Batch RNAi selector: a standalone program to predict specific siRNA candidates in batches with enhanced sensitivity

RNA interference (RNAi) is a popular and effective method for silencing gene expression. siRNAs should be gene-specific and effective to achieve specific and potent gene silencing. However, most currently available siRNA design programs are web-based programs that either require each sequence be submitted individually, making large-batch analyses difficult to conduct, or only provide limited options for searching off-target candidates (e.g. NCBI-BLAST). We have developed a stand-alone, enhanced RNAi design program that overcomes these shortcomings. We have implemented WU-BLAST, FASTA and SSEARCH homology searches for siRNA candidates to improve gene specific siRNA selection and to identity siRNA candidates that could lead to off-target gene silencing. We also included many new features such as siRNA score calculation and calculation of siRNA internal stability to help select highly potent siRNAs. This program is freely available for academic and commercial use (), and can be installed and run on any Linux machine. Our program automates the search for siRNAs and the resulting data files including a list of siRNA primers with scores and database search results for each siRNA candidate are stored locally for easy retrieval and inspection when needed.     

Orthographic Structure Versus Morphological Structure: Principles of Lexical Organization in a Given Language.

Most models of visual word recognition in alphabetic orthographies assume that words are lexically organized according to orthographic similarity. Support for this is provided by form-priming experiments that demonstrate robust facilitation when primes and targets share similar sequences of letters. The authors examined form-orthographic priming effects in Hebrew, Arabic, and English. Hebrew and Arabic have an alphabetic writing system but a Semitic morphological structure. Hebrew morphemic units are composed of noncontiguous phonemic (and letter) sequences in a given word. Results demonstrate that form-priming effects in Hebrew or Arabic are unreliable, whereas morphological priming effects with minimal letter overlap are robust. Hebrew bilingual subjects, by contrast, showed robust form-priming effects with English material, suggesting that Semitic words are lexically organized by morphological rather than orthographic principles. The authors conclude that morphology can constrain lexical organization even in alphabetic orthographies and that visual processing of words is first determined by morphological characteristics. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

The Octave Illusion Revisited Again.

The octave illusion (D. Deutsch, 1974) occurs when 2 tones separated by an octave are alternated repeatedly, such that when the right ear receives the high tone, the left ear receives the low tone, and vice versa. Most subjects in the original study reported hearing a single tone that alternated from ear to ear, whose pitch also alternated from octave to octave, and D. Deutsch (1975a) proposed an explanation in terms of separate what and where auditory pathways. C. D. Chambers, J. B. Mattingley, and S. A. Moss (2002) argued that the perceived pitch difference generally corresponds more to a semitone and proposed an alternative explanation in terms of diplacusis. This article argues that Chambers et al. used problematic procedures and reports a new experiment on the octave illusion. The findings confirm that an octave difference is generally perceived, and they agree with the model of Deutsch (1975a) but are at variance with the diplacusis hypothesis. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

On human–machine relations

Cognition, Technology & Work - This paper presents an approach to human–machine interactions based on the concept of teamwork and the psychological theory of object relations. We envision...     

Constrained Smoothing of Histograms and Scatterplots With Simulated Annealing

Histogram and scatterplot models are often required for statistical inference. In the field of petroleum engineering, stochastic simulation algorithms require, among other statistics, a model for the histogram of the petrophysical attribute (porosity/permeability) being simulated. Often this model is taken to be the deciustered distribution of the sample data. When there are many data (say, greater than l,000), this histogram may be reasonably informed. Most often, however, the sample histogram shows multiple sawtoothlike spikes that are not representative of the entire population; the sample histogram must be smoothed. A simulated annealing-based procedure is proposed for smoothing one-variable (univariate) histograms and two-variable scatterplots (bivariate histograms). The smoothed histograms are constrained to the sample mean, variance, specified quantiles, and a measure of smoothness. In the bivariate case, the distribution must be consistent with both marginal histograms and can be additionally constrained to a linear correlation coefficient. Several examples with real reservoir data are presented.     

Studies on the O/C-Arylation of Cyclic β-Diketones with activated aryl fluorides

The reaction of nitrosubstituted aryl fluorides 1 with cyclic β-diketones 2 proceeds at 20–80°C in the presence of bases, such as KOH, KF or NaOEt, leading to the aryl ethers 3a – m . Depending on the base the reaction of dimedone 2a or 1,3-cyclohexanedione 2b with 2,4-dinitrofluorobenzene 1a or 4-fluoro-3-nitrobenzonitrile 1b furnishes C- and/or O-arylated products. Upon heating of 3g , e and 3m at 40–100°C in DMF/K₂CO₃, the C-arylated ketones 4a – c are formed in good yields. Starting from 3a we obtained the chromenedione 5 under the same conditions.     

Pulsed photothermal radiometry of human artery

Pulsed photothermal radiometry (PPTR) has been used to measure, in vitro, the optical attenuation coefficients of normal and diseased human artery at four wavelengths (308, 351, 488, 532 nm) in the near UV and visible spectrum. The advantages and limitations of this noncontact method of measuring the optical properties of biological material, as well as other potential applications, are discussed.     

The effect of life-cycle cost disclosure on consumer behavior: evidence from a field experiment with cooling appliances

Theory suggests that providing consumers with an estimated life-cycle cost (LCC) may make them buy more energy-efficient household appliances in cases where energy efficiency is cost effective. This article evaluates the link between the provision of LCC and consumer behavior by using an online field experiment for cooling appliances. Internet users arriving at a commercially operating price comparison website were randomly assigned to two experimental groups, and the groups were exposed to different visual stimuli. The control group received regular product price information, whereas the treatment group was offered additional information about estimated operating cost and total LCC. Consumers’ click behavior was evaluated with multiple regression controlling for several product characteristics (n = 1,969 clicks). We find that LCC disclosure reduces the mean specific energy use of chosen cooling appliances by 2.5% (p < 0.01), making it a potentially interesting approach for environmental policy regarding the market transformation toward more energy-efficient household appliances. However, LCC disclosure also decreases the number of clicks from the price comparison website to final retailers by about 23% (p < 0.01), which makes it—in the format chosen here—undesirable from a business perspective. Therefore, future research should clarify under what (if any) conditions can monetary energy cost disclosure be associated with more positive effects for price comparison websites.