Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

A Viking Lander 1 image was modeled as mixtures of reflectance spectra of palagonite dust, gray andesitelike rock, and a coarse rocklike soil. The rocks are covered to varying degrees by dust but otherwise appear unweathered. Rocklike soil occurs as lag deposits in deflation zones around stones and on top of a drift and as a layer in a trench dug by the lander. This soil probably is derived from the rocks by wind abrasion and/or spallation. Dust is the major component of the soil and covers most of the surface. The dust is unrelated spectrally to the rock but is equivalent to the global-scale dust observed telescopically. A new method was developed to model a multispectral image as mixtures of end-member spectra and to compare image spectra directly with laboratory reference spectra. The method for the first time uses shade and secondary illumination effects as spectral end-members; thus the effects of topography and illumination on all scales can be isolated or removed. The image was calibrated absolutely from the laboratory spectra, in close agreement with direct calibrations. The method has broad applications to interpreting multispectral images, including satellite images.

Spectral mixture modeling - A new analysis of rock and soil types at the Viking Lander 1 site. [on Mars]

Introduction Japanese encephalitis (JE) is among the most important viral encephalitides in Asia, especially in rural and suburban areas where rice culture and pig farming coexist. (1-3) It has also occurred rarely and sporadically in northern Australia and parts of the Western Pacific. (4-6) JE is due to infection with the JE virus (JEV), a mosquito-borne flavivirus. The main JEV transmission cycle involves Culex tritaeniorhynchus mosquitoes and similar species that lay eggs in rice paddies and other open water sources, with pigs and aquatic birds as principal vertebrate amplifying hosts. (1,2,7) Humans are generally thought to be dead-end JEV hosts, i.e. they seldom develop enough viremia to infect feeding mosquitoes. Fewer than 1% of human JEV infections result in JE. Approximately 20-30% of JE cases are fatal and 30-50% of survivors have significant neurologic sequelae. (8) JE is primarily a disease of children and most adults in endemic countries have natural immunity after childhood infection, but all age groups are affected. In most temperate areas of Asia, JEV is transmitted mainly during the warm season, when large epidemics can occur. In the tropics and subtropics, transmission can occur year-round but often intensifes during the rainy season. (1-3) The global incidence of JE is unknown because the intensity and quality of JE surveillance and the availability of diagnostic laboratory testing vary throughout the world. Countries that have implemented high-quality childhood JE vaccination programmes have seen a dramatic decline in JE incidence. Although JE is reportable to the World Health Organization (WHO) by its Member States, reporting is highly variable and incomplete. In the late 1980s, Burke and Leake estimated that 50 000 new cases of JE occurred annually among the 2.4 billion people living in the 16 Asian countries considered endemic at the time (approximate overall annual incidence: 2 per 100 000). (2) In the intervening two decades, despite major population growth, urbanization, changes in agricultural practices and increased use of the JE vaccine in many countries, this figure has been widely quoted, including very recently. (9-13) In 2000, assuming an annual, age-group-specific incidence of 25 cases per 100 000, Tsai estimated that in the absence of vaccination 175 000 cases of JE would occur annually among Asian children aged 0-14 years living in rural areas. (14) The current study used more recent, published, local or national incidence estimates and current population data to produce an updated estimate of the annual global incidence of JE. Methods We approximated the JE-affected territory of each of the 24 countries endemic for JE using a recent update (15) of an earlier approximation by Tsai (16) with some modifications (Table 1, available at: http://www.who.int/bulletin/ volumes/89/10/10-085233). Based on these same approximations, (15,16) we then stratified the JE-affected territory of some countries (e.g. China excluding Taiwan, India and Nepal) into two or more incidence strata. Because suitable studies of JE incidence were not available for every endemic country or incidence stratum, we sorted JE-endemic countries and incidence strata into 10 incidence groups (A, B, C1, C2 and D through I) based primarily on geographic proximity, ecologic similarity, vaccine programme similarity. Table 1 briefly describes the status of each endemic country's JE vaccination programme as of 2009, according to recent publications and unpublished sources. (8,17-20) Incidence data We identified studies that contained potentially useful data on the incidence of JE in Asia in a manner similar to the one used in a recent study of global typhoid fever incidence. (21) Whenever possible, this review followed the relevant guidelines for Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA). (22) The review process is described as follows and no protocol is available. …

Estimated Global Incidence of Japanese Encephalitis: A Systematic review/Estimation De L'incidence Mondiale De L'encephalite Japonaise: Une Evaluation Systematique/ Incidencia Global Estimada De la Encefalitis Japonesa: Una Revision Sistematica

Use of nanoparticles for oil production applications

Accurate and efficient numerical methods to simulate dynamic earthquake rupture and wave propagation in complex media and complex fault geometries are needed to address fundamental questions in earthquake dynamics, to integrate seismic and geodetic data into emerging approaches for dynamic source inversion, and to generate realistic physics-based earthquake scenarios for hazard assessment. Modeling of spontaneous earthquake rupture and seismic wave propagation by a high-order discontinuous Galerkin (DG) method combined with an arbitrarily high-order derivatives (ADER) time integration method was introduced in two dimensions by de la Puente et al. (2009). The ADER-DG method enables high accuracy in space and time and discretization by unstructured meshes. Here we extend this method to three-dimensional dynamic rupture problems. The high geometrical flexibility provided by the usage of tetrahedral elements and the lack of spurious mesh reflections in the ADER-DG method allows the refinement of the mesh close to the fault to model the rupture dynamics adequately while concentrating computational resources only where needed. Moreover, ADER-DG does not generate spurious high-frequency perturbations on the fault and hence does not require artificial Kelvin-Voigt damping. We verify our three-dimensional implementation by comparing results of the SCEC TPV3 test problem with two well-established numerical methods, finite differences, and spectral boundary integral. Furthermore, a convergence study is presented to demonstrate the systematic consistency of the method. To illustrate the capabilities of the high-order accurate ADER-DG scheme on unstructured meshes, we simulate an earthquake scenario, inspired by the 1992 Landers earthquake, that includes curved faults, fault branches, and surface topography.

Three-dimensional dynamic rupture simulationwith a high-order discontinuous Galerkin methodon unstructured tetrahedral meshes

A discontinuous Galerkin method for simulating the effects of arbitrary discrete fractures on elastic wave propagation

Evaluation of hydraulic fractures has been under intensive study since the last decade. Among published works, only a few have included casing effects. This paper focuses on the through-casing electromagnetic (EM) induction imaging method that evaluates hydraulic fractures with enhanced contrasts. An experimental system and an inverse scattering algorithm are presented. The laboratory scaled experimental system is built for the feasibility study of the EM induction imaging method for the through-casing hydraulic fracture evaluation. To develop the inverse scattering algorithm, fractures outside boreholes with metallic casing are modeled by a novel hybrid approximation method. This method combines the distorted Born approximation and the mixed order stabilized bi-conjugate gradient fast Fourier transform method to solve the forward scattering problem. The variational Born iterative method is applied to solve the nonlinear inverse problem iteratively. Experimental results show that the inverse scattering algorithm is effective for EM contrast enhanced through-casing hydraulic fracture evaluation.

Through-Casing Hydraulic Fracture Evaluation by Induction Logging II: The Inversion Algorithm and Experimental Validations

The Anopheles hyrcanus group includes 25 species, and is widely distributed in the Oriental and Palaearctic regions. Several species within this group are vectors of malaria, lymphatic filariasis and Japanese encephalitis. It is difficult or impossible to identify cryptic species based on their morphological characteristics, with some closely related species of the Hyrcanus Group have similar adult morphological characteristics. Thus, their molecular identification has been an important complementary method to traditional morphological taxonomy. We used 461 ribosomal DNA (rDNA) internal transcribed spacer 2 (ITS2) sequences relating to 19 species to reconstruct the molecular phylogeny of the Hyrcanus Group across its range. In addition, we compared the performance of rDNA ITS2 to that of mitochondrial DNA (mtDNA) cytochrome c oxidase subunit 1 gene (cox1) to assess the genetic divergence of Hyrcanus Group sibling species. Based on Kimura’s 2-parameter (K2P) distance model, the average conspecific ITS2 divergence was 0.003, whereas sequence divergence between species averaged 0.480. Average ITS2 sequence divergences were almost 160 times higher among the Hyrcanus Group members than within each species. Two sets of sibling species, An. lesteri Baisas & Hu, 1936 and An. paraliae Sandosham, 1959; and An. sinensis Wiedemann, 1828, An. belenrae Rueda, 2005, and An. kleini Rueda, 2005, were resolved by ITS2. Each of these species was represented as an independent lineage in the phylogenetic tree. Results suggest that An. pseudopictus Grassi, 1899 and An. hyrcanus (Pallas, 1771) are most likely a single species. We uncovered two new ITS2 lineages that require further study before resolving their true taxonomic status, and designed a diagnostic polymerase chain reaction (PCR) assay to distinguish five morphologically similar species. Nuclear and mitochondrial genes generally provided consistent results for subgroup division. Compared to cox1, ITS2 is a more reliable tool for studying phylogenetic relationships among closely related mosquito taxa. Based on species-specific differences in ITS2 sequences, the multiplex PCR assay developed here can be used to improve the efficiency of vector identification. Thus, this research will promote the progress of malaria vector surveillance in both epidemic and non-epidemic areas of South and East Asia.

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Molecular phylogeny of Anopheles hyrcanus group members based on ITS2 rDNA.

Remote Imaging of Proppants in Hydraulic Fracture Networks Using Electromagnetic Methods: Results of Small-Scale Field Experiments

Continuous vector pathogen surveillance is essential for preventing outbreaks of mosquito-borne diseases. Several mosquito species acting as vectors of Japanese encephalitis virus (JEV), dengue virus, Zika virus, malaria parasites and other pathogens are primary mosquito species in Shanghai, China. However, few surveys of human pathogenic arboviruses in mosquitoes in Shanghai have been reported in the last ten years. Therefore, in this study, we evaluated mosquito activity in Shanghai, China during 2016 and tested for the presence of alphaviruses, flaviviruses, orthobunyaviruses and several parasitic pathogens. Five pooled samples were JEV-positive [4/255 pools of Culex tritaeniorhynchus and 1/256 pools of Cx. pipiens (s.l.)] based on analysis of the NS5 gene. Alphaviruses, orthobunyaviruses, Plasmodium and filariasis were not found in this study. Phylogenetic and molecular analyses revealed that the JEV strains belonged to genotype I. Moreover, newly detected Shanghai JEV strains were genetically close to previously isolated Shandong strains responsible for transmission during the 2013 Japanese encephalitis (JE) outbreak in Shandong Province, China but were more distantly related to other Shanghai strains detected in the early 2000s. The E proteins of the newly detected Shanghai JEV strains differed from that in the live attenuated vaccine SA14-14-2-derived strain at six amino residues: E130 (Ile→Val), E222 (Ala→Ser), E327 (Ser→Thr), E366 (Arg→Ser/Pro), E393 (Asn→Ser) and E433 (Val→Ile). However, no differences were observed in key amino acid sites related to antigenicity. Minimum JEV infection rates were 1.01 and 0.65 per 1000 Cx. tritaeniorhynchus and Cx. pipiens (s.l.), respectively. Five new Shanghai JEV genotype I strains, detected after a ten-year hiatus in local mosquito surveillance, were genetically close to strains involved in the 2013 Shandong JE outbreak. Because JEV is still circulating, vaccination in children should be extensively and continuously promoted. Moreover, JEV mosquito surveillance programmes should document the genotype variation, intensity and distribution of circulating viruses for use in the development and implementation of disease prevention and control strategies.

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Yuan Fang

Papers

A discontinuous Galerkin method for simulating the effects of arbitrary discrete fractures on elastic wave propagation

Through-Casing Hydraulic Fracture Evaluation by Induction Logging II: The Inversion Algorithm and Experimental Validations

Molecular phylogeny of Anopheles hyrcanus group members based on ITS2 rDNA.

Remote Imaging of Proppants in Hydraulic Fracture Networks Using Electromagnetic Methods: Results of Small-Scale Field Experiments

New strains of Japanese encephalitis virus circulating in Shanghai, China after a ten-year hiatus in local mosquito surveillance.