NuGO contributions to GenePattern.

NuGO, the European Nutrigenomics Organization, utilizes 31 powerful computers for, e.g., data storage and analysis. These so-called black boxes (NBXses) are located at the sites of different partners. NuGO decided to use GenePattern as the preferred genomic analysis tool on each NBX. To handle the custom made Affymetrix NuGO arrays, new NuGO modules are added to GenePattern. These NuGO modules execute the latest Bioconductor version ensuring up-to-date annotations and access to the latest scientific developments. The following GenePattern modules are provided by NuGO: NuGOArrayQualityAnalysis for comprehensive quality control, NuGOExpressionFileCreator for import and normalization of data, LimmaAnalysis for identification of differentially expressed genes, TopGoAnalysis for calculation of GO enrichment, and GetResultForGo for retrieval of information on genes associated with specific GO terms. All together, these NuGO modules allow comprehensive, up-to-date, and user friendly analysis of Affymetrix data. A special feature of the NuGO modules is that for analysis they allow the use of either the standard Affymetrix or the MBNI custom CDF-files, which remap probes based on current knowledge. In both cases a .chip-file is created to enable GSEA analysis. The NuGO GenePattern installations are distributed as binary Ubuntu (.deb) packages via the NuGO repository.

Effect on the partial least-squares prediction of yarn properties combining raman and infrared measurements and applying wavelength selection.

The combination of Raman and infrared spectroscopy on the one hand and wavelength selection on the other hand is used to improve the partial least-squares (PLS) prediction of seven selected yarn properties. These properties are important for on-line quality control during production. From 71 yarn samples, the Raman and infrared spectra are measured and reference methods are used to determine the selected properties. Making separate PLS models for all yarn properties using the Raman and infrared spectra, prior to wavelength selection, reveals that Raman spectroscopy outperforms infrared spectroscopy. If wavelength selection is applied, the PLS prediction error decreases and the correlation coefficient increases for all properties. However, a substantial wavelength selection effect is present for the infrared spectra compared to the Raman spectra. For the infrared spectra, wavelength selection results in PLS prediction errors comparable with the prediction performance of the Raman spectra prior to wavelength selection. Concatenating the Raman and infrared spectra does not enhance the PLS prediction performance, not even after wavelength selection. It is concluded that an infrared spectrometer, combined with a wavelength selection procedure, can be used if no (suitable) Raman instrument is available.

Proximal interphalangeal joint silicone arthroplasty for posttraumatic arthritis.

The long-term results of 16 silicone implant arthroplasties following severe destruction of the proximal interphalangeal joint and surrounding soft tissue in 14 patients were evaluated. Two implants were revised (1 arthrodesis and 1 amputation) and are not included in the results. On a visual analog scale of 0 to 100, the subjective evaluation relating to the quality of function and the ability to perform activities of daily living scored 73 on average (range, 0-100; median, 75). The range of active motion compared with the opposite side ranged from 0% to 100% (average, 47%; median, 56%). The lateral deviation, either radial or ulnar, averaged 4 degrees (range, 0 degrees to 9 degrees; median, 4 degrees). Rotational deformity, either radial or ulnar, averaged 8 (range, 0 degrees to 32 degrees; median, 4 degrees). Pinch strength of the operated finger on average was 75% of the opposite nonoperated finger (range, 14% to 164%; median, 70%). Possible statistical correlation between objective and subjective results was evaluated. Subjectively, most patients were satisfied because they were pain free. Objectively, notable rotational deformity, alignment deviation, and loss of pinch strength and range of motion were observed, but these did not correlate well with the subjective assessment. Silicone implant arthroplasty for posttraumatic arthrosis should be used for those cases in which associated adhesions may be corrected by simple tenolysis, allowing for active range of motion shortly following arthroplasty. Even in these cases, the objective results of silicone arthroplasty may not be as good as its subjective outcome.

Punctuated quadrature phase-shifting interferometry.

We describe a method and algorithm for reducing the sensitivity of phase-shifting interferometry to external vibrations. Using an interline-transfer camera, a shutter, and a fast phase shifter, we acquire a series of paired interferograms in quadrature, with the pairs spaced to maximize residual phase-error cancellation. The rapid acquisition of quadrature pairs significantly improves resistance of interferometry to low-frequency vibrations.

Interferometric back focal plane microellipsometry.

We present a technique for ellipsometric analysis of materials with high lateral resolution. A Michelson-type phase-shifting interferometer measures the phase distribution in the back focal plane of a high numerical aperture objective. Local measurements of the ellipsometric parameter delta are performed over the entire spectrum of angles of incidence. We show that delta is to leading order linearly proportional to the phase change on reflection of normally incident light. We furthermore invert the Fresnel reflection equations and derive expressions for the real and imaginary parts of the refractive index as functions of the phase change on reflection and the reflectivity at normal incidence, both of which are measurable with the same apparatus. Hence we accomplish local measurements of the refractive indices of our samples. Determination of the phase change on reflection permits correction of interferometric topography measurements of heterogeneous specimens.

Lack of difference in sensibility between the dominant and non-dominant hands as tested with Semmes-Weinstein monofilaments.

The sensibility of the dominant hand was compared with that of the non-dominant hand using Semmes-Weinstein monofilaments in each of 22 bilateral palmar sites in 50 healthy volunteers. No difference in sensibility was found in 51% of all 2,200 tested palmar sites. Statistically significant superior sensibility was found in the non-dominant hand at 34% of all sites, whereas the dominant side showed superior sensibility in the remaining 15%.

Grating interferometer for flatness testing.

Two diffraction gratings placed in front of a f lat surface generate an interference pattern representing the surface deformations. The interference pattern is achromatic and has an equivalent wavelength between 4 and 40 microm, depending on the grating frequencies and the viewing angle. Using phase-shifting techniques, the grating interferometer provides high-precision profile measurements of both smooth and rough surfaces.

Numerical simulations of vibration in phase-shifting interferometry.

Computer simulations predict the expected rms measurement error in a phase-shifting interferometer in the presence of mechanical vibrations. The simulations involve a numerical resolution of a nonlinear mathematical model and are performed over a range of vibrational frequencies and amplitudes for three different phase-shift algorithms. Experimental research with an interference microscope and comparison with analytical solutions verify the numerical model.

Difference in sensibility between the dominant and nondominant index finger as tested using the Semmes-Weinstein monofilaments pressure aesthesiometer.

In 130 active subjects aged 7 to 76 years, sensibility of both index fingers were tested using Semmes-Weinstein monofilaments. Subsequently, subjects were asked to indicate their dominant side. The gathered data was analysed statistically to try and find a possible difference in sensibility between the dominant and nondominant side. No difference was found in the majority of our series (76). The index at the nondominant side was found to have superior sensibility in 35 out of 130 subjects, while the reverse was true in the remaining subjects (19). In case there is a difference in sensibility between the two hands, the less sensitive side shows 'normal' distribution of light touch thresholds, whereas at the more sensitive side these thresholds usually scored one nylon rod marker lower.

Index finger extension and strength after extensor indicis proprius transfer.

We reviewed the long-term morbidity of the donor index finger following extensor indicis proprius tendon transfer in 34 patients with an average follow-up period of 8 years. An extension lag of the donor index was found to present in 24 patients. In all patients a reduced extension strength of the donor index finger was noticed, either measured dependently (with concurrent long finger extension) or independently (without long finger extension). Despite these findings, 30 of the patients described no limitations in their daily life activities. In nearly all patients the dependent extension strength was superior to the independent extension strength. To prevent an extension lag, the surgeon should avoid surgical trauma to the dorsal aponeurosis ("hood") by sectioning the index tendon proximal to the hood.

Extending the unambiguous range of two-color interferometers.

The unambiguous distance measurement range in two-color interferometry is generally understood to be limited to the equivalent or synthetic wavelength, which is inversely proportional to the wavelength separation of the two colors. Here it is shown that one may extend the unambiguous range well beyond this limit by using optical phase information to determine the synthetic-wavelength fringe order.

Backscatter-modulation velocimetry with an external-cavity laser diode.

Feedback phenomena in lasers induce modulation signals that can be used for ranging and velocimetry. The modulation depth of a backscatter-modulated semiconductor laser diode is considerably enhanced by operating the diode near the lasing threshold. In the present work an external cavity is used to maintain a spectral linewidth of less than 1 MHz in a diode running at 2.5% of its rated power of 30 mW, resulting in a modulation depth enhancement by a factor of 30 over the high-power limit. Coherent velocimetry has been performed for targets at a distance of 50 m, or 20 times farther than the previously published operational range for backscatter-modulated laser diodes. Light power of less than 10 pW at the collection aperture produces useful modulation signals.

Reconfigurable bipolar analog optical crossbar switch.

A differential technique is proposed for obtaining bipolar analog {-1 . . . 0 . . . 1} inputs, outputs, and connection weights in a mask-type optical crossbar switch. The technique compensates for the limitations of current component technology and permits the use of inexpensive, low-contrast spatial light modulators for reconfigurable switching matrices. The conclusions of this work may be extended to design improvements in a wide variety of optical computing implementations.

Ranging and velocimetry signal generation in a backscatter-modulated laser diode.

A compact self-aligning laser radar has been constructed for coheren ranging and velocimetry using a laser diode modulated by feedback from light scattered from a diffusing target. The phenomenology of beat-signal generation in the device is discussed from both experimental and theoretical points of view. The ac-coupled modulation waveform is asymmetric (similar to a sawtooth) and different for the two propagation directions of the light leaving the diode. Atheoreticalmodel, based on the mode structure ofathree-mirrorFabry-Perot cavity, describes signal generation in these experiments and accounts for the asymmetric waveform.