A robust association test with multiple genetic variants and covariates.

Due to the advancement of genome sequencing techniques, a great stride has been made in exome sequencing such that the association study between disease and genetic variants has become feasible. Some powerful and well-known association tests have been proposed to test the association between a group of genes and the disease of interest. However, some challenges still remain, in particular, many factors can affect the performance of testing power, e.g., the sample size, the number of causal and non-causal variants, and direction of the effect of causal variants. Recently, a powerful test, called TREM , is derived based on a random effects model. TREM has the advantages of being less sensitive to the inclusion of non-causal rare variants or low effect common variants or the presence of missing genotypes. However, the testing power of TREM can be low when a portion of causal variants has effects in opposite directions. To improve the drawback of TREM , we propose a novel test, called TROB , which keeps the advantages of TREM and is more robust than TREM in terms of having adequate power in the case of variants with opposite directions of effect. Simulation results show that TROB has a stable type I error rate and outperforms TREM when the proportion of risk variants decreases to a certain level and its advantage over TREM increases as the proportion decreases. Furthermore, TROB outperforms several other competing tests in most scenarios. The proposed methodology is illustrated using the Shanghai Breast Cancer Study.

Therapeutic effectiveness of percutaneous drainage and factors for performing an interval appendectomy in pediatric appendiceal abscess.

BACKGROUND: In this study, we studied the therapeutic effectiveness of percutaneous drainage with antibiotics and the need for an interval appendectomy for treating appendiceal abscess in children with a research-oriented dataset released by the Bureau of National Health Insurance in Taiwan through the Collaboration Center for Health Information Application (CCHIA). METHODS: We identified 1225 patients under 18 years of age who had non-surgical treatment for an appendiceal abscess between 2007 and 2012 in a Taiwan CCHIA dataset. The treatment included percutaneous drainage with antibiotics or antibiotics alone. We also analyzed data of patient's baseline characteristics, outcomes of percutaneous drainage, and indicating factors for performing an interval appendectomy. RESULTS: Totally, 6190 children had an appendiceal abscess, an 1225 patients received non-operative treatment. Of 1225 patients, 150 patients received treatment with percutaneous drainage and antibiotics, 78 had recurrent appendicitis, 185 went on to receive an interval appendectomy, and 10 had postoperative complications after the interval appendectomy. We found that patients treated with percutaneous drainage and antibiotics had a significantly lower rate of recurrent appendicitis (p < 0.05), a significantly smaller chance of receiving an interval appendectomy (p < 0.05), and significantly fewer postoperative complications after the interval appendectomy (p < 0.05) than those without percutaneous drainage treatment. Older children (13 ~ 18 years) patients were found to have a significantly smaller need to receive an interval appendectomy than those who were ≤ 6 years of age (odd ratio (OR) = 2.071, 95 % confidence interval (CI) = 1.34-3.19, p < 0.01), and those who were 7 ~ 12 years old (OR = 1.662, 95 % CI = 1.15-2.41, p < 0.01). In addition, those treated with percutaneous drainage were significantly less indicated to receive an interval appendectomy later (OR = 2.249, 95 % CI = 1.19 ~ 4.26, p < 0.05). In addition, those with recurrent appendicitis had a significantly increased incidence of receiving an interval appendectomy later (OR = 3.231, 95 % CI = 1.95 ~ 5.35, p < 0.001). CONCLUSIONS: In this study, we used nationwide data to demonstrate therapeutic effectiveness of percutaneous drainage and antibiotics was more beneficial than only antibiotics in treating patients with an appendiceal abscess. We also found three factors that were significantly associated with receiving an interval appendectomy: recurrent appendicitis, being aged ≤ 13 years, and treatment with antibiotics only.

A powerful and robust test in genetic association studies.

There are several well-known single SNP tests presented in the literature for detecting gene-disease association signals. Having in place an efficient and robust testing process across all genetic models would allow a more comprehensive approach to analysis. Although some studies have shown that it is possible to construct such a test when the variants are common and the genetic model satisfies certain conditions, the model conditions are too restrictive and in general difficult to verify. In this paper, we propose a powerful and robust test without assuming any model restrictions. Our test is based on the selected 2 × 2 tables derived from the usual 2 × 3 table. By signals from these tables, we show through simulations across a wide range of allele frequencies and genetic models that this approach may produce a test which is almost uniformly most powerful in the analysis of low- and high-frequency variants. Two cancer studies are used to demonstrate applications of the proposed test.

National trends in therapeutic approaches and outcomes for pediatric appendicitis: a Taiwanese nationwide cohort study.

PURPOSE: To define the pattern of therapeutic approaches for pediatric appendicitis and compare their benefits in Taiwan, we analyzed a research-oriented dataset released by the Bureau of National Health Insurance in Taiwan through the Collaboration Center for Health Information Application (CCHIA) to document the impact of the rise of laparoscopic treatment on outcomes. METHODS: We identified 22,161 patients under 18 years who had been hospitalized with a diagnosis of acute appendicitis between 2007 and 2012 in the CCHIA. Statistical comparisons between the Laparoscopic appendectomy (LA) and open appendectomy (OA, control) groups were computed using a Chi squared test. The odds ratios (ORs) and 95% confidence intervals (CIs) of risk factors for intra-abdominal abscess (IAA) and postoperative bowel obstruction (PBO) were derived from multivariate logistic regression models. RESULTS: In each respective year, the incidence of LA increased from 29.17% in 2007 to 57.4% in 2012, while that of OA decreased from 70.83% in 2007 to 42.60% in 2012; incidences of non-perforated appendicitis and perforated appendicitis with LA or OA seemed similar. The length of hospitalization between an LA and OA for non-perforated appendicitis was the same, but that with an LA was shorter for perforated appendicitis. The adjusted ORs for IAA and PBO for those patients with perforated and non-perforated appendicitis were 6.30 (95% CI = 5.09-7.78; p < 0.001) and 6.49 (95% CI = 4.45-9.48; p < 0.001); while for those cases undergoing an LA and OA, they were 0.50 (95 % CI = 0.40-0.62; p < 0.001) and 2.07 (95% CI = 1.45-2.95; p < 0.001), respectively. The ORs of IAA and PBO for those patients ≤6 and 7-12 years of age were 1.67 (95% CI = 1.23-2.25; p = 0.001) and 1.20 (95% CI = 0.97-1.49; p = 0.095), and 1.88 (95% CI = 1.08-3.24; p = 0.025) and 1.47 (95% CI = 1.01-2.14; p = 0.043), respectively, compared to those aged 13-18 years. CONCLUSIONS: Our study demonstrated that young age and perforated appendicitis can affect postoperative IAA and PBO. LA appeared beneficial in reducing the length of hospitalization and postoperative IAA, but had an increasing risk of PBO. Although laparoscopic approach for pediatric appendectomy is increasing in our country, the different hospital levels and pediatric surgeon's laparoscopic experience must be evaluated in further study.

Asymptomatic ratio for seasonal H1N1 influenza infection among schoolchildren in Taiwan.

BACKGROUND: Studies indicate that asymptomatic infections do indeed occur frequently for both seasonal and pandemic influenza, accounting for about one-third of influenza infections. Studies carried out during the 2009 pH1N1 pandemic have found significant antibody response against seasonal H1N1 and H3N2 vaccine strains in schoolchildren receiving only pandemic H1N1 monovalent vaccine, yet reported either no symptoms or only mild symptoms. METHODS: Serum samples of 255 schoolchildren, who had not received vaccination and had pre-season HI Ab serotiters <40, were collected from urban, rural areas and an isolated island in Taiwan during the 2005-2006 influenza season. Their hemagglutination inhibition antibody (HI Ab) serotiters against the 2005 A/New Caledonia/20/99 (H1N1) vaccine strain at pre-season and post-season were measured to determine the symptoms with the highest correlation with infection, as defined by 4-fold rise in HI titer. We estimate the asymptomatic ratio, or the proportion of asymptomatic infections, for schoolchildren during the 2005-6 influenza season when this vaccine strain was found to be antigenically related to the circulating H1N1 strain. RESULTS: Fever has the highest correlation with the 2005-06 seasonal influenza A(H1N1) infection, followed by headache, cough, vomiting, and sore throat. Asymptomatic ratio for the schoolchildren is found to range between 55.6% (95% CI: 44.7-66.4)-77.9% (68.8-87.0) using different sets of predictive symptoms. Moreover, the asymptomatic ratio was 66.9% (56.6-77.2) when using US-CDC criterion of fever + (cough/sore throat), and 73.0 (63.3-82.8) when under Taiwan CDC definition of Fever + (cough or sore throat or nose) + ( headache or pain or fatigue). CONCLUSIONS: Asymptomatic ratio for children is found to be substantially higher than that of the general population in literature. In providing reasonable quantification of the asymptomatic infected children spreading pathogens to others in a seasonal epidemic or a pandemic, our estimates of symptomatic ratio of infected children has important clinical and public health implications.

Geographical heterogeneity and influenza infection within households.

BACKGROUND: Although it has been suggested that schoolchildren vaccination reduces influenza morbidity and mortality in the community, it is unknown whether geographical heterogeneity would affect vaccine effectiveness. METHODS: A 3-year prospective, non-randomized sero-epidemiological study was conducted during 2008-2011 by recruiting schoolchildren from both urban and rural areas. Respective totals of 124, 206, and 176 households were recruited and their household contacts were followed. Serum samples were collected pre-vaccination, one-month post-vaccination and post-season from children and household contacts for hemagglutination inhibition (HI) assay. A multivariate logistic model implemented with generalized estimation equations (GEE) was fitted with morbidity or a four-fold increase in HI titer of the household contacts for two consecutive sera as the dependent variable; with geographical location, vaccination status of each household and previous vaccination history as predictor variables. RESULTS: Although our results show no significant reduction in the proportion of infection or clinical morbidity among household contacts, a higher risk of infection, indicated by odds ratio>1, was consistently observed among household children contacts from the un-vaccinated households after adjusting for confounding variables. Interestingly, a statistically significant lower risk of infection was observed among household adult contacts from rural area when compared to those from urban area (OR=0.89; 95% CI: 0.82-0.97 for Year 2 and OR=0.85; 95% CI: 0.75-0.96 for Year 3). CONCLUSIONS: A significant difference in the risk of influenza infection among household adults due to geographical heterogeneity, independent of schoolchildren vaccination status, was revealed in this study. Its impact on vaccine effectiveness requires further study.

A method for analyzing clustered interval-censored data based on Cox's model.

Methods for analyzing interval-censored data are well established. Unfortunately, these methods are inappropriate for the studies with correlated data. In this paper, we focus on developing a method for analyzing clustered interval-censored data. Our method is based on Cox's proportional hazard model with piecewise-constant baseline hazard function. The correlation structure of the data can be modeled by using Clayton's copula or independence model with proper adjustment in the covariance estimation. We establish estimating equations for the regression parameters and baseline hazards (and a parameter in copula) simultaneously. Simulation results confirm that the point estimators follow a multivariate normal distribution, and our proposed variance estimations are reliable. In particular, we found that the approach with independence model worked well even when the true correlation model was derived from Clayton's copula. We applied our method to a family-based cohort study of pandemic H1N1 influenza in Taiwan during 2009-2010. Using the proposed method, we investigate the impact of vaccination and family contacts on the incidence of pH1N1 influenza.

Assessment of performance of survival prediction models for cancer prognosis.

BACKGROUND: Cancer survival studies are commonly analyzed using survival-time prediction models for cancer prognosis. A number of different performance metrics are used to ascertain the concordance between the predicted risk score of each patient and the actual survival time, but these metrics can sometimes conflict. Alternatively, patients are sometimes divided into two classes according to a survival-time threshold, and binary classifiers are applied to predict each patient's class. Although this approach has several drawbacks, it does provide natural performance metrics such as positive and negative predictive values to enable unambiguous assessments. METHODS: We compare the survival-time prediction and survival-time threshold approaches to analyzing cancer survival studies. We review and compare common performance metrics for the two approaches. We present new randomization tests and cross-validation methods to enable unambiguous statistical inferences for several performance metrics used with the survival-time prediction approach. We consider five survival prediction models consisting of one clinical model, two gene expression models, and two models from combinations of clinical and gene expression models. RESULTS: A public breast cancer dataset was used to compare several performance metrics using five prediction models. 1) For some prediction models, the hazard ratio from fitting a Cox proportional hazards model was significant, but the two-group comparison was insignificant, and vice versa. 2) The randomization test and cross-validation were generally consistent with the p-values obtained from the standard performance metrics. 3) Binary classifiers highly depended on how the risk groups were defined; a slight change of the survival threshold for assignment of classes led to very different prediction results. CONCLUSIONS: 1) Different performance metrics for evaluation of a survival prediction model may give different conclusions in its discriminatory ability. 2) Evaluation using a high-risk versus low-risk group comparison depends on the selected risk-score threshold; a plot of p-values from all possible thresholds can show the sensitivity of the threshold selection. 3) A randomization test of the significance of Somers' rank correlation can be used for further evaluation of performance of a prediction model. 4) The cross-validated power of survival prediction models decreases as the training and test sets become less balanced.

Gout and subsequent increased risk of cardiovascular mortality in non-diabetics aged 50 and above: a population-based cohort study in Taiwan.

BACKGROUND: Limited data are available on the risk ratios for fatal cardiovascular disease (CVD) outcome from gout and chronic kidney disease (CKD) in non-diabetic individuals. METHODS: Nationwide population-based retrospective prospective study with a 5-year follow-up to investigate the association between physician-diagnosed gout and CKD in non-diabetics aged 50 and above who had no pre-existing serious CVD and the subsequent risk of death from CVD. Hazard ratios (HR) of CVD mortality were adjusted for gender, age, smoking- and alcoholism-related diagnoses, hypertension, hyperlipidemia, atrial fibrillation and Charlson's comorbidity index score. RESULTS: A case cohort (n=164,463) having gout and a control cohort (n=3,694,377) having no gout were formed. The prevalence of gout in this study was 4.26% whereas that of gout plus CKD was 8.17%. Male to female ratio among the individuals with gout was 3.2:1. The relative risk (RR) of subsequent cardiovascular mortality between the case and control cohort was 1.71 (95% confidence interval (CI), 1.66-1.75). The presence of CKD in nondiabetic subjects with no gout (control group) has a RR of CVD mortality at 3.05 (95% CI, 2.94-3.15). The presence of gout has protective effect on subjects with CKD with a RR of 1.84 (95% CI, 1.71-1.98). As compared with individuals with no gout, the adjusted HR (aHR) for CVD mortality among the individuals with gout was 1.10 (95% CI 1.07-1.13). In a Cox model, when compared with subjects having neither gout nor CKD, the aHR in subjects with no gout but with CKD is 1.76 (95% CI, 1.70-1.82); in subjects with gout but without CKD, 1.10 (1.07-1.13); interestingly, the aHR is attenuated in subjects with concomitant gout plus CKD which is 1.38 (1.29-1.48). CONCLUSIONS: Among non-diabetic individuals aged 50 years or above who had no preceding serious CVD, those with gout were 1.1 times more likely to die from CVD as were individuals without gout. The presence of gout appears to attenuate the risk of subsequent CV mortality in subjects with CKD. Further studies should focus on finding an explanation for the protective effect of gout on CV mortality in patients with CKD.

Survival analysis of pediatric dialysis patients in Taiwan.

AIM: The long-term survival of Taiwanese children with end-stage renal disease (ESRD) has not been reported before. This study aimed to determine the long-term survival, mortality hazards and causes of death in paediatric patients receiving dialysis. METHODS: Paediatric patients (aged 19 years and younger) with incident ESRD who were reported to the Taiwan Renal Registry from 1995 to 2004 were included. A total of 319 haemodialysis (HD) and 156 peritoneal dialysis (PD) patients formed the database. After stratification by dialysis modality, multivariate Cox proportional-hazards model was constructed with age, sex and co-morbidity as predictive variables. RESULTS: The annual paediatric ESRD incidence rate was 8.12 per million of age-related populations. The overall 1-, 5-, and 10-year survival rates for PD patients were 98.1%, 88.0% and 68.4%, respectively, and were 96.9%, 87.3% and 78.5% for HD patients. The survival analysis showed no significant difference between HD and PD (P = 0.4878). Using '15-19 years' as a reference group, the relative risk (RR) of the youngest group (0-4 years) was 6.60 (95% CI: 2.50-17.38) for HD, and 5.03 (95% CI: 1.23-20.67) for PD. The death rate was 24.66 per 1000 dialysis patient-years. The three major causes of death were infection (23.4%), cardiovascular disease (13.0%) and cerebrovascular disease (10.4%). Hemorrhagic stroke (87.5%) was the main type of foetal cerebrovascular accident. CONCLUSION: We conclude that there was no significant difference of paediatric ESRD patient survival between HD and PD treatment in Taiwan. The older paediatric ESRD patients had better survival than younger patients.

Transmissibility and temporal changes of 2009 pH1N1 pandemic during summer and fall/winter waves.

BACKGROUND: In order to compare the transmissibility of the 2009 pH1N1 pandemic during successive waves of infections in summer and fall/winter in the Northern Hemisphere, and to assess the temporal changes during the course of the outbreak in relation to the intervention measures implemented, we analyze the epidemiological patterns of the epidemic in Taiwan during July 2009-March 2010. METHODS: We utilize the multi-phase Richards model to fit the weekly cumulative pH1N1 epidemiological data (numbers of confirmed cases and hospitalizations) as well as the daily number of classes suspended under a unique "325" partial school closing policy in Taiwan, in order to pinpoint the turning points of the summer and fall/winter waves, and to estimate the reproduction numbers R for each wave. RESULTS: Our analysis indicates that the summer wave had slowed down by early September when schools reopened for fall. However, a second fall/winter wave began in late September, approximately 4 weeks after the school reopened, peaking at about 2-3 weeks after the start of the mass immunization campaign in November. R is estimated to be in the range of 1.04-1.27 for the first wave, and between 1.01-1.05 for the second wave. CONCLUSIONS: Transmissibility of the summer wave in Taiwan during July-early September, as measured by R, was lower than that of the earlier spring outbreak in North America and Europe, as well as that of the winter outbreak in Southern Hemisphere. Furthermore, transmissibility during fall/winter in Taiwan was noticeably lower than that of the summer, which is attributable to population-level immunity acquired from the earlier summer wave and also to the intervention measures that were implemented prior to and during the fall/winter wave.

Survival analysis: comparing peritoneal dialysis and hemodialysis in Taiwan.

OBJECTIVES: Comparisons of survival in patients on peritoneal dialysis (PD) and on hemodialysis (HD) have been conducted in many Western countries, but publications on this subject in Asian populations are scarce. The present study estimated the survival and the relative mortality hazard for HD and PD patients in Taiwan. METHODS: Incident end-stage renal disease patients reported to the Taiwan Renal Registry during 1995 - 2002 were included in the study. Patients had to be 20 years of age or older and had to have survived for the first 90 days on dialysis. A total of 45,820 incident HD and 2,809 incident PD patients formed the study population. Patients on PD were treated mainly with traditional glucose-based solutions. Using an intent-to-treat analysis, the Cox proportional hazards (CPH) model was applied to identify the factors that predict survival by treatment modality. Subgroup analyses were conducted by stratifying patients according to sex, comorbidity, age, and diabetes status. Kaplan-Meier estimates were used to explore the survival of HD and PD patients. Adjustments were implemented using the CPH model. RESULTS: The overall 1-year, 2-year, 3-year, 5-year and 10-year survival rates for PD patients were 89.8%, 77.6%, 67.6%, 55.5%, and 35% respectively. The equivalent survival rates for HD patients were 87.5%, 76.6%, 68.1%, 54.3%, and 33.8%. The differences were not statistically significant (p = 0.125). The CPH analysis stratified by diabetes status and age revealed that PD patients 55 years of age or younger and nondiabetic had a lower mortality ratio (MR) of 0.94. But the MR increased to 1.31 for nondiabetic patients older than 55. The MR for PD versus HD further increased to 1.72 for diabetic patients 55 years of age or younger, and to 1.99 for diabetic patients older than 55. CONCLUSIONS: After adjusting for both demographic and clinical case-mix differences, PD and HD patients were observed to have similar long-term survival. Subgroup analyses revealed that, among diabetic patients and patients older than 55, those on HD experienced better survival than did those on PD.

Risk factors for 14-day rehospitalization following trauma with new traumatic spinal cord injury diagnosis: A 10-year nationwide study in Taiwan.

OBJECTIVES: Fourteen-day rehospitalization with new traumatic spinal cord injury (tSCI) diagnosis is used as an indicator for the diagnostic quality of the first hospitalization. In this nationwide population-based cohort study, we identified risk factors for this indicator. METHODS: We conducted a nested case-control study by using the data of patients who received a first hospitalization for trauma between 2001 and 2011. The data were retrieved from Taiwan's National Health Insurance Research Database. Variables including demographic and trauma characteristics were compared between patients diagnosed with tSCI at the first hospitalization and those receiving a 14-day rehospitalization with new tSCI diagnosis. RESULTS: Of the 23 617 tSCI patients, 997 had 14-day rehospitalization with new tSCI diagnosis (incidence rate, 4.22%). The risk of 14-day rehospitalization with new tSCI diagnosis was significantly lower in patients with severe (injury severity score [ISS] = 16-24; odds ratio [OR], 0.17; 95% confidence interval [CI], 0.13-0.21) and profound (ISS > 24; OR, 0.11; 95% CI, 0.07-0.18) injuries. Interhospital transfer (OR, 8.20; 95% CI, 6.48-10.38) was a significant risk factor, along with injuries at the thoracic (OR, 1.62; 95% CI, 1.21-2.18), lumbar (OR, 1.30; 95% CI, 1.02-1.65), and multiple (OR, 3.23; 95% CI, 1.86-5.61) levels. Brain (OR, 2.82), chest (OR, 2.99), and abdominal (OR, 2.74) injuries were also identified as risk factors. In addition, the risk was higher in patients treated at the orthopedic department (OR, 2.26; 95% CI, 1.78-2.87) and those of other surgical disciplines (OR, 1.89; 95% CI, 1.57-2.28) than in those treated at the neurosurgery department. CONCLUSIONS: Delayed tSCI diagnoses are not uncommon, particularly among trauma patients with ISSs < 16 or those who are transferred from lower-level hospitals. Further validation and implementation of evidence-based decision rules is essential for improving the diagnostic quality of traumatic thoracolumbar SCI.

Detecting rare variants in case-parents association studies.

Despite the success of genome-wide association studies (GWASs) in detecting common variants (minor allele frequency ≥0.05) many suggested that rare variants also contribute to the genetic architecture of diseases. Recently, researchers demonstrated that rare variants can show a strong stratification which may not be corrected by using existing methods. In this paper, we focus on a case-parents study and consider methods for testing group-wise association between multiple rare (and common) variants in a gene region and a disease. All tests depend on the numbers of transmitted mutant alleles from parents to their diseased children across variants and hence they are robust to the effect of population stratification. We use extensive simulation studies to compare the performance of four competing tests: the largest single-variant transmission disequilibrium test (TDT), multivariable test, combined TDT, and a likelihood ratio test based on a random-effects model. We find that the likelihood ratio test is most powerful in a wide range of settings and there is no negative impact to its power performance when common variants are also included in the analysis. If deleterious and protective variants are simultaneously analyzed, the likelihood ratio test was generally insensitive to the effect directionality, unless the effects are extremely inconsistent in one direction.

Brain cancer associated with environmental lead exposure: evidence from implementation of a National Petrol-Lead Phase-Out Program (PLPOP) in Taiwan between 1979 and 2007.

BACKGROUND AND OBJECTIVE: In 1981, a Petrol-Lead Phase-Out Program (PLPOP) was launched in Taiwan for the abatement of environmental lead emissions. The present study was intended to examine whether the high Petrol-Lead Emission Areas (PLEA) would result in an increase in the incidence rate of brain cancer based on a national data bank. METHODS: The national brain cancer incidence data was obtained from the Taiwan National Cancer Registry. Age standardized incidence rates were calculated based on the 2000 WHO world standard population, and gasoline consumption data was obtained from the Bureau of Energy. The differences in the trend tests for age-standardized incidence rates of brain cancer between high, median, low, and small PLEA were analyzed. RESULTS: A significant increase was found from small to high PLEA in age-standardized incidence rates of brain cancer. By taking six possible confounders into account, the age-standardized incidence rates for brain cancer were highly correlated with the median and high PLEA by reference to the small PLEA. CONCLUSION: After being adjusted for a number of relevant confounders, it could be concluded that high PLEA might result in an increase in the incidence rate of brain cancer resulting from high lead exposures.

Improved candidate biomarker detection based on mass spectrometry data using the Hilbert-Huang transform.

Mass spectrometry biomarker discovery may assist patient's diagnosis in time and realize the characteristics of new diseases. Our previous work built a preprocess method called HHTmass which is capable of removing noise, but HHTmass only a proof of principle to be peak detectable and did not tested for peak reappearance rate and used on medical data. We developed a modified version of biomarker discovery method called Enhance HHTMass (E-HHTMass) for MALDI-TOF and SELDI-TOF mass spectrometry data which improved old HHTMass method by removing the interpolation and the biomarker discovery process. E-HHTMass integrates the preprocessing and classification functions to identify significant peaks. The results show that most known biomarker can be found and high peak appearance rate achieved comparing to MSCAP and old HHTMass2. E-HHTMass is able to adapt to spectra with a small increasing interval. In addition, new peaks are detected which can be potential biomarker after further validation.

Characterization and prediction of mRNA polyadenylation sites in human genes.

The accurate identification of potential poly(A) sites has contributed to all many studies with regard to alternative polyadenylation. The aim of this study was the development of a machine-learning methodology that will help to discriminate real polyadenylation signals from randomly occurring signals in genomic sequence. Since previous studies have revealed that RNA secondary structure in certain genes has significant impact, the authors tried to computationally pinpoint common structural patterns around the poly(A) sites and to investigate how RNA secondary structure may influence polyadenylation. This involved an initial study on the impact of RNA structure and it was found using motif search tools that hairpin structures might be important. Thus, it was propose that, in addition to the sequence pattern around poly(A) sites, there exists a widespread structural pattern that is also employed during human mRNA polyadenylation. In this study, the authors present a computational model that uses support vector machines to predict human poly(A) sites. The results show that this predictive model has a comparable performance to the current prediction tool. In addition, it was identified common structural patterns associated with polyadenylation using several motif finding programs and this provides new insight into the role of RNA secondary structure plays in polyadenylation.

Health impacts associated with the implementation of a national petrol-lead phase-out program (PLPOP): evidence from Taiwan between 1981 and 2007.

BACKGROUND AND OBJECTIVE: In 1981, a petrol-lead phase-out program (PLPOP) was launched in Taiwan for the abatement of environmental lead emissions. The present study was set out to examine whether the reduction of environmental lead emissions would result in the decrease in mortality rates of various diseases based on national data between 1981 and 2007. METHOD: The national mortality data were obtained from the Office of Statistics of the Taiwan Department of Health (Taiwan DOH). Standardized mortality ratios (SMRs) were calculated based on 2000 WHO world standard population. Gasoline consumptions were obtained from the Bureau of Energy. RESULTS: The mean blood lead levels (BLLs) had decreased dramatically from approximately 20.14µg/dl in the leaded petrol phase to 3µg/dl or lower in the unleaded petrol phase. From 1981 to 2007, the mortality (per 100,000 people) was decreased from 146.2 to 43.8 for cerebrovascular disease, from 85.3 to 44.4 for heart disease, from 35.4 to 6.6 for hypertensive disease, from 21.3 to 17.3 for nephrosis, and from 810.2 to 491.6 for all causes. By taking the confounders (including economic growth rate, per capita income, tobacco consumption, and medical resources) into account, the decreases in SMRs for all causes, cerebrovascular disease, and nephrosis were found to be highly correlated with the decrease in petrol lead emissions (p-values=0.001, <0.001, 0.020, respectively). CONCLUSION: Our results clearly show that the implementation of the PLPOP was associated with a decline in mortality rates in several diseases that have been associated with lead exposure, even after adjustment for a number of relevant confounders.

Serological response and persistence in schoolchildren with high baseline seropositive rate after receiving 2009 pandemic influenza A(H1N1) vaccine.

The serological response of the current 2009 H1N1 pandemic influenza monovalent vaccine in children exhibiting high baseline seropositive rate was evaluated though a community-based household study. Seroprotection rate of >90% and seroconversion rate of >50% were observed in children one month after receiving the pandemic vaccine. Among children with low baseline antibody titer, a significant lower seroconversion rate (55%) was observed in children who received seasonal trivalent inactivated vaccine (TIV) prior to pandemic vaccine, when compared with those receiving the pandemic vaccine only (86%). Persistence of antibody against the pandemic influenza virus was observed 6 months after vaccination in >80% of children presenting seroprotective antibody levels.

Serological evidence of subclinical transmission of the 2009 pandemic H1N1 influenza virus outside of Mexico.

BACKGROUND: Relying on surveillance of clinical cases limits the ability to understand the full impact and severity of an epidemic, especially when subclinical cases are more likely to be present in the early stages. Little is known of the infection and transmissibility of the 2009 H1N1 pandemic influenza (pH1N1) virus outside of Mexico prior to clinical cases being reported, and of the knowledge pertaining to immunity and incidence of infection during April-June, which is essential for understanding the nature of viral transmissibility as well as for planning surveillance and intervention of future pandemics. METHODOLOGY/PRINCIPAL FINDINGS: Starting in the fall of 2008, 306 persons from households with schoolchildren in central Taiwan were followed sequentially and serum samples were taken in three sampling periods for haemagglutination inhibition (HI) assay. Age-specific incidence rates were calculated based on seroconversion of antibodies to the pH1N1 virus with an HI titre of 1:40 or more during two periods: April-June and September-October in 2009. The earliest time period with HI titer greater than 40, as well as a four-fold increase of the neutralization titer, was during April 26-May 3. The incidence rates during the pre-epidemic phase (April-June) and the first wave (July-October) of the pandemic were 14.1% and 29.7%, respectively. The transmissibility of the pH1N1 virus during the early phase of the epidemic, as measured by the effective reproductive number R(0), was 1.16 (95% confidence interval (CI): 0.98-1.34). CONCLUSIONS: Approximately one in every ten persons was infected with the 2009 pH1N1 virus during the pre-epidemic phase in April-June. The lack of age-pattern in seropositivity is unexpected, perhaps highlighting the importance of children as asymptomatic transmitters of influenza in households. Although without virological confirmation, our data raise the question of whether there was substantial pH1N1 transmission in Taiwan before June, when clinical cases were first detected by the surveillance network.