Molecular diagnosis of medical viruses.

The diagnosis of infectious diseases has been revolutionized by the development of molecular techniques, foremost with the applications of the polymerase chain reaction (PCR). The achievable high sensitivity and ease with which the method can be used to detect any known genetic sequence have led to its wide application in the life sciences. More recently, real-time PCR assays have provided additional major contributions, with the inclusion of an additional fluorescent probe detection system resulting in an increase in sensitivity over conventional PCR, the ability to confirm the amplification product and to quantitate the target concentration. Further, nucleotide sequence analysis of the amplification products has facilitated epidemiological studies of infectious disease outbreaks, and the monitoring of treatment outcomes for infections, in particular with viruses which mutate at high frequency. This review discusses the applications of qualitative and quantitative real-time PCR, nested PCR, multiplex PCR, nucleotide sequence analysis of amplified products and quality assurance with nucleic acid testing (NAT) in diagnostic laboratories

Testing theories of post-error slowing

People tend to slow down after they make an error. This phenomenon, generally referred to as post-error slowing, has been hypothesized to reflect perceptual distraction, time wasted on irrelevant processes, an a priori bias against the response made in error, increased variability in a priori bias, or an increase in response caution. Although the response caution interpretation has dominated the empirical literature, little research has attempted to test this interpretation in the context of a formal process model. Here, we used the drift diffusion model to isolate and identify the psychological processes responsible for post-error slowing. In a very large lexical decision data set, we found that post-error slowing was associated with an increase in response caution and—to a lesser extent—a change in response bias. In the present data set, we found no evidence that post-error slowing is caused by perceptual distraction or time wasted on irrelevant processes. These results support a response-monitoring account of post-error slowing

On the interpretation of removable interactions: A survey of the field 33 years after Loftus

In a classic 1978 Memory &Cognition article, Geoff Loftus explained why noncrossover interactions are removable. These removable interactions are tied to the scale of measurement for the dependent variable and therefore do not allow unambiguous conclusions about latent psychological processes. In the present article, we present concrete examples of how this insight helps prevent experimental psychologists from drawing incorrect conclusions about the effects of forgetting and aging. In addition, we extend the Loftus classification scheme for interactions to include those on the cusp between removable and nonremovable. Finally, we use various methods (i.e., a study of citation histories, a questionnaire for psychology students and faculty members, an analysis of statistical textbooks, and a review of articles published in the 2008 issue of Psychology andAging) to show that experimental psychologists have remained generally unaware of the concept of removable interactions. We conclude that there is more to interactions in a 2 × 2 design than meets the eye

Cortical topography of intracortical inhibition influences the speed of decision making

The neocortex contains orderly topographic maps; however, their functional role remains controversial. Theoretical studies have suggested a role in minimizing computational costs, whereas empirical studies have focused on spatial localization. Using a tactile multiple-choice reaction time (RT) task before and after the induction of perceptual learning through repetitive sensory stimulation, we extend the framework of cortical topographies by demonstrating that the topographic arrangement of intracortical inhibition contributes to the speed of human perceptual decision-making processes. RTs differ among fingers, displaying an inverted U-shaped function. Simulations using neural fields show the inverted U-shaped RT distribution as an emergent consequence of lateral inhibition. Weakening inhibition through learning shortens RTs, which is modeled through topographically reorganized inhibition. Whereas changes in decision making are often regarded as an outcome of higher cortical areas, our data show that the spatial layout of interaction processes within representational maps contributes to selection and decision-making processes

Statistical properties of thermodynamically predicted RNA secondary structures in viral genomes

By performing a comprehensive study on 1832 segments of 1212 complete genomes of viruses, we show that in viral genomes the hairpin structures of thermodynamically predicted RNA secondary structures are more abundant than expected under a simple random null hypothesis. The detected hairpin structures of RNA secondary structures are present both in coding and in noncoding regions for the four groups of viruses categorized as dsDNA, dsRNA, ssDNA and ssRNA. For all groups hairpin structures of RNA secondary structures are detected more frequently than expected for a random null hypothesis in noncoding rather than in coding regions. However, potential RNA secondary structures are also present in coding regions of dsDNA group. In fact we detect evolutionary conserved RNA secondary structures in conserved coding and noncoding regions of a large set of complete genomes of dsDNA herpesviruses.Comment: 9 pages, 2 figure

The spatial distribution of coronae on Venus

Coronae on Venus are large, generally circular surface features that have distinctive tectonic, volcanic, and topographic expressions. They range in diameter from less than 200 km to at least 1000 km. Data from the Magellan spacecraft have now allowed complete global mapping of the spatial distribution of coronae on the planet. Unlike impact craters, which show a random (i.e., Poisson) spatial distribution, the distribution of coronae appears to be nonrandom. We investigate the distribution here in detail, and explore its implications in terms of mantle convection and surface modification processes

Spectroscopy with random and displaced random ensembles

Due to the time reversal invariance of the angular momentum operator J^2, the average energies and variances at fixed J for random two-body Hamiltonians exhibit odd-even-J staggering, that may be especially strong for J=0. It is shown that upon ensemble averaging over random runs, this behaviour is reflected in the yrast states. Displaced (attractive) random ensembles lead to rotational spectra with strongly enhanced BE2 transitions for a certain class of model spaces. It is explained how to generalize these results to other forms of collectivity.Comment: 4 pages, 4 figure

Investigating the impact of mindfulness meditation training on working memory: A mathematical modeling approach

We investigated whether mindfulness training (MT) influences information processing in a working memory task with complex visual stimuli. Participants were tested before (T1) and after (T2) participation in an intensive one-month MT retreat, and their performance was compared with that of an age- and education-matched control group. Accuracy did not differ across groups at either time point. Response times were faster and significantly less variable in the MT versus the control group at T2. Since these results could be due to changes in mnemonic processes, speed–accuracy trade-off, or nondecisional factors (e.g., motor execution), we used a mathematical modeling approach to disentangle these factors. The EZ-diffusion model (Wagenmakers, van der Maas, & Grasman, Psychonomic Bulletin & Review 14:(1), 3–22, 2007) suggested that MT leads to improved information quality and reduced response conservativeness, with no changes in nondecisional factors. The noisy exemplar model further suggested that the increase in information quality reflected a decrease in encoding noise and not an increase in forgetting. Thus, mathematical modeling may help clarify the mechanisms by which MT produces salutary effects on performance