An adaptable method using human mixed tissue ratiometric controls for benchmarking performance on gene expression microarrays in clinical laboratories

<p>Abstract</p> <p>Background</p> <p>Molecular biomarkers that are based on mRNA transcripts are being developed for the diagnosis and treatment of a number of diseases. DNA microarrays are one of the primary technologies being used to develop classifiers from gene expression data for clinically relevant outcomes. Microarray assays are highly multiplexed measures of comparative gene expression but have a limited dynamic range of measurement and show compression in fold change detection. To increase the clinical utility of microarrays, assay controls are needed that benchmark performance using metrics that are relevant to the analysis of genomic data generated with biological samples.</p> <p>Results</p> <p>Ratiometric controls were prepared from commercial sources of high quality RNA from human tissues with distinctly different expression profiles and mixed in defined ratios. The samples were processed using six different target labeling protocols and replicate datasets were generated on high density gene expression microarrays. The area under the curve from receiver operating characteristic plots was calculated to measure diagnostic performance. The reliable region of the dynamic range was derived from log₂ratio deviation plots made for each dataset. Small but statistically significant differences in diagnostic performance were observed between standardized assays available from the array manufacturer and alternative methods for target generation. Assay performance using the reliable range of comparative measurement as a metric was improved by adjusting sample hybridization conditions for one commercial kit.</p> <p>Conclusions</p> <p>Process improvement in microarray assay performance was demonstrated using samples prepared from commercially available materials and two metrics - diagnostic performance and the reliable range of measurement. These methods have advantages over approaches that use a limited set of external controls or correlations to reference sets, because they provide benchmark values that can be used by clinical laboratories to help optimize protocol conditions and laboratory proficiency with microarray assays.</p

Characterization of the effect of sample quality on high density oligonucleotide microarray data using progressively degraded rat liver RNA

<p>Abstract</p> <p>Background</p> <p>The interpretability of microarray data can be affected by sample quality. To systematically explore how RNA quality affects microarray assay performance, a set of rat liver RNA samples with a progressive change in RNA integrity was generated by thawing frozen tissue or by <it>ex vivo </it>incubation of fresh tissue over a time course.</p> <p>Results</p> <p>Incubation of tissue at 37°C for several hours had little effect on RNA integrity, but did induce changes in the transcript levels of stress response genes and immune cell markers. In contrast, thawing of tissue led to a rapid loss of RNA integrity. Probe sets identified as most sensitive to RNA degradation tended to be located more than 1000 nucleotides upstream of their transcription termini, similar to the positioning of control probe sets used to assess sample quality on Affymetrix GeneChip^®arrays. Samples with RNA integrity numbers less than or equal to 7 showed a significant increase in false positives relative to undegraded liver RNA and a reduction in the detection of true positives among probe sets most sensitive to sample integrity for <it>in silico </it>modeled changes of 1.5-, 2-, and 4-fold.</p> <p>Conclusion</p> <p>Although moderate levels of RNA degradation are tolerated by microarrays with 3'-biased probe selection designs, in this study we identify a threshold beyond which decreased specificity and sensitivity can be observed that closely correlates with average target length. These results highlight the value of annotating microarray data with metrics that capture important aspects of sample quality.</p

Quantitative MRI maps of human neocortex explored using cell type-specific gene expression analysis

Quantitative magnetic resonance imaging (qMRI) allows extraction of reproducible and robust parameter maps. However, the connection to underlying biological substrates remains murky, especially in the complex, densely packed cortex. We investigated associations in human neocortex between qMRI parameters and neocortical cell types by comparing the spatial distribution of the qMRI parameters longitudinal relaxation rate (${R_{1}}$), effective transverse relaxation rate (${R_{2}}^{\ast }$), and magnetization transfer saturation (MTsat) to gene expression from the Allen Human Brain Atlas, then combining this with lists of genes enriched in specific cell types found in the human brain. As qMRI parameters are magnetic field strength-dependent, the analysis was performed on MRI data at 3T and 7T. All qMRI parameters significantly covaried with genes enriched in GABA- and glutamatergic neurons, i.e. they were associated with cytoarchitecture. The qMRI parameters also significantly covaried with the distribution of genes enriched in astrocytes (${R_{2}}^{\ast }$ at 3T, ${R_{1}}$ at 7T), endothelial cells (${R_{1}}$ and MTsat at 3T), microglia (${R_{1}}$ and MTsat at 3T, ${R_{1}}$ at 7T), and oligodendrocytes and oligodendrocyte precursor cells (${R_{1}}$ at 7T). These results advance the potential use of qMRI parameters as biomarkers for specific cell types

Linear and nonlinear rheology of wormlike micelles

Several surfactant molecules self-assemble in solution to form long, cylindrical, flexible wormlike micelles. These micelles can be entangled with each other leading to viscoelastic phases. The rheological properties of such phases are very interesting and have been the subject of a large number of experimental and theoretical studies in recent years. We shall report on our recent work on the macrorheology, microrheology and nonlinear flow behaviour of dilute aqueous solutions of a surfactant CTAT (Cetyltrimethylammonium Tosilate). This system forms elongated micelles and exhibits strong viscoelasticity at low concentrations ($\sim$ 0.9 wt%) without the addition of electrolytes. Microrheology measurements of $G(\omega)$ have been done using diffusing wave spectroscopy which will be compared with the conventional frequency sweep measurements done using a cone and plate rheometer. The second part of the paper deals with the nonlinear rheology where the measured shear stress $\sigma$ is a nonmonotonic function of the shear rate $\dot{\gamma}$. In stress-controlled experiments, the shear stress shows a plateau for $\dot{\gamma}$ larger than some critical strain rate, similar to the earlier reports on CPyCl/NaSal system. Cates et al have proposed that the plateau is a signature of mechanical instability in the form of shear bands. We have carried out extensive experiments under controlled strain rate conditions, to study the time-dependence of shear stress. The measured time series of shear stress has been analysed in terms of correlation integrals and Lyapunov exponents to show unambiguously that the behaviour is typical of low dimensional dynamical systems.Comment: 15 pages, 10 eps figure

How quantum bound states bounce and the structure it reveals

We investigate how quantum bound states bounce from a hard surface. Our analysis has applications to ab initio calculations of nuclear structure and elastic deformation, energy levels of excitons in semiconductor quantum dots and wells, and cold atomic few-body systems on optical lattices with sharp boundaries. We develop the general theory of elastic reflection for a composite body from a hard wall. On the numerical side we present ab initio calculations for the compression of alpha particles and universal results for two-body states. On the analytical side we derive a universal effective potential that gives the reflection scattering length for shallow two-body states.Comment: final publication version, new lattice results on alpha particle compression, 5 pages, 2 figure

An in vitro comparison between two methods of electrical resistance measurement for occlusal caries detection

Because of different measurement techniques and the easier design of the CRM prototype, this in vitro study aimed to compare the diagnostic performance and reproducibility of two electrical methods (Electronic Caries Monitor III, ECM and Cariometer 800, CRM) for occlusal caries detection, and to evaluate the effect of staining/ discoloration of fissures on diagnostic performance. Hundred and seventeen third molars with no apparent occlusal cavitation were selected. Six examiners inspected all specimens independently, using the CRM, and a subgroup of 4 using the ECM. Histological validation using a stereomicroscope was performed after hemisectioning. Intra- and interexaminer reproducibility was assessed by Lin's concordance correlation coefficient (CCC) and Bland and Altman analysis. Diagnostic performance parameters included sensitivity (SE), specificity (SP) and area under the ROC curve (A(z)). The CCC yielded an intra- and interexaminer reproducibility of 0.69/0.62 (ECM) and of 0.79/0.74 (CRM). The mean intra- and interexaminer 95% range of measurements (range between Bland and Altman limits of agreement) given in percentages of the instrument reading were 67%/65% for the ECM and 28%/33% for the CRM. A(z) at the D3-4 level was 0.74 (ECM) and 0.78 (CRM). The CRM showed at least equivalent diagnostic performance to the ECM. However, improvement is still desirable. Diagnostic performance appeared to be enhanced in discolored lesions; however, this may be related to sample lesion distribution characteristics. Copyright (C) 2006 S. Karger AG, Basel

Diffusing-wave spectroscopy of nonergodic media

We introduce an elegant method which allows the application of diffusing-wave spectroscopy (DWS) to nonergodic, solid-like samples. The method is based on the idea that light transmitted through a sandwich of two turbid cells can be considered ergodic even though only the second cell is ergodic. If absorption and/or leakage of light take place at the interface between the cells, we establish a so-called "multiplication rule", which relates the intensity autocorrelation function of light transmitted through the double-cell sandwich to the autocorrelation functions of individual cells by a simple multiplication. To test the proposed method, we perform a series of DWS experiments using colloidal gels as model nonergodic media. Our experimental data are consistent with the theoretical predictions, allowing quantitative characterization of nonergodic media and demonstrating the validity of the proposed technique.Comment: RevTeX, 12 pages, 6 figures. Accepted for publication in Phys. Rev.

Infant behavioral reactivity predicts change in amygdala volume 12 years later

The current study examined the link between temperamental reactivity in infancy and amygdala development in middle childhood. A sample (n = 291) of four-month-old infants was assessed for infant temperament, and two groups were identified: those exhibiting negative reactivity (n = 116) and those exhibiting positive reactivity (n = 106). At 10 and 12 years of age structural imaging was completed on a subset of these participants (n = 75). Results indicate that, between 10 and 12 years of age, left amygdala volume increased more slowly in those with negative compared to positive reactive temperament. These results provide novel evidence linking early temperament to distinct patterns of brain development over middle childhood

Childhood abuse and reduced cortical thickness in brain regions involved in emotional processing

Alterations in gray matter development represent a potential pathway through which childhood abuse is associated with psychopathology. Several prior studies find reduced volume and thickness of prefrontal (PFC) and temporal cortex regions in abused compared to non-abused adolescents, although most prior research is based on adults and volume-based measures. The current study tests the hypothesis that child abuse, independent of parental education, predicts reduced cortical thickness in prefrontal and temporal cortices as well as reduced gray mater volume (GMV) in subcortical regions during adolescence

The natural resources of Elkhorn Slough: their present and future use

This report summarizes the history of the slough, ecological attractions, educational value, and problems facing its continued existence. Appended references provide the interested and concerned citizen with sources of more specific information. As a result of the initial survey of estuarine areas of California (California Department of Fish and Game, 1969), the critical status of the coastal marshes became obvious. This report on Elkhorn Slough is part of the high priority inventory and assessment of coastal wetlands by the Department of Fish and Game, and it is intended as a guide for citizens, planners, administrators, and all others interested in the use and development of coastal lands and waters. As such, this report transcends local issues on pollution and development and, in fact, documents the status and future of natural resources that should be a part of the inheritance of following generations. This publication is one of a scheduled series. It follows similar documents on Upper Newport Bay (orange county), Goleta Slough (Santa Barbara County) and the Bolinas Lagoon (Marin county). (Document has 126 pages