Delineating Boundaries for Imprecise Regions

In geographic information retrieval, queries often name geographic regions that do not have a well-defined boundary, such as “Southern France.” We provide two algorithmic approaches to the problem of computing reasonable boundaries of such regions based on data points that have evidence indicating that they lie either inside or outside the region. Our problem formulation leads to a number of subproblems related to red-blue point separation and minimum-perimeter polygons, many of which we solve algorithmically. We give experimental results from our implementation and a comparison of the two approaches. This research is supported by the EU-IST Project No. IST-2001-35047 (SPIRIT) and by grant WO 758/4-2 of the German Research Foundation (DFG).     

SNORE: spike noise removal and detection

A method for detection and removal of random spike noise in magnetic resonance (MR) raw data (k-space data) is described. This method would reduce or eliminate the corduroy-type and higher than usual level artifacts in MR images resulting from random spike noise in k-space data. The method described involves applying a spatially varying threshold to be k-space data. Any data point that has a magnitude greater than that of the threshold value at that location will be replaced by a local complex average of the neighboring data points or some other suitable data replacement scheme.     

Mosaic organization of DNA nucleotides

Long-range power-law correlations have been reported recently for DNA sequences containing noncoding regions. We address the question of whether such correlations may be a trivial consequence of the known mosaic structure ("patchiness") of DNA. We analyze two classes of controls consisting of patchy nucleotide sequences generated by different algorithms--one without and one with long-range power-law correlations. Although both types of sequences are highly heterogenous, they are quantitatively distinguishable by an alternative fluctuation analysis method that differentiates local patchiness from long-range correlations. Application of this analysis to selected DNA sequences demonstrates that patchiness is not sufficient to account for long-range correlation properties.     

Long-range correlation properties of coding and noncoding DNA sequences: GenBank analysis

An open question in computational molecular biology is whether long-range correlations are present in both coding and noncoding DNA or only in the latter. To answer this question, we consider all 33301 coding and all 29453 noncoding eukaryotic sequences--each of length larger than 512 base pairs (bp)--in the present release of the GenBank to dtermine whether there is any statistically significant distinction in their long-range correlation properties. Standard fast Fourier transform (FFT) analysis indicates that coding sequences have practically no correlations in the range from 10 bp to 100 bp (spectral exponent beta=0.00 +/- 0.04, where the uncertainty is two standard deviations). In contrast, for noncoding sequences, the average value of the spectral exponent beta is positive (0.16 +/- 0.05) which unambiguously shows the presence of long-range correlations. We also separately analyze the 874 coding and the 1157 noncoding sequences that have more than 4096 bp and find a larger region of power-law behavior. We calculate the probability that these two data sets (coding and noncoding) were drawn from the same distribution and we find that it is less than 10(-10). We obtain independent confirmation of these findings using the method of detrended fluctuation analysis (DFA), which is designed to treat sequences with statistical heterogeneity, such as DNA's known mosaic structure ("patchiness") arising from the nonstationarity of nucleotide concentration. The near-perfect agreement between the two independent analysis methods, FFT and DFA, increases the confidence in the reliability of our conclusion.     

Recent advances in CKD and ESRD: A literature update

The past year has seen interesting publications in the fields of chronic kidney disease and end stage renal disease. This review highlights some of these important papers and places their findings in the context of clinical care.     

The "first generation" of endovascular stent-grafts for patients with aneurysms of the descending thoracic aorta

OBJECTIVE: Our goal was to determine whether endovascular stent-grafting is feasible and effective for patients with aneurysms of the descending thoracic aorta. METHODS: Starting in July 1992, we conducted a prospective, uncontrolled clinical trial in 103 patients (mean age 69 years [range 34-89 years]) who underwent endovascular treatment of aneurysms of the descending thoracic aorta using a custom-fabricated, self-expanding stent-graft device. Follow-up was 100% complete and averaged 22 months. Sixty-two patients (60%) were judged not to be reasonable candidates for a conventional "open" surgical procedure. RESULTS: Complete thrombosis of the aneurysm was ultimately achieved in 86 (83%) patients. The early mortality rate was 9% +/- 3% (+/- 70% CL). Multivariable analysis revealed that myocardial infarction or stroke was linked with a higher likelihood of early death (P = .001). Early serious complications included paraplegia in 3% +/- 2% and stroke in 7% +/- 3%. Actuarial survival estimates at 1 year and 2 years were 81% +/- 4% and 73% +/- 5% (+/- 1 SE), respectively; being judged not to be a surgical candidate portended a higher probability of death (P = .003). According to the intent-to-treat principle, "treatment failure" (including all late sudden unexplained deaths) occurred in 38 patients; 53% +/- 10% of patients were free from treatment failure at 3.7 years. Stent-graft related complications occurred commonly and were linked with several anatomic, technical, and patient-related risk factors. CONCLUSIONS: This 5-year clinical trial involving use of a "first generation" device indicates that endovascular stent-grafting of descending thoracic aortic aneurysms is feasible with acceptable medium-term results. More refined, commercially developed devices available today offer less traumatic and more precise stent-graft deployment; these major technical advantages, coupled with important lessons we have learned over time and better patient selection, should be associated with more salutary clinical results in the future.     

Ice-crystal absorption: a comparison between theory and implications for remote sensing

The problem of the disagreement between cirrus crystal sizes determined remotely and by in situ measurements is shown to be due to inappropriate application of Mie theory. We retrieved the absorption optical depth at 8.3 and 11.1 mum from 11 tropical anvil cirrus clouds, using data from the High Resolution Infrared Radiation Sounder (HIRS). We related the absorption optical depth ratio between the two wavelengths to crystal size (the size was defined in terms of the crystal median mass dimension) by assuming Mie theory applied to ice spheres and anomalous diffraction theory (ADT) applied to hexagonal columns, hexagonal plates, bullet rosettes, and aggregates (polycrystals). The application of Mie theory to retrievals yielded crystal sizes approximately one third those obtained with ADT. The retrievals of crystal size by use of HIRS data are compared with measurements of habit and crystal size obtained from in situ measurements of tropical anvil cirrus particles. The results of the comparison show that ADT provides the more realistic retrieval. Moreover, we demonstrate that at infrared wavelengths retrieval of crystal size depends on assumed habit. The reason why Mie theory predicts smaller sizes than ADT is shown to result from particle geometry and enhanced absorption owing to the capture of photons from above the edge of the particle (tunneling). The contribution of particle geometry to absorption is three times greater than from tunneling, but this process enhances absorption by a further 35%. The complex angular momentum and T-matrix methods are used to show that the contribution to absorption by tunneling is diminished as the asphericity of spheroidal particles is increased. At an aspect ratio of 6 the contribution to the absorption that is due to tunneling is substantially reduced for oblate particles, whereas for prolate particles the tunneling contribution is reduced by 50% relative to the sphere.     

Conformations and folding of lysozyme ions in vacuo

Proton transfer reactivity of isolated charge states of the protein hen egg-white lysozyme shows that multiple distinct conformations of this protein are stable in the gas phase. The reactivities of the 9+ and 10+ charge state ions, formed by electrospray ionization of "native" (disulfide-intact) and "denatured" (disulfide-reduced) solutions, are consistent with values calculated for ions in their crystal structure and fully denatured conformations, respectively. Charge states below 8+ of both forms, formed by proton stripping, have similar or indistinguishable reactivities, indicating that the disulfide-reduced ions fold in the gas phase to a more compact conformation.     

Interaction of guided light in rib polymer waveguides with dielectrophoretically controlled nanoparticles

This work demonstrates an optofluidic system, where dielectrophoretically controlled suspended nanoparticles are used to manipulate the properties of an optical waveguide. This optofluidic device is composed of a multimode polymeric rib waveguide and a microfluidic channel as its upper cladding. This channel integrates dielectrophoretic (DEP) microelectrodes and is infiltrated with suspended silica and tungsten trioxide nanoparticles. By applying electrical signals with various intensities and frequencies to the DEP microelectrodes, the nanoparticles can be concentrated close to the waveguide surface significantly altering the optical properties in this region. Depending on the particle refractive indices, concentrations, positions and dimensions, the light remains confined or is scattered into the surrounding media in the microfluidic channel.