Detection of spatiotemporal patterns of rainfall trends, using non-parametric statistical techniques, in Karnataka state, India.

The unpredictability of the climate has drawn a lot of interest worldwide, especially that of the annual mean temperatures and rainfall. In this study, non-parametric tests such as the LOWESS curve method, Mann-Kendall (MK), SNHT test, Pettitt's test (PT), and Buishand range test (BRT) were used to evaluate long-term (2000-2020) rainfall data series to examine rainfall variability. The Dakshina Kannada district has the highest average rainfall is 3495.6 mm with a magnitude change% of about 26.2, while the Koppala district has the lowest average rainfall roughly about 530.4 mm, with a magnitude change % of about 11.49 mm in a year. The statistics from the fitted prediction line were utilized to determine the maximum coefficient determination (R2 = 0.8808) in the Uttara Kannada region. Because of the commencement of the present rising era, 2015 is the shift year in rainfall with the highest potential of being a change point in the state's Western Ghats region. It was also revealed that the majority of the districts exhibit positive trends before the change point and vice versa. The current research can be used to plan for and minimize the agricultural and water resource challenges in the state of Karnataka. To link observable patterns to climate variability, the next inquiry must identify the source of these changes. Overall, the study's findings will help organize and improve drought, flood, and water resource management techniques in the state.

ModInterv COVID-19: An online platform to monitor the evolution of epidemic curves.

We present the software ModInterv as an informatics tool to monitor, in an automated and user-friendly manner, the evolution and trend of COVID-19 epidemic curves, both for cases and deaths. The ModInterv software uses parametric generalized growth models, together with LOWESS regression analysis, to fit epidemic curves with multiple waves of infections for countries around the world as well as for states and cities in Brazil and the USA. The software automatically accesses publicly available COVID-19 databases maintained by the Johns Hopkins University (for countries as well as states and cities in the USA) and the Federal University of Viçosa (for states and cities in Brazil). The richness of the implemented models lies in the possibility of quantitatively and reliably detecting the distinct acceleration regimes of the disease. We describe the backend structure of software as well as its practical use. The software helps the user not only to understand the current stage of the epidemic in a chosen location but also to make short term predictions as to how the curves may evolve. The app is freely available on the internet (http://fisica.ufpr.br/modinterv), thus making a sophisticated mathematical analysis of epidemic data readily accessible to any interested user.

Evaluation of Time-Varying Biomarkers in Mortality Outcome in COVID-19: an Application of Extended Cox Regression Model.

Background: COVID-19 pandemic has created many challenges for clinicians. The monitoring trend for laboratory biomarkers is helpful to provide additional information to determine the role of those in the severity status and death outcome. Objective: This article aimed to evaluate the time-varying biomarkers by LOWESS Plot, check the proportional hazard assumption, and use to extended Cox model if it is violated. Methods: In the retrospective study, we evaluated a total of 1641 samples of confirmed patients with COVID-19 from October until March 2021 and referred them to the central hospital of Ayatollah Rohani Hospital affiliated with Babol University of medical sciences, Iran. We measured four biomarkers AST, LDH, NLR, and lymphocyte in over the hospitalization to find out the influence of those on the rate of death of COVID-19 patients. Results: The standard Cox model suggested that all biomarkers were prognostic factors of death (AST: HR=2.89, P<0.001, Lymphocyte: HR=2.60, P=0.004, LDH: HR=2.60, P=0.006, NLR: HR=1.80, P<0.001). The additional evaluation showed that the PH assumption was not met for the NLR biomarker. NLR biomarkers had a significant time-varying effect, and its effect increase over time (HR(t)=exp (0.234+0.261×log(t)), p=0.001). While the main effect of NLR did not show any significant effect on death outcome (HR=1.26, P=0.097). Conclusion: The reversal of results between the Cox PH model and the extended Cox model provides insight into the value of considering time-varying covariates in the analysis, which can lead to misleading results otherwise.

Relationship Between Initial Urine Output and Mortality in Patients Hospitalized in Cardiovascular Intensive Care Units: More Is Not Better.

Backgrounds: Decreased urine output (UO) is associated with adverse outcomes in certain patients, but this effect in patients admitted for cardiovascular diseases is still unproven. Moreover, the relationship between increased UO and prognosis is also unclear. Objective: To investigate the relationship between decreased or increased UO and outcomes in patients with the cardiovascular intensive care unit (CICU). Methods: This study was a retrospective cohort analysis based on the medical information mart for intensive care III (MIMIC-III) database. The patients' data were extracted from the Beth Israel Deaconess Medical Center (Boston, MA) between 2001 and 2012. With the initial 24-h UO range from 0.5 to 1.0 ml/kg/h as the reference, participants were divided into the several groups. The primary outcome was 30-day mortality. The secondary outcomes were 90-day mortality, ICU mortality, hospital mortality, use of mechanical ventilation (MV), and vasopressor agents in the first 24-h of ICU. The association between UO and mortality was assessed by multivariable logistic regression. Results: A total of 13,279 patients admitted to CICU were included. Low UO (< 0.5 ml/kg/h) was strongly associated with 30-day mortality (unadjusted OR = 3.993, 95% CI: 3.447-4.625, p < 0.001), and very high UO (≥ 2.0 ml/kg/h) was also a significantly risk factor for 30-day mortality (Unadjusted OR = 2.069, 95% CI: 1.701-2.516, p < 0.001) compared with the reference. The same effects also were shown in the multivariable logistic regression, adjusted by age, gender, vital signs, common comorbidities, and use of diuretics, with an adjusted OR of 2.023 (95% CI: 1.693-2.417, p < 0.001) for low UO and 1.771 (95% CI: 1.389-2.256, p < 0.001) for very high UO. Moreover, both decreased UO and increased UO were risk factors for 90-day mortality, ICU mortality, hospital mortality, use of MV and vasopressor agents. Conclusion: The decreased and increased UO both were significantly associated with short-term mortality, the relationship between UO and mortality was U-shape rather than linear.

Interhospital competition and hospital charges and costs for patients undergoing cranial neurosurgery.

OBJECTIVE: Research has documented significant growth in neurosurgical expenditures and practice consolidation. The authors evaluated the relationship between interhospital competition and inpatient charges or costs in patients undergoing cranial neurosurgery. METHODS: The authors identified all admissions in 2006 and 2009 from the National Inpatient Sample. Admissions were classified into 5 subspecialties: cerebrovascular, tumor, CSF diversion, neurotrauma, or functional. Hospital-specific interhospital competition levels were quantified using the Herfindahl-Hirschman Index (HHI), an economic metric ranging continuously from 0 (significant competition) to 1 (monopoly). Inpatient charges (hospital billing) were multiplied with reported cost-to-charge ratios to calculate costs (actual resource use). Multivariate regressions were used to assess the association between HHI and inpatient charges or costs separately, controlling for 17 patient, hospital, severity, and economic factors. The reported ß-coefficients reflect percentage changes in charges or costs (e.g., ß-coefficient = 1.06 denotes a +6% change). All results correspond to a standardized -0.1 change in HHI (increase in competition). RESULTS: In total, 472,938 nationwide admissions for cranial neurosurgery treated at 896 unique hospitals met inclusion criteria. Hospital HHIs ranged from 0.099 to 0.724 (mean 0.298 ± 0.105). Hospitals in more competitive markets had greater charge/cost markups (ß-coefficient = 1.10, p < 0.001) and area wage indices (ß-coefficient = 1.04, p < 0.001). Between 2006 and 2009, average neurosurgical charges and costs rose significantly ($62,098 to $77,812, p < 0.001; $21,385 to $22,389, p < 0.001, respectively). Increased interhospital competition was associated with greater charges for all admissions (ß-coefficient = 1.07, p < 0.001) as well as cerebrovascular (ß-coefficient = 1.08, p < 0.001), tumor (ß-coefficient = 1.05, p = 0.039), CSF diversion (ß-coefficient = 1.08, p < 0.001), neurotrauma (ß-coefficient = 1.07, p < 0.001), and functional neurosurgery (ß-coefficient = 1.11, p = 0.037) admissions. However, no significant associations were observed between HHI and costs, except for CSF diversion surgery (ß-coefficient = 1.03, p = 0.021). Increased competition was not associated with important clinical outcomes, such as inpatient mortality, favorable discharge disposition, or complication rates, except for lower mortality for brain tumors (OR 0.78, p = 0.026), but was related to greater length of stay for all admissions (ß-coefficient = 1.06, p < 0.001). For a sensitivity analysis adjusting for outcomes, all findings for charges and costs remained the same. CONCLUSIONS: Hospitals in more competitive markets exhibited higher charges for admissions of patients undergoing an in-hospital cranial procedure. Despite this, interhospital competition was not associated with increased inpatient costs except for CSF diversion surgery. There was no corresponding improvement in outcomes with increased competition, with the exception of a potential survival benefit for brain tumor surgery.

Variance-Preserving Estimation of Intensity Values Obtained From Omics Experiments.

Faced with the lack of reliability and reproducibility in omics studies, more careful and robust methods are needed to overcome the existing challenges in the multi-omics analysis. In conventional omics data analysis, signal intensity values (denoted by M and values) are estimated neglecting pixel-level uncertainties, which may reflect noise and systematic artifacts. For example, intensity values from two-color microarray data are estimated by taking the mean or median of the pixel intensities within the spot and then subjected to a within-slide normalization by LOWESS. Thus, focusing on estimation and normalization of gene expression profiles, we propose a spot quantification method that takes into account pixel-level variability. Also, to preserve relevant variation that may be removed in LOWESS normalization with poorly chosen parameters, we propose a parameter selection method that is parsimonious and considers intrinsic characteristics of microarray data, such as heteroskedasticity. The usefulness of the proposed methods is illustrated by an application to real intestinal metaplasia data. Compared with the conventional approaches, the analysis is more robust and conservative, identifying fewer but more reliable differentially expressed genes. Also, the variability preservation allowed the identification of new differentially expressed genes. Using the proposed approach, we have identified differentially expressed genes involved in pathways in cancer and confirmed some molecular markers already reported in the literature.

Acute kidney injury after aneurysmal subarachnoid hemorrhage and its effect on patient outcome: an exploratory analysis.

OBJECTIVE: Acute kidney injury (AKI) is associated with death in critically ill patients, but this complication has not been well characterized after aneurysmal subarachnoid hemorrhage (aSAH). The purpose of this study was to determine the incidence of AKI after aSAH and to identify risk factors for renal dysfunction. Secondary objectives were to examine what effect AKI has on patient mortality and functional outcome at 12 weeks post-aSAH. METHODS: The authors performed a post hoc analysis of the Clazosentan to Overcome Neurological Ischemia and Infarction Occurring After Subarachnoid Hemorrhage (CONSCIOUS-1) trial data set (clinical trial registration no.: NCT00111085, https://clinicaltrials.gov). The primary outcome of interest was the development of AKI, which was defined according to the Kidney Disease: Improving Global Outcomes (KDIGO) guidelines. Secondary outcomes of interest were death and a modified Rankin Scale score greater than 2 at 12 weeks post-aSAH. Propensity score matching was used to assess for a significant treatment effect related to clazosentan administration and AKI. Univariate analysis, locally weighted scatterplot smoothing (LOWESS) curves, and stepwise logistic regression models were used to evaluate for associations between baseline or disease-related characteristics and study outcomes. RESULTS: One hundred fifty-six (38%) of the 413 patients enrolled in the CONSCIOUS-1 trial developed AKI during their ICU stay. A history of hypertension (p < 0.001) and the number of nephrotoxic medications administered (p = 0.029) were independent predictors of AKI on multivariate analysis. AKI was an independent predictor of death (p = 0.028) but not a poor functional outcome (p = 0.21) on multivariate testing. Unresolved renal dysfunction was the strongest independent predictor of death in this cohort (p < 0.001). CONCLUSIONS: AKI is a common complication following aSAH. Patients with premorbid hypertension and those treated with nephrotoxic medications may be at greater risk for renal dysfunction. AKI appears to confer an increased probability of death after aSAH.

Magnetic resonance-guided focused ultrasound thalamotomy for essential tremor: a 5-year single-center experience.

OBJECTIVE: The authors report their experience in treating patients suffering from medication-resistant essential tremor (ET) with MR-guided focused ultrasound (MRgFUS) thalamotomy over a 5-year period. METHODS: Forty-four ET patients treated with unilateral MRgFUS ventral intermediate nucleus (VIM) thalamotomy were assessed using the Clinical Rating Scale for Tremor (CRST) score and the Quality of Life in Essential Tremor Questionnaire (QUEST) over a 5-year span. RESULTS: Tremor was significantly improved immediately following MRgFUS in all patients and ceased completely in 24 patients. CRST scores in the treated hand at baseline (median 19; range 7-32, 44 patients) improved by a median of 16 at 1 month (44 patients; p < 0.0001), 17 at 6 months (31 patients; p < 0.0001), 15 at 1 year (24 patients; p < 0.0001), 18 at 2 years (15 patients; p < 0.0001), 19 at 3 years, (10 patients; p < 0.0001), 21 at 4 years (6 patients; p < 0.01), and 23 at 5 years (2 patients, significance not tested). Return of tremor that impacted activities of daily living was reported in 5 patients (11%). QUEST scores showed significant improvement, with median change of 35 points (p < 0.0001; 44 patients) at 1 month, 33 (p < 0.0001; 31 patients) at 6 months, 27 (p < 0.0001; 24 patients) at 1 year, 26 (p < 0.001; 15 patients) at 2 years, 25 (p < 0.001; 10 patients) at 3 years, 33 (p < 0.001; 6 patients) at 4 years, and 28 (significance not tested, 2 patients) at 5 years. Adverse events after the procedure were reversible in all but 5 patients (11%). CONCLUSIONS: MRgFUS thalamotomy for ET is an effective and safe procedure that provides long-term tremor relief and improvement in quality of life even in patients with medication-resistant disabling tremor. Additional studies with a larger group of patients is needed to substantiate these favorable results.

Significance of fluctuations in serum sodium levels following aneurysmal subarachnoid hemorrhage: an exploratory analysis.

OBJECTIVE: Fluctuations in patient serum sodium levels are common after aneurysmal subarachnoid hemorrhage (aSAH), but their effect on patient outcome is not well described in the literature. The goal of this work was to better characterize the relationship between fluctuations in serum sodium levels, outcome, and the development of delayed cerebral ischemia (DCI) after aSAH. METHODS: The authors performed a post hoc analysis of data from the Clazosentan to Overcome Neurological Ischemia and Infarction Occurring After Subarachnoid Hemorrhage (CONSCIOUS-1) trial. Patients had their serum sodium values recorded daily for 14 days post-aSAH. Average and average absolute daily differences in sodium levels were calculated for each patient based on 3 reference points: admission sodium levels, a normal sodium level (defined as 140 mmol/L), and the previous day's sodium level. These variables were also calculated for the classic "vasospasm window" (days 3-12) post-aSAH. A stepwise logistic regression model, locally weighted scatterplot smoothing curves, and receiver operator characteristic curve analysis were used to evaluate the relationship between alterations in serum sodium levels and clinical outcome or the development of DCI after aSAH. Poor outcome was defined as a modified Rankin Scale (mRS) score of > 2 at 3 months. RESULTS: The average daily difference in sodium values from baseline (p < 0.001), average daily difference from a normal sodium level (p < 0.001), average absolute daily difference from a normal sodium level (p = 0.015), and average absolute daily difference from the previous day's sodium level (p = 0.017) were significant predictors of poor outcome in a stepwise multivariate regression model. There was a trend toward significance for average absolute daily difference from admission sodium levels during the vasospasm window as an independent predictor of DCI (p = 0.052). There was no difference in the predictive capacity for DCI when sodium fluctuations from post-aSAH days 1-14 were compared with those from the classic vasospasm window (days 3-12). CONCLUSIONS: Fluctuations in serum sodium levels may play a role in clinical outcome and the development of DCI after aSAH. The timing of these fluctuations appears to have no significant effect on the development of DCI.

Verification of water environment monitoring network representativeness under estuary backwater effects.

The multi-functional weirs constructed as part of the Four Major River Restoration Project in Korea are operated for water level management and may have a backwater effect in estuaries. If the main channel of the Nakdong River flows backward and affects the estuary water, the water quality in the estuaries may not be representative of the tributary water quality. In this study, we confirmed the representativeness of the existing water quality monitoring networks using spatiotemporally disperse electrical conductivity observations, self-organizing maps (SOMs) for monthly pattern analysis, and the LOcally WEighted Scatter plot Smoother (LOWESS) technique for trend analysis. The results show that the Namgang 4-1 site, which is located in the Nam River estuary, is not affected by the Nakdong River, while the Baekcheon (Sunwongyo) site in the Baekcheon estuary is always affected by the Nakdong River. Therefore, it is necessary to relocate the existing monitoring network or establish a new monitoring network for locations affected by mainstream backflow, as is seen in Baekcheon (Sunwongyo). The methods proposed in this study, including spatiotemporally diverse electrical conductivity measurement, dimensionless fluctuation values, SOMs, and LOWESS, can be used to verify the representativeness of water quality measurement networks in other regions.

The use of hippocampal volumetric measurements to improve diagnostic accuracy in pediatric patients with mesial temporal sclerosis.

OBJECTIVE Many patients with medically intractable epilepsy have mesial temporal sclerosis (MTS), which significantly affects their quality of life. The surgical excision of MTS lesions can result in marked improvement or even complete resolution of the epileptic episodes. Reliable radiological diagnosis of MTS is a clinical challenge. The purpose of this study was to evaluate the utility of volumetric mapping of the hippocampi for the identification of MTS in a case-controlled series of pediatric patients who underwent resection for medically refractory epilepsy, using pathology as a gold standard. METHODS A cohort of 57 pediatric patients who underwent resection for medically intractable epilepsy between 2005 and 2015 was evaluated. On pathological investigation, this group included 24 patients with MTS and 33 patients with non-MTS findings. Retrospective quantitative volumetric measurements of the hippocampi were acquired for 37 of these 57 patients. Two neuroradiologists with more than 10 years of experience who were blinded to the patients' MTS status performed the retrospective review of MR images. To produce the volumetric data, MR scans were parcellated and segmented using the FreeSurfer software suite. Hippocampal regions of interest were compared against an age-weighted local regression curve generated with data from the pediatric normal cohort. Standard deviations and percentiles of specific subjects were calculated. The sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) were determined for the original clinical read and the expert readers. Receiver operating characteristic curves were generated for the methods of classification to compare results from the readers with the authors' results, and an optimal threshold was determined. From that threshold the sensitivity, specificity, PPV, and NPV were calculated for the volumetric analysis. RESULTS With the use of quantitative volumetry, a sensitivity of 72%, a specificity of 95%, a PPV of 93%, an NPV of 78%, and an area under the curve of 0.84 were obtained using a percentage difference of normalized hippocampal volume. The resulting specificity (95%) and PPV (93%) are superior to the original clinical read and to Reader A and Reader B's findings (range for specificity 74%-86% and for PPV 64%-71%). The sensitivity (72%) and NPV (78%) are comparable to Reader A's findings (73% and 81%, respectively) and are better than those of the original clinical read and of Reader B (sensitivity 45% and 63% and NPV 71% and 70%, respectively). CONCLUSIONS Volumetric measurement of the hippocampi outperforms expert readers in specificity and PPV, and it demonstrates comparable to superior sensitivity and NPV. Volumetric measurements can complement anatomical imaging for the identification of MTS, much like a computer-aided detection tool would. The implementation of this approach in the daily clinical workflow could significantly improve diagnostic accuracy.

[Responses of the Benthic Diatom Community to Nutrients and the Identification of Nutrient Thresholds in Three Aquatic Ecoregions of the Huntai River, Northeast China].

Benthic diatom communities and nutrient gradients were investigated from 287 sampling sites in three aquatic ecoregions (AE) of the Huntai River to characterize the spatial distribution of nutrients and the benthic diatom communities. Locally weighted scatterplot smoothing (LOWESS) was used to analyze the thresholds for nitrogen and phosphorus. The results showed that:① The concentration of ammonia nitrogen and total phosphorus significantly differs in the three AEs, and shows a tendency of AEⅠ < AE Ⅱ < AE Ⅲ. ② To reveal the structure of benthic diatom communities, various benthic diatom indexes, including the sportive diatom percentage, sensitive diatom percentage, stipitate diatom percentage, Pielou evenness index, specific polluosensitivity index (IPS), biological diatom index (IBD), and generic diatom index (IDG) were analyzed. The sportive diatom percentage varied significantly in AEI, AEⅡ, and AE Ⅲ, with the highest percentage observed in AEⅢ and the lowest in AEⅠ. However, the other six indexes exhibited an opposite trend. All revealed that AE Ⅲ has been seriously damaged, while AEⅠ is less disturbed than AEⅡ and AE Ⅲ. ③ LOWESS fitting curves show thresholds for ammonia nitrogen (NH4+ -N) in the three aquatic ecoregions as 0.13, 0.30, and 1.98 mg·L-1, respectively and for total phosphorous (TP) were 0.04, 0.06, and 0.20 mg·L-1. All results were tested by independent-sample T tests. This study will provide assistance for effectively protecting the benthic diatom community in different aquatic ecoregions and also provide a theoretical basis for water management.

A novel framework for discharge uncertainty quantification applied to 500 UK gauging stations.

A generalized framework for discharge uncertainty estimation is presentedAllows estimation of place-specific discharge uncertainties for many catchmentsLocal conditions dominate in determining discharge uncertainty magnitudes.

Non-high-density lipoprotein cholesterol: distribution and prevalence of high serum levels in children and adolescents: United States National Health and Nutrition Examination Surveys, 2005-2010.

OBJECTIVES: To estimate age-related changes for serum concentration of non-high-density lipoprotein cholesterol (HDL-C), describe non-HDL-C distribution, and examine the prevalence of high non-HDL-C levels in children and adolescents by demographic characteristics and weight status. STUDY DESIGN: Data from 7058 participants ages 6-19 years in the 2005-2010 National Health and Nutrition Examination Surveys were analyzed. A high level of non-HDL-C was defined as a non-HDL-C value ≥ 145 mg/dL. RESULTS: Locally weighted scatterplot smoothing-smoothed curves showed that non-HDL-C levels increased from 101 mg/dL at age 6 to 111 mg/dL at age 10, decreased to 101 mg/dL at age 14, and then increased to 122 mg/dL at age 19 in non-Hispanic white males. Non-HDL-C levels generally were greater in female than male subjects, lower in non-Hispanic black subjects, and similar in male and slightly lower in female Mexican American subjects, compared with non-Hispanic white subjects. The overall mean was 108 (SE 0.5), and the percentiles were 67 (5th), 74 (10th), 87 (25th), 104 (50th), 123 (75th), 145 (90th), and 158 (95th) mg/dL. Mean and percentiles were greater among age groups 9-11 and 17-19 years than others and greater among non-Hispanic white than non-Hispanic black subjects. The prevalence of high non-HDL-C was 11.8% (95% CI 9.9%-14.0%) and 15.0% (95% CI 12.9%-17.3%) for the age groups 9-11 and 17-19, respectively. It varied significantly by race/ethnicity and overweight/obesity status. CONCLUSION: Non-HDL-C levels vary by age, sex, race/ethnicity, and weight classification status. Evaluation of non-HDL-C in youth should account for its normal physiologic patterns and variations in demographic characteristics and weight classification.

Preparation of archival formalin-fixed paraffin-embedded mouse liver samples for use with the Agilent gene expression microarray platform.

INTRODUCTION: Tissue samples are routinely formalin-fixed and paraffin-embedded (FFPE) for long term preservation. Gene expression analysis of archival FFPE tissues may advance knowledge of the molecular perturbations contributing to disease. However, formalin causes extensive degradation of RNA. METHODS: We compared RNA quality/yield from FFPE samples using six commercial FFPE RNA extraction kits. In addition we compared four DNA microarray protocols for the Agilent 8×60K platform using 16year old FFPE mouse liver samples treated with phenobarbital or vehicle. RESULTS: Despite low quality RNA, archival phenobarbital samples exhibited strong induction of the positive control genes Cyp2b9 and Cyp2b10 by quantitative real-time PCR (qPCR). We tested one- and two-color microarray designs and evaluated the effects of increasing the amount of hybridized cDNA. Canonical gene responders to phenobarbital were measurably induced under each experimental condition. Increasing the amount of labeled cDNA did not improve the overall signal intensity. One-color experiments yielded larger fold changes than two-color and the number of differentially expressed genes varied between protocols. Gene expression changes were validated by qPCR and literature searches. Individual protocols exhibited high rates of false positives; however, pathway analysis revealed that nine of the top ten canonical pathways were consistent across experiments. Genes that were differentially expressed in more than one experiment were more likely to be validated. Thus, we recommend that experiments on FFPE samples be done in duplicate to reduce false positives. DISCUSSION: In this analysis of archival FFPE samples we were able to identify pathways that are consistent with phenobarbital's mechanism of action. Therefore, we conclude that FFPE samples can be used for meaningful microarray gene expression analyses.

Reference charts for height and weight of school children from west malaysia in comparison with the United States centers for disease control and prevention.

BACKGROUND: Reference charts are widely used in healthcare as a screening tool. This study aimed to produce reference growth charts for school children from West Malaysia in comparison with the United States Centers for Disease Control and Prevention (CDC) chart. METHODS: A total of 14,360 school children ranging from 7 to 17 years old from six states in West Malaysia were collected. A two-stage stratified random sampling technique was used to recruit the subjects. Curves were adjusted using Cole's LMS method. The LOWESS method was used to smooth the data. RESULTS: The means and standard deviations for height and weight for both genders are presented. The results showed good agreement with growth patterns in other countries, i.e., males tend to be taller and heavier than females for most age groups. Height and weight of females reached a plateau at 17 years of age; however, males were still growing at this age. The growth charts for West Malaysian school children were compared with the CDC 2000 growth charts for school children in the United States. CONCLUSION: The height and weight for males and females at the start of school-going ages were almost similar. The comparison between the growth charts from this study and the CDC 2000 growth charts indicated that the growth patterns of West Malaysian school children have improved, although the height and weight of American school children were higher than those for West Malaysian school children.

Effect of local background intensities in the normalization of cDNA microarray data with a skewed expression profiles

Normalization of the data of cDNA microarray is an obligatory step during microarray experiments due to the relatively frequent non-specific errors. Generally, normalization of microarray data is based on the null hypothesis and variance model. In the Yang's model (Yang et al., 2001), at least two types of noises are included. The one is additive noise and the other is multiplicative noise. Usually, background is considered as one of additive noise to the signal and the variation between the signal pixels is the representative multiplicative noise. In this study, the relation between the signal (spot intensity minus background intensity) and background was observed and the influence of background on normalization as a representative additive factor was investigated. Although the relation has not been considered as a factor affecting the normalization, it could improve the accuracy of microarray data when the normalization was carried out considering signal/background ratio. The background dependent normalization decreased the number of genes whose expression levels were changed significantly and it could make their distribution more consistent through the whole range of signal intensities. In this study, printing pin dependent normalization was also carried out regarding the printing pin as a representative multiplicative noise. It improved the distribution of spots in the Cy3-Cy5 scatter plot, but its effect was slight. These studies suggest that there are some influences of the signals on the local backgrounds and they must be considered for the normalization of cDNA microarray data.