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Ames, S. K., Gardner, S. N., Marti, J. M., Slezak, T. R., Gokhale, M. B., & Allen, J. E. (2015). Using populations of human and microbial genomes for organism detection in metagenomes. Genome Res., 25(7), 1056–1067.
Abstract: Identifying causative disease agents in human patients from shotgun metagenomic sequencing (SMS) presents a powerful tool to apply when other targeted diagnostics fail. Numerous technical challenges remain, however, before SMS can move beyond the role of research tool. Accurately separating the known and unknown organism content remains difficult, particularly when SMS is applied as a last resort. The true amount of human DNA that remains in a sample after screening against the human reference genome and filtering nonbiological components left from library preparation has previously been underreported. In this study, we create the most comprehensive collection of microbial and reference-free human genetic variation available in a database optimized for efficient metagenomic search by extracting sequences from GenBank and the 1000 Genomes Project. The results reveal new human sequences found in individual Human Microbiome Project (HMP) samples. Individual samples contain up to 95% human sequence, and 4% of the individual HMP samples contain 10% or more human reads. Left unidentified, human reads can complicate and slow down further analysis and lead to inaccurately labeled microbial taxa and ultimately lead to privacy concerns as more human genome data is collected.
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Barrio, J., Etxebeste, A., Lacasta, C., Muñoz, E., Oliver, J. F., Solaz, C., et al. (2015). Performance of VATA64HDR16 ASIC for medical physics applications based on continuous crystals and SiPMs. J. Instrum., 10, P12001–12pp.
Abstract: Detectors based on Silicon Photomultipliers (SiPMs) coupled to continuous crystals are being tested in medical physics applications due to their potential high resolution and sensitivity. To cope with the high granularity required for a very good spatial resolution, SiPM matrices with a large amount of elements are needed. To be able to read the information coming from each individual channel, dedicated ASICs are employed. The VATA64HDR16 ASIC is a 64-channel, charge-sensitive amplifier that converts the collected charge into a proportional current or voltage signal. A complete assessment of the suitability of that ASIC for medical physics applications based on continuous crystals and SiPMs has been carried out. The input charge range is linear from 20 pC up to 55 pC. The energy resolution obtained at 511 keV is 10% FWHM with a LaBr3 crystal and 16% FWHM with a LYSO crystal. A coincidence timing resolution of 24 ns FWHM is obtained with two LYSO crystals.
Keywords: Solid state detectors; Photon detectors for UV, visible and IR photons (solid-state) (PIN diodes, APDs, Si-PMTs, G-APDs, CCDs, EBCCDs, EMCCDs etc); Front-end electronics for detector readout; Gamma detectors (scintillators, CZT, HPG, HgI etc)
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Doncel, M., Cederwall, B., Martin, S., Quintana, B., Gadea, A., Farnea, E., et al. (2015). Conceptual design of a high resolution Ge array with tracking and imaging capabilities for the DESPEC (FAIR) experiment. J. Instrum., 10, P06010–15pp.
Abstract: We present results of Monte Carlo simulations for the conceptual design of the high-resolution DESPEC Germanium Array Spectrometer (DEGAS) proposed for the Facility for Ion and Antiproton Research (FAIR) under construction at Darmstadt, Germany. The project is carried out in three phases, although only results for the two first phases will be addressed in this work. The first phase will consist of a re-arrangement of the EUROBALL cluster detectors previously used in the RISING campaign at GSI. The second phase is based on coupling AGATA-type triple-cluster detectors with EUROBALL cluster detectors in a compact geometry around the active ion implantation target of DESPEC.
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Palomo, R., Pujades, M. C., Gimeno-Olmos, J., Carmona, V., Lliso, F., Candela-Juan, C., et al. (2015). Evaluation of lens absorbed dose with Cone Beam IGRT procedures. J. Radiol. Prot., 35(4), N33–N41.
Abstract: The purpose of this work is to evaluate the absorbed dose to the eye lenses due to the cone beam computed tomography (CBCT) system used to accurately position the patient during head-and-neck image guided procedures. The on-board imaging (OBI) systems (v. 1.5) of Clinac iX and TrueBeam (Varian) accelerators were used to evaluate the imparted dose to the eye lenses and some additional points of the head. All CBCT scans were acquired with the Standard-Dose Head protocol from Varian. Doses were measured using thermoluminescence dosimeters (TLDs) placed in an anthropomorphic phantom. TLDs were calibrated at the beam quality used to reduce their energy dependence. Average dose to the lens due to the OBI systems of the Clinac iX and the TrueBeam were 0.71 +/- 0.07 mGy/CBCT and 0.70 +/- 0.08 mGy/CBCT, respectively. The extra absorbed dose received by the eye lenses due to one CBCT acquisition with the studied protocol is far below the 500 mGy threshold established by ICRP for cataract formation (ICRP 2011 Statement on Tissue Reactions). However, the incremental effect of several CBCT acquisitions during the whole treatment should be taken into account.
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Torres-Espallardo, I., Diblen, F., Rohling, H., Solevi, P., Gillam, J., Watts, D., et al. (2015). Evaluation of resistive-plate-chamber-based TOF-PET applied to in-beam particle therapy monitoring. Phys. Med. Biol., 60(9), N187–N208.
Abstract: Particle therapy is a highly conformal radiotherapy technique which reduces the dose deposited to the surrounding normal tissues. In order to fully exploit its advantages, treatment monitoring is necessary to minimize uncertainties related to the dose delivery. Up to now, the only clinically feasible technique for the monitoring of therapeutic irradiation with particle beams is Positron Emission Tomography (PET). In this work we have compared a Resistive Plate Chamber (RPC)-based PET scanner with a scintillation-crystal-based PET scanner for this application. In general, the main advantages of the RPC-PET system are its excellent timing resolution, low cost, and the possibility of building large area systems. We simulated a partial-ring scannerbeam monitoring, which has an intrinsically low positron yield compared to diagnostic PET. In addition, for in-beam PET there is a further data loss due to the partial ring configuration. In order to improve the performance of the RPC-based scanner, an improved version of the RPC detector (modifying the thickness of the gas and glass layers), providing a larger sensitivity, has been simulated and compared with an axially extended version of the crystal-based device. The improved version of the RPC shows better performance than the prototype, but the extended version of the crystal-based PET outperforms all other options. based on an RPC prototype under construction within the Fondazione per Adroterapia Oncologica (TERA). For comparison with the crystal-based PET scanner we have chosen the geometry of a commercially available PET scanner, the Philips Gemini TF. The coincidence time resolution used in the simulations takes into account the current achievable values as well as expected improvements of both technologies. Several scenarios (including patient data) have been simulated to evaluate the performance of different scanners. Initial results have shown that the low sensitivity of the RPC hampers its application to hadron
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