-Hsin Chen

Selection of DDX5 as a novel internal control for Q-RT-PCR from microarray data using a block bootstrap re-sampling scheme

BackgroundThe development of microarrays permits us to monitor transcriptomes on a genome-wide scale. To validate microarray measurements, quantitative-real time-reverse transcription PCR (Q-RT-PCR) is one of the most robust and commonly used approaches. The new challenge in gene quantification analysis is how to explicitly incorporate statistical estimation in such studies. In the realm of statistical analysis, the various available methods of the probe level normalization for microarray analysis may result in distinctly different target selections and variation in the scores for the correlation between microarray and Q-RT-PCR. Moreover, it remains a major challenge to identify a proper internal control for Q-RT-PCR when confirming microarray measurements.ResultsSixty-six Affymetrix microarray slides using lung adenocarcinoma tissue RNAs were analyzed by a statistical re-sampling method in order to detect genes with minimal variation in gene expression. By this approach, we identified DDX5 as a novel internal control for Q-RT-PCR. Twenty-three genes, which were differentially expressed between adjacent normal and tumor samples, were selected and analyzed using 24 paired lung adenocarcinoma samples by Q-RT-PCR using two internal controls, DDX5 and GAPDH. The percentage correlation between Q-RT-PCR and microarray were 70% and 48% by using DDX5 and GAPDH as internal controls, respectively.ConclusionTogether, these quantification strategies for Q-RT-PCR data processing procedure, which focused on minimal variation, ought to significantly facilitate internal control evaluation and selection for Q-RT-PCR when corroborating microarray data.

Effect of granulocyte-macrophage colony-stimulating factor on oral mucositis in head and neck cancer patients after cisplatin, fluorouracil, and leucovorin chemotherapy.

PURPOSE To evaluate prospectively the efficacy of granulocyte-macrophage colony-stimulating factor (GM-CSF) in the reduction of chemotherapy-induced oral mucositis. PATIENTS AND METHODS Twenty patients with stage IV squamous cell carcinoma of head and neck were studied. Two-cycles (periods) of identical doses of cisplatin, fluorouracil (5-FU), and leucovorin (PFL) chemotherapy with cisplatin 20 mg/m2/d, 5-FU 800 mg/m2/d, leucovorin 90 mg/m2/d by 96-hour continuous intravenous infusion every 3 weeks were given to each patient. After PFL chemotherapy, GM-CSF 4 micrograms/kg subcutaneously from days 5 to 14 or no therapy was given by a randomized self-controlled crossover study design. Oral mucositis was graded with modified Radiation Therapy Oncology Group criteria. RESULTS In the first cycle of PFL chemotherapy, GM-CSF significantly reduced the incidence, mean duration, and mean area under the curve (AUC) of severe oral gross mucositis (grade > or = 3) compared with no therapy. These beneficial effects continued into the second cycle of PFL chemotherapy after crossover to no GM-CSF. The incidence of severe mucositis was reduced when GM-CSF was given in the second cycle of PFL. Analysis of variance indicated significant direct GM-CSF treatment effects on the mean AUC of gross/functional scores and duration of moderate gross mucositis (grade > or = 2) over both periods. There was a significant period effect in favor of giving GM-CSF in the first cycle of chemotherapy. CONCLUSION GM-CSF can significantly reduce the severity and duration of chemotherapy-induced oral mucositis after PFL chemotherapy.

A Randomized Controlled Trial on the Treatment for Acute Partial Ischemic Stroke with Acupuncture

The effectiveness of acupuncture in acute stroke remains largely untested and unproved. A randomized, controlled trial was carried out to study the feasibility of acupuncture in combination with conventional supportive treatment for acute stroke patients. A total of 30 patients, aged 46-74, with the onset of symptoms within 36 h were enrolled into the study after appropriate screening. All patients gave informed consent. Basing on the same supportive treatment, patients were randomly assigned to a treatment with or without acupuncture. The procedure and acupoint selection were discussed and decided through several meetings of a group of senior acupuncture doctors in Taiwan. Acupuncture was applied 3 times/week for 4 weeks. During the study period, there were no problems in conducting this trial in terms of patient availability and acceptance, and physician cooperation. A significantly better neurologic outcome was observed in the acupuncture group on day 28 and day 90. The improvement in neurologic status was greatest in patients with a poor neurologic score at baseline. There were no important side effects except for one episode of dizziness related to acupuncture treatment. The data and results of this study will be used as a guideline for planning a full-scale clinical trial, e.g. sample size calculation, method of randomization with stratification of prognostic factors, choosing acupuncture points and technique of acupuncture.

Prevalence of obesity in children after therapy for acute lymphoblastic leukemia.

To confirm an impression that many survivors of acute lymphoblastic leukemia (ALL) are overweight or obese, we retrospectively examined the medical records of 414 patients for height and weight at diagnosis, at completion of treatment, and at annual intervals thereafter. The body mass index, weight/height2, was used as a measure of fatness; population norms for the index were established from 9,003 people between the ages of 1 and 30 years who were examined in a national health survey. The percentile of each patients index was determined at each observation date. At diagnosis, the study sample was skewed toward leanness; however, at cessation of therapy, the fatness distribution resembled population norms. Statistically significant increases in fatness occurred during the first year off therapy, at the end of which 35% of the children were above the 80th percentile (i.e., overweight) and 12% were above the 95th percentile (i.e., obese). Only 12% were below the 20th percentile. This skewed distribution persisted during the subsequent 4-year follow-up period. Cranial irradiation was associated with a large increase of fatness in one group available for comparisons. Our findings indicate that the first year following cessation of therapy is a time of excessive weight gain among pediatric ALL patients.

Symptom patterns and subgrouping of schizophrenic patients: significance of negative symptoms assessed on admission

This study subgroups schizophrenic patients based on symptoms assessed on admission and examines the validity of the subgrouping using follow-up data and other clinical outcome variables. Schizophrenic patients (n=163) from consecutive admission received ratings on the positive and negative syndrome scale (PANSS) on admission and during a 1-year follow-up course. An exploratory graphic analysis on the admission PANSS derived four symptom dimensions: negative symptoms, disorganized thought, hostility/excitement and delusions/hallucinations. This yielded two subgroups of patients on admission, a group with marked negative (GWNEG) and a group without marked negative (GONEG) symptoms. Compared with the GONEG, the GWNEG had a poorer recovery rate, more impairment in attention, a slower response of the delusion/hallucination symptoms to neuroleptic treatment and a longer duration of index hospitalization. At a one-year follow-up, the GWNEG assessed on admission had persistently higher scores on the negative symptom and disorganized thought syndromes, less relapse rate, a shorter duration on job, as well as worse social functioning than the GONEG. Thus, the GONEG might comprise patients having a pure paranoid syndrome with quick and better treatment response, while the GWNEG comprises patients with the blunt-disorganization syndrome having a poorer outcome.

The prevalence of heavy proteinuria and progression risk factors in children undergoing urinary screening

Abstract To evaluate the prevalence and incidence density of heavy proteinuria and chronic renal insufficiency (CRI) and the factors related to disease progression, 10,288,620 urinary screenings of elementary and junior high-school students from 1992 to 1996 were studied retrospectively. Urinary screening included pH, protein, occult blood, and glucose measurements. Blood sample analysis included total protein, albumin, A/G ratio, blood urea nitrogen, creatinine (Cr), antistreptolysin O titer, C3, cholesterol, hepatitis B virus surface antigen, IgA, and fasting blood sugar. The results showed that the 4-year prevalence of proteinuria was higher in girls than in boys (6.87×10–4 vs. 4.83×10–4 respectively). There were 189 cases with disease progression into CRI among the 10,288,620 students screened and followed continuously, with the prevalence of disease progression into CRI higher in boys than in girls (2.24×10–5 vs. 1.41×10–5 respectively). Of the 119 cases (63%) presenting with CRI since the first urine screening and blood sampling, only 14 had serum Cr levels higher than 6.0 mg/dl. There were 1,289 patients (10.5%) with proteinuria in 1992 and 705 patients (7.1%) in 1996. The absolute number of patients with heavy proteinuria decreased. The percentage of underlying glomerulonephritis in children on dialysis also decreased from 63.2% in 1992 to 47.0% in 1996. Logistic regression analysis showed that a persistent serum cholesterol level higher than 220 mg/dl, an albumin level lower than 3.5 g/dl, total protein less than 6 g/dl, and diastolic pressure higher than 90 mmHg were the significant risk factors for disease progression to CRI. We conclude that early detection of students with heavy proteinuria by mass urinary screening, early appropriate treatment, and monitoring of significant risk factors may help to decrease or delay the progression of renal disease, delay the introduction of dialysis in these pre-dialysis CRI patients and maintain their growth and development.

Diagnostic plots in Cox's regression model.

Two diagnostic plots are presented for validating the fitting of a Cox proportional hazards model. The added variable plot is developed to assess the effect of adding a covariate to the model. The constructed variable plot is applied to detect nonlinearity of a fitted covariate. Both plots are also useful for identifying influential observations on the issues of interest. The methods are illustrated on examples of multiple myeloma and lung cancer data.

The Product-Moment Correlation Coefficient and Linear Regression for Truncated Data

Abstract The random truncation model has been considered extensively in the literature. Tsai has noted that many previous results hold under the weaker assumption of quasi-independence between the failure time and the truncation time in the observable region of truncated data. We generalize the Pearson product-moment correlation coefficient to measure the association between both time variables in the observable region. We show that if the failure time and the truncation time follow a truncated bivariate normal distribution, then a zero value of the generalized correlation coefficient is equivalent to the quasi-independence. We propose a corresponding sample correlation coefficient and consider its asymptotic behavior. We also study an application of quasi-independence to truncated linear regression with its asymptotic results. The proposed estimator, stemming directly from the least-squares approach, is computationally much simpler and has a natural extension to multiple linear regression. A simulation s...

Predictive effect of serial serum alanine aminotransferase levels on spontaneous HBeAg seroconversion in chronic genotype B and C HBV-infected children.

Objective: The present study aimed to investigate the association between serial serum alanine aminotransferase (ALT) and spontaneous hepatitis B e antigen (HBeAg) seroconversion age in chronic hepatitis B virus (HBV)–infected children. Patients and Methods: One hundred four HBeAg-positive chronic genotype B or C HBV–infected patients were included in this long-term prospective cohort study (mean initial age 7.20 years). Serial serum ALT levels and HBV serology markers were measured every 6 to 12 months. The 104 subjects made a total of 2525 visits during the study period, and the majority (93.6%) of visits were within a 1-year interval apart from previous visits. Cox proportional hazards model with time-dependent covariates was used in the survival analysis of HBeAg in these subjects. Results: During the chronic course of HBV infection, the median remaining times to spontaneous HBeAg seroconversion were 8.35, 5.14, 4.25, 3.95, and 2.80 years after the ALT levels crossed 20, 30, 40, 60, and 150 IU/L, respectively. The incidence rate of spontaneous HBeAg seroconversion within 6 months when a subject entered the phase of ALT between 60 and 150 IU/L was 5.57 times that of the phase with ALT < 60 IU/L. The incidence rate of HBeAg seroconversion once ALT levels were above 150 IU/L was 9.87 times that of the phase of ALT < 60 IU/L. Conclusions: The ALT levels above 30 IU/L served as a cutoff of the inflammatory phase in chronic genotype B and C HBV–infected patients. Serial ALT levels in chronic HBV–infected subjects offer a predicted effect on the occurrence of spontaneous HBeAg seroconversion.

Effectiveness of a nationwide aftercare program for suicide attempters.

BACKGROUND The effectiveness of large-scale interventions to prevent suicide among persons who previously attempted suicide remains to be determined. The National Suicide Surveillance System (NSSS), launched in Taiwan in 2006, is a structured nationwide intervention program for people who survived their suicide attempts. This naturalistic study examined its effectiveness using data from the first 3 years of its operation. Method Effectiveness of the NSSS aftercare services was examined using a logistic/proportional odds mixture model, with eventual suicide as the outcome of interest. As well, we examined time until death for those who died and factors associated with eventual suicide. RESULTS Receipt of aftercare services was associated with reduced risk for subsequent suicide; for service recipients who eventually killed themselves, there was a prolonged duration between the index and fatal attempts. Elderly attempters were particularly prone to a shorter duration between the index and fatal attempts. Male gender, the lethality potential of the index attempt, and a history of having had a mental disorder also were associated with higher risk. CONCLUSIONS The structured aftercare program of the NSSS appears to decrease suicides and to delay time to death for those who remained susceptible to suicide.