Assessing the accuracy and reproducibility of computer-assisted analysis of (123) I-FP-CIT SPECT using BasGan (V2).

BACKGROUND AND PURPOSE: Over the last two decades (123) I-FP-CIT-SPECT, has been used to discriminate neurodegenerative Parkinsonian syndrome from other diseases. BasGan is a freely available software that assists (123) I-FP-CIT-SPECT evaluation by estimating semiquantitative values for each basal nucleus and compares the results to a database of healthy subjects. The aims of this study were: (1) to assess the accuracy of qualitative analysis and of semiquantitative, BasGan-assisted evaluations of (123) I-FP-CIT-SPECT; (2) to compare the accuracy of both methods when applied to "doubtful" cases; (3) to appreciate the reproducibility of the BasGan-assisted evaluations. MATERIALS AND METHODS: Seventy-eight patients were included in this 4-year follow-up study. The diagnostic cut-off for semiquantitative uptake values of each basal nucleus was determined based on ROC curves analysis. Accuracy scores were calculated for the entire population and for "doubtful" cases. Intra- and interoperator reproducibility was assessed. RESULTS: Accuracy of the software-assisted analyses was high for data from each nucleus. In "doubtful" exams accuracy was higher when using BasGan as opposed to relying solely on visual assessment. Intra- and interoperator reproducibility of the BasGan-assisted evaluations was good to excellent. CONCLUSION: BasGan-assisted evaluations of (123) I-FP-CIT-SPECT were very useful, particularly in "doubtful" cases. Multicenter studies are mandatory before routine use of BasGan.

Direct microcontact printing of oligonucleotides for biochip applications.

BACKGROUND: A critical step in the fabrication of biochips is the controlled placement of probes molecules on solid surfaces. This is currently performed by sequential deposition of probes on a target surface with split or solid pins. In this article, we present a cost-effective procedure namely microcontact printing using stamps, for a parallel deposition of probes applicable for manufacturing biochips. RESULTS: Contrary to a previous work, we showed that the stamps tailored with an elastomeric poly(dimethylsiloxane) material did not require any surface modification to be able to adsorb oligonucleotides or PCR products. The adsorbed DNA molecules are subsequently printed efficiently on a target surface with high sub-micron resolution. Secondly, we showed that successive stamping is characterized by an exponential decay of the amount of transferred DNA molecules to the surface up the 4th print, then followed by a second regime of transfer that was dependent on the contact time and which resulted in reduced quality of the features. Thus, while consecutive stamping was possible, this procedure turned out to be less reproducible and more time consuming than simply re-inking the stamps between each print. Thirdly, we showed that the hybridization signals on arrays made by microcontact printing were 5 to 10-times higher than those made by conventional spotting methods. Finally, we demonstrated the validity of this microcontact printing method in manufacturing oligonucleotides arrays for mutations recognition in a yeast gene. CONCLUSION: The microcontact printing can be considered as a new potential technology platform to pattern DNA microarrays that may have significant advantages over the conventional spotting technologies as it is easy to implement, it uses low cost material to make the stamp, and the arrays made by this technology are 10-times more sensitive in term of hybridization signals than those manufactured by conventional spotting technology.

Two-dimensional and quasi-three-dimensional dosimetry of hadron and photon beams with the Magic Cube and the Pixel Ionization Chamber.

Two detectors for fast two-dimensional (2D) and quasi-three-dimensional (quasi-3D) verification of the dose delivered by radiotherapy beams have been developed at University and Istituto Nazionale di Fisica Nucleare (INFN) of Torino. The Magic Cube is a stack of strip-segmented ionization chambers interleaved with water-equivalent slabs. The parallel plate ionization chambers have a sensitive area of 24 x 24 cm2, and consist of 0.375 cm wide and 24 cm long strips. There are a total of 64 strips per chamber. The Magic Cube has been tested with the clinical proton beam at Loma Linda University Medical Centre (LLUMC), and was shown to be capable of fast and precise quasi-3D dose verification. The Pixel Ionization Chamber (PXC) is a detector with pixel anode segmentation. It is a 32 x 32 matrix of 1024 cylindrical ionization cells arranged in a square 24 x 24 cm2 area. Each cell has 0.4 cm diameter and 0.55 cm height, at a pitch of 0.75 cm separates the centre of adjacent cells. The sensitive volume of each single ionization cell is 0.07 cm3. The detectors are read out using custom designed front-end microelectronics and a personal computer-based data acquisition system. The PXC has been used to verify dynamic intensity-modulated radiotherapy for head-and-neck and breast cancers.

Dosimetric characterization of a large area pixel-segmented ionization chamber.

A pixel-segmented ionization chamber has been designed and built by Torino University and INFN. The detector features a 24 x 24 cm2 active area divided in 1024 independent cylindrical ionization chambers and can be read out in 500 micros without introducing dead time; the digital charge quantum can be adjusted between 100 fC and 800 fC. The sensitive volume of each single ionization chamber is 0.07 cm3. The purpose of the detector is to ease the two-dimensional (2D) verifications of fields with complex shapes and large gradients. The detector was characterized in a PMMA phantom using 60Co and 6 MV x-ray photon beams. It has shown good signal linearity with respect to dose and dose rate to water. The average sensitivity of a single ionization chamber was 2.1 nC/Gy, constant within 0.5% over one month of daily measurements. Charge collection efficiency was 0.985 at the operating polarization voltage of 400 V and 3.5 Gy/min dose rate. Tissue maximum ratio and output factor have been compared with a Farmer ionization chamber and were found in good agreement. The dose profiles have been compared with the ones obtained with an ionization chamber in water phantom for the field sizes supplied by a 3D-Line dynamic multileaf collimator. These results show that this detector can be used for 2D dosimetry of x-ray photon beams, supplying a good spatial resolution and sensibly reducing the time spent in dosimetric verification of complex radiation fields.

Labeling during cleavage of nucleic acids for their detection on DNA chips.

A new and efficient strategy for labeling of nucleic acids prior to their hybridization on high density DNA chip has been developed. Our approach which combines the fragmentation and the labeling is based on the reactivity of the terminal phosphates of cleaved DNA and RNA fragments with a reporter molecule bearing aryldiazomethane group.

Fluorescent labelling of oligodeoxyribonucleotides by the oxyamino-aldehyde coupling reaction.

We describe the reaction of oligonucleotides containing an aldehydic group at the 5'-end or inside the sequence with an oxyamino label. The reaction was found to be highly selective and represents an efficient method for derivatization of oligonucleotides.