Relative luminosity generated by the colours of the CRT

This paper describes a computer-controlled method presented on a CRT, which is capable of defining the relative luminosity generated by the primary colors of the monitor. The relative luminance ratio of the different primary colors of the monitor generating the same luminance sensation has been identified. The method is based on heterochromatic photometry. Theoretical calculation of the luminosity generated by the primary colors is also presented in the paper. Analysis shows little difference between theoretical calculation results and actual measurement data. An interesting byproduct of the theoretical calculation is that the additive mixture of the equal luminosity primary colors results to purple colour rather than white. At the end the feasibility of a color vision test based on individual luminance sensation compensation and carried out on a computer-controlled color CRT is discussed

More complete gene silencing by fewer siRNAs: transparent optimized design and biophysical signature

Highly accurate knockdown functional analyses based on RNA interference (RNAi) require the possible most complete hydrolysis of the targeted mRNA while avoiding the degradation of untargeted genes (off-target effects). This in turn requires significant improvements to target selection for two reasons. First, the average silencing activity of randomly selected siRNAs is as low as 62%. Second, applying more than five different siRNAs may lead to saturation of the RNA-induced silencing complex (RISC) and to the degradation of untargeted genes. Therefore, selecting a small number of highly active siRNAs is critical for maximizing knockdown and minimizing off-target effects. To satisfy these needs, a publicly available and transparent machine learning tool is presented that ranks all possible siRNAs for each targeted gene. Support vector machines (SVMs) with polynomial kernels and constrained optimization models select and utilize the most predictive effective combinations from 572 sequence, thermodynamic, accessibility and self-hairpin features over 2200 published siRNAs. This tool reaches an accuracy of 92.3% in cross-validation experiments. We fully present the underlying biophysical signature that involves free energy, accessibility and dinucleotide characteristics. We show that while complete silencing is possible at certain structured target sites, accessibility information improves the prediction of the 90% active siRNA target sites. Fast siRNA activity predictions can be performed on our web server at

MEASURING WAVELENGTH DISCRIMINATION THRESHOLD ALONG THE ENTIRE VISIBLE SPECTRUM

The wavelength discrimination threshold can be characterized by the difference of two monochromatic lights´ wavelengths (Δ λ) that subject can hardly detect. The detection of small differences in hue, present in a colour simulation is of great interest from a scientific viewpoint. A new instrument was built to measure wavelength discrimination threshold. A bipartite light is located in 2° visual angles within a white adaptation field. A monochromatic reference light is projected into one half of the field, while an adjustable monochromatic target light is projected into the other half of the field. Both lights have the same brightness. The examined subject has to adjust the wavelength of the target light until the difference between the reference and the target light can be seen. Measuring wavelength discrimination threshold along the entire spectrum the Δ λ (λ reference light) function can be established. Wavelength discrimination threshold function describes the subject´s color discrimination ability. Our experiences with the newly set up instrument are presented in this paper

Measurement of color defective and normal color vision subjects´ color and luminance contrast threshold functions on CRT

To perform a more complete diagnosis on the effect of color vision deficiency on visual performance we measured luminance and color contrast threshold functions. Measurements were carried out on CRT for a range of spatial frequencies on color deficient and normal color vision individuals. Luminance and color contrast threshold is a measure of the recognition limits of low luminance and color contrast patterns. Both of them are function of the image features and spatial frequency. In our test patterns of stripes with a sinusoidal luminance profile were displayed on the monitor. The subject´s task was to detect the presence and orientation of these gratings. In the study 6 normal and 6 anomalous trichromats were measured. In the case of color contrast threshold measurement it is essential to apply colors with identical luminance sensation, otherwise the test person might be able to differentiate between the presented colors not based on hue but based on luminance. The increasing accessibility of computers and color monitors provides a platform for color vision tests based on brightness sensation correction. In our experiment we define the subject´s relative luminance sensation stimulated by the primary colors of the monitor with the method of direct heterochromatic photometry. Although, there were no significant differences in luminance contrast threshold between normal color vision and color deficient subjects, we found significant reduction in red-green color contrast threshold at all color defectives. The results prove the assumption that color deficiency has a negative effect on noticing details in color environment

ChIPathlon: A competitive assessment for gene regulation tools.

When gene regulation of the cell cycle malfunctions, it frequently causes cancer. Adult, differentiated cells can be reprogrammed to induced pluripotent stem cell; which can then be reprogrammed to heart muscle, skin, etc, to repair damaged tissue (to limited extent in clinical practice). ChIPathlon: Evaluate the performance of all transcription factor mapping (peak calling) methods. To this end, we will develop a scalable and easy to use super computing pipeline to stage data, compare many different peak calling and differential binding site tools, and store all results into a single database

ChIPathlon: A competitive assessment for gene regulation tools.

When gene regulation of the cell cycle malfunctions, it frequently causes cancer. Adult, differentiated cells can be reprogrammed to induced pluripotent stem cell; which can then be reprogrammed to heart muscle, skin, etc, to repair damaged tissue (to limited extent in clinical practice). ChIPathlon: Evaluate the performance of all transcription factor mapping (peak calling) methods. To this end, we will develop a scalable and easy to use super computing pipeline to stage data, compare many different peak calling and differential binding site tools, and store all results into a single database

Practical guidelines for the comprehensive analysis of ChIP-seq data.

Mapping the chromosomal locations of transcription factors, nucleosomes, histone modifications, chromatin remodeling enzymes, chaperones, and polymerases is one of the key tasks of modern biology, as evidenced by the Encyclopedia of DNA Elements (ENCODE) Project. To this end, chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) is the standard methodology. Mapping such protein-DNA interactions in vivo using ChIP-seq presents multiple challenges not only in sample preparation and sequencing but also for computational analysis. Here, we present step-by-step guidelines for the computational analysis of ChIP-seq data. We address all the major steps in the analysis of ChIP-seq data: sequencing depth selection, quality checking, mapping, data normalization, assessment of reproducibility, peak calling, differential binding analysis, controlling the false discovery rate, peak annotation, visualization, and motif analysis. At each step in our guidelines we discuss some of the software tools most frequently used. We also highlight the challenges and problems associated with each step in ChIP-seq data analysis. We present a concise workflow for the analysis of ChIP-seq data in Figure 1 that complements and expands on the recommendations of the ENCODE and modENCODE projects. Each step in the workflow is described in detail in the following sections

Weakly Positioned Nucleosomes Enhance the Transcriptional Competency of Chromatin

Background: Transcription is affected by nucleosomal resistance against polymerase passage. In turn, nucleosomal resistance is determined by DNA sequence, histone chaperones and remodeling enzymes. The contributions of these factors are widely debated: one recent title claims ‘‘… DNA-encoded nucleosome organization…’’ while another title states that ‘‘histone-DNA interactions are not the major determinant of nucleosome positions.’’ These opposing conclusions were drawn from similar experiments analyzed by idealized methods. We attempt to resolve this controversy to reveal nucleosomal competency for transcription. Methodology/Principal Findings: To this end, we analyzed 26 in vivo, nonlinked, and in vitro genome-wide nucleosome maps/replicates by new, rigorous methods. Individual H2A nucleosomes are reconstituted inaccurately by transcription, chaperones and remodeling enzymes. At gene centers, weakly positioned nucleosome arrays facilitate rapid histone eviction and remodeling, easing polymerase passage. Fuzzy positioning is not due to artefacts. At the regional level, transcriptional competency is strongly influenced by intrinsic histone-DNA affinities. This is confirmed by reproducing the high in vivo occupancy of translated regions and the low occupancy of intergenic regions in reconstitutions from purified DNA and histones. Regional level occupancy patterns are protected from invading histones by nucleosome excluding sequences and barrier nucleosomes at gene boundaries and within genes. Conclusions/Significance: Dense arrays of weakly positioned nucleosomes appear to be necessary for transcription. Weak positioning at exons facilitates temporary remodeling, polymerase passage and hence the competency for transcription. At regional levels, the DNA sequence plays a major role in determining these features but positions of individual nucleosomes are typically modified by transcription, chaperones and enzymes. This competency is reduced at intergenic regions by sequence features, barrier nucleosomes, and proteins, preventing accessibility regulation of untargeted genes. This combination of DNA- and protein-influenced positioning regulates DNA accessibility and competence for regulatory protein binding and transcription. Interactive nucleosome displays are offered at http://chromatin.unl.edu/cgi-bin/skyline.cgi

Selection of hyperfunctional siRNAs with improved potency and specificity

One critical step in RNA interference (RNAi) experiments is to design small interfering RNAs (siRNAs) that can greatly reduce the expression of the target transcripts, but not of other unintended targets. Although various statistical and computational approaches have been attempted, this remains a challenge facing RNAi researchers. Here, we present a new experimentally validated method for siRNA design. By analyzing public siRNA data and focusing on hyperfunctional siRNAs, we identified a set of sequence features as potency selection criteria to build an siRNA design algorithm with support vector machines. Additional bioinformatics filters were also included in the algorithm to increase RNAi specificity by reducing potential sequence cross-hybridization or microRNA-like effects. Independent validation experiments were performed, which indicated that the newly designed siRNAs have significantly improved performance, and worked effectively even at low concentrations. Furthermore, our cell-based studies demonstrated that the siRNA off-target effects were significantly reduced when the siRNAs were delivered into cells at the 3 nM concentration compared to 30 nM. Thus, the capability of our new design program to select highly potent siRNAs also renders increased RNAi specificity because these siRNAs can be used at a much lower concentration. The siRNA design web server is available at http://www5.appliedbiosystems.com/tools/siDesign/