Amplitude and phase evolution of optical fields inside periodic photonic structures

Optical amplitude distributions of light inside periodic photonic structures are visualized with subwavelength resolution. In addition, using a phase-sensitive photon scanning tunneling microscope, we simultaneously map the phase evolution of light. Two different structures, which consist of a ridge wave-guide containing periodic arrays of nanometer scale features, are investigated. We determine the wavelength dependence of the exponential decay rate inside the periodic arrays. Furthermore, various interference patterns are observed, which we interpret as interference between light reflected by the substrate and light inside the waveguide. The phase information obtained reveals scattering phenomena around the periodic array, which gives rise to phase jumps and phase singularities. Locally around the air rods, we observe an unexpected change in effective refractive index, a possible indication for anomalous dispersion resulting from the periodicity of the array

FISH mapping and molecular organization of the major repetitive sequences of tomato

This paper presents a bird's-eye view of the major repeats and chromatin types of tomato. Using fluorescence in-situ hybridization (FISH) with Cot-1, Cot-10 and Cot-100 DNA as probes we mapped repetitive sequences of different complexity on pachytene complements. Cot-100 was found to cover all heterochromatin regions, and could be used to identify repeat-rich clones in BAC filter hybridization. Next we established the chromosomal locations of the tandem and dispersed repeats with respect to euchromatin, nucleolar organizer regions (NORs), heterochromatin, and centromeres. The tomato genomic repeats TGRII and TGRIII appeared to be major components of the pericentromeres, whereas the newly discovered TGRIV repeat was found mainly in the structural centromeres. The highly methylated NOR of chromosome 2 is rich in [GACA](4), a microsatellite that also forms part of the pericentromeres, together with [GA](8), [GATA](4) and Ty1-copia. Based on the morphology of pachytene chromosomes and the distribution of repeats studied so far, we now propose six different chromatin classes for tomato: (1) euchromatin, (2) chromomeres, (3) distal heterochromatin and interstitial heterochromatic knobs, (4) pericentromere heterochromatin, (5) functional centromere heterochromatin and (6) nucleolar organizer regio

MOTIFATOR: detection and characterization of regulatory motifs using prokaryote transcriptome data

Summary: Unraveling regulatory mechanisms (e.g. identification of motifs in cis-regulatory regions) remains a major challenge in the analysis of transcriptome experiments. Existing applications identify putative motifs from gene lists obtained at rather arbitrary cutoff and require additional manual processing steps. Our standalone application MOTIFATOR identifies the most optimal parameters for motif discovery and creates an interactive visualization of the results. Discovered putative motifs are functionally characterized, thereby providing valuable insight in the biological processes that could be controlled by the motif.

Molecular Dynamics Simulation of Solvent-Polymer Interdiffusion. I. Fickian diffusion

The interdiffusion of a solvent into a polymer melt has been studied using large scale molecular dynamics and Monte Carlo simulation techniques. The solvent concentration profile and weight gain by the polymer have been measured as a function of time. The weight gain is found to scale as t^{1/2}, which is expected for Fickian type of diffusion. The concentration profiles are fit very well assuming Fick's second law with a constant diffusivity. The diffusivity found from fitting Fick's second law is found to be independent of time and equal to the self diffusion constant in the dilute solvent limit. We separately calculated the diffusivity as a function of concentration using the Darken equation and found that the diffusivity is essentially constant for the concentration range relevant for interdiffusion.Comment: 17 pages and 7 figure

How effortful is cognitive control? Insights from a novel method measuring single-trial evoked beta-adrenergic cardiac reactivity

The ability to adjust attentional focus to varying levels of task demands depends on the adaptive recruitment of cognitive control processes. The present study investigated for the first time whether the mobilization of cognitive control during response-conflict trials in a flanker task is associated with effort-related sympathetic activity as measured by changes in the RZinterval at a single-trial level, thus providing an alternative to the pre-ejection period (PEP) which can only be reliably measured in ensemble-averaged data. We predicted that response conflict leads to a physiological orienting response (i.e. heart rate slowing) and increases in effort as reflected by changes in myocardial beta-adrenergic activity (i.e. decreased RZ interval). Our results indeed showed that response conflict led to cardiac deceleration and decreased RZ interval. However, the temporal overlap of the observed heart rate and RZ interval changes suggests that the effect on the latter reflects a change in cardiac pre-load (Frank-Starling mechanism). Our study was thus unable to provide evidence for the expected link between cognitive control and cardiovascular effort. However, it demonstrated that our single-trial analysis enables the assessment of transient changes in cardiac sympathetic activity, thus providing a promising tool for future studies that aim to investigate effort at a single-trial level

Predictors for outcome of failure of balloon dilatation in patients with achalasia

Background: Pneumatic balloon dilatation (PD) is a regular treatment modality for achalasia. The reported success rates of PD vary. Recurrent symptoms often require repeated PD or surgery. Objective: To identify predicting factors for symptom recurrence requiring repeated treatment. Methods: Between 1974 and 2006, 336 patients were treated with PD and included in this longitudinal cohort study. The median follow-up was 129 months (range 1-378). Recurrence of achalasia was defined as symptom recurrence in combination with increased lower oesophageal sphincter (LOS) pressure on manometry, requiring repeated treatment. Patient characteristics, results of timed barium oesophagram and manometry as well as baseline PD characteristics were evaluated as predictors of disease recurrence with Kaplan-Meier curves and Cox regression analysis. Results: 111 patients had symptom recurrence requiring repeated treatment. Symptoms recurred after a mean follow-up of 51 months (range 1-348). High recurrence percentages were found in patients younger than 21 years in whom the 5 and 10-year risks of recurrence were 64% and 72%, respectively. These risks were respectively 28% and 36% in patients with classic achalasia, respectively 48% and 60% in patients without complete obliteration of the balloon's waist during PD and respectively 25% and 33% in patients with a LOS pressure greater than 10 mm Hg at 3 months post-dilatation. These four predictors remained statistically significant in a multivariable Cox analysis. Conclusion: Although PD is an effective primary treatment in patients with primary achalasia, patients are at risk of recurrent disease, with this risk increasing during long-term follow-up. Young age at presentation, classic achalasia, high LOS pressure 3 months after PD and incomplete obliteration of the balloon's waist during PD are the most important predicting factors for the need for repeated treatment during follow-up. Patients who meet one or more of these characteristics may be considered earlier for alternative treatment, such as surgery

Sampling Time Effects for Persistence and Survival in Step Structural Fluctuations

The effects of sampling rate and total measurement time have been determined for single-point measurements of step fluctuations within the context of first-passage properties. Time dependent STM has been used to evaluate step fluctuations on Ag(111) films grown on mica as a function of temperature (300-410 K), on screw dislocations on the facets of Pb crystallites at 320K, and on Al-terminated Si(111) over the temperature range 770K - 970K. Although the fundamental time constant for step fluctuations on Ag and Al/Si varies by orders of magnitude over the temperature ranges of measurement, no dependence of the persistence amplitude on temperature is observed. Instead, the persistence probability is found to scale directly with t/Dt where Dt is the time interval used for sampling. Survival probabilities show a more complex scaling dependence which includes both the sampling interval and the total measurement time tm. Scaling with t/Dt occurs only when Dt/tm is a constant. We show that this observation is equivalent to theoretical predictions that the survival probability will scale as Dt/L^z, where L is the effective length of a step. This implies that the survival probability for large systems, when measured with fixed values of tm or Dt should also show little or no temperature dependence.Comment: 27 pages, 10 figure