GATE (Geant4 Application for Emission Tomography) is a Monte Carlo simulation platform developed by the OpenGATE collaboration since 2001 and first publicly released in 2004. Dedicated to the ...modelling of planar scintigraphy, single photon emission computed tomography (SPECT) and positron emission tomography (PET) acquisitions, this platform is widely used to assist PET and SPECT research. A recent extension of this platform, released by the OpenGATE collaboration as GATE V6, now also enables modelling of x-ray computed tomography and radiation therapy experiments. This paper presents an overview of the main additions and improvements implemented in GATE since the publication of the initial GATE paper (Jan et al 2004 Phys. Med. Biol. 49 4543-61). This includes new models available in GATE to simulate optical and hadronic processes, novelties in modelling tracer, organ or detector motion, new options for speeding up GATE simulations, examples illustrating the use of GATE V6 in radiotherapy applications and CT simulations, and preliminary results regarding the validation of GATE V6 for radiation therapy applications. Upon completion of extensive validation studies, GATE is expected to become a valuable tool for simulations involving both radiotherapy and imaging.
ABSTRACT
We used extensive ground‐based multisite and archival spectroscopy to derive observational constraints for a seismic modelling of the magnetic β Cep star V2052 Ophiuchi. The line‐profile ...variability is dominated by a radial mode (f1 = 7.148 46 d−1) and by rotational modulation (Prot = 3.638 833 d). Two non‐radial low‐amplitude modes (f2 = 7.756 03 d−1 and f3 = 6.823 08 d−1) are also detected. The four periodicities that we found are the same as the ones discovered from a companion multisite photometric campaign and known in the literature. Using the photometric constraints on the degrees ℓ of the pulsation modes, we show that both f2 and f3 are prograde modes with (ℓ, m) = (4, 2) or (4, 3). These results allowed us to deduce ranges for the mass (M ∈ 8.2, 9.6 M⊙) and central hydrogen abundance (Xc ∈ 0.25, 0.32) of V2052 Oph, to identify the radial orders n1 = 1, n2 = −3 and n3 = −2, and to derive an equatorial rotation velocity veq ∈ 71, 75 km s−1. The model parameters are in full agreement with the effective temperature and surface gravity deduced from spectroscopy. Only models with no or mild core overshooting (αov ∈ 0, 0.15 local pressure scale heights) can account for the observed properties. Such a low overshooting is opposite to our previous modelling results for the non‐magnetic β Cep star θ Oph having very similar parameters, except for a slower surface rotation rate. We discuss whether this result can be explained by the presence of a magnetic field in V2052 Oph that inhibits mixing in its interior.
Proton resonance frequency shift (PRFS) MR thermometry (MRT) is the generally preferred method for monitoring thermal ablation, typically implemented with gradient-echo (GRE) sequences. Standard PRFS ...MRT is based on the subtraction of a temporal reference phase map and is, therefore, intrinsically sensitive to tissue motion (including deformation) and to external perturbation of the magnetic field. Reference-free (or reference-less) PRFS MRT has been previously described by Rieke and was based on a 2-D polynomial fit performed on phase data from outside the heated region, to estimate the background phase inside the region of interest. While their approach was undeniably a fundamental progress in terms of robustness against tissue motion and magnetic perturbations, the underlying mathematical formalism requires a thick unheated border and may be subject to numerical instabilities with high order polynomials. A novel method of reference-free PRFS MRT is described here, using a physically consistent formalism, which exploits mathematical properties of the magnetic field in a homogeneous or near-homogeneous medium.
Arsenic mobilization from aquatic sediments is an issue of concern, as water-borne arsenic can migrate into pristine areas, endangering aquatic organisms and people. Such mobilization in the Aberjona ...Watershed has distributed nearly 20 t of arsenic throughout river and lake sediments. To gain an understanding of possible biological mechanisms contributing to this transport, mobilization of solid-phase arsenic was investigated in upper Aberjona sediment microcosms. Microcosms catalyzed rapid dissolution of arsenic from iron arsenate, a solid-phase surrogate for sedimentary arsenic, mobilizing 20−28% of the arsenic present. Sterilization prevented this transformation. Reduction of arsenate to arsenite accompanied iron arsenate dis solution, suggesting that reduction was driving dissolution. Sediment-conditioned, filter-sterilized medium showed no arsenic-transforming activity. A native enrichment culture of sulfate-reducing bacteria possessed one-fifth of the microcosm activity, while strain MIT-13, a native arsenate-reducing microorganism, showed much greater activity, dissolving 38% of the arsenic present. Furthermore, strain MIT-13 mobilized arsenic from presterilized, unamended upper Aberjona sediments. These observations indicate that a direct microbial arsenic-mobilizing activity exists in the sedi ments, show that strain MIT-13 is a strong arsenic-transforming agent native to the sediments, and suggest that dissimilatory arsenic reduction may contribute to arsenic flux from anoxic sediments in the most arsenic-contaminated region of the Aberjona Watershed.
Aim To compare the diagnostic accuracy of the digital breast tomosynthesis (DBT) with coned compression magnification mammography (CCMM). Materials and methods The study design included two reading ...sessions completed by seven experienced radiologists. In the first session, all readers read bilateral standard two-view mammograms and a CCMM view of the lesion before giving a combined score for assessment. In the second session, readers read bilateral standard two-view mammograms plus one-view DBT. The two reading sessions of the experiment were separated by at least 2 weeks to reduce the chance of reader memory of the images read in the previous session from influencing the performance in the subsequent session. Results Three hundred and fifty-four lesions were assessed and receiver-operative characteristic (ROC) analysis was used to evaluate the difference between the two modes. For standard two-view mammography plus CCMM, the area under the curve (AUC) was 0.87 95% confidence interval (CI): 0.83–0.91 and for standard two-view mammography plus DBT the AUC was 0.93 (95% CI: 0.91–0.95). The difference between the AUCs was 0.06 with p -value of 0.0014. Conclusion Two-view mammography with one-view DBT showed significantly improved accuracy compared to two-view mammography and CCMM in the assessment of mammographic abnormalities. These results show that DBT can be used effectively in the further evaluation of mammographic abnormalities found at screening and in symptomatic diagnostic practice.
The discovery of lithium-rich giants contradicts expectations from canonical stellar evolution. Here we report on the serendipitous discovery of 20 Li-rich giants observed during the Gaia-ESO Survey, ...which includes the first nine Li-rich giant stars known towards the CoRoT fields. Most of our Li-rich giants have near-solar metallicities and stellar parameters consistent with being before the luminosity bump. This is difficult to reconcile with deep mixing models proposed to explain lithium enrichment, because these models can only operate at later evolutionary stages: at or past the luminosity bump. In an effort to shed light on the Li-rich phenomenon, we highlight recent evidence of the tidal destruction of close-in hot Jupiters at the sub-giant phase. We note that when coupled with models of planet accretion, the observed destruction of hot Jupiters actually predicts the existence of Li-rich giant stars, and suggests that Li-rich stars should be found early on the giant branch and occur more frequently with increasing metallicity. A comprehensive review of all known Li-rich giant stars reveals that this scenario is consistent with the data. However, more evolved or metal-poor stars are less likely to host close-in giant planets, implying that their Li-rich origin requires an alternative explanation, likely related to mixing scenarios rather than external phenomena.
To evaluate whether digital breast tomosynthesis (DBT) can predict if circumscribed masses are benign or malignant by assessing margin sharpness.
Circumscribed masses were evaluated on co-registered ...two-dimensional digital mammography (2DDM) and DBT. Lesions were categorised as follows: category 1=visible sharp border 0–25% of the total margin; category 2 = 26–50% category 3= 51–75%, and category 4=76–100%. Changes in category between 2DDM and DBT were analysed; if the category was lower on DBT the change was negative, if higher the change was positive.
Of 759 lesions, 121 masses classified as circumscribed on DBT were included; 25 were malignant and 96 benign. Of the benign lesions, 8/96 were within category 3 or 4 on 2DDM compared with 48/96 benign lesions within category 3 or 4 on DBT (Fisher's exact test p<0.000527). Forty-eight of 51 (94.1%) lesions categorised as 3 or 4 on DBT were benign and 65/67 (97.01%) of the positive category change group were benign. Lesions in category 1 on DBT had 45.4% chance of being malignant (20/44) compared with 22.72% (20/88) on 2DDM (chi-squared test p<0.001). Sixty-five of 67 (97.01%) lesions in the positive category change group were benign and 23/54 (42.6%) lesions with either no or negative category change were malignant.
The present study demonstrates 97% accuracy in predicting circumscribed lesions as benign when using positive category change and 94% accuracy when >50% of the margin is sharply defined on DBT.
•Significant improvement in accuracy at predicting whether a lesion is benign or malignant was demonstrated.•The potential implications for patient care are to reduce biopsy rates in the assessment clinic.•Potential to reduce recall rates in the context of breast screening with DBT.
Aims. Recent magnetic field surveys in O- and B-type stars revealed that about 10% of the core-hydrogen-burning massive stars host large-scale magnetic fields. The physical origin of these fields is ...highly debated. To identify and model the physical processes responsible for the generation of magnetic fields in massive stars, it is important to establish whether magnetic massive stars are found in very young star-forming regions or whether they are formed in close interacting binary systems. Methods. In the framework of our ESO Large Program, we carried out low-resolution spectropolarimetric observations with FORS 2 in 2013 April of the three most massive central stars in the Trifid nebula, HD 164492A, HD 164492C, and HD 164492D. These observations indicated a strong longitudinal magnetic field of about 500–600 G in the poorly studied component HD 164492C. To confirm this detection, we used HARPS in spectropolarimetric mode on two consecutive nights in 2013 June. Results. Our HARPS observations confirmed the longitudinal magnetic field in HD 164492C. Furthermore, the HARPS observations revealed that HD 164492C cannot be considered as a single star as it possesses one or two companions. The spectral appearance indicates that the primary is most likely of spectral type B1–B1.5 V. Since in both observing nights most spectral lines appear blended, it is currently unclear which components are magnetic. Long-term monitoring using high-resolution spectropolarimetry is necessary to separate the contribution of each component to the magnetic signal. Given the location of the system HD 164492C in one of the youngest star formation regions, this system can be considered as a Rosetta Stone for our understanding of the origin of magnetic fields in massive stars.
Blast disease (causal agent Magnaporthe oryzae) has presented as a new and serious field disease of wheat in South America. Here, we investigated the responses of wheat to both adapted and nonadapted ...isolates of the blast fungus Magnaporthe, examining cellular defence and transcriptional changes. Resistance towards the nonadapted isolate was associated with the formation of appositions, here termed halos, beneath attempted Magnaporthe grisea penetration sites that wheat-adapted, M. oryzae isolates were able to breach. Transcriptome analysis indicated extensive transcriptional reprogramming following inoculation with both wheat-adapted and nonadapted isolates of Magnaporthe. Functional annotation of many of the differentially expressed transcripts classified into the categories: cell rescue and defence, plant metabolism, cellular transport and regulation of transcription (although a significant number of transcripts remain unclassified). Defence-related transcripts induced in common by adapted and nonadapted isolates were differentially regulated in response to M. oryzae and M. grisea isolates over time. Differential expression of genes involved in cellular transport indicated the importance of this process in plant defence. Functional characterisation of these transcripts and their role in defence may eventually lead to the identification of broad-spectrum resistance mechanisms in wheat towards Magnaporthe.
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