On the implementation of acollinearity in PET Monte Carlo simulations.

Objective.Acollinearity of annihilation photons (APA) introduces spatial blur in positron emission tomography (PET) imaging. This phenomenon increases proportionally with the scanner diameter and it has been shown to follow a Gaussian distribution. This last statement can be interpreted in two ways: the magnitude of the acollinearity angle, or the angular deviation of annihilation photons from perfect collinearity. As the former constitutes the partial integral of the latter, a misinterpretation could have significant consequences on the resulting spatial blurring. Previous research investigating the impact of APA in PET imaging has assumed the Gaussian nature of its angular deviation, which is consistent with experimental results. However, a comprehensive analysis of several simulation software packages for PET data acquisition revealed that the magnitude of APA was implemented as a Gaussian distribution.Approach.We quantified the impact of this misinterpretation of APA by comparing simulations obtained with GATE, which is one of these simulation programs, to an in-house modification of GATE that models APA deviation as following a Gaussian distribution.Main results.We show that the APA misinterpretation not only alters the spatial blurring profile in image space, but also considerably underestimates the impact of APA on spatial resolution. For an ideal PET scanner with a diameter of 81 cm, the APA point source response simulated under the first interpretation has a cusp shape with 0.4 mm FWHM. This is significantly different from the expected Gaussian point source response of 2.1 mm FWHM reproduced under the second interpretation.Significance.Although this misinterpretation has been found in several PET simulation tools, it has had a limited impact on the simulated spatial resolution of current PET scanners due to its small magnitude relative to the other factors. However, the inaccuracy it introduces in estimating the overall spatial resolution of PET scanners will increase as the performance of newer devices improves.

Timing Estimation and Limits in TOF-PET Detectors Producing Prompt Photons.

The production of prompt photons providing high photon time densities is a promising avenue to reach ultrahigh coincidence time resolution (CTR) in time-of-flight PET. Detectors producing prompt photons are receiving high interest experimentally, ignited by past exploratory theoretical studies that have anchored some guiding principles. Here, we aim to consolidate and extend the foundations for the analytical modeling of prompt generating detectors. We extend the current models to a larger range of prompt emission kinetics where more stringent requirements on the prompt photon yield rapidly emerge as a limiting factor. Lower bound and estimator evaluations are investigated with different underlying models, notably by merging or keeping separate the prompt and scintillation photon populations. We further show the potential benefits of knowing the proportion of prompt photons within a detection set to improve the CTR by mitigating the detrimental effect of population (prompt vs scintillation) mixing. Taking into account the fluctuations on the average number of detected prompt photons in the model reveals a limited influence when prompt photons are accompanied by fast scintillation (e.g., LSO:Ce:Ca) but a more significant effect when accompanied by slower scintillation (e.g., BGO). Establishing performance characteristics and limitations of prompt generating detectors is paramount to gauging and targeting the best possible timing capabilities they can offer.

Improvement of Spatial Resolution with Iterative PET Reconstruction using UltraFast TOF.

The impact of Time-of-Flight (TOF) on positron emission tomography (PET) spatial resolution is generally considered negligible. In this work, a two-step approach based on simulations of two-dimensional scanner configurations is taken to show that ultra-fast TOF has the potential to overcome the limitation induced by the physical size of detectors on spatial resolution. An estimation of the lower bound on spatial resolution using point sources is provided, followed by a qualitative assessment of the resolution obtained using a Hot Spot phantom. The impact of detector width, TOF resolution and TOF binning on the achieved spatial resolution is also studied. While gain beyond the expected blur due to detector size is demonstrated, the detector size remains one limiting factor albeit less prominent. The dependence on acquisition statistics to reach the full potential of TOF-induced gain in spatial resolution is demonstrated. A simulated brain phantom acquired with a fictive three-dimensional PET scanner was qualitatively analyzed and structures smaller than the typical limit are clearly made visible by reconstructing the images with a ∼13-ps TOF resolution. A potential application of this feature of ultra-fast TOF would be the design of clinical PET scanners achieving spatial resolution beyond the current state-of-the-art.

DOI estimation through signal arrival time distribution: a theoretical description including proof of concept measurements.

The challenge to reach 10 ps coincidence time resolution (CTR) in time-of-flight positron emission tomography (TOF-PET) is triggering major efforts worldwide, but timing improvements of scintillation detectors will remain elusive without depth-of-interaction (DOI) correction in long crystals. Nonetheless, this momentum opportunely brings up the prospect of a fully time-based DOI estimation since fast timing signals intrinsically carry DOI information, even with a traditional single-ended readout. Consequently, extracting features of the detected signal time distribution could uncover the spatial origin of the interaction and in return, provide enhancement on the timing precision of detectors. We demonstrate the validity of a time-based DOI estimation concept in two steps. First, experimental measurements were carried out with current LSO:Ce:Ca crystals coupled to FBK NUV-HD SiPMs read out by fast high-frequency electronics to provide new evidence of a distinct DOI effect on CTR not observable before with slower electronics. Using this detector, a DOI discrimination using a double-threshold scheme on the analog timing signal together with the signal intensity information was also developed without any complex readout or detector modification. As a second step, we explored by simulation the anticipated performance requirements of future detectors to efficiently estimate the DOI and we proposed four estimators that exploit either more generic or more precise features of the DOI-dependent timestamp distribution. A simple estimator using the time difference between two timestamps provided enhanced CTR. Additional improvements were achieved with estimators using multiple timestamps (e.g. kernel density estimation and neural network) converging to the Cramér-Rao lower bound developed in this work for a time-based DOI estimation. This two-step study provides insights on current and future possibilities in exploiting the timing signal features for DOI estimation aiming at ultra-fast CTR while maintaining detection efficiency for TOF PET.

Performance evaluation of the mouse version of the LabPET II PET scanner.

The LabPET II is a new positron emission tomography technology platform designed to achieve submillimetric spatial resolution imaging using fully pixelated avalanche photodiodes-based detectors and highly integrated parallel front-end processing electronics. The detector was designed as a generic building block to develop devices for preclinical imaging of small to mid-sized animals and for clinical imaging of the human brain. The aim of this work is to assess the physical characteristics and imaging performance of the mouse version of LabPET II scanner following the NEMA NU4-2008 standard and using high resolution phantoms and in vivo imaging applications. A reconstructed spatial resolution of 0.78 mm (0.5 µ l) is measured close to the center of the radial field of view. With an energy window of 350 650 keV, the system absolute sensitivity is 1.2% and its maximum noise equivalent count rate reaches 61.1 kcps at 117 MBq. Submillimetric spatial resolution is achieved in a hot spot phantom and tiny bone structures were resolved with unprecedented contrast in the mouse. These results provide convincing evidence of the capabilities of the LabPET II technology for biomolecular imaging in preclinical research.

The Cellular Response to Lanthanum Is Substrate Specific and Reveals a Novel Route for Glycerol Metabolism in Pseudomonas putida KT2440.

Ever since the discovery of the first rare earth element (REE)-dependent enzyme, the physiological role of lanthanides has become an emerging field of research due to the environmental implications and biotechnological opportunities. In Pseudomonas putida KT2440, the two pyrroloquinoline quinone-dependent alcohol dehydrogenases (PQQ-ADHs) PedE and PedH are inversely regulated in response to REE availability. This transcriptional switch is orchestrated by a complex regulatory network that includes the PedR2/PedS2 two-component system and is important for efficient growth on several alcoholic volatiles. To study whether cellular responses beyond the REE switch exist, the differential proteomic responses that occur during growth on various model carbon sources were analyzed. Apart from the Ca2+-dependent enzyme PedE, the differential abundances of most identified proteins were conditional. During growth on glycerol-and concomitant with the proteomic changes-lanthanum (La3+) availability affected different growth parameters, including the onset of logarithmic growth and final optical densities. Studies with mutant strains revealed a novel metabolic route for glycerol utilization, initiated by PedE and/or PedH activity. Upon oxidation to glycerate via glyceraldehyde, phosphorylation by the glycerate kinase GarK most likely yields glycerate-2-phosphate, which is eventually channeled into the central metabolism of the cell. This new route functions in parallel with the main degradation pathway encoded by the glpFKRD operon and provides a growth advantage to the cells by allowing an earlier onset of growth with glycerol as the sole source of carbon and energy.IMPORTANCE The biological role of REEs has long been underestimated, and research has mainly focused on methanotrophic and methylotrophic bacteria. We have recently demonstrated that P. putida, a plant growth-promoting bacterium that thrives in the rhizosphere of various food crops, possesses a REE-dependent alcohol dehydrogenase (PedH), but knowledge about REE-specific effects on physiological traits in nonmethylotrophic bacteria is still scarce. This study demonstrates that the cellular response of P. putida to lanthanum (La3+) is mostly substrate specific and that La3+ availability highly affects the growth of cells on glycerol. Further, a novel route for glycerol metabolism is identified, which is initiated by PedE and/or PedH activity and provides a growth advantage to this biotechnologically relevant organism by allowing a faster onset of growth. Overall, these findings demonstrate that lanthanides can affect physiological traits in nonmethylotrophic bacteria and might influence their competitiveness in various environmental niches.

Experimental validation of a coincidence time resolution metric including depth-of-interaction bias for TOF-PET.

Depth-of-interaction (DOI) variability of annihilation photons is known to be a source of coincidence time resolution (CTR) degradation for fast time-of-flight-positron emission tomography detectors. An analytical model was recently proposed to explicitly include the DOI time bias separately from variance-related statistical factors, such as scintillation photon emission and photosensor jitter, in the CTR evaluation. In the present work, an experimental validation of this new model is provided. An unconventional signal readout configuration was used to magnify the DOI bias with 20 mm long LYSO:Ce crystals. In a head-to-head orientation of the crystals, simulations performed using the metric with DOI bias exhibited a much better agreement (within 21 ps) with the experimentally measured CTR of 413 ± 8 ps full-width at half maximum, whereas simulations without DOI bias underestimated the CTR by 138 ps. The metric including DOI bias was shown to also be effective at predicting the CTR of the head-to-head setup (without DOI information) using data from a DOI-collimated experimental setup (with partial DOI information). With the development of new low-variance ultra-fast detectors, the DOI timing blur will become increasingly important and will need to be taken into account in analytical predictions and in some experimental measurements through the proposed metric.

Analytical model of DOI-induced time bias in ultra-fast scintillation detectors for TOF-PET.

In positron emission tomography (PET), long crystals ([Formula: see text]20 mm) are used to enhance detection efficiency and increase scanner sensitivity. However, for fast time-of-flight (TOF) scanners, this may affect the achievable coincidence time resolution (CTR) due to depth-of-interaction (DOI) induced blur on timing. Currently, the effect of DOI on CTR evaluation with analytical modeling is incorporated using the probability density function (PDF) for attenuation of the annihilation photons with the PDFs of the other scintillation processes. However, we show that the resulting PDF would not describe accurately the variation in timestamps distribution at different DOIs. We propose a new analytical model for the CTR evaluation, which consists of computing a DOI dependent CTR weighted by the DOI probability in coincidence. The CTR was thus defined as the weighted root-mean-square error (RMSE) of the DOI-wise variance and bias in order to explicitly describe the positioning bias induced by coincident annihilation photons at different DOIs. The effect of DOI bias on CTR was investigated by using four classic estimators found in the literature, each applied on contemporary scintillation detectors and nearly ideal detectors. A limited difference in the calculated CTR was found for typical scintillation detectors when assessing RMSE with and without DOI time offset correction. This was expected since the DOI bias remains negligible against other phenomena in such case. However, the difference becomes significant for nearly ideal scintillation detectors, where optimal CTR would only be attainable with DOI correction. For these nearly ideal cases, the revised model has better predictive power since the DOI time offset correction is included. Investigation with analytical approaches for realistically achievable ultra-fast CTR in TOF-PET detectors should be performed with a model that genuinely takes into account the DOI effect. We show that the proposed model is a valid candidate for such a task.

Performance Simulation of an Ultra-High Resolution Brain PET Scanner Using 1.2-mm Pixel Detectors.

The concept of a new ultra-high resolution positron emission tomography (PET) brain scanner featuring truly pixelated detectors based on the LabPET II technology is presented. The aim of this study is to predict the performance of the scanner using GATE simulations. The NEMA procedures for human and small animal PET scanners were used, whenever appropriate, to simulate spatial resolution, scatter fraction, count rate performance and the sensitivity of the proposed system compared to state-of-the-art PET scanners that would currently be the preferred choices for brain imaging, namely the HRRT dedicated brain PET scanner and the Biograph Vision wholebody clinical PET scanner. The imaging performance was also assessed using the NEMA-NU4 image quality phantom, a mini hot spot phantom and a 3-D voxelized brain phantom. A reconstructed nearly isotropic spatial resolution of 1.3 mm FWHM is obtained at 10 mm from the center of the field of view. With an energy window of 250-650 keV, the system absolute sensitivity is estimated at 3.4% and its maximum NECR reaches 16.4 kcps at 12 kBq/cc. The simulation results provide evidence of the promising capabilities of the proposed scanner for ultra-high resolution brain imaging.

Genome Sequences of 11 Conspecific Streptomyces sp. Strains.

The genomes of 11 conspecific Streptomyces strains, i.e., from the same species and inhabiting the same ecological niche, were sequenced and assembled. This data set offers an ideal framework to assess the genome evolution of Streptomyces species in their ecological context.

Massive Gene Flux Drives Genome Diversity between Sympatric Streptomyces Conspecifics.

In this work, by comparing genomes of closely related individuals of Streptomyces isolated at a spatial microscale (millimeters or centimeters), we investigated the extent and impact of horizontal gene transfer in the diversification of a natural Streptomyces population. We show that despite these conspecific strains sharing a recent common ancestor, all harbored significantly different gene contents, implying massive and rapid gene flux. The accessory genome of the strains was distributed across insertion/deletion events (indels) ranging from one to several hundreds of genes. Indels were preferentially located in the arms of the linear chromosomes (ca. 12 Mb) and appeared to form recombination hot spots. Some of them harbored biosynthetic gene clusters (BGCs) whose products confer an inhibitory capacity and may constitute public goods that can favor the cohesiveness of the bacterial population. Moreover, a significant proportion of these variable genes were either plasmid borne or harbored signatures of actinomycete integrative and conjugative elements (AICEs). We propose that conjugation is the main driver for the indel flux and diversity in Streptomyces populations.IMPORTANCE Horizontal gene transfer is a rapid and efficient way to diversify bacterial gene pools. Currently, little is known about this gene flux within natural soil populations. Using comparative genomics of Streptomyces strains belonging to the same species and isolated at microscale, we reveal frequent transfer of a significant fraction of the pangenome. We show that it occurs at a time scale enabling the population to diversify and to cope with its changing environment, notably, through the production of public goods.

Diversity and antimicrobial activities of Streptomyces isolates from Fetzara Lake, north eastern Algeria.

A total of 125 Streptomyces strains were isolated from an Algerian wetland (Fetzara Lake) and characterized by growth on different culture media. Phylogenetic analyses were carried out by 16S rRNA sequence comparison after PCR amplification using universal primers. Antibacterial bioassays performed by the agar diffusion method enabled us to retain 33 Streptomyces isolates for their activity against two Gram-positive bacteria (Bacillus subtilis and Micrococcus luteus) and one Gram-negative bacteria (Escherichia coli). Among them, six isolates inhibited all three indicator strains. Antibacterial compounds were then extracted from the solid culture media with ethanol and ethyl acetate as organic solvents. The minimal inhibitory concentration (% v/v) of the extracts was evaluated by a standardized broth dilution method against different clinical-resistant bacterial isolates and Candida albicans. The most active crude extracts were selected for further characterization by chromatographic analysis (RP-HPLC).

Whole-cell biosensor of cellobiose and application to wood decay detection.

Fungal biodegradation of wood is one of the main threats regarding its use as a material. So far, the detection of this decaying process is empirically assessed by loss of mass, when the fungal attack is advanced and woody structure already damaged. Being able to detect fungal attack on wood in earlier steps is thus of special interest for the wood economy. In this aim, we designed here a new diagnostic tool for wood degradation detection based on the bacterial whole-cell biosensor technology. It was designed in diverting the soil bacteria Streptomyces CebR sensor system devoted to cellobiose detection, a cellulolytic degradation by-product emitted by lignolytic fungi since the onset of wood decaying process. The conserved regulation scheme of the CebR system among Streptomyces allowed constructing a molecular tool easily transferable in different strains or species and enabling the screen for optimal host strains for cellobiose detection. Assays are performed in microplates using one-day culture lysates. Diagnostic is performed within one hour by a spectrophotometric measuring of the cathecol deshydrogenase activity. The selected biosensor was able to detect specifically cellobiose at concentrations similar to those measured in decaying wood and in a spruce leachate attacked by a lignolytic fungus, indicating a high potential of applicability to detect ongoing wood decay process.

Taxonomic and functional diversity of Streptomyces in a forest soil.

In this work we report the isolation and the characterization of 79 Streptomyces isolates from a French forest soil. The 16S rRNA gene phylogeny indicated that a great diversity of Streptomyces was present in this soil, with at least nine different and potentially new species. Growth plate assays showed that most Streptomyces lineages exhibit cellulolytic and hemicellulolytic capacities and potentially participate in wood decomposition. Molecular screening for a specific hydrogenase also indicated a widespread potential for atmospheric H2 uptake. Co-culture experiments with representative strains showed antagonistic effects between Streptomyces of the same population and between Streptomyces and various fungi. Interestingly, in certain conditions, growth promotion of some fungi also occurred. We conclude that in forest soil, Streptomyces populations exhibit many important functions involved in different biogeochemical cycles and also influence the structure of soil microbial communities.