Exploiting the noise: improving biomarkers with ensembles of data analysis methodologies.

BackgroundThe advent of personalized medicine requires robust, reproducible biomarkers that indicate which treatment will maximize therapeutic benefit while minimizing side effects and costs. Numerous molecular signatures have been developed over the past decade to fill this need, but their validation and up-take into clinical settings has been poor. Here, we investigate the technical reasons underlying reported failures in biomarker validation for non-small cell lung cancer (NSCLC).MethodsWe evaluated two published prognostic multi-gene biomarkers for NSCLC in an independent 442-patient dataset. We then systematically assessed how technical factors influenced validation success.ResultsBoth biomarkers validated successfully (biomarker #1: hazard ratio (HR) 1.63, 95% confidence interval (CI) 1.21 to 2.19, P = 0.001; biomarker #2: HR 1.42, 95% CI 1.03 to 1.96, P = 0.030). Further, despite being underpowered for stage-specific analyses, both biomarkers successfully stratified stage II patients and biomarker #1 also stratified stage IB patients. We then systematically evaluated reasons for reported validation failures and find they can be directly attributed to technical challenges in data analysis. By examining 24 separate pre-processing techniques we show that minor alterations in pre-processing can change a successful prognostic biomarker (HR 1.85, 95% CI 1.37 to 2.50, P < 0.001) into one indistinguishable from random chance (HR 1.15, 95% CI 0.86 to 1.54, P = 0.348). Finally, we develop a new method, based on ensembles of analysis methodologies, to exploit this technical variability to improve biomarker robustness and to provide an independent confidence metric.ConclusionsBiomarkers comprise a fundamental component of personalized medicine. We first validated two NSCLC prognostic biomarkers in an independent patient cohort. Power analyses demonstrate that even this large, 442-patient cohort is under-powered for stage-specific analyses. We then use these results to discover an unexpected sensitivity of validation to subtle data analysis decisions. Finally, we develop a novel algorithmic approach to exploit this sensitivity to improve biomarker robustness

Estimating the impact of unsafe water, sanitation and hygiene on the global burden of disease: evolving and alternative methods.

The 2010 global burden of disease (GBD) study represents the latest effort to estimate the global burden of disease and injuries and the associated risk factors. Like previous GBD studies, this latest iteration reflects a continuing evolution in methods, scope and evidence base. Since the first GBD Study in 1990, the burden of diarrhoeal disease and the burden attributable to inadequate water and sanitation have fallen dramatically. While this is consistent with trends in communicable disease and child mortality, the change in attributable risk is also due to new interpretations of the epidemiological evidence from studies of interventions to improve water quality. To provide context for a series of companion papers proposing alternative assumptions and methods concerning the disease burden and risks from inadequate water, sanitation and hygiene, we summarise evolving methods over previous GBD studies. We also describe an alternative approach using population intervention modelling. We conclude by emphasising the important role of GBD studies and the need to ensure that policy on interventions such as water and sanitation be grounded on methods that are transparent, peer-reviewed and widely accepted

The Art and Science of Immunosuppression: The Fifth Annual American Society of Transplant Surgeon's State-of-the-Art Winter Symposium

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/72057/1/j.1600-6143.2005.01187.x.pd

Age-related differences in human skin proteoglycans

Previous work has shown that versican, decorin and a catabolic fragment of decorin, termed decorunt, are the most abundant proteoglycans in human skin. Further analysis of versican indicates that four major core protein species are present in human skin at all ages examined from fetal to adult. Two of these are identified as the V0 and V1 isoforms, with the latter predominating. The other two species are catabolic fragments of V0 and V1, which have the amino acid sequence DPEAAE as their carboxyl terminus. Although the core proteins of human skin versican show no major age-related differences, the glycosaminoglycans (GAGs) of adult skin versican are smaller in size and show differences in their sulfation pattern relative to those in fetal skin versican. In contrast to human skin versican, human skin decorin shows minimal age-related differences in its sulfation pattern, although, like versican, the GAGs of adult skin decorin are smaller than those of fetal skin decorin. Analysis of the catabolic fragments of decorin from adult skin reveals the presence of other fragments in addition to decorunt, although the core proteins of these additional decorin catabolic fragments have not been identified. Thus, versican and decorin of human skin show age-related differences, versican primarily in the size and the sulfation pattern of its GAGs and decorin in the size of its GAGs. The catabolic fragments of versican are detected at all ages examined, but appear to be in lower abundance in adult skin compared with fetal skin. In contrast, the catabolic fragments of decorin are present in adult skin, but are virtually absent from fetal skin. Taken together, these data suggest that there are age-related differences in the catabolism of proteoglycans in human skin. These age-related differences in proteoglycan patterns and catabolism may play a role in the age-related changes in the physical properties and injury response of human ski

Determining the effects of training duration on the behavioral expression of habitual control in humans: a multi-laboratory investigation

It has been suggested that there are two distinct and parallel mechanisms for controlling instrumental behavior in mammals: goal-directed actions and habits. To gain an understanding of how these two systems interact to control behavior, it is essential to characterize the mechanisms by which the balance between these systems is influenced by experience. Studies in rodents have shown that the amount of training governs the relative expression of these two systems: behavior is goal-directed following moderate training, but the more extensively an instrumental action is trained, the more it becomes habitual. It is less clear whether humans exhibit similar training effects on the expression of goal-directed and habitual behavior, as human studies have reported contradictory findings. To tackle these contradictory findings, we formed a consortium, where four laboratories undertook a pre-registered experimental induction of habits by manipulating the amount of training. There was no statistical evidence for a main effect of the amount of training on the formation and expression of habits. However, exploratory analyses suggest a moderating effect of the affective component of stress on the impact of training over habit expression. Participants who were lower in affective stress appeared to be initially goal-directed, but became habitual with increased training, whereas participants who were high in affective stress were already habitual even after moderate training, thereby manifesting insensitivity to overtraining effects. Our findings highlight the importance of the role of moderating variables such as individual differences in stress and anxiety when studying the experimental induction of habits in humans

CpG Island microarray probe sequences derived from a physical library are representative of CpG Islands annotated on the human genome

An effective tool for the global analysis of both DNA methylation status and protein–chromatin interactions is a microarray constructed with sequences containing regulatory elements. One type of array suited for this purpose takes advantage of the strong association between CpG Islands (CGIs) and gene regulatory regions. We have obtained 20 736 clones from a CGI Library and used these to construct CGI arrays. The utility of this library requires proper annotation and assessment of the clones, including CpG content, genomic origin and proximity to neighboring genes. Alignment of clone sequences to the human genome (UCSC hg17) identified 9595 distinct genomic loci; 64% were defined by a single clone while the remaining 36% were represented by multiple, redundant clones. Approximately 68% of the loci were located near a transcription start site. The distribution of these loci covered all 23 chromosomes, with 63% overlapping a bioinformatically identified CGI. The high representation of genomic CGI in this rich collection of clones supports the utilization of microarrays produced with this library for the study of global epigenetic mechanisms and protein–chromatin interactions. A browsable database is available on-line to facilitate exploration of the CGIs in this library and their association with annotated genes or promoter elements

Cell Cycle Re-Entry and Mitochondrial Defects in Myc-Mediated Hypertrophic Cardiomyopathy and Heart Failure

While considerable evidence supports the causal relationship between increases in c-Myc (Myc) and cardiomyopathy as a part of a “fetal re-expression” pattern, the functional role of Myc in mechanisms of cardiomyopathy remains unclear. To address this, we developed a bitransgenic mouse that inducibly expresses Myc under the control of the cardiomyocyte-specific MHC promoter. In adult mice the induction of Myc expression in cardiomyocytes in the heart led to the development of severe hypertrophic cardiomyopathy followed by ventricular dysfunction and ultimately death from congestive heart failure. Mechanistically, following Myc activation, cell cycle markers and other indices of DNA replication were significantly increased suggesting that cell cycle-related events might be a primary mechanism of cardiac dysfunction. Furthermore, pathological alterations at the cellular level included alterations in mitochondrial function with dysregulation of mitochondrial biogenesis and defects in electron transport chain complexes I and III. These data are consistent with the known role of Myc in several different pathways including cell cycle activation, mitochondrial proliferation, and apoptosis, and indicate that Myc activation in cardiomyocytes is an important regulator of downstream pathological sequelae. Moreover, our findings indicate that the induction of Myc in cardiomyocytes is sufficient to cause cardiomyopathy and heart failure, and that sustained induction of Myc, leading to cell cycle re-entry in adult cardiomyocytes, represents a maladaptive response for the mature heart

Safe distances between groundwater-based water wells and pit latrines at different hydrogeological conditions in the Ganges Atrai floodplains of Bangladesh.

BACKGROUND: Groundwater drawn from shallow tubewells in Bangladesh is often polluted by nearby pit latrines, which are commonly used toilets in rural and sub-urban areas of the country. METHODS: To determine the minimum safe distance of a tubewell from a pit latrine in different hydrogeological conditions of Bangladesh, 20 monitoring wells were installed at three study sites (Manda, Mohanpur and Bagmara) with the vertical and horizontal distances ranging from 18-47 to 2-15 m, respectively. Water samples were collected three times in three seasons and tested for faecal coliforms (FC) and faecal streptococci (FS) as indicators of contamination. Soil samples were analysed for texture, bulk density and hydraulic conductivity following standard procedures. Sediment samples were collected to prepare lithological logs. RESULTS: When the shallow aquifers at one of the three sites (Mohanpur) were overlained by 18-23-m-thick aquitards, the groundwater of the monitoring wells was found contaminated with a lateral and vertical distances of 2 and 31 m, respectively. However, where the aquitard was only 9 m thick, contamination was found up to lateral and vertical distances of 4.5 and 40.5 m, respectively. The soil textures of all the sites were mainly composed of loam and sandy loam. The hydraulic conductivities in the first aquifer at Manda, Mohanpur and Bagmara were 5.2-7.3, 8.2 and 1.4-15.7 m/h, respectively. CONCLUSIONS: The results showed that the safe distance from the tubewell to the pit latrine varied from site to site depending on the horizontal and vertical distances of the tubewell as well as hydrogeological conditions of a particular area