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S Xu

Publications and source records attributed to S Xu.

At least 19 recordsLinked to original sources
PubMed2006

A multivariate model for ordinal trait analysis.

Many economically important characteristics of agricultural crops are measured as ordinal traits. Statistical analysis of the genetic basis of ordinal traits appears to be quite different from regular quantitative traits. The generalized linear model methodology implemented via the Newton-Raphson algorithm offers improved efficiency in the analysis of such data, but does not take full advantage of the extensive theory developed in the linear model arena. Instead, we develop a multivariate model for ordinal trait analysis and implement an EM algorithm for parameter estimation. We also propose a method for calculating the variance-covariance matrix of the estimated parameters. The EM equations turn out to be extremely similar to formulae seen in standard linear model analysis. Computer simulations are performed to validate the EM algorithm. A real data set is analyzed to demonstrate the application of the method. The advantages of the EM algorithm over other methods are addressed. Application of the method to QTL mapping for ordinal traits is demonstrated using a simulated baclcross (BC) population.

Algorithms↗
PubMed2006

Diverse signals converge at MAPK cascades in plant.

Mitogen-activated protein kinases (MAPKs) are important signal transducing enzymes that connects diverse receptors/sensors to a wide range of cellular responses in mammals, yeasts and plants. In recent years, a large number of different components of plant MAPK cascades were isolated. Molecular and biochemical studies have revealed that plant MAPKs play important role in the response to a broad variety of biotic and abiotic stresses, including wounding, pathogen infection, temperature, drought, salinity, but also in the signaling of plant hormones and the cell division. This review briefly summaries the recent research results about the cross-talk and complexity of MAP kinase cascades in plant obtained from functional analyses.

Acclimatization↗
PubMed2006

Mechanisms of the reactions of W AND W+ with H2O: computational studies.

The mechanism of the reactions of W and W(+) with the water molecule have been studied for several lower-lying electronic states of tungsten centers at the CCSD(T)/6-311G(d,p)+SDD and B3LYP/6-31G(d,p)+SDD levels of theory. It is shown that these reactions are essentially multistate processes, during which lower-lying electronic states of the systems cross several times. They start with the formation of initial prereaction M(H(2)O) complexes with M-H(2)O bonding energies of 9.6 and 48.2 kcal/mol for M = W and W(+), followed by insertion of the metal center into an O-H bond with 20.0 and 53.3 kcal/mol barriers for neutral and cationic systems, respectively. The overall process of M + H(2)O --> t-HM(OH) is calculated to be highly exothermic, 48.4 and 48.8 kcal/mol for M = W and W(+). From the HM(OH) intermediate the reaction may proceed via several different channels, among which the stepwise HM(OH) --> HMO + H --> (H)(2)MO and concerted HM(OH) --> (H)(2)MO pathways are more favorable and can compete (energetically) with each other. For the neutral system (M = W), the concerted process is the most favorable, whereas for the charged system (M = W(+)), the stepwise pathway is slightly more favorable. From the energetically most favorable intermediate (H)(2)MO the reactions proceed via H(2)-molecule formation with a 53.1 kcal/mol activation barrier for the neutral system. For the cationic system, H-H formation and dissociation is an almost barrierless process. The overall reaction of W and W(+) with the water molecule leading to H(2) + MO formation is found to be exothermic by 48.2 and 39.8 kcal/mol, respectively. In the gas phase with the collision-less conditions the reactions W((7)S) + H(2)O --> H(2) + WO((3)Sigma(+)), and W(+)((6)D) + H(2)O --> H(2) + WO(+)((4)Sigma(+)) are expected to proceed via a 10.4 and 5.1 kcal/mol overall energy barrier corresponding to the first O-H dissociation at the TS1. On the basis of these PESs, we predict kinetic rate constants for the reactions of W and W(+) with H(2)O.

Journal Article↗
PubMed2006

Progressive proliferative and dysplastic typhlocolitis in aging syrian hamsters naturally infected with Helicobacter spp.: a spontaneous model of inflammatory bowel disease.

Helicobacter spp. have been implicated in a variety of gastrointestinal tract diseases, including peptic ulcer disease, gastric cancer, and inflammatory bowel disease (IBD), in humans and animals. Although most models of IBD are experimentally induced, spontaneous or natural models of IBD are rare. Herein, we describe a long-term study of chronic, progressive lesions that develop in the distal portion of the large bowel of unmanipulated Syrian hamsters naturally infected with Helicobacter spp. Twenty-four Syrian hamsters of three age groups (group A, 1 month [n = 4], group B, 7-12 months [n = 12], group C, 18-24 months [n = 12]), underwent complete postmortem examination. Results of microbial isolation and polymerase chain reaction and restriction fragment length polymorphism analyses confirmed the presence of Helicobacter spp. infection in the distal portion of the large bowel of all animals. Additionally, confounding pathogens, such as Clostridium difficile, Lawsonia intracellularis, and Giardia spp. that can cause proliferative enteritis, were absent in the hamsters of this study. Histopathologic scores for inflammation (P < 0.01), hyperplasia (P < 0.01), and dysplasia (P < 0.05) were significantly higher in the ileocecocolic (ICC) junction of animals in group C, relative to group A. Dysplastic lesions of various grades were detected in 5 of 11 hamsters in group C. Interestingly, the segment of the bowel that is usually colonized by Helicobacter spp. in hamsters had the most severe lesions. One hamster of group C developed a malignant fibrous histiocytoma, whereas another hamster developed a round cell sarcoma originating from the ICC junction. Thus, lesions in the distal portion of the large bowel of aging hamsters naturally colonized with Helicobacter spp. warrants developing the hamster as an animal model of IBD and potentially IBD-related cancer.

Animals↗
PubMed2005

Water clusters on graphite: methodology for quantum chemical a priori prediction of reaction rate constants.

The properties, interactions, and reactions of cyclic water clusters (H(2)O)(n=1-5) on model systems for a graphite surface have been studied using pure B3LYP, dispersion-augmented density functional tight binding (DFTB-D), and integrated ONIOM(B3LYP:DFTB-D) methods. Coronene C(24)H(12) as well as polycircumcoronenes C(96)H(24) and C(216)H(36) in monolayer, bilayer, and trilayer arrangements were used as model systems to simulate ABA bulk graphite. Structures, binding energies, and vibrational frequencies of water clusters on mono- and bilayer graphite models have been calculated, and structural changes and frequency shifts due to the water cluster-graphite interactions are discussed. ONIOM(B3LYP:DFTB-D) with coronene and water in the high level and C(96)H(24) in the low level mimics the effect of extended graphite pi-conjugation on the water-graphite interaction very reasonably and suggests that water clusters only weakly interact with graphite surfaces, as suggested by the fact that water is an excellent graphite lubricant. We use the ONIOM(B3LYP:DFTB-D) method to predict rate constants for model pathways of water dissociative adsorption on graphite. Quantum chemical molecular dynamics (QM/MD) simulations of water clusters and water addition products on the C(96)H(24) graphite model are presented using the DFTB-D method. A three-stage strategy is devised for a priori investigations of high temperature corrosion processes of graphite surfaces due to interaction with water molecules and fragments.

Journal Article↗
PubMed2005

Ion drag force in plasmas at high electronegativity.

The electric as well as the positive- and negative-ion drag forces on an isolated dust grain in an electronegative plasma are studied for large negative-ion densities, when the negative ions are not Boltzmann distributed. The investigation is carried out for submicrometer dust particles, so that the theory of Coulomb scattering is applicable for describing ion-dust interaction. Among the forces acting on the dust grain, the negative-ion drag force is found to be important. The effects of the negative-ion density, neutral-gas pressure, and dust-grain size on the forces are also considered. It is shown that by increasing the density of the negative ions one can effectively manipulate the dust grains. Our results imply that both dust voids and balls can be formed.

Journal Article↗
PubMed2005

HCHs and DDTs in sediment-dwelling animals from the Yangtze Estuary, China.

HCHs and DDTs in sediment-dwelling animals including mollusks and crabs from the Yangtze Estuary were determined by GC-ECD. Levels of t-HCH were in the range of 1.2-5.5 ng g(-1) and averaged 3.5 ng g(-1) in mollusks, while t-DDT concentrations ranged from 26.0 to 68.8 ng g(-1), with a mean of 34.5 ng g(-1). In crabs t-HCH concentrations varied from 2.0 to 25.7 ng g(-1) and averaged 13.8 ng g(-1), whereas the concentrations of t-DDT were in the range of 1.5-24.8 ng g(-1) with a mean value of 5.9 ng g(-1). The HCHs and DDTs levels depend on geographical position and sources, showing the high levels at fresh water area in the estuary, such as XP, CM and LHK sites, and lower at brackish water area, such as FX site, and little difference between species. Results also indicate there was no significant relationship between t-HCH (t-DDT) concentrations and lipid contents both in mollusks and crabs because of non-equilibrium state under a specific estuarine dynamics; smaller individuals accumulated more HCHs and DDTs than larger individuals of mollusks at LHK site, showing different uptake rate for these pesticides; moreover, HCHs and DDTs levels were lower in female crab bodies than male crab bodies suggesting that the release of spawning. BSAFs (Biota- Sediment Accumulation Factors) from sediment-dwelling animals for HCHs and DDTs show a significant "one high with two low" and "one low with two high" effect in the Yangtze Estuary.

Animals↗
PubMed2005

HCHs and DDTs in salt marsh plants (Scirpus) from the Yangtze estuary and nearby coastal areas, China.

HCHs and DDTs in salt marsh plants taken from intertidal flats in the Yangtze estuary and coastal area in April and July 2002 were determined by GC-ECD. A significant seasonal effect was observed for HCHs and DDTs in sources and concentration levels in different sample types including above-ground tissues and roots as well as the whole plants and rhizospheric sediments. The results indicated that the concentration of t-HCH was higher in the above-ground tissues than in their roots in April; however, the partitioning of DDTs between contaminated sediments and the roots showed the higher concentrations of t-DDT in their roots. HCHs and DDTs concentration levels were higher in above-ground tissues than in roots in July. BCFs of HCHs and DDTs exhibited lower values with higher levels of contaminants in sediments, and higher values with lower levels in sediments.

China↗
PubMed2005

Proton magnetic resonance spectroscopy in immunocompetent patients with primary central nervous system lymphoma.

BACKGROUND: Magnetic resonance spectroscopy imaging (MRSI) non-invasively evaluates the metabolic profile of normal and abnormal brain tissue. Primary central nervous system lymphoma (PCNSL) is a highly aggressive tumor responsive to high-dose methotrexate based regimens. Patients often have complete responses but relapses are common. We characterized the MR spectra of PCNSL patients, correlated MRSI with MRI and evaluated whether early recurrence could be detected by MRSI. METHODS: Patients with PCNSL had multi-voxel MRSI before, during, and after treatment. The region of interest was defined using axial FLAIR images. Metabolites assessed were N-acetyl-aspartate (NAA), choline (Cho), creatine (Cr), lipid, and lactate. Ratios of Cho/Cr, NAA/Cho, and NAA/Cr were calculated and correlated with MRI. Overall survival (OS), progression free survival (PFS), and relative risks of each of the ratios were determined. RESULTS: MRSI was performed on 11 men and seven women; median age of 59. Sixty-seven MRSI studies were performed, 17 baseline and 48 follow-up studies. Median ratios in 16 pretreated patients were Cho/Cr-1.90, NAA/Cho-0.39, and NAA/Cr-1.27. Two patients had lipid at baseline, five had lactate and two had both. MRSI correlated with tumor response or progression on MRI; in three patients MRSI suggested disease progression prior to changes on MRI. Univariate analysis of metabolite ratios, lipid, and lactate revealed that none significantly affected PFS or OS. Kaplan-Meier analysis of the presence or absence of lipid, lactate or both revealed a trend for increased PFS. CONCLUSION: MRSI and MRI correlate with tumor response or progression and may allow early detection of disease recurrence. The presence or absence of lipid and/or lactate may have prognostic significance. Further research using MRSI needs to be done to validate our findings and determine the role of MRSI in PCNSL.

Adult↗
PubMed2005

A Monte Carlo algorithm for computing the IBD matrices using incomplete marker information.

Identity-By-Descent (IBD) is a general measurement of the relationship between two groups of genes. If the two groups consist of two homologous genes, one from each individual, the IBD is called the coancestry between the two individuals. Coancestry is an important concept in both population and quantitative genetics. It is the probability that both genes are copies of the same gene in the genealogy. The average coancestry value at a random locus in a population reflects the level of population diversity, effective population size, the level of inbreeding and other attributes. Coancestry is also the building block for the covariance structure used to estimate the additive genetic variance component for a quantitative trait. There are many other types of IBD matrices, depending on the natures of the genes included in each group, and these IBD matrices vary from locus to locus. Molecular markers distributed along the genome provide information that can be used to infer these locus-specific IBD matrices. As a result, we can estimate and test the variance components of a quantitative trait contributed by these loci using the inferred IBD matrices. In this study, we develop the concept of locus-specific epistatic IBD matrices and a Monte Carlo method to infer these IBD matrices. The method is suitable for large pedigrees with arbitrary complexity and various levels of missing marker information. With these locus-specific IBD matrices, we are ready to search for quantitative trait loci along the genome in complicated pedigrees.

Algorithms↗
PubMed2005

An EM algorithm for mapping quantitative resistance loci.

Many disease resistance traits in plants have a polygenic background and the disease phenotypes are modified by environmental factors. As a consequence, the phenotypic values usually show a quantitative variation. The phenotypes of such disease traits, however, are often measured in discrete but ordered categories. These traits are called ordinal traits. In terms of disease resistance, they are called quantitative resistance traits, as opposed to qualitative resistance traits, and are controlled by the quantitative resistance loci (QRL). Classical quantitative trait locus mapping methods are not optimal for ordinal trait analysis because the assumption of normal distribution is violated. Methods for mapping binary trait loci are not suitable either because there are more than two categories in ordinal traits. We developed a maximum likelihood method to map these QRL. The method is implemented via a multicycle expectation-conditional-maximization (ECM) algorithm under the threshold model, where we can estimate both the QRL effects and the thresholds that link the disease liability and the categorical phenotype. The method is verified in simulated data under various combinations of the parameters. An SAS program is available to implement the multicycle ECM algorithm. The program can be downloaded from our website at www.statgen.ucr.edu.

Algorithms↗
PubMed2005

A quantitative genetics model for viability selection.

Viability selection will change gene frequencies of loci controlling fitness. Consequently, the frequencies of marker loci linked to the viability loci will also change. In genetic mapping, the change of marker allelic frequencies is reflected by the departure from Mendelian segregation ratio. The non-Mendelian segregation of markers has been used to map viability loci along the genome. However, current methods have not been able to detect the amount of selection (s) and the degree of dominance (h) simultaneously. We developed a method to detect both s and h using an F2 mating design under the classical fitness model. We also developed a quantitative genetics model for viability selection by proposing a continuous liability controlling the viability of individuals. With the liability model, mapping viability loci has been formulated as mapping quantitative trait loci. As a result, nongenetic systematic environmental effects can be easily incorporated into the model and subsequently separated from the genetic effects of the viability loci. The quantitative genetic model has been verified with a series of Monte Carlo simulation experiments.

Algorithms↗
PubMed2005

A penalized maximum likelihood method for estimating epistatic effects of QTL.

Although epistasis is an important phenomenon in the genetics and evolution of complex traits, epistatic effects are hard to estimate. The main problem is due to the overparameterized epistatic genetic models. An epistatic genetic model should include potential pair-wise interaction effects of all loci. However, the model is saturated quickly as the number of loci increases. Therefore, a variable selection technique is usually considered to exclude those interactions with negligible effects. With such techniques, we may run a high risk of missing some important interaction effects by not fully exploring the extremely large parameter space of models. We develop a penalized maximum likelihood method. The method developed here adopts a penalty that depends on the values of the parameters. The penalized likelihood method allows spurious QTL effects to be shrunk towards zero, while QTL with large effects are estimated with virtually no shrinkage. A simulation study shows that the new method can handle a model with a number of effects 15 times larger than the sample size. Simulation studies also show that results of the penalized likelihood method are comparable to the Bayesian shrinkage analysis, but the computational speed of the penalized method is orders of magnitude faster.

Bayes Theorem↗
PubMed2005

Metabolic activation of a pentafluorophenylethylamine derivative: formation of glutathione conjugates in vitro in the rat.

The aim was to investigate the metabolic activation potential of a pentafluorophenylethylamine derivative (compound I) in vitro in the rat and to identify the cytochrome P450 (CYP) enzymes that catalyse these metabolic activation processes. Reduced glutathione (GSH) was fortified in rat hepatocytes and liver microsomes to trap possible reactive intermediates. Four glutathione conjugates (M1-4) were identified by LC-MS(n) following incubation of compound I in GSH-enriched rat hepatocytes and liver microsomes. Three of these conjugates (M2-4) have not been reported previously for pentafluorophenyl derivatives. Elemental composition analysis of these conjugates was obtained using high-resolution quadrupole time-of-flight mass spectrometry. The formation of GSH conjugate M1 was rationalized as a direct nucleophilic replacement of fluoride by glutathione, whereas the formation of the GSH conjugates M2-4 was proposed to occur by NADPH-dependent metabolic activation of the pentafluorophenyl ring via arene oxide, quinone and/or quinoneimine reactive intermediates. Formation of these conjugates was enhanced three- to five-fold in liver microsomes obtained from phenobarbital- and dexamethasone-treated rats. In incubations with pooled rat liver microsomes and recombinant rat CYP3A1 and CYP3A2, troleandomycin (TAO) reduced the formation of GSH conjugates M2-4 by 80-90%, but it had no effect on the formation of M1. Incubation of compound I with rat supersomes indicated that only CYP3A1 and CYP3A2 were capable of mediating these metabolic activation processes.

Animals↗
PubMed2004

Coregionalization analysis of heavy metals in the surface soil of Inner Mongolia.

Due to potential problems associated with their deficiencies or toxicities, heavy metals in soils are of great environmental concern. To evaluate heavy metal contents and their relationships in the surface soil of Inner Mongolia, soil samples were collected from 344 sites and contents of copper, lead, zinc, cadmium, nickel, chromium, mercury, cobalt, vanadium and manganese were determined. In this article, coregionalization of these ten heavy metals is investigated using factorial kriging. Vegetation type, parent material type and soil pH, with respective characteristic ranges of 200, 400 and over 1000 km, are identified as the primary factors that control the spatial distribution of soil heavy metals. At the scale of 200 km, heavy metal relationships mainly reflect the result of biocycling. Their relationships at the intermediate scale (400 km) are thought to be derived from the atomic substitution of metals in the parent materials. Effects of soil pH on the adsorption of heavy metals by soil organic materials could explain their relationships at the large spatial scale (over 1000 km).

China↗
PubMed2004

Evaluation of coastal zone sustainability: an integrated approach applied in Shanghai Municipality and Chong Ming Island.

A systems approach has been applied to the examination of sustainable development in the coastal zone. This complex system is envisaged as comprising three sub-systems: environment and resources, economic development and society. A sustainability indicator system based on these three sub-systems has been set up to evaluate the nature of development in the coastal zone. The administrative regions of the Municipality of Shanghai and Chong Ming Island (in the Yangtze Estuary) have been selected as two coastal zones in which to demonstrate the feasibility and effectiveness of the approach. The approach indicated that the development process in Shanghai is one of weak sustainability with relatively rapid social and economic development at the cost of environment and resource degradation. In contrast, social and economic development in Chong Ming County has been limited to protect the regional environment and resources indicating a more sustainable approach to development.

Algorithms↗
PubMed2004

Human neutrophil lipocalin: normal levels and use as a marker for invasive infection in the newborn.

AIM: To evaluate human neutrophil lipocalin (HNL) as a marker of neonatal invasive infection and determine the normal serum levels of HNL in newborns. METHODS: HNL is released from neutrophil granulocytes and is regarded as a specific marker of neutrophil activity. In 81 newborns < or = 28 d of age with signs of infection on a total of 87 occasions, HNL and C-reactive protein (CRP) were measured at inclusion and on the three following days. As controls, term healthy newborns were recruited at birth (cord blood, n = 45) and at ages 3-5 d (n = 46). Serum HNL was measured by a radioimmunoassay. RESULTS: 25/87 episodes were classified as infection and 62 as non-proven infection. HNLmax was significantly higher in the infected group (mean 587.6 microg/l) than in the non-proven infected group (mean 217.7 microg/, p < 0.001). HNL peaked at inclusion, 1 d earlier than CRP. In the healthy controls. HNL was the same at 3-5 d of age as at birth (mean 82.4-81.7 microg/l) and similar to normal adult levels. CONCLUSIONS: The release of HNL is not increased in healthy newborns at birth, but neonatal neutrophils rapidly release HNL upon microbial stimulation in vivo. HNL might be useful as an early marker of neonatal infection.

Acute-Phase Proteins↗