Rui Feng

Both maternal and paternal disease history can be important predictors of the risk of common conditions such as heart disease or cancer because of shared environmental and genetic risk factors. Sometimes maternal and paternal history can have remarkably different effects on offspring's status. The results are often affected by how the maternal and paternal disease histories are quantified. We proposed using the log-rank score (LRS) to investigate the separate effect of maternal and paternal history on diseases, which takes parental disease status and the age of their disease onset into account. Through simulation studies, we compared the performance of the maternal and paternal LRS with simple binary indicators under two different mechanisms of unbalanced parental effects. We applied the LRS to a national cohort study to further segregate family risks for heart diseases. We demonstrated using the LRS rather than binary indicators can improve the prediction of disease risks and b...

To investigate the Churg-Strauss syndrome (CSS) associated lung involvement, concentrating on clinical characteristics, pathological findings of lung involvements, response to treatment, and prognosis. We retrospectively analyzed the characters of the clinical manifestations, thin-section CT and pathological findings of CSS. The study involved 16 patients. Clinical data were obtained by chart review. All patients underwent transbronchial lung biopsy (TBLB). Six of them underwent surgical lung biopsy as well. The patients included 7 men and 9 women, aged from 14 to 61 years (median, 47.5 years). Extrathoracic organs involved included nervous system (7/16) and skin (5/16). Respiratory symptoms included cough (12/16), exertional dyspnea (11/16), hemoptysis (4/16), and chest pain (3/16). CT findings included bilateral ground-glass opacities (12/16), bilateral patchy opacities (12/16), and centrilobular nodules (6/16). The pathological findings of TBLB demonstrated increased eosinophils ...

In this study, a sensor for the sensitive determination of ascorbic acid (AA) has been fabricated based on meso-tetra-(3,5-dibromo-4-hydroxydroxyphenyl) porphyrin copper (II) (T(DBHP)P-Cu) modified Au electrode through l-cysteine (l-cys). Firstly, l-cys modified Au electrode was prepared through self-assembled technology. Then T(DBHP)P-Cu was adsorbed on l-cys/Au through covalent binding. The fabrication process and electrochemical behavior of T(DBHP)P-Cu/l-cys/Au were studied by cyclic

Nano-montmorillonites belong to aluminosilicate clay minerals with innocuity, high specific surface area, ion exchange, and favorable adsorption property. Due to the excellent properties, montmorillonites can be used as labels for the electrochemical immunosensors. In this study, nano-montmorillonites were converted to sodium montmorillonites (Na-Mont) and further utilized for the immobilization of thionine (TH), horseradish peroxidase (HRP) and the secondary anti-zeranol antibody (Ab(2)). The modified particles, Na-Mont-TH-HRP-Ab(2) were used as labels for immunosensors to detect zeranol. This protocol was used to prepare the immunosensor with the primary antibody (Ab(1)) immobilized onto the nanoporous gold films (NPG) modified glassy carbon electrode (GCE) surface. Within zeranol concentration range (0.01-12ng mL(-1)), a linear calibration plot (Y=0.4326+8.713X, r=0.9996) was obtained with a detection limit of 3pg mL(-1) under optimal conditions. The proposed immunosensor showed ...

Parent-of-origin effects have been pointed out to be one plausible source of the heritability that was unexplained by genome-wide association studies. Here, we consider a case-control mother-child pair design for studying parent-of-origin effects of offspring genes on neonatal/early-life disorders or pregnancy-related conditions. In contrast to the standard case-control design, the case-control mother-child pair design contains valuable parental information and therefore permits powerful assessment of parent-of-origin effects. Suppose the region under study is in Hardy-Weinberg equilibrium, inheritance is Mendelian at the diallelic locus under study, there is random mating in the source population, and the SNP under study is not related to risk for the phenotype under study because of linkage disequilibrium (LD) with other SNPs. Using a maximum likelihood method that simultaneously assesses likely parental sources and estimates effect sizes of the two offspring genotypes, we investigate the extent of power increase for testing parent-of-origin effects through the incorporation of genotype data for adjacent markers that are in LD with the test locus. Our method does not need to assume the outcome is rare because it exploits supplementary information on phenotype prevalence. Analysis with simulated SNP data indicates that incorporating genotype data for adjacent markers greatly help recover the parent-of-origin information. This recovery can sometimes substantially improve statistical power for detecting parent-of-origin effects. We demonstrate our method by examining parent-of-origin effects of the gene PPARGC1A on low birth weight using data from 636 mother-child pairs in the Jerusalem Perinatal Study.

An ionic liquid, 1-allyl-3-methyl imidazole chloride (AMIMCl), was synthesized to modify a terminal-vinyl organic-inorganic hybrid silica monolithic column by free-radical polymerization procedure using 2,2′-azodiisobutyronitrile (AIBN) as an initiator. Nucleotide monophosphates, phenols and benzoic acid compounds were successfully separated on this column under acidic conditions. The electroosmotic flow (EOF) was in the direction opposite to electrophoretic migration, and separation selectivity was

Nanoporous PtCo alloy was designed as an antibody carrier for preparation of a highly sensitive immunosensor. The immunosensor was constructed by assembling the capture zeranol antibody on thionine decorated graphene nanosheets modified glassy carbon electrode. With an enzyme-free immunosensor mode, the nanoporous PtCo alloy, synthesized by dealloying method, had shown strong electrocatalytic activity toward antigen-antibody reaction. The use of PtCo alloy carrier offered a high amount of antibody on each immunoconjugate, hence amplified the detectable signal from the electro-reaction of dissolved oxygen. Cyclic voltammetry and electrochemical impedance spectroscopy were used to characterize the recognition of zeranol. Due to the poor conductivity of zeranol, a small amount of zeranol immobilized onto the electrode could result in great change in the electron-transfer resistance. Some factors that would affect the performance of the immunosensor were studied, such as concentration of PtCo, pH, and the ratio of TH to GS. With zeranol concentration range (0.05 to 5.0 ng/mL), the immunosensor exhibited a highly sensitive response to zeranol with a detection limit of 13 pg/mL. The immunosensor was evaluated for bovine urine sample, receiving satisfactory results.

The goals were to isolate and to estimate the genetic susceptibility to retinopathy of prematurity. A retrospective study (1994-2004) from 3 centers was performed with zygosity data for premature twins who were born at a gestational age of < or = 32 weeks and survived beyond a postmenstrual age of 36 weeks. Retinopathy of prematurity was diagnosed and staged by pediatric ophthalmologists at each center. Data analyses were performed with mixed-effects logistic regression analysis and latent variable probit modeling. A total of 63 monozygotic and 137 dizygotic twin pairs were identified and analyzed. Data on gestational age, birth weight, gender, respiratory distress syndrome, retinopathy of prematurity, bronchopulmonary dysplasia, duration of ventilation and supplemental oxygen use, and length of stay were comparable between monozygotic and dizygotic twins. In the mixed-effects logistic regression analysis for retinopathy of prematurity, gestational age and duration of supplemental oxygen use were significant covariates. After controlling for known and unknown nongenetic factors, genetic factors accounted for 70.1% of the variance in liability for retinopathy of prematurity. In addition to prematurity and environmental factors, there is a strong genetic predisposition to retinopathy of prematurity.

Oxidant stress pathway activation during ischemia reperfusion injury may contribute to the development of primary graft dysfunction (PGD) after lung transplantation. We hypothesized that oxidant stress gene variation in recipients and donors is associated with PGD. Donors and recipients from the Lung Transplant Outcomes Group (LTOG) cohort were genotyped using the Illumina IBC chip filtered for oxidant stress pathway genes. Single nucleotide polymorphisms (SNPs) grouped into SNP sets based on haplotype blocks within 49 oxidant stress genes selected from gene ontology pathways and literature review were tested for PGD association using a sequencing kernel association test. Analyses were adjusted for clinical confounding variables and population stratification. Three hundred ninety-two donors and 1038 recipients met genetic quality control standards. Thirty percent of patients developed grade 3 PGD within 72 hours. Donor NADPH oxidase 3 (NOX3) was associated with PGD (P = .01) with 5 individual significant loci (P values between .006 and .03). In recipients, variation in glutathione peroxidase (GPX1) and NRF-2 (NFE2L2) was significantly associated with PGD (P = .01 for both). The GPX1 association included 3 individual loci (P values between .006 and .049) and the NFE2L2 association included 2 loci (P = .03 and .05). Significant epistatic effects influencing PGD susceptibility were evident between 3 different donor blocks of NOX3 and recipient NFE2L2 (P = .026, P = .017, and P = .031). Our study has prioritized GPX1, NOX3, and NFE2L2 genes for future research in PGD pathogenesis, and highlights a donor-recipient interaction of NOX3 and NFE2L2 that increases the risk of PGD.

ABSTRACT Background and objective Twin and family studies support large genetic influences on variability in body mass index (BMI), with heritability estimates ranging from 47% to over 90%. Our objective was to study the relative contributions of genetics and environment to BMI, evaluating sex differences, in an adolescent twin sample from Valencia, Spain. Material and methods Five hundred eighty-four pairs of adolescent twins between 13 and 18 years of age completed the study (82 monozygotic [MZ] and 87 dizygotic [DZ] pairs of male twins, 118 MZ and 102 DZ pairs of female twins, and 195 opposite-sex pairs of DZ twins). To determine zygosity, teachers responded a questionnaire on physical similarity. They also measured the participant's height and weight. BMI was calculated and weight status was determined according to age. We used twin models to assess genetic and environmental (common and unique) factors affecting BMI. Results There was a 7.1% frequency of overweight and 2.8% of obesity. The estimated heritability of BMI was 88.0% in boys and 72.1% in girls, with the remaining variance attributable to non-shared environment in boys (12.0%) and 8.8% in girls. It was only in girls that common environment had an effect on BMI. Conclusions Genetics appears to play an important role in explaining the variability in BMI in the adolescence, with slight variations between boys and girls. Common environmental factors exert their influence on BMI only in girls.

We consider estimation and variable selection in high-dimensional Cox regression when a prior knowledge of the relationships among the covariates, described by a network or graph, is available. A limitation of the existing methodology for survival analysis with high-dimensional genomic data is that a wealth of structural information about many biological processes, such as regulatory networks and pathways, has often been ignored. In order to incorporate such prior network information into the analysis of genomic data, we propose a network-based regularization method for high-dimensional Cox regression; it uses an ℓ1-penalty to induce sparsity of the regression coefficients and a quadratic Laplacian penalty to encourage smoothness between the coefficients of neighboring variables on a given network. The proposed method is implemented by an efficient coordinate descent algorithm. In the setting where the dimensionality p can grow exponentially fast with the sample size n, we establish model selection consistency and estimation bounds for the proposed estimators. The theoretical results provide insights into the gain from taking into account the network structural information. Extensive simulation studies indicate that our method outperforms Lasso and elastic net in terms of variable selection accuracy and stability. We apply our method to a breast cancer gene expression study and identify several biologically plausible subnetworks and pathways that are associated with breast cancer distant metastasis.

Infants with congenital diaphragmatic hernia (CDH) can develop pulmonary hypertension (PH) from decreased number and abnormal muscularization of pulmonary arteries. Normally pulmonary vascular growth and remodeling parallel airspace growth and alveolarization, which exhibits a wide morphologic variation in CDH. To assess whether infants with CDH and PH have greater abnormalities in infant pulmonary function testing (IPFT) compared to those without PH. We reviewed results of IPFTs and echocardiograms performed on infants with CDH from 2004 to June 2011. Lung volumes, forced flows and tidal mechanics were standardized according to available reference values. Comparisons between infants with and without PH were performed using linear regression, adjusting for potential confounders. Sixty-six infants were included; 18 had PH and 48 did not. Z-score values for functional residual capacity (FRC), residual volume (RV), FRC/total lung capacity (TLC), and RV/TLC were significantly higher in infants with CDH and PH compared to those without PH. Z-score values for forced flows including forced expiratory volume in the first 0.5 sec (FEV0.5) and FEV0.5/forced vital capacity were significantly lower in infants with CDH and PH compared to those without PH. For 29 infants studied on ≥2 occasions, the slopes of FRC, RV, and TLC versus length were significantly higher in those with persistent PH compared to those without. Infants with CDH and persistent PH demonstrate greater airspace overdistension with growth compared to those without. Therapies that modify disrupted pulmonary vascular and alveolar formation could potentially improve future care of these patients. Pediatr Pulmonol. © 2014 Wiley Periodicals, Inc.

In genetical genomics studies, it is important to jointly analyze gene expression data and genetic variants in exploring their associations with complex traits, where the dimensionality of gene expressions and genetic variants can both be much larger than the sample size. Motivated by such modern applications, we consider the problem of variable selection and estimation in high-dimensional sparse instrumental variables models. To overcome the difficulty of high dimensionality and unknown optimal instruments, we propose a two-stage regularization framework for identifying and estimating important covariate effects while selecting and estimating optimal instruments. The methodology extends the classical two-stage least squares estimator to high dimensions by exploiting sparsity using sparsity-inducing penalty functions in both stages. The resulting procedure is efficiently implemented by coordinate descent optimization. For the representative L 1 regularization and a class of concave regularization methods, we establish estimation, prediction, and model selection properties of the two-stage regularized estimators in the high-dimensional setting where the dimensionality of co-variates and instruments are both allowed to grow exponentially with the sample size. The practical performance of the proposed method is evaluated by simulation studies and its usefulness is illustrated by an analysis of mouse obesity data. Supplementary materials for this article are available online.

The role of genetics in the development of acute lung injury (ALI)/acute respiratory distress syndrome (ARDS) from direct or indirect lung injury has not been specifically investigated. The aim of this study was to identify genetic variants contributing to ALI/ARDS from pulmonary or extrapulmonary causes. We conducted a multistage genetic association study. We first performed a large-scale genotyping (50K ITMAT-Broad_CARe Chip) in 1717 critically ill Caucasian patients with either pulmonary or extrapulmonary injury, to identify single nucleotide polymorphisms (SNPs) associated with the development of ARDS from direct or indirect insults to the lung. Identified SNPs (p≤0.0005) were validated in two separated populations (Stage II), with trauma (Population I; n=765) and pneumonia/pulmonary sepsis (Population II; n=838), as causes for ALI/ARDS. Genetic variants replicating their association with trauma related-ALI in Stage II were validated in a second trauma-associated ALI population (n=224, Stage III). In Stage I, non-overlapping SNPs were significantly associated with ARDS from direct/indirect lung injury, respectively. The association between rs1190286 (POPDC3) and reduced risk of ARDS from pulmonary injury was validated in Stage II (p<0.003). SNP rs324420 (FAAH) was consistently associated with increased risk of ARDS from extrapulmonary causes in two independent ALI-trauma populations (p<0.006, Stage II;…

The major histocompatibility complex (MHC) (Chromosome 6p21.3) is a dynamic, immune gene-rich region that is associated with multiple diseases. Haplotype-tagging single-nucleotide polymorphism (htSNP) panels for the MHC can aid association studies but have only been reported for African, Asian and Caucasian populations to date. We genotyped 2154 SNPs spanning a 3.8-Mb region of the classical MHC in 94 healthy African Americans using Illumina BeadArray technology. We describe the haplotype structure of the MHC in African Americans, calculate the recombination rate (0.35 cM Mb(-1)) across the region, identify recombination hot spots and develop a panel of htSNPs for future genetic association studies in this population. We conclude that while patterns of LD and recombination are similar within the MHC to that reported in other populations, differences in minor allele frequency at specific markers necessitates an htSNP panel unique to African Americans, which we provide here for use in future genetic association studies.

Acute respiratory distress syndrome (ARDS) behaves as a complex genetic trait, yet knowledge of genetic susceptibility factors remains incomplete. To identify genetic risk variants for ARDS using large scale genotyping. A multistage genetic association study was conducted of three critically ill populations phenotyped for ARDS. Stage I, a trauma cohort study (n = 224), was genotyped with a 50K gene-centric single-nucleotide polymorphism (SNP) array. We tested SNPs associated with ARDS at P < 5 × 10(-4) for replication in stage II, a trauma case-control population (n = 778). SNPs replicating their association in stage II (P < 0.005) were tested in a stage III nested case-control population of mixed subjects in the intensive care unit (n = 2,063). Logistic regression was used to adjust for potential clinical confounders. We performed ELISA to test for an association between ARDS-associated genotype and plasma protein levels. A total of 12 SNPs met the stage I threshold for an association with ARDS. rs315952 in the IL1RN gene encoding IL-1 receptor antagonist (IL1RA) replicated its association with reduced ARDS risk in stages II (P < 0.004) and III (P < 0.02), and was robust to clinical adjustment (combined odds ratio = 0.81; P = 4.2 × 10(-5)). Plasma IL1RA level was associated with rs315952C in a subset of critically ill subjects. The effect of rs315952 was independent from the tandem repeat variant in IL1RN. The IL1RN SNP rs315952C is associated with decreased risk of ARDS in three populations with heterogeneous ARDS risk factors, and with increased plasma IL1RA response. IL1RA may attenuate ARDS risk.

Elevated long pentraxin-3 (PTX3) levels are associated with the development of primary graft dysfunction (PGD) after lung transplantation. Abnormalities in innate immunity, mediated by PTX3 release, may play a role in PGD pathogenesis. Our goal was to test whether variants in the gene encoding PTX3 are risk factors for PGD. We performed a candidate gene association study in recipients from the multicenter, prospective Lung Transplant Outcomes Group cohort enrolled between July 2002 and July 2009. The primary outcome was International Society for Heart and Lung Transplantation grade 3 PGD within 72 hours of transplantation. Targeted genotyping of 10 haplotype-tagging PTX3 single-nucleotide polymorphisms (SNPs) was performed in lung transplant recipients. The association between PGD and each SNP was evaluated by logistic regression, adjusting for pretransplantation lung disease, cardiopulmonary bypass use, and population stratification. The association between SNPs and plasma PTX3 levels was tested across genotypes in a subset of recipients with idiopathic pulmonary fibrosis. Six hundred fifty-four lung transplant recipients were included. The incidence of PGD was 29%. Two linked 5' region variants, rs2120243 and rs2305619, were associated with PGD (odds ratio, 1.5; 95% confidence interval, 1.1 to 1.9; P = 0.006 and odds ratio, 1.4; 95% confidence interval, 1.1 to 1.9; P = 0.007, respectively). The minor allele of rs2305619 was significantly associated with higher plasma PTX3 levels measured pretransplantation (P = 0.014) and at 24 hours (P = 0.047) after transplantation in patients with idiopathic pulmonary fibrosis. Genetic variants of PTX3 are associated with PGD after lung transplantation, and are associated with increased PTX3 plasma levels.