Search

DNA metabarcoding of benthic diatoms has been successfully applied for biomonitoring at the national scale and can now be considered technically ready for routine application. However, protocols and methods still vary between and within countries, limiting their transferability and the comparability of results. In order to overcome this, routine use of DNA metabarcoding for diatom biomonitoring requires knowledge of the sources of variability introduced by the different steps of the procedure. Here, we examine how elements of routine procedures contribute to variability between European laboratories. A set of four experiments were performed focusing on DNA extraction and PCR amplification steps to evaluate their reproducibility between different laboratories and the variability introduced by different protocols currently applied by the scientific community. Under the guidance of a reference laboratory, 17 participants from 14 countries performed DNA extraction and PCR amplification in parallel, using the same fixed protocol and their own choice of protocol. Experiments were performed by each participant on a set of standardised DNA and biofilm samples (river, lake and mock community) to investigate potential systematic and random errors. Our results revealed the successful transferability of a protocol amongst labs and a highly similar and consistent ecological assessment outcome obtained regardless of the protocols used by each participant. We propose an “all for one but prove them all” strategy, suggesting that distinct protocols can be used within the scientific community, as long as their consistency is be proven by following minimum standard requirements.

Proton therapy (PT) is an advancing radiotherapy modality increasingly integrated into clinical settings, transitioning from research facilities to hospital environments. A critical aspect of the commissioning of a proton pencil beam scanning delivery system is the acquisition of experimental beam data for accurate beam modelling within the treatment planning system (TPS). These guidelines describe in detail the acquisition of proton pencil beam modelling data. First, it outlines the intrinsic characteristics of a proton pencil beam—energy distribution, angular-spatial distribution and particle number. Then, it lists the input data typically requested by TPSs. Finally, it describes in detail the set of experimental measurements recommended for the acquisition of proton pencil beam modelling data—integrated depth-dose curves, spot maps in air, and reference dosimetry. The rigorous characterization of these beam parameters is essential for ensuring the safe and precise delivery of proton therapy treatments.

Streptomycetes are gram-positive actinobacteria largely represented in the plant root microbiota. The genetic determinants involved in the adaption of Streptomyces in the rhizosphere environment are mostly unknown but can rely on the ability to release phytohormones, degrade plant cell-wall polysaccharides, and produce specialized metabolites notably involved in microbial competition. Here, we sequenced the genome of the rhizospheric and plant defense-stimulating strain Streptomyces sp. AgN23. We found that it belongs to the soil- and plant root-dwelling S. violaceusniger clade. The genome annotation of AgN23 revealed the genetic potential of the bacterium to degrade the plant cell wall with a large repertoire of carbohydrate degrading enzymes, to synthesize auxin, a major regulator of plant development, and to produce antimicrobials (rustmicin, mediomycin, niphimycin, nigericin) and plant bioactive compounds (nigericin, echosides, elaiophylin) through a set of biosynthetic gene clusters. We also found that these genomic features are well conserved among members of the S. violaceusniger clade. In addition, AgN23 displays original events of biosynthetic gene cluster acquisitions and losses, which may account for its interaction with plants. Taken together, our work supports the hypothesis that evolution of a large set of conserved hydrolytic enzymes directed against plant polymers and specialized metabolite repertoires can mediate the adaptation of S. violaceusniger strains to the rhizospheric ecological niches. [Figure: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

A novel irradiation platform for preclinical proton therapy studies foresees proton imaging for accurate setup and treatment planning. Imaging at modern synchrocyclotron-based proton therapy centers with high instantaneous particle flux is possible with an integration mode setup. The aim of this work is to determine an object’s water-equivalent thickness (WET) with a commercially available large-area CMOS sensor. Image contrast is achieved by recording the proton energy deposition in detector pixels for several incoming beam energies (here, called probing energies) and applying a signal decomposition method that retrieves the water-equivalent thickness. A single planar 114 mm × 65 mm CMOS sensor (49.5 µm pixel pitch) was used for this study, aimed at small-animal imaging. In experimental campaigns, at two isochronous cyclotron-based facilities, probing energies suitable for small-animal-sized objects were produced once with built-in energy layer switching and the other time, using a custom degrader wheel. To assess water-equivalent thickness accuracy, a micro-CT calibration phantom with 10 inserts of tissue-mimicking materials was imaged at three phantom-to-detector distances: 3 mm, 13 mm, and 33 mm. For 3 mm and 13 mm phantom-to-detector distance, the average water-equivalent thickness error compared to the ground truth was about 1% and the spatial resolution was 0.16(3) mm and 0.47(2) mm, respectively. For the largest separation distance of 33 mm air gap, proton scattering had considerable impact and the water-equivalent thickness relative error increased to 30%, and the spatial resolution was larger than 1.75 mm. We conclude that a pixelated CMOS detector with dedicated post-processing methods can enable fast proton radiographic imaging in a simple and compact setup for small-animal-sized objects with high water-equivalent thickness accuracy and spatial resolution for reasonable phantom-to-detector distances.

PurposeThe Bragg peak located at the end of the ion beam range is one of the main advantages of ion beam therapy compared to X-Ray radiotherapy. However, verifying the exact position of the Bragg peak within the patient online is a major challenge. The goal of this work was to achieve submillimeter proton beam range verification for pulsed proton beams of an energy of up to 220 MeV using ionoacoustics for a clinically relevant dose deposition of typically 2 Gy per fraction by i) using optimal proton beam characteristics for ionoacoustic signal generation and ii) improved signal detection by correlating the signal with simulated filter templates.MethodsA water tank was irradiated with a preclinical 20 MeV proton beam using different pulse durations ranging from 50 ns up to 1 μs in order to maximise the signal-to-noise ratio (SNR) of ionoacoustic signals. The ionoacoustic signals were measured using a piezo-electric ultrasound transducer in the MHz frequency range. The signals were filtered using a cross correlation-based signal processing algorithm utilizing simulated templates, which enhances the SNR of the recorded signals. The range of the protons is evaluated by extracting the time of flight (ToF) of the ionoacoustic signals and compared to simulations from a Monte Carlo dose engine (FLUKA).ResultsOptimised SNR of 28.0 ± 10.6 is obtained at a beam current of 4.5 μA and a pulse duration of 130 ns at a total peak dose deposition of 0.5 Gy. Evaluated ranges coincide with Monte Carlo simulations better than 0.1 mm at an absolute range of 4.21 mm. Higher beam energies require longer proton pulse durations for optimised signal generation. Using the correlation-based post-processing filter a SNR of 17.8 ± 5.5 is obtained for 220 MeV protons at a total peak dose deposition of 1.3 Gy. For this clinically relevant dose deposition and proton beam energy, submillimeter range verification was achieved at an absolute range of 303 mm in water.ConclusionOptimal proton pulse durations ensure an ideal trade-off between maximising the ionoacoustic amplitude and minimising dose deposition. In combination with a correlation-based post-processing evaluation algorithm, a reasonable SNR can be achieved at low dose levels putting clinical applications for online proton or ion beam range verification into reach.

Myelination optimizes conduction speed of excitatory neurons. However, whether myelination of interneurons (INs) refines cortical networks is unclear. Here, the authors show that INs myelination shapes feedforward inhibition of mouse cortical sensory circuits and impacts whisker-mediated behaviour.

The wine industry must face many challenges because of climate change. One of them is the increase in temperatures and droughts events. These changes sometimes lead to yield losses and can also impact the quality of the wine produced (e.g., increased alcohol content). The management of available water is also a sensitive issue as water requirements for vineyard irrigation are quickly increasing in the south of France. In this context, there is a need for a decision tool that can help evaluate the vine water status through the entire growth season at a large scale. To address this issue, we have previously developed a model (see Laroche-Pinel et al. 2021a) which predicts the vine Stem Water Potential (Ψstem) using Sentinel-2 (S2) images. This model was developed based on a field campaign over three years. The present study now aims to investigate the feedback of winegrowers on the outputs of our model. Therefore, it was applied on the plots of five wine estates that do not belong to the set used in the initial paper. The qualitative results show interesting spatial and temporal consistency in accordance with winegrower knowledge, irrigation data, and weather forecast. The predicted Ψstemhighlights spatial variability in vine fields where a water source emerges and reflects the differences between vine fields with a drip or sparkling irrigation or without an irrigation system. The predicted Ψstem also clearly reacts to a peak in temperature. According to their feedback, three of the five winegrowers would be glad to use this service in the years to come.

BackgroundThe conventional dose rate of radiation therapy is 0.01–0.05 Gy per second. According to preclinical studies, an increased dose rate may offer similar anti-tumoral effect while dramatically improving normal tissue protection. This study aims at evaluating the early toxicities for patients irradiated with high dose rate pulsed proton therapy (PT).Materials and MethodsA single institution retrospective chart review was performed for patients treated with high dose rate (10 Gy per second) pulsed proton therapy, from September 2016 to April 2020. This included both benign and malignant tumors with ≥3 months follow-up, evaluated for acute (≤2 months) and subacute (>2 months) toxicity after the completion of PT.ResultsThere were 127 patients identified, with a median follow up of 14.8 months (3–42.9 months). The median age was 55 years (1.6–89). The cohort most commonly consisted of benign disease (55.1%), cranial targets (95.1%), and were treated with surgery prior to PT (56.7%). There was a median total PT dose of 56 Gy (30–74 Gy), dose per fraction of 2 Gy (1–3 Gy), and CTV size of 47.6 ml (5.6–2,106.1 ml). Maximum acute grade ≥2 toxicity were observed in 49 (38.6%) patients, of which 8 (6.3%) experienced grade 3 toxicity. No acute grade 4 or 5 toxicity was observed. Maximum subacute grade 2, 3, and 4 toxicity were discovered in 25 (19.7%), 12 (9.4%), and 1 (0.8%) patient(s), respectively.ConclusionIn this cohort, utilizing high dose rate proton therapy (10 Gy per second) did not result in a major decrease in acute and subacute toxicity. Longer follow-up and comparative studies with conventional dose rate are required to evaluate whether this approach offers a toxicity benefit.

Abstract Background Brevibacterium strains are widely used for the manufacturing of surface-ripened cheeses, contributing to the breakdown of lipids and proteins and producing volatile sulfur compounds and red-orange pigments. The objective of the present study was to perform comparative genomic analyses in order to better understand the mechanisms involved in their ability to grow on the cheese surface and the differences between the strains. Results The genomes of 23 Brevibacterium strains, including twelve strains isolated from cheeses, were compared for their gene repertoire involved in salt tolerance, iron acquisition, bacteriocin production and the ability to use the energy compounds present in cheeses. All or almost all the genomes encode the enzymes involved in ethanol, acetate, lactate, 4-aminobutyrate and glycerol catabolism, and in the synthesis of the osmoprotectants ectoine, glycine-betaine and trehalose. Most of the genomes contain two contiguous genes encoding extracellular proteases, one of which was previously characterized for its activity on caseins. Genes encoding a secreted triacylglycerol lipase or involved in the catabolism of galactose and D-galactonate or in the synthesis of a hydroxamate-type siderophore are present in part of the genomes. Numerous Fe3+/siderophore ABC transport components are present, part of them resulting from horizontal gene transfers. Two cheese-associated strains have also acquired catecholate-type siderophore biosynthesis gene clusters by horizontal gene transfer. Predicted bacteriocin biosynthesis genes are present in most of the strains, and one of the corresponding gene clusters is located in a probable conjugative transposon that was only found in cheese-associated strains. Conclusions Brevibacterium strains show differences in their gene repertoire potentially involved in the ability to grow on the cheese surface. Part of these differences can be explained by different phylogenetic positions or by horizontal gene transfer events. Some of the distinguishing features concern biotic interactions with other strains such as the secretion of proteases and triacylglycerol lipases, and competition for iron or bacteriocin production. In the future, it would be interesting to take the properties deduced from genomic analyses into account in order to improve the screening and selection of Brevibacterium strains, and their association with other ripening culture components.

Objective: The purpose of this systematic literature review is to appraise contemporary research literature examining the effects of mentoring on graduate registered nurses’ transition to practice objectively and systematically. These areas, specifically examined, are competence, job satisfaction, and retention. Three themes emerged from the research in this area. The themes are informal mentoring effectiveness, the extent of mentoring, and mentoring efficacy. Methods: The PRISMA method was implemented. Articles reviewed were written in English and published between December 2015 and December 2020 and obtained from the Griffith University Library electronic catalogue. A quality assessment of each record not excluded in the title and abstract analysis was undertaken using the method described by Kmet.[1] Those with a quality rating of 16 as a minimum are included in this systematic literature review. Results: Three quantitative, two qualitative and two - method research studies emerged after applying inclusion criteria, selection, and quality assessment. The analysis demonstrated the positive effects of mentoring on all three avenues with one mixed-method study that documented a downward trend in job satisfaction at six months. Conclusions: Mentoring is an effective transition to practice strategy for novice nurses. It affects competence, job satisfaction and retention positively. Retention and resignation rates worsen following 12 months of employment. Robust and rigorous studies are essential to justify long-term mentoring programs’ cost-effectiveness.