The Automatic Inversion of Attribute Grammars

Over the last decade there has developed an acute awareness of the need to introduce abstraction and mathematical rigor into the programming process. This increased formality allows for the automatic manipulation of software, increasing productivity and, even more importantly, the manageability of complex systems. Along these lines, attribute grammars constitute a formal mechanism (or specifying translations between languages; from a Cormal description of the translation a translator can be automatically constructed. In this paper we consider taking this process one step further: given an attribute grammar specifying the translation from language L1 to the language L2, we address the question of whether the inverse attribute grammar specifying the inverse translation from L2 to L1 can be automatically generated. We show how to solve this problem for a restricted subset of attribute grammars. This inversion process allows for compatible two-way translators to be generated from a single description. To show the practical feasibility of attribute grammar inversion, we relate our experience in inverting an attribute grammar used as an interface for a formal database accessing language, SQL. The attribute grammar is used to paraphrase SQL database queries in English

Development and Applications of Terahertz Near-Field Microscopes for Surface Plasmon Imaging

The confined nature of surface plasmons (SPs) often imposes challenges on their experimental detection and makes specific near-field probes necessary. While various SP detection methods have been developed in the optical domain, only a few examples of SP imaging have been reported in the terahertz range. In this thesis, specific problems of current terahertz near-field detection systems have been addressed which has led to the development of two new SP imaging methods. In the first method, SP imaging is demonstrated using the integrated subwavelength aperture near-field probe. The photoconductive antenna inside the probe is sensitive to the SP electric-field despite the orthogonal spatial orientation between the antenna and the SP polarisation. This enables SP imaging directly on a metallic surface employing a photoconductive antenna. This unexpected sensitivity has been applied to SP imaging in two examples: first, the SP propagation has been imaged on a resonant THz bow-tie antenna and second, the SP excitation by a strongly focused terahertz beam directly on the metallic probe surface has been investigated. The second method presents an electro-optic micro-resonator for SP imaging. A micro-resonator structure has the potential to provide a better sensitivity and spatial resolution, as well as a lower level of invasiveness compared to bulk crystals, which are commonly used in terahertz near-field systems. The micro-resonator design is explained in detail and the impact of the micro-resonator geometry on the probe performance is discussed. This micro-resonator has then been fabricated and embedded into an electro-optic detection system. This detection system has been fully characterised with the focus on two functional units which are essential for its performance: a tapered parallel plate waveguide for broadband terahertz transmission and the balanced detector for noise reduction. The overall performance of the detection system has been evaluated for its use as a terahertz near-field microscope

Near-Field Analysis of Terahertz Pulse Generation From Photo-Excited Charge Density Gradients

Excitation of photo-current transients at semiconductor surfaces by subpicosecond optical pulses gives rise to emission of electromagnetic pulses of terahertz (THz) frequency radiation. To correlate the THz emission with the photo-excited charge density distribution and the photo-current direction, we mapped near-field and far-field distributions of the generated THz waves from GaAs and Fe-doped InGaAs surfaces. The experimental results show that the charge dynamics in the plane of the surface can radiate substantially stronger THz pulses than the charge dynamics in the direction normal to the surface, which is generally regarded as the dominant origin of the emission

Modality-specific effects of mental fatigue in multitasking

The mechanisms underlying increased dual-task costs in the comparison of modality compatible stimulus-response mappings (e.g., visual-manual, auditory-vocal) and modality incompatible mappings (e.g., visual-vocal, auditory-manual) remain elusive. To investigate whether additional control mechanisms are at work in simultaneously processing two modality incompatible mappings, we applied a transfer logic between both types of dual-task mappings in the context of a mental fatigue induction. We expected an increase in dual-task costs for both modality mappings after a fatigue induction with modality compatible tasks. In contrast, we expected an additional, selective increase in modality incompatible dual-task costs after a fatigue induction with modality incompatible tasks. We tested a group of 45young individuals (19–30 years) in an online pre-post design, in which participants were assigned to one of three groups. The two fatigue groups completed a 90-min time-on-task intervention with a dual task comprising either compatible or incompatible modality mappings. The third group paused for 90 min as a passive control group. Pre and post-session contained single and dual tasks in both modality mappings for all participants. In addition to behavioral performance measurements, seven subjective items (effort, focus, subjective fatigue, motivation, frustration, mental and physical capacity) were analyzed. Mean dual-task performance during and after the intervention indicated a practice effect instead of the presumed fatigue effect for all three groups. The modality incompatible intervention group showed a selective performance improvement for the modality incompatible mapping but no transfer to the modality compatible dual task. In contrast, the compatible intervention group showed moderately improved performance in both modality mappings. Still, participants reported increased subjective fatigue and reduced motivation after the fatigue intervention. This dynamic interplay of training and fatigue effects suggests that high control demands were involved in the prolonged performance of a modality incompatible dual task, which are separable from modality compatible dual-task demands

Mapping the distribution of photo-currents responsible for generation of terahertz pulses at semiconductor surfaces

Photo-excited charge carriers at semiconductor surfaces generate pulses of terahertz (THz) radiation. By mapping the spatial distribution of the THz radiation in the near-field and the angular emission pattern in the far-field, we link the THz generation process to the photo-current direction. We find that inplane carrier dynamics play an important role and can even be the dominant source of THz radiation

A Revised Design for Microarray Experiments to Account for Experimental Noise and Uncertainty of Probe Response

Background Although microarrays are analysis tools in biomedical research, they are known to yield noisy output that usually requires experimental confirmation. To tackle this problem, many studies have developed rules for optimizing probe design and devised complex statistical tools to analyze the output. However, less emphasis has been placed on systematically identifying the noise component as part of the experimental procedure. One source of noise is the variance in probe binding, which can be assessed by replicating array probes. The second source is poor probe performance, which can be assessed by calibrating the array based on a dilution series of target molecules. Using model experiments for copy number variation and gene expression measurements, we investigate here a revised design for microarray experiments that addresses both of these sources of variance. Results Two custom arrays were used to evaluate the revised design: one based on 25 mer probes from an Affymetrix design and the other based on 60 mer probes from an Agilent design. To assess experimental variance in probe binding, all probes were replicated ten times. To assess probe performance, the probes were calibrated using a dilution series of target molecules and the signal response was fitted to an adsorption model. We found that significant variance of the signal could be controlled by averaging across probes and removing probes that are nonresponsive or poorly responsive in the calibration experiment. Taking this into account, one can obtain a more reliable signal with the added option of obtaining absolute rather than relative measurements. Conclusion The assessment of technical variance within the experiments, combined with the calibration of probes allows to remove poorly responding probes and yields more reliable signals for the remaining ones. Once an array is properly calibrated, absolute quantification of signals becomes straight forward, alleviating the need for normalization and reference hybridizations

Physico-chemical foundations underpinning microarray and next-generation sequencing experiments

Hybridization of nucleic acids on solid surfaces is a key process involved in high-throughput technologies such as microarrays and, in some cases, next-generation sequencing (NGS). A physical understanding of the hybridization process helps to determine the accuracy of these technologies. The goal of a widespread research program is to develop reliable transformations between the raw signals reported by the technologies and individual molecular concentrations from an ensemble of nucleic acids. This research has inputs from many areas, from bioinformatics and biostatistics, to theoretical and experimental biochemistry and biophysics, to computer simulations. A group of leading researchers met in Ploen Germany in 2011 to discuss present knowledge and limitations of our physico-chemical understanding of high-throughput nucleic acid technologies. This meeting inspired us to write this summary, which provides an overview of the state-of-the-art approaches based on physico-chemical foundation to modeling of the nucleic acids hybridization process on solid surfaces. In addition, practical application of current knowledge is emphasized

Hybridization thermodynamics of NimbleGen Microarrays

Background While microarrays are the predominant method for gene expression profiling, probe signal variation is still an area of active research. Probe signal is sequence dependent and affected by probe-target binding strength and the competing formation of probe-probe dimers and secondary structures in probes and targets. Results We demonstrate the benefits of an improved model for microarray hybridization and assess the relative contributions of the probe-target binding strength and the different competing structures. Remarkably, specific and unspecific hybridization were apparently driven by different energetic contributions: For unspecific hybridization, the melting temperature Tm was the best predictor of signal variation. For specific hybridization, however, the effective interaction energy that fully considered competing structures was twice as powerful a predictor of probe signal variation. We show that this was largely due to the effects of secondary structures in the probe and target molecules. The predictive power of the strength of these intramolecular structures was already comparable to that of the melting temperature or the free energy of the probe-target duplex. Conclusions This analysis illustrates the importance of considering both the effects of probe-target binding strength and the different competing structures. For specific hybridization, the secondary structures of probe and target molecules turn out to be at least as important as the probe-target binding strength for an understanding of the observed microarray signal intensities. Besides their relevance for the design of new arrays, our results demonstrate the value of improving thermodynamic models for the read-out and interpretation of microarray signals

Coherent terahertz photonics

We present a review of recent developments in THz coherent systems based on photonic local oscillators. We show that such techniques can enable the creation of highly coherent, thus highly sensitive, systems for frequencies ranging from 100 GHz to 5 THz, within an energy efficient integrated platform. We suggest that such systems could enable the THz spectrum to realize its full applications potential. To demonstrate how photonics-enabled THz systems can be realized, we review the performance of key components, show recent demonstrations of integrated platforms, and give examples of applications