Over the last decade, the introduction of microarray technology has had a profound impact on gene expression research. The publication of studies with dissimilar or altogether contradictory results, obtained using different microarray platforms to analyze identical RNA samples, has raised concerns about the reliability of this technology. The MicroArray Quality Control (MAQC) project was initiated to address these concerns, as well as other performance and data analysis issues. Expression data on four titration pools from two distinct reference RNA samples were generated at multiple test sites using a variety of microarray-based and alternative technology platforms. Here we describe the experimental design and probe mapping efforts behind the MAQC project. We show intraplatform consistency across test sites as well as a high level of interplatform concordance in terms of genes identified as differentially expressed. This study provides a resource that represents an important first step toward establishing a framework for the use of microarrays in clinical and regulatory settings.

We studied the receptive field organization and contrast sensitivity of ganglion cells located within the central 80 (radius of 40) deg of the macaque retina. Ganglion cell activity was monitored as synaptic (S) potentials recorded extracellularly in the lateral geniculate nuclei of anesthetized and paralyzed monkeys. Receptive field center and surround regions of magnocellularly-projecting (M) and parvocellularly-projecting (P) cells increase in area with distance from the fovea, with the center radii of M cells being about twice those of neighboring P cells. Peak sensitivities of center and surround regions are inversely proportional to the regions' areas, so that integrated contrast sensitivities (contrast gains) are constant across the visual field, with the gain of M cells being, on average, six times that of P cells. For both M and P cells, the average ratio of surround/center gain is 0.55. Constant gain of P cells across the visual field is achieved by increasing sensitivity to stimuli falling on the peripheral retina to an extent that counteracts the aberrations introduced by the eye's optics.

Background: Reproducibility is a fundamental requirement in scientific experiments. Some recent publications have claimed that microarrays are unreliable because lists of differentially expressed genes (DEGs) are not reproducible in similar experiments. Meanwhile, new statistical methods for identifying DEGs continue to appear in the scientific literature. The resultant variety of existing and emerging methods exacerbates confusion and continuing debate in the microarray community on the appropriate choice of methods for identifying reliable DEG lists.

The primate visual system uses form cues-such as hue, contrast polarity, luminance, and texture-to segment complex retinal images into the constituent objects of the visual scene. We investigated whether segmentation of dynamic images on the basis of hue, luminance contrast polarity, or luminance contrast amplitude aids discrimination of motion direction. Human subjects viewed dynamic displays of randomly positioned dots, in which a variable proportion of the dots moved in the same direction at the same speed ("signal" dots) while the remaining dots were randomly displaced ("noise" dots). In agreement with previous reports, we observed a reliable relationship between the strength of the motion signal and subjects' ability to discriminate motion direction, enabling the measurement of thresholds for direction discrimination. When signal dots had a different luminance contrast amplitude than noise dots, direction discrimination performance was directly related to the relative contrast of the signal dots, demonstrating the importance of matching the perceived contrast amplitude of signal and noise tokens when testing the effects of segmentation by other cues. When Michelson luminance contrast was matched, distinguishing signal from noise dots by hue or by luminance contrast polarity strongly improved direction discrimination, lowering thresholds by an average factor of five. These results reveal a strong influence of form cues on motion processing in the human visual system, and suggest that segmentation on the basis of form cues occurs prior to motion processing.

Single-chain Fvs (scFvs) are commonly used building blocks for creating engineered diagnostic and therapeutic antibody molecules. Bispecific antibodies (BsAbs) hold particular interest due to their ability to simultaneously bind and engage two distinct targets. We describe a technology for producing stable, scalable IgG-like bispecific and multivalent antibodies based on methods for rapidly engineering thermally stable scFvs. Focused libraries of mutant scFvs were designed using a combination of sequence-based statistical analyses and structure-, and knowledge-based methods. Libraries encoding these designs were expressed in E. coli and culture supernatants-containing soluble scFvs screened in a high-throughput assay incorporating a thermal challenge prior to an antigen-binding assay. Thermally stable scFvs were identified that retain full antigen-binding affinity. Single mutations were found that increased the measured T(m) of either the V(H) or V(L) domain by as much as 14 degrees C relative to the wild-type scFv. Combinations of mutations further increased the T(m) by as much as an additional 12 degrees C. Introduction of a stability-engineered scFv as part of an IgG-like BsAb enabled scalable production and purification of BsAb with favorable biophysical properties.