Homocysteine, hyperhomocysteinemia and H-type hypertension.

Homocysteine (Hcy) is a sulfur-containing nonessential amino acid derived from the intermediate metabolites of methionine. Methionine is obtained from dietary proteins, such as poultry, meat, eggs, seafood, and dairy products. Abnormalities in Hcy metabolic pathways, deficiencies in dietary methionine, folate, and vitamins B12, B6 and B2 and genetic defects, polymorphisms, or mutations in Hcy metabolism-related enzymes may lead to an increase in plasma Hcy levels. Generally, a plasma Hcy level higher than 10 µmol/L or 15 µmol/L has been defined as hyperhomocysteinemia (HHcy). An individual with essential hypertension complicated with HHcy is considered to have H-type hypertension (HTH). Currently, HHcy is considered a novel independent risk factor for various cardiovascular diseases. To provide a useful reference for clinicians, the research progress on Hcy, HHcy and HTH in recent years was systematically reviewed here, with a focus on the source and metabolic pathways of Hcy, plasma Hcy levels and influencing factors, detection methods for plasma Hcy levels, relationship between Hcy concentration and hypertension, pathogenesis of HTH, cardiovascular complications of HTH, and treatment of HTH.

Application of the metal ions as potential population biomarkers for wastewater-based epidemiology: estimating tobacco consumption in Southern China.

Wastewater-based epidemiology (WBE) is an objective approach for the estimation of population-level exposure to a wide range of substances, in which the use of a population biomarker (PB) could significantly reduce back-calculation errors. Although some endogenous or exogenous compounds such as cotinine and other hormones have been developed as PBs, more PBs still need to be identified and evaluated. This study aimed to propose a novel method to estimate population parameters from the mass load of metal ion biomarkers in wastewater, and estimate the consumption of tobacco in 24 cities in Southern China using the developed method. Daily wastewater samples were collected from 234 wastewater treatment plants (WWTPs) in 24 cities in Southern China. Atomic absorption spectroscopy (AAS) was applied to determine the concentrations of common health-related metal ions in wastewater, including sodium (Na), potassium (K), magnesium (Mg), calcium (Ca), iron (Fe), and zinc (Zn), and compared them with the daily mass load of cotinine corresponding to catchment populations. The concentrations of cotinine in wastewater samples were measured using liquid chromatography-tandem mass spectrometry. There were clear and strong correlations between the target metal ion equivalent population and census data. The correlation coefficients (R) were RK = 0.78, RNa = 0.66, RCa = 0.81, RMg = 0.77, and RFe = 0.69, at p < 0.01 and R2 > 0.6. Subsequently, the combination of WBE and metal ion PBs was used to estimate tobacco consumption. Daily consumption of nicotine was estimated to be approximately 1.76 ± 1.19 mg/d/capita, equivalent to an average of 13.0 ± 8.75 cigarettes/d being consumed by smokers. The data on tobacco consumption in this study were consistent with those in traditional surveys in Southern China. The metal ion potassium is an appropriate PB for reflecting the real-time population and could be used to evaluate the tobacco consumption in WBE study.

Identification of hsa_circ_0001445 of a novel circRNA-miRNA-mRNA regulatory network as potential biomarker for coronary heart disease.

Objects: To evaluate the hsa_circ_0001445 level in peripheral blood leukocytes of patients with coronary heart disease (CHD) and its related clinical factors, and predict its circRNA-miRNA-mRNA regulatory network in CHD pathogenesis via bioinformatics analysis. Methods: Peripheral blood leukocytes were isolated from the whole blood samples of 94 CHD patients (aged 65.96 ± 9.78 years old) and 126 healthy controls (aged 60.75 ± 8.81 years old). qRT-PCR was used to quantify the expression level of circRNA and subsequently analyze its association with CHD clinical parameters. Via bioinformatics algorithm and GEO datasets, differential miRNA expression was evaluated using the Limma package. A miRNA-mRNA regulatory network was predicted by cyTargetLinker. ClusterProfiler was employed to perform functional enrichment analysis of the circRNA network to investigate its role in CHD pathogenesis. Results: The expression of hsa_circ_0001445 in peripheral blood leukocytes of CHD patients was downregulated compared with that of healthy controls. Positive correlations were evident between hsa_circ_0001445 expression level and the levels of hemoglobin, triglycerides, high- and low-density lipoprotein cholesterol. A significant negative correlation was also found between hsa_circ_0001445 expression level and age and the neutrophil level. Low expression of hsa_circ_0001445 exhibited a discriminatory ability between CHD patients and healthy controls with a sensitivity of 67.5% and a specificity of 76.6% (p < 0.05). By bioinformatics analysis, 405 gene ontology terms were identified. The Kyoto Encyclopedia of Genes and Genomes terms focused principally on the PI3K-Akt signaling pathway. hsa_circ_0001445 was associated with the expression of three miRNAs that may regulate 18 genes involved in KEGG processes: hsa-miR-507, hsa-miR-375-3p, and hsa-miR-942-5p. Conclusion: The hsa_circ_0001445 level in peripheral blood leukocytes may serve as a biomarker for CHD diagnosis. Our work on circRNA-miRNA-mRNA networks suggests a potential role for hsa_circ_0001445 in CHD development.

When to initiate cancer screening exam?

A probability method is developed to decide when to initiate cancer screening for asymptomatic individuals. The probability of incidence is a function of screening sensitivity, time duration in the disease-free state and sojourn time in the preclinical state; and it is monotonically increasing as time increases, given a person's current age. So a unique solution of the first screening time can be found by limiting this probability to a small value, such as 10% or 20%. That is, with 90% or 80% probability, one will not be a clinical incident case before the first exam. After this age is found, we can further estimate the lead time distribution and probability of over-diagnosis if one would be diagnosed with cancer at the first exam. Simulations were carried out under different scenarios; and the method was applied to two heavy smoker cohorts in the National Lung Screening Trial using low-dose computerized tomography. The method is applicable to other kinds of cancer screening. The predictive information can be used by physicians or individuals at risk to make informed decisions on when to initiate screening.

Estimation of Preclinical State Onset Age and Sojourn Time for Heavy Smokers in Lung Cancer.

Estimation of the three key parameters: onset age of the preclinical state, sojourn time and screening sensitivity is critical in cancer screening, since all other terms are functions of the three. A novel link function to connect sensitivity with time in the preclinical state and the likelihood method were used in this project; since sensitivity depends on how long one has entered the preclinical state relative to the total sojourn time. Simulations using Markov Chain Monte Carlo and maximum likelihood estimate were carried out to estimate the key parameters for male and female heavy smokers separately in the low-dose computed tomography group of the National Lung Screening Trial. Sensitivity for male and female heavy smokers were 0.883 and 0.915 respectively at the onset of the preclinical state, and increased to 0.972 and 0.981 at the end. The mean age to make the transition into the preclinical state was 70.94 or 71.15 for male and female heavy smokers respectively, and 90% of heavy smokers at risk for lung cancer would enter the preclinical state in age interval (55.7, 85.8) for males and (54.2, 87.7) for females, and the transition peaked around age 69 for both genders. The mean sojourn time in the preclinical state was 1.43 and 1.49 years, and the 99% credible intervals for the sojourn time were (0.21, 2.96) and (0.37, 2.69) years for male and female heavy smokers correspondingly. Based on the result, low-dose CT should be started at age 55 and ended before 85 for heavy smokers. This provided important information to policy makers.

Inference of Onset Age of Preclinical State and Sojourn Time for Breast Cancer.

Aims: Accurate estimation of the three key parameters (sensitivity, time duration in disease-free state and sojourn time in preclinical state) in cancer screening are critical. Likelihood method with a new link function was applied to the Health Insurance Plan of Greater New York (HIP) breast cancer screening data, to estimate the onset age of preclinical state and the sojourn time in the preclinical state for breast cancer. Materials and Methods: A new link function to model sensitivity as a function of time in the preclinical state and the sojourn time was adopted. Markov Chain Monte Carlo simulations were used to obtain posterior samples and make inference on the three key parameters. Maximum likelihood estimate was also used for comparison. Results: The onset age of the preclinical state has a wide range for breast cancer; the peak onset age was 65.07 years (95% credible interval [C.I.], 55.76 to 73.02). The mean sojourn time was 2.00 years (95% C.I., 0.85 to 2.95). The 95 % C.I. for the sojourn time was 0.16 to 5.53 years. Sensitivity at onset of the preclinical state was 0.75 (95% C.I., 0.54 to 0.88); and sensitivity at the end of the preclinical state was 0.84 (95% C.I., 0.67 to 0.88). Conclusion: The HIP study was the oldest breast cancer mass screening. The estimates reflect key parameters in those days with lower screening sensitivity. However, it is helpful to know other parameters in the planning for future breast cancer screening.

Preoperative Cardiac Index as a Predictor of Maturation and Primary Patency of Radiocephalic Arteriovenous Fistula in Hemodialysis.

BACKGROUND: Radiocephalic arteriovenous fistula (RCAVF) is the best access modality to be considered initially when planning arteriovenous fistula (AVF) for maintenance hemodialysis. Considering the higher incidence of RCAVF failed maturation (M), it is important to perform proper preoperative evaluation and identification of high-risk patients. There has been no study on the influence of preoperative cardiac function on the M and patency of AVFs. The purpose of this investigation is to determine whether preoperative cardiac index (CI) is a predictor of M and primary patency of RCAVF. METHOD: A total of 365 end-stage renal disease patients undergoing RCAVF surgery were consecutively enrolled with a median follow-up time of 20 months in this prospective cohort study. Demographics, vascular diameters measured by duplex ultrasound examination, and CI measured by echocardiography, were analyzed for effect on RCAVF primary functional M and primary patency. RESULT: Patients in the group achieving primary RCAVF functional M had a significantly larger mean CI than the group with early RCAVF failure (2.93 ± 0.77 vs. 3.57 ± 0.76 L/min/m2, p < 0.001). The receiver operating characteristic curve was plotted and demonstrated that preoperative vein diameter and CI can predict failure of RCAVF M. The AUC of CI was higher (0.745 vs. 0.666). Multivariate regression analysis, adjusted for age, sex, diabetes, preoperative dialysis status and vessel diameters, showed that decreased CI remained associated with increased risk of failure of M (FM) and worse primary unassisted patency. The Kaplan-Meier survival analysis suggested that patients with CI <3 L/min/m2 had a worse primary unassisted patency rate at all time points compared with patients with CI ≥3 L/min/m2. CONCLUSION: This study demonstrated that preoperative CI was associated with RCAVF M and long-term patency. A decreased CI may be a possible predictor of an increased risk of FM and a shorter primary patency time.

Differential effects of hyperhomocysteinemia on the lipid profiles and lipid ratios between patients with and without coronary artery disease: A retrospective observational study.

This study aimed to investigate the differential effects of hyperhomocysteinemia (HHcy) on lipid profiles and lipid ratios between patients with coronary artery disease (CAD) and without CAD. The data of 872 CAD patients and 774 non-CAD controls were extracted from the information system of hospitalized patients. Serum homocysteine (Hcy), total cholesterol (TC), triglycerides (TGs), high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), apolipoprotein (Apo) AI, and ApoB concentrations were detected. HHcy was defined as a serum level of Hcy ≥ 15 µmol/L. The CAD patients had lower levels of HDL-C and ApoAI and higher levels of Hcy than the controls (P < .05). Serum TGs and HDL-C were negatively correlated with Hcy in controls. Serum HDL-C and ApoAI were negatively correlated with Hcy, and the ratios of TC/HDL-C, TG/HDL-C, LDL/HDL-C, and ApoB/ApoAI were positively correlated with Hcy in the CAD patients (P < .05). Although the trends for HHcy to decrease the lipid profiles were not different between the CAD and controls (Pinteraction > 0.05), CAD with HHcy had lower HDL-C and ApoAI levels than those of subjects with normal Hcy; controls with HHcy had lower TC, LDL-C, and ApoB levels than those of subjects with normal Hcy (P < .05). There were different HHcy trends affecting the ratios of TC/HDL-C and LDL/HDL-C between the CAD patients and controls (Pinteraction for TC/HDL-C = 0.025; Pinteraction for LDL/HDL-C = 0.033). CAD patients with HHcy had a higher ratio of TC/HDL-C (P = .022) and LDL/HDL-C (P = .045) than those of patients with normal Hcy, but in the controls, the subjects with HHcy exhibited a trend toward a decreased ratio of TC/HDL-C (P = .481) and LDL/HDL-C (P = .303). There were differential effects of HHcy on the lipid ratios between CAD and non-CAD patients. HHcy was related to higher ratios of TC/HDL-C and LDL/HDL-C in patients with CAD.

Inference of Sojourn Time and Transition Density using the NLST X-ray Screening Data in Lung Cancer.

AIMS: The aim of this study is to provide statistical inference of the sojourn time and the transition probability from the disease free to the preclinical state of lung cancer for male and female smokers using lung cancer data from the National Lung Screening Trial (NLST). MATERIALS AND METHODS: We applied a likelihood function to the lung cancer data, to obtain Bayesian inference of the transition probability and the sojourn time distribution. A log-normal distribution was used for the transition probability density function multiplied by 30%, and a Weibull distribution was used to model the sojourn time in the preclinical state. RESULTS: The estimate of screening sensitivity is 0.61 for males and 0.62 for females. Early transition happened before age 50 and lasted until after age 90. The transition probability from the disease free to the preclinical state has a single maximum at around age 73 for males and 72 for females. For male, the Bayesian posterior mean, and median sojourn time are 1.33 and 1.27 years, respectively. For female, the corresponding posterior mean, and median sojourn time are 1.23 and 1.21 years, respectively. CONCLUSION: Our estimation showed that male smokers are more vulnerable to lung cancer, because they have a higher transition probability density than the same aged female smokers. The female smokers have a slightly shorter mean sojourn time than the male, meaning that they are quicker to develop clinical symptom of lung cancer.

Identification and monitoring of fentanyls-related substances in east China sewage water samples by LC-MS for drug enforcement.

Fentanyls abuse is a persistent international concern. New fentanyl derivatives are constantly appearing, circumventing national and international laws. In this study, laboratory degradation experiment with different conditions such as pH, light, temperature and oxygen availability were compared to improve the understanding of the fentanyls degradation pathways. Twelve major degradants of sufentanil and alfentanil were detected and identified together using UHPLC-QTOF-MS. A total of thirty nine fentanyls including twelve typical fentanyl new psychoactive substances, eighteen manufacturing process-related substances and nine key degradants of sufentanil and alfentanil were screened in 120 sewage water samples collected from 20 sewage water treatment plants chosen among 6 urban cities in east China from July to August in 2020 using a validated UHPLC-MS/MS method. Three fentanyls (fentanyl, sufentanil, alfentanil), seven degradants and six manufacturing process-related substances were found in the test samples. The study could provide a useful tool for the monitoring of the abuses, illegal manufacturing or pharmaceuticals related pollutions of fentanyls and their analogs.

High expression of protein phosphatase 2 regulatory subunit B'' alpha predicts poor outcome in hepatocellular carcinoma patients after liver transplantation.

BACKGROUND: Protein phosphatase 2 regulatory subunit B'' alpha (PPP2R3A) gene has been reported in other tumors, but the influence of PPP2R3A gene expression on the occurrence, development, and prognosis of hepatocellular carcinoma (HCC) remains unclear. AIM: To investigate whether the PPP2R3A gene could be used to predict tumor recurrence and survival of HCC patients after liver transplantation (LT). METHODS: Diseased liver tissues of HCC patients after LT were collected as well as their clinical data and follow-up information. The immunohistochemical method was used to detect the expression of PPP2R3A protein in the tissues of 108 patients with primary liver cancer. The χ 2 test was used to analyze the relationship between PPP2R3A protein expression levels and the clinicopathological features of tumors. The Kaplan-Meier method was used to analyze overall postoperative survival. The COX proportional hazard model was used to analyze adverse prognostic factors. RESULTS: Immunohistochemistry showed that the PPP2R3A protein was mainly expressed in the cytoplasm of HCC cells. Compared to corresponding peritumoral tissues, expression was higher in HCC tissues (P ≤ 0.001). Correlation analysis showed that high PPP2R3A expression was correlated with preoperative serum alpha-fetoprotein (AFP) levels (P = 0.003), tumor-node-metastasis-t stage (P ≤ 0.001), and envelope invasion (P = 0.001). Univariate analysis showed that overall survival (P ≤ 0.001) and recurrence-free survival (P = 0.025) of patients with high PPP2R3A expression (≥ 4 points) were poor compared to those with low expression (< 4 points). The overall survival rates or recurrence-free survival rates at 1, 2, and 3 years with high PPP2R3A expression were 73%, 38%, and 23% or 31%, 23%, and 23%, respectively. Multivariate analysis showed that high PPP2R3A expression (hazard ratio = 2.900, 95% confidence interval: 1.411-5.960, P = 0.004) was an independent survival risk factor of HCC patients after LT, and it was also an independent predictor of postoperative tumor recurrence. This study also showed in patients with AFP ≥ 400 ng/mL, the overall survival (P ≤ 0.001) and recurrence-free survival (P = 0.023) of those with high PPP2R3A expression were significantly worse compared to those with low PPP2R3A expression. When PPP2R3A expression was low, the overall survival rate (P = 0.461) or recurrence-free survival rate (P = 0.072) after LT in patients with AFP < 400 ng/mL and ≥ 400 ng/mL was not significantly difference. The 1, 2, and 3 year survival rate of patients with low PPP2R3A expression and AFP < 400 ng/mL were 98%, 80%, and 69%, respectively, while patients who met Hangzhou criteria had a post-transplant 1, 2, and 3 years overall survival rate of 89%, 66%, and 55%, respectively. CONCLUSION: High expression of PPP2R3A might be a potential marker for predicting poor prognosis of HCC after LT. Combined with serum AFP levels, PPP2R3A might enhance the accuracy of predicting HCC outcome in patients after LT and supplement the efficacy of the Hangzhou criteria.

Sex-Specific Influence of the SCARB1 Rs5888 SNP on the Serum Lipid Response to Atorvastatin in Patients with Acute Coronary Syndrome Undergoing Percutaneous Coronary Intervention.

BACKGROUND: Epidemiological studies have shown that there are sex differences in blood lipid levels and lipid responses to statins. Previous studies have shown that the rs5888 single nucleotide polymorphism (SNP) in the scavenger receptor class B type 1 (SCARB1) gene is associated with serum lipid levels in a sex-specific manner. The present study was undertaken to detect the sex-specific influence of the SCARB1 rs5888 SNP on the serum lipid response to atorvastatin in patients with acute coronary syndrome (ACS) undergoing percutaneous coronary intervention (PCI). METHODS: A total of 158 unrelated ACS patients (108 males, 50 females) were enrolled, and all patients received atorvastatin 20 mg/daily after PCI. Genotyping of the rs5888 SNP was performed by polymerase chain reaction and direct sequencing. Serum lipid profiles were determined before treatment and after an average follow-up time of one year. RESULTS: The baseline serum total cholesterol (TC), low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C) and apolipoprotein (Apo)AI levels were higher in females than in males (P<0.05). After treatment with atorvastatin, serum TC, LDL-C, and ApoB were decreased, and ApoAI was increased (P<0.05). The effects of atorvastatin on serum lipid levels were different between males and females, and females had greater decreases in TC, LDL-C and ApoB levels than males (P<0.05). The genotypic frequencies of the rs5888 SNP were not different between males and females. The atorvastatin response was not associated with the rs5888 SNP in males (P > 0.05). Nonetheless, in female individuals carrying the rs5888 T-allele, we observed a greater reduction in TC, LDL-C, and ApoB levels after the use of 20 mg/day atorvastatin (P<0.05). CONCLUSION: This study indicates that the SCARB1 rs5888 T-allele was associated with a greater reduction in serum TC, LDL-C, and ApoB after atorvastatin treatment in female patients with ACS undergoing PCI.

Impurity profiling of alfentanil hydrochloride by liquid chromatography/quadrupole time-of-flight high-resolution mass spectrometric techniques for drug enforcement.

RATIONALE: Fentanyl and its analogues play important roles in the hospital and clinic setting as anesthetics. However, illicitly manufactured fentanyl as well as the new psychoactive substances (NPS) account for 30% of all deaths in the United States. Since fentanyl derivatives and NPS are designed to produce similar effects, their related substances are similar or even have the same active groups. A comprehensive analysis of the related substances of alfentanil hydrochloride can provide a basis for the identification and supervision of fentanyl derivatives and NPS. METHODS: A liquid chromatography/quadrupole time-of-flight tandem mass spectrometry (LC/QTOF-MS/MS) method was developed for the separation and characterization of related substances in alfentanil hydrochloride. Degradation studies were conducted according to the ICH-prescribed stress conditions. The compounds were identified mainly through positive electrospray ionization QTOF high-resolution mass spectrometric measurements of the accurate masses of the precursor and product ions and their calculated elemental compositions. Their formation mechanisms were also discussed. RESULTS: Seventeen related substances were detected in alfentanil hydrochloride and its stressed samples. Among them, nine were process-related substances and the other eight were degradation products. The stress study results demonstrated that alfentanil hydrochloride was unstable under acid, alkaline, and oxidative stress conditions, while relatively stable under dry photolytic and thermal stress conditions. Alfentanil hydrochloride was most susceptible for degradation at the N-phenylpropanamide and piperidine sites. CONCLUSIONS: Process-related alfentanil hydrochloride compounds are useful for determination of synthetic routes and entangling of fentanyl analogues. The stress study results can provide a sound scientific basis for the waste water monitoring of alfentanil. These results are important for routine quality control in the manufacturing and storage of alfentanil hydrochloride, as well as for drug enforcement of fentanyl and its analogues.

Changes in Homocysteine Levels Affect Serum Lipid Response to Atorvastatin in Patients With Acute Coronary Syndrome: A Retrospective Observational Study.

OBJECTIVE: The present study investigated whether changes in serum homocysteine (Hcy) levels modify the effects of atorvastatin treatment on blood lipid parameters in patients with acute coronary syndrome (ACS). METHODS: A total of 159 patients with ACS who received regular, long-term treatment with 20 mg/d atorvastatin were included. Depending on the changes in Hcy parameters, they were divided into Hcy reduction (HR) and Hcy elevation (HE) groups. RESULTS: After long-term atorvastatin treatment, total cholesterol (TC), triglycerides (TGs), low-density lipoprotein cholesterol (LDL-C), apolipoprotein (Apo) B, and Hcy levels were decreased (P < .05), and the ApoAI level was increased (P < .01). Correlation and stratified analysis showed that Hcy or hyperhomocysteinemia was correlated with blood lipids. In both the HE and HR groups, the TC, LDL-C, and ApoB levels after treatment were lower than those before treatment (P < .01), and the ApoAI level was increased compared with that before treatment (P < .05). There was no difference in the reduction of TC, LDL-C, and ApoB levels or in the increase of ApoAI level (P interaction > .05) between the 2 groups. However, there was a clear opposite trend of the effect of atorvastatin on TG and high-density lipoprotein cholesterol (HDL-C) levels between the HR and HE groups (P interaction < .05). In the HR group, the HDL-C level was increased (P < .05), and TGs were decreased compared with those before treatment (P < .01). Nevertheless, in the HE group, the HDL-C level was decreased (P < .05), and TGs (P < .05) were increased compared with those before treatment. CONCLUSION: The effects of atorvastatin on TGs and HDL-C depend on changes in Hcy levels. Patients with a reduced Hcy level after atorvastatin treatment had more favorable lipid parameters.

Electrocardiographic findings of Wellens syndrome due to coronary artery-pulmonary artery fistula.

A coronary artery fistula (CAF) is an abnormal connection between a coronary artery and any of the four cardiac chambers, the large vessels, or other vascular structures. Wellens syndrome is an ST-segment elevation myocardial infarction equivalent. Although both Wellens syndrome and CAFs have been reported in the literature, they have rarely been reported in the same patient. We herein report a case clinically diagnosed as Wellens syndrome by electrocardiography (ECG) findings; coronary angiography subsequently showed a fistula originating from the left anterior descending artery and draining into the pulmonary artery. The ECG findings then returned to normal after the fistula had been closed by controlled-release coils. These events confirmed that the abnormal ECG findings of Wellens syndrome were due to the CAF.

Sample size calculations for the differential expression analysis of RNA-seq data using a negative binomial regression model.

High throughput RNA sequencing (RNA-seq) technology is increasingly used in disease-related biomarker studies. A negative binomial distribution has become the popular choice for modeling read counts of genes in RNA-seq data due to over-dispersed read counts. In this study, we propose two explicit sample size calculation methods for RNA-seq data using a negative binomial regression model. To derive these new sample size formulas, the common dispersion parameter and the size factor as an offset via a natural logarithm link function are incorporated. A two-sided Wald test statistic derived from the coefficient parameter is used for testing a single gene at a nominal significance level 0.05 and multiple genes at a false discovery rate 0.05. The variance for the Wald test is computed from the variance-covariance matrix with the parameters estimated from the maximum likelihood estimates under the unrestricted and constrained scenarios. The performance and a side-by-side comparison of our new formulas with three existing methods with a Wald test, a likelihood ratio test or an exact test are evaluated via simulation studies. Since other methods are much computationally extensive, we recommend our M1 method for quick and direct estimation of sample sizes in an experimental design. Finally, we illustrate sample sizes estimation using an existing breast cancer RNA-seq data.

Estimation of Lead Time via Low-Dose CT in the National Lung Screening Trial.

Based on recent reports from the National Lung Screening Trial (NLST), smokers who were screened by low-dose computer tomography (LDCT) had a 20% lower chance of dying from lung cancer than those screened by chest X-rays. However, due to the complexities of lead time bias and over diagnosis, no formal test has been shown to reduce lung cancer mortality. To correctly evaluate survival benefit due to early detection, it is critical to estimate lead time, the length of time that detection of a disease is advanced by screening. We applied a recently developed probability method to estimate lead time, using the LDCT data from NLST, where human lifetime was treated as random and derived from the actuarial life table of the US Social Security Administration. Using Bayesian posterior samples of key parameters extracted from the NLST-LDCT data, simulations on lead time were carried out on 16 hypothetical cohorts with four initial ages (55, 60, 65, and 70) and four future screening intervals (12, 18, 24, and 30 months). For each scenario, the estimated lead time for both screen-detected and interval cases is reported. Results show that the probability of no-early-detection (interval cases) increases monotonically when the screening interval increases for both genders. A male heavy smoker with an initial screening age at 60 has 11.65% (female 6.76%) chance of no-early-detection with annual screenings. This probability increases to 36.35% (female 28.26%) if the screenings were biennial. The mean lead time appears longer for women than for men. The mean lead time decreases when the screening interval increases, but it appears stable across different initial age groups. These results lay a foundation to evaluate survival benefit accurately with LDCT and to schedule future screening exams.

A comparison of per sample global scaling and per gene normalization methods for differential expression analysis of RNA-seq data.

Normalization is an essential step with considerable impact on high-throughput RNA sequencing (RNA-seq) data analysis. Although there are numerous methods for read count normalization, it remains a challenge to choose an optimal method due to multiple factors contributing to read count variability that affects the overall sensitivity and specificity. In order to properly determine the most appropriate normalization methods, it is critical to compare the performance and shortcomings of a representative set of normalization routines based on different dataset characteristics. Therefore, we set out to evaluate the performance of the commonly used methods (DESeq, TMM-edgeR, FPKM-CuffDiff, TC, Med UQ and FQ) and two new methods we propose: Med-pgQ2 and UQ-pgQ2 (per-gene normalization after per-sample median or upper-quartile global scaling). Our per-gene normalization approach allows for comparisons between conditions based on similar count levels. Using the benchmark Microarray Quality Control Project (MAQC) and simulated datasets, we performed differential gene expression analysis to evaluate these methods. When evaluating MAQC2 with two replicates, we observed that Med-pgQ2 and UQ-pgQ2 achieved a slightly higher area under the Receiver Operating Characteristic Curve (AUC), a specificity rate > 85%, the detection power > 92% and an actual false discovery rate (FDR) under 0.06 given the nominal FDR (≤0.05). Although the top commonly used methods (DESeq and TMM-edgeR) yield a higher power (>93%) for MAQC2 data, they trade off with a reduced specificity (<70%) and a slightly higher actual FDR than our proposed methods. In addition, the results from an analysis based on the qualitative characteristics of sample distribution for MAQC2 and human breast cancer datasets show that only our gene-wise normalization methods corrected data skewed towards lower read counts. However, when we evaluated MAQC3 with less variation in five replicates, all methods performed similarly. Thus, our proposed Med-pgQ2 and UQ-pgQ2 methods perform slightly better for differential gene analysis of RNA-seq data skewed towards lowly expressed read counts with high variation by improving specificity while maintaining a good detection power with a control of the nominal FDR level.

Compound Identification Using Penalized Linear Regression on Metabolomics.

Compound identification is often achieved by matching the experimental mass spectra to the mass spectra stored in a reference library based on mass spectral similarity. Because the number of compounds in the reference library is much larger than the range of mass-to-charge ratio (m/z) values so that the data become high dimensional data suffering from singularity. For this reason, penalized linear regressions such as ridge regression and the lasso are used instead of the ordinary least squares regression. Furthermore, two-step approaches using the dot product and Pearson's correlation along with the penalized linear regression are proposed in this study.