. Furthermore, for rectangular LSLs of lower symmetry they lead us to predict a strongly anisotropic resistance tensor, with high- and low-resistance directions which can be interchanged by tuning the externally applied magnetic field.Comment: 12 pages, 9 figure

First-principles study of the structural energetics of PdTi and PtTi

The structural energetics of PdTi and PtTi have been studied using first-principles density-functional theory with pseudopotentials and a plane-wave basis. We predict that in both materials, the experimentally reported orthorhombic $B19$ phase will undergo a low-temperature phase transition to a monoclinic $B19'$ ground state. Within a soft-mode framework, we relate the $B19$ structure to the cubic $B2$ structure, observed at high temperature, and the $B19'$ structure to $B19$ via phonon modes strongly coupled to strain. In contrast to NiTi, the $B19$ structure is extremely close to hcp. We draw on the analogy to the bcc-hcp transition to suggest likely transition mechanisms in the present case.Comment: 8 pages 5 figure

QED_3 theory of underdoped high temperature superconductors II: the quantum critical point

We study the effect of gapless quasiparticles in a d-wave superconductor on the T=0 end point of the Kosterlitz-Thouless transition line in underdoped high-temperature superconductors. Starting from a lattice model that has gapless fermions coupled to 3D XY phase fluctuations of the superconducting order parameter, we propose a continuum field theory to describe the quantum phase transition between the d-wave superconductor and the spin-density-wave insulator. Without fermions the theory reduces to the standard Higgs scalar electrodynamics (HSE), which is known to have the critical point in the inverted XY universality class. Extending the renormalization group calculation for the HSE to include the coupling to fermions, we find that the qualitative effect of fermions is to increase the portion of the space of coupling constants where the transition is discontinuous. The critical exponents at the stable fixed point vary continuously with the number of fermion fields $N$, and we estimate the correlation length exponent (nu = 0.65) and the vortex field anomalous dimension(eta_Phi=-0.48) at the quantum critical point for the physical case N=2. The stable critical point in the theory disappears for the number of Dirac fermions N > N_c, with N_c ~ 3.4 in our approximation. We discuss the relationship between the superconducting and the chiral (SDW) transitions, and point to some interesting parallels between our theory and the Thirring model.Comment: 13 pages including figures in tex

QED3 theory of underdoped high temperature superconductors

Low-energy theory of d-wave quasiparticles coupled to fluctuating vortex loops that describes the loss of phase coherence in a two dimensional d-wave superconductor at T=0 is derived. The theory has the form of 2+1 dimensional quantum electrodynamics (QED3), and is proposed as an effective description of the T=0 superconductor-insulator transition in underdoped cuprates. The coupling constant ("charge") in this theory is proportional to the dual order parameter of the XY model, which is assumed to be describing the quantum fluctuations of the phase of the superconducting order parameter. The principal result is that the destruction of phase coherence in d-wave superconductors typically, and immediately, leads to antiferromagnetism. The transition can be understood in terms of the spontaneous breaking of an approximate "chiral" SU(2) symmetry, which may be discerned at low enough energies in the standard d-wave superconductor. The mechanism of the symmetry breaking is analogous to the dynamical mass generation in the QED3, with the "mass" here being proportional to staggered magnetization. Other insulating phases that break chiral symmetry include the translationally invariant "d+ip" and "d+is" insulators, and various one dimensional charge-density and spin-density waves. The theory offers an explanation for the rounded d-wave-like dispersion seen in ARPES experiments on Ca2CuO2Cl2 (F. Ronning et. al., Science 282, 2067 (1998)).Comment: Revtex, 20 pages, 5 figures; this is a much extended follow-up to the Phys. Rev. Lett. vol.88, 047006 (2002) (cond-mat/0110188); improved presentation, many additional explanations, comments, and references added, sec. IV rewritten. Final version, to appear in Phys. Rev.

Current- and Wave-Generated Bedforms on Mixed Sand–Clay Intertidal Flats: A New Bedform Phase Diagram and Implications for Bed Roughness and Preservation Potential

The effect of bedforms on frictional roughness felt by the overlying flow is crucial to the regional modelling of estuaries and coastal seas. Bedforms are also a key marker of palaeoenvironments. Experiments have shown that even modest biotic and abiotic cohesion in sand inhibits bedform formation, modifies bedform size, and slows bedform development, but this has rarely been tested in nature. The present study used a comprehensive dataset recorded over a complete spring–neap cycle on an intertidal flat to investigate bedform dynamics controlled by a wide range of wave and current conditions, including the effects of wave–current angle and bed cohesion. A detailed picture of different bedform types and their relationship to the flow, be they equilibrium, non-equilibrium, or relict, was produced, and captured in a phase diagram that integrates wave-dominated, current-dominated, and combined wave–current bedforms. This bedform phase diagram incorporates a substantially wider range of flow conditions than previous phase diagrams, including bedforms related to near-orthogonal wave–current angles, such as ladderback ripples. Comparison with laboratory-derived bedform phase diagrams indicates that washed-out ripples, lunate interference ripples and upper-stage plane beds replace the subaqueous dune field; such bedform distributions may be a key characteristic of intertidal flats. The field data also provide a means of predicting the dimensions of these bedforms, which can be transferred to other areas and grain sizes. We show that an equation for the prediction of equilibrium bedform size is sufficient to predict the roughness, even though the bedforms are highly variable in character and only in equilibrium with the flow for approximately half the time. Whilst the effect of cohesive clay is limited under more active spring conditions, clay does play a role in reducing the bedform dimensions under more quiescent neap conditions. We also investigated which combinations of waves, currents, and bed clay contents in the intertidal zone have the highest potential for bedform preservation in the geological record. This shows that combined wave–current bedforms have the lowest preservation potential and equilibrium current ripples have the highest preservation potential, even in the presence of moderate and storm waves. Hence, the absence of wave ripples and combined-flow bedforms and their primary stratification in sedimentary successions cannot be taken as evidence that waves were absent at the time of deposition