Threshold estimation based on a p-value framework in dose-response and regression settings

We use p-values to identify the threshold level at which a regression function leaves its baseline value, a problem motivated by applications in toxicological and pharmacological dose-response studies and environmental statistics. We study the problem in two sampling settings: one where multiple responses can be obtained at a number of different covariate levels, and the other the standard regression setting involving limited number of response values at each covariate. Our procedure involves testing the hypothesis that the regression function is at its baseline at each covariate value and then computing the potentially approximate p-value of the test. An estimate of the threshold is obtained by fitting a piecewise constant function with a single jump discontinuity, known as a stump, to these observed p-values, as they behave in markedly different ways on the two sides of the threshold. The estimate is shown to be consistent and its finite sample properties are studied through simulations. Our approach is computationally simple and extends to the estimation of the baseline value of the regression function, heteroscedastic errors and to time series. It is illustrated on some real data applications.

Use of genomic data in risk assessment case study: II. Evaluation of the dibutyl phthalate toxicogenomic data set

An evaluation of the toxicogenomic data set for dibutyl phthalate (DBP) and male reproductive developmental effects was performed as part of a larger case study to test an approach for incorporating genomic data in risk assessment. The DBP toxicogenomic data set is composed of nine in vivo studies from the published literature that exposed rats to DBP during gestation and evaluated gene expression changes in testes or Wolffian ducts of male fetuses. The exercise focused on qualitative evaluation, based on a lack of available dose-response data, of the DBP toxicogenomic data set to postulate modes and mechanisms of action for the male reproductive developmental outcomes, which occur in the lower dose range. A weight-of-evidence evaluation was performed on the eight DBP toxicogenomic studies of the rat testis at the gene and pathway levels. The results showed relatively strong evidence of DBP-induced downregulation of genes in the steroidogenesis pathway and lipid/sterol/cholesterol transport pathway as well as effects on immediate early gene/growth/differentiation, transcription, peroxisome proliferator-activated receptor signaling and apoptosis pathways in the testis. Since two established modes of action (MOAs), reduced fetal testicular testosterone production and Insl3 gene expression, explain some but not all of the testis effects observed in rats after in utero DBP exposure, other MOAs are likely to be operative. A reanalysis of one DBP microarray study identified additional pathways within cell signaling, metabolism, hormone, disease, and cell adhesion biological processes. These putative new pathways may be associated with DBP effects on the testes that are currently unexplained. This case study on DBP identified data gaps and research needs for the use of toxicogenomic data in risk assessment. Furthermore, this study demonstrated an approach for evaluating toxicogenomic data in human health risk assessment that could be applied to future chemicals.

Steady and oscillatory fluid flows produce a similar osteogenic phenotype

Mechanical loading induces positive changes in the skeleton due to direct effects on bone cells, which may include regulation of transcription factors that support osteoblast differentiation and function. Flow effects on osteoblast transcription factors have generally been evaluated after short exposures. In this work, we assayed flow effects on osteogenic genes at early and late time points in a preosteoblast (CIMC-4) cell line and evaluated both steady and oscillatory flows. Four hours of steady unidirectional flow decreased the level of RANKL mRNA 53 ± 7% below that of nonflowed cells, but increases in Runx2 and osterix mRNA (44 ± 22% and 129 ± 12%, respectively) were significant only after 12-19 h of continuous flow. Late flow effects on RANKL and osterix were also induced by an intermittent flow-rest protocol (four cycles of 1 h on/1 h off + overnight rest). Four hours of oscillatory flow decreased RANKL mRNA at this early time point (63 ± 2%) but did not alter either osterix or Runx2. When oscillatory flow was delivered using the intermittent flow-rest protocol, Runx2 and osterix mRNA increased significantly (85 ± 19% and 161 ± 22%, respectively). Both β-catenin and ERK1/2, known to be involved in RANKL regulation, were rapidly activated by steady flow. Inhibition of flow-activated ERK1/2 prevented the increase in osterix mRNA but not Runx2; Runx2 phosphorylation was increased by flow, an effect which likely contributes to osterix induction. This work shows that both steady and oscillatory fluid flows can support enhancement of an osteogenic phenotype.

A case report of right ventricular mass

Primary Cardiac tumors are uncommon during infancy and childhood. Myxomas originating in the right ventricles are even less common in paediatric patient. Our patient baby Rani, 3 months of age presented with shortness of breath and chest indrawing. Antenatal history and delivery was uneventful. The baby was under weight and also malnourished but there was no cyanosis and clubbing. Her respiratory rate was 25/minute. On precordium examination, first heart sound (S1) was normal but pulmonary component of second heart sound (P2) was soft. There was an ejection systolic murmur (Grade-3/6) in the left upper para-sternal area. Chest X-ray revealed cardiomegaly. Echocardiogram revealed a large mass (11x10mm) in the right ventricle, dynamically obstructing the right ventricular out-flow tract and compressing the left ventricle. There was a Tricuspid regurgitation (Grade-2) and moderate pulmonary hypertension (PASP-50 mmHg).

Pathway modeling of microarray data: a case study of pathway activity changes in the testis following in utero exposure to dibutyl phthalate (DBP)

Pathway activity level analysis, the approach pursued in this study, focuses on all genes that are known to be members of metabolic and signaling pathways as defined by the KEGG database. The pathway activity level analysis entails singular value decomposition (SVD) of the expression data of the genes constituting a given pathway. We explore an extension of the pathway activity methodology for application to time-course microarray data. We show that pathway analysis enhances our ability to detect biologically relevant changes in pathway activity using synthetic data. As a case study, we apply the pathway activity level formulation coupled with significance analysis to microarray data from two different rat testes exposed in utero to Dibutyl Phthalate (DBP). In utero DBP exposure in the rat results in developmental toxicity of a number of male reproductive organs, including the testes. One well-characterized mode of action for DBP and the male reproductive developmental effects is the repression of expression of genes involved in cholesterol transport, steroid biosynthesis and testosterone synthesis that lead to a decreased fetal testicular testosterone. Previous analyses of DBP testes microarray data focused on either individual gene expression changes or changes in the expression of specific genes that are hypothesized, or known, to be important in testicular development and testosterone synthesis. However, a pathway analysis may inform whether there are additional affected pathways that could inform additional modes of action linked to DBP developmental toxicity. We show that Pathway activity analysis may be considered for a more comprehensive analysis of microarray data.

Correlation of platelet count and acute ST-elevation in myocardial infarction

The role of platelets in the pathogenesis of ST-elevation myocardial infarction (STEMI) has been substantiated by studies that demonstrated significant clinical benefits associated with antiplatelet therapy. Initial platelet counts in Acute Myocardial Infarction (AMI) may be a useful adjunct for identifying those patients who may or may not respond to fibrinolytic agents. Patient with acute STEMI has variable level of platelet count and with higher platelet count have poor in hospital outcome. There are many predictors of poor outcome in Acute Myocardial Infarction (AMI) like cardiac biomarkers (Troponin I, Troponin T and CK-MB), C-Reactive Protien (CRP) and WBC (White Blood Cell) counts. Platelet count on presentation of STEMI is one of them. Higher platelet count is associated with higher rate of adverse clinical outcome in ST-Elevation Myocardial Infarction (STEMI), like heart failure, arrhythmia, re-infarction & death. So, categorization of patient with STEMI on the basis of platelet counts may be helpful for risk stratification and management of these patients.

Food choice among homebound older adults: motivations and perceived barriers

OBJECTIVES

The purpose of this paper is to identify: motivations and perceived barriers associated with food choices made by homebound older adults; whether motivations and perceived barriers vary according to social demographic characteristics; and whether motivations and perceived barriers are associated with dietary quality.

DESIGN

This was an observational study using standard interview methods where participants were administered a questionnaire and completed three 24-hour dietary recalls.

SETTING

Participants were interviewed in their homes.

PARTICIPANTS

185 homebound older adults were included.

MEASUREMENT

Motivations were assessed using a modification of The Food Choice Questionnaire and perceived barriers were assessed using the Vailas Food Enjoyment Questionnaire. Participants answered questions regarding social demographic characteristics. Dietary quality measures of adequate intakes of calories, protein, vitamin D, and vitamin B12 were obtained from the three 24-hour dietary recalls.

RESULTS

Mean age was 78.9; 80% were female; and 36% were African American. Key motivations in food choice included sensory appeal, convenience, and price. Key barriers included health, being on a special diet, and being unable to shop. These varied little by social demographics, except for age. Dietary quality varied according to different motivations and barriers.

CONCLUSION

Food choices are based upon a complex interaction between the social and environmental context, the individual, and the food. Efforts to change eating behaviors, especially community-based interventions involving self-management approaches, must carefully take into account individuals' self-perceived motivations and barriers to food selection. Incorporating foods that are tasty, easy to prepare, inexpensive, and that involve caregivers are critical for successful interventions.

Volkmann sign of non-ischaemic origin

This paper presents six cases who had a contracture of the long flexor tendons of the fingers and exhibited Volkmann's sign due to a chronic abscess or cysticercosis in the belly of the flexor digitorum profundus. All of them were treated conservatively, with full functional recovery in all the cases and with no recurrence.

Transcriptional responses to complex mixtures—A review

Exposure of people to hazardous compounds is primarily through complex environmental mixtures, those that occur through media such as air, soil, water, food, cigarette smoke, and combustion emissions. Microarray technology offers the ability to query the entire genome after exposure to such an array of compounds, permitting a characterization of the biological effects of such exposures. This review summarizes the published literature on the transcriptional profiles resulting from exposure of cells or organisms to complex environmental mixtures such as cigarette smoke, diesel emissions, urban air, motorcycle exhaust, carbon black, jet fuel, and metal ore and fumes. The majority of the mixtures generally up-regulate gene expression, with heme oxygenase 1 and CYP1A1 being up-regulated by all of the mixtures. Most of the mixtures altered the expression of genes involved in oxidative stress response (OH-1, metallothioneins), immune/inflammation response (IL-1b, protein kinase), xenobiotic metabolism (CYP1A1, CYP1B1), coagulation and fibrinolysis (plasminogen activator/inhibitor), proto-oncogenes (FUS1, JUN), heat-shock response (HSP60, HSP70), DNA repair (PCNA, GADD45), structural unit of condensed DNA (Crf15Orf16, DUSP 15), and extracellular matrix degradation (MMP1, 8, 9, 11, 12). Genes involved in aldehyde metabolism, such as ALDH3, appeared to be uniquely modulated by cigarette smoke. Cigarette smoke-exposed populations have been successfully distinguished from control nonexposed populations based on the expression pattern of a subset of genes, thereby demonstrating the utility of this approach in identifying biomarkers of exposure and susceptibility. The analysis of gene-expression data at the pathway and functional level, along with a systems biology approach, will provide a more comprehensive insight into the biological effects of complex mixtures and will improve risk assessment of the same. We suggest critical components of study design and reporting that will achieve this goal.

Identification of interspecies concordance of mechanisms of arsenic-induced bladder cancer

Exposure to arsenic causes cancer by inducing a variety of responses that affect the expression of genes associated with numerous biological pathways leading to altered cell growth and proliferation, signaling, apoptosis and oxidative stress response. Affymetrix GeneChip arrays were used to detect gene expression changes following dimethylarsinic acid (DMA) exposure to human bladder cells (UROtsa) or rat bladder cells (MYP3) and rat bladder epithelium in vivo at comparable doses. Using different experimental models coupled with transcriptional profiling allowed investigation of the correlation of mechanisms of DMA-induced toxicity between in vitro and in vivo treatment and across species. Our observations suggest that DMA-induced gene expression in UROtsa cells is distinct from that observed in the MYP3 cells. Principal component analysis shows a more distinct separation by treatment and dose in MYP3 cells as compared to UROtsa cells. However, at the level of pathways and biological networks, DMA affects both common and unique processes in the bladder transitional cells of human and rats. Twelve pathways were found common between human in vitro, rat in vitro and rat in vivo systems. These included signaling pathways involved in adhesion, cellular growth and differentiation. Fifty-five genes found to be commonly expressed between rat in vivo and rat in vitro systems were involved in diverse functions such as cell cycle regulation, lipid metabolism and protein degradation. Many of the genes, processes and pathways have previously been associated with arsenic-induced toxicity. Our finding reiterates and also identifies new biological processes that might provide more information regarding the mechanisms of DMA-induced toxicity. The results of our analysis further suggest that gene expression profiles can address pertinent issues of relevance to risk assessment, namely interspecies extrapolation of mechanistic information as well as comparison of in vitro to in vivo response.