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Over the last decades, the use of artificial intelligence, machine learning and deep learning in medical fields has skyrocketed. Well known for their results in segmentation, motion management and posttreatment outcome tasks, investigations of machine learning and deep learning models as fast dose calculation or quality assurance tools have been present since 2000. The main motivation for this increasing research and interest in artificial intelligence, machine learning and deep learning is the enhancement of treatment workflows, specifically dosimetry and quality assurance accuracy and time points, which remain important time-consuming aspects of clinical patient management. Since 2014, the evolution of models and architectures for dose calculation has been related to innovations and interest in the theory of information research with pronounced improvements in architecture design. The use of knowledge-based approaches to patient-specific methods has also considerably improved the accuracy of dose predictions. This paper covers the state of all known deep learning architectures and models applied to external radiotherapy with a description of each architecture, followed by a discussion on the performance and future of deep learning predictive models in external radiotherapy.

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In a previous work, a PENELOPE Monte Carlo model of a Cyberknife system equipped with fixed collimator was developed and validated for in-field dose evaluation. The aim of this work is to extend it to evaluate peripheral doses and to determine the precision of the treatment planning system (TPS) Multiplan in evaluating the off-axis doses. The Cyberknife® head model was completed with surrounding components based on manufacturer drawings. The contribution of the different head parts on the out-of-field dose was studied. To model the attenuation and the modification of particle energy caused by components not modelled, the photon transport was modified in one of the added components. The model was iteratively adjusted to fit dose profiles measured with EBT3 films and an ionization chamber for several collimator sizes. Finally, dose profiles were calculated using the two Multiplan TPS algorithms and were compared to our simulations. The contributions to out-of-field dose were identified as scattered radiation from the phantom and head leakage and scatter originating at the secondary collimator level. Particle transport in the additional pieces was modified to model this radiation. The maximum differences between simulated and measured doses are of 20.4%. Regarding the detector responses away from axis, EBT3 films and the Farmer chamber give similar response (less than 20% difference). The TPS Monte Carlo algorithm underestimates the doses away from axis more importantly for the smaller field sizes (up to 98%). Besides, RayTracing simplifies peripheral dose to a constant value with no inclusion of particle transport. A Monte Carlo model of a Cyberknife system for the determination of out-of-field doses up to 14 cm off-axis was successfully developed and validated for different depths and field sizes in comparison with measurements. This study also confirms that TPS algorithms do not model peripheral dose properly.

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PURPOSE: This study aims at characterising the properties of TruView™ and ClearView™ two new gel dosimeters (Modus Medical Devices Inc.) and at studying the feasibility of relative dosimetry using these dosimeters and the Vista™ Optical CT scanner to accurately evaluate dose. METHODS: In this work, we investigated key dosimetric aspects (dose response, energy and dose rate dependence) and stability of these radiochromic gels initiated in preliminary works (Huet et al., 2017; Colnot et al., 2017) using spectrophotometric measurements. Moreover, by mean of optical CT scanning (Vista™), their performances to measure relative depth dose (PDD) and cross profiles were analysed. RESULTS: TruView™ and ClearView™ present a linear dose response up to 20 Gy and up to 80 Gy respectively, independent of both photon beam energy (4-18 MV) and dose rate (up to 9.9 Gy/min) (Huet et al., 2017; Colnot et al., 2017). ClearView™ response proves to be stable for a week post-irradiation and uniform within the batch whereas TruView™ presents an unstable but uniform response. Optical CT scanning generates errors due to stray light that need to be corrected in order to use these gels; ClearView™ scanning particularly requires important precautions. After corrections, those gels used in combination with the Vista™ scanner show promising spatial and dosimetric precision (dose difference <5%). Finally, TruView™ is reusable and presents excellent reproducible response (maximum 3% difference) and the ClearView™ dosimeter presents good spatial stability (0.5% difference after 6 days). CONCLUSION: This study provides important knowledge about two gel dosimeters presenting interesting dosimetric properties. A study is ongoing to benchmark those promising candidates for clinical dose verification.

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Dental prostheses made of high density material contribute to modify dose distribution in head and neck cancer treatment. Our objective is to quantify dose perturbation due to high density inhomogeneity with experimental measurements and Monte Carlo simulations. Firstly, measurements were carried in a phantom representing a human jaw with thermoluminescent detectors (GR200A) and EBT2 Gafchromic films in the vicinity of three samples: a healthy tooth, a tooth with amalgam and a Ni-Cr crown, irradiated in clinical configuration. Secondly, Monte Carlo simulations (BEAMnrc code) were assessed in an identical configuration. Experimental measurements and simulation results confirm the two well-known phenomena: firstly the passage from a low density medium to a high density medium induces backscattered electrons causing a dose increase at the interface, and secondly, the passage from a high density medium to a low density medium creates a dose decrease near the interface. So, the results show a 1.4% and 23.8% backscatter dose rise and attenuation after sample of 26.7% and 10.9% respectively for tooth with amalgam and crown compared to the healthy tooth. Although a tooth with amalgam has a density of about 12-13, the changes generated are not significant. However, the results for crown (density of 8) are very significant and the discordance observed may be due to calculation point size difference 0.8 mm and 0.25 mm respectively for TLD and Monte Carlo. The use of Monte Carlo simulations and experimental measurements provides objective evidence to evaluate treatment planning system results with metal dental prostheses.

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An LED based illumination device for mechanistic studies on photochemical reactions by means of NMR spectroscopy is presented. The LEDs are directly switched by the NMR spectrometer with the help of a one-stage electronic circuit. This allows for continuous or alternatively pulsed operation of the LEDs. Continuous operation provides direct comparability with conditions in synthetic chemistry, in pulsed operation the short time light power can be enhanced ninefold. The LEDs are efficiently coupled to a 1000 µm core optical fiber guiding the light into the spectrometer by simply bringing it in close contact to the fiber. The tip of the fiber is roughened by sandblasting and thus emits light in a uniform and efficient way over the full length of the receiver coil. The combination of these techniques tremendously increases the amount of light brought into the NMR sample and makes LEDs an easy, versatile and handy light source for the in situ illumination of NMR samples allowing even for single millisecond time resolved Photo-CIDNP spectroscopy.

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PURPOSE: A way to improve the accuracy of lung radiotherapy for a patient is to get a better understanding of its lung motion. Indeed, thanks to this knowledge it becomes possible to follow the displacements of the clinical target volume (CTV) induced by the lung breathing. This paper presents a feasibility study of an original method to simulate the positions of points in patient's lung at all breathing phases. PATIENTS AND METHODS: This method, based on an artificial neural network, allowed learning the lung motion on real cases and then to simulate it for new patients for which only the beginning and the end breathing data are known. The neural network learning set is made up of more than 600 points. These points, shared out on three patients and gathered on a specific lung area, were plotted by a MD. RESULTS: The first results are promising: an average accuracy of 1mm is obtained for a spatial resolution of 1 × 1 × 2.5mm(3). CONCLUSION: We have demonstrated that it is possible to simulate lung motion with accuracy using an artificial neural network. As future work we plan to improve the accuracy of our method with the addition of new patient data and a coverage of the whole lungs.

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We present herein the first indications for dimeric structures in cometal-free asymmetric conjugate addition reactions of dialkylzinc reagents with aldehydes. These are revealed by nonlinear effect (NLE) studies. A monomer-dimer equilibrium can be assumed which explains the increase of the ee value in the product over time. Also, DOSY NMR spectroscopic measurements indicate the existence of the catalyst as [LZnEt](n) complexes in solution. Additionally, the first X-ray structure of a zinc complex with a [2.2]paracyclophane ligand was determined. The structures of the zinc complexes are supported by DFT calculations of monomeric and dimeric species.

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Breathing-adapted techniques in external radiotherapy lead to the improvement of the taken into account of the tumour motion during the patient treatment. Indeed, this motion involves dosimetric uncertainties, in particular during a dynamic treatment (intensity-modulated radiation therapy, dynamic wedge...). As tumoral movement is complex and is carried out in various directions of space, a dynamic platform moving in one or two plans was conceived. This article approaches the technical aspects of design and functioning of this prototype. A study of the dosimetric effects of the respiratory movement on one and two plans during a dynamic treatment without gating will be presented. Films were irradiated while varying the rates with wedged fields at various speeds. The penumbra of beams were compared with the static case and appeared twice broader in the majority of the cases. The results highlighted the contributions of the longitudinal and the axial components of the motion on the form of the dose distribution. These results were completed with gamma index measurements to determine an internal margin. Moreover, this platform proves to be a promising tool for breathing-adapted treatment, in particularly to test the synchronisation of RPM system in fluoroscopic mode in board imaging system.

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As the population become aged, many patients with hip prosthesis are treated for a pelvic cancer. The recommended ballistic must avoid to pass in the prosthesis, but sometimes it is inevitable. So it is essential to quantify with accuracy the dose modifications linked to the presence of metallic implant. The aim of this study is to analyze by Monte Carlo method these modifications in simple and complex models (anthropomorphic phantom) which take into account the geometry and the composition of the prosthesis and its coatings. Then, this methodology was used to study the behaviour of a treatment planning system in theses extreme conditions.

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The main goal of external beam radiotherapy is the treatment of tumours, while sparing, as much as possible, surrounding healthy tissues. In order to master and optimize the dose distribution within the patient, dosimetric planning has to be carried out. Thus, for determining the most accurate dose distribution during treatment planning, a compromise must be found between the precision and the speed of calculation. Current techniques, using analytic methods, models and databases, are rapid but lack precision. Enhanced precision can be achieved by using calculation codes based, for example, on Monte Carlo methods. However, in spite of all efforts to optimize speed (methods and computer improvements), Monte Carlo based methods remain painfully slow. A newer way to handle all of these problems is to use a new approach in dosimetric calculation by employing neural networks. Neural networks (Wu and Zhu 2000 Phys. Med. Biol. 45 913-22) provide the advantages of those various approaches while avoiding their main inconveniences, i.e., time-consumption calculations. This permits us to obtain quick and accurate results during clinical treatment planning. Currently, results obtained for a single depth-dose calculation using a Monte Carlo based code (such as BEAM (Rogers et al 2003 NRCC Report PIRS-0509(A) rev G)) require hours of computing. By contrast, the practical use of neural networks (Mathieu et al 2003 Proceedings Journees Scientifiques Francophones, SFRP) provides almost instant results and quite low errors (less than 2%) for a two-dimensional dosimetric map.

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The gcpE and lytB gene products control the terminal steps of isoprenoid biosynthesis via the 2-C-methyl-D-erythritol 4-phosphate pathway in Escherichia coli. In lytB-deficient mutants, a highly immunogenic compound accumulates significantly, compared to wild-type E. coli, but is apparently absent in gcpE-deficient mutants. Here, this compound was purified from E. coli DeltalytB mutants by preparative anion exchange chromatography, and identified by mass spectrometry, (1)H, (13)C and (31)P NMR spectroscopy, and NOESY analysis as (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate (HMB-PP). HMB-PP is 10(4) times more potent in activating human Vgamma9/Vdelta2 T cells than isopentenyl pyrophosphate.

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H-Li distances and (1)H-(1)H dipolar interactions in Me(2)CuLiLiCN and Me(2)CuLi in diethyl ether (Et(2)O), obtained by NMR spectroscopy, were used to gain structural information about the contact ion pair of the salt-containing organocuprate Me(2)CuLiLiCN in this solvent. The H-Li distances of Me(2)CuLiLiCN and Me(2)CuLi in Et(2)O, resulting from the initial buildup rates in conjunction with the motional correlation times, are almost identical, indicating a similar homodimeric core structure [Me(2)CuLi](2) for both samples. However, the H-Li distances obtained for Me(2)CuLiLiCN do not rigorously exclude a heterodimeric structure [Me(2)CuLiLiCN] as proposed by ab initio calculations. Therefore, (1)H-(1)H dipolar interactions were investigated by SYM-BREAK-NOE/ROE-HSQC experiments, which allow for the observation of NOEs between equivalent protons. Since these experiments showed similar (1)H-(1)H dipolar interactions of Me(2)CuLiLiCN and Me(2)CuLi, we propose that for Me(2)CuLiLiCN a homodimeric core structure [Me(2)CuLi](2) indeed is predominant in Et(2)O.

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The basidiolipids of six mushroom species, i.e. the basidiomycetes Amanita virosa (engl., death cup), Calvatia exipuliformis (engl., puffball), Cantharellus cibarius (engl., chanterelle), Leccinum scabrum (engl., red birch boletus), Lentinus edodes (jap., Shiitake), and Pleurotus ostreatus (engl., oystermushroom), were isolated, and their chemical structures investigated. All glycolipids are structurally related to those of the Agaricales (engl., field mushroom). They are glycoinositolphosphosphingolipids, their ceramide moiety consisting of t18:0-trihydroxysphinganine and an alpha-hydroxy long-chain fatty acid. In contrast to a previous study [Jennemann, R., Bauer, B.L., Bertalanffy, H., Geyer, R., Gschwind, R.M., Selmer, T. & Wiegandt, H. (1999) Eur. J. Biochem. 259, 331--338], the glycoside anomery of the hexose (mannose) connected to the inositol of all investigated basidiomycete glycolipids, including the basidiolipids of Agaricus bisporus, was determined unequivocally to be alpha. Therefore, the root structure of all basidiolipids consists of alpha-DManp-2Ins1-[PO(4)]-Cer. In addition, for some mushroom species, the occurrence of an inositol substitution position variant, alpha-Manp-4Ins1-[PO(40]-Cer, is shown. The carbohydrate of chanterelle basidiolipids consists solely of mannose, i.e. Cc1, Man alpha-3 or -6Man alpha; Cc2, Man alpha-3(Man alpha-6)Man alpha-. All other species investigated show extension of the alpha-mannoside in the 6-position by beta-galactoside, which, in some instances, is alpha-fucosylated in 2-position (Fuc alpha-2)Gal beta-6Man alpha-. Further sugar chain elongation at the beta-galactoside may be in 3- and/or 6-position by alpha-galactoside, e.g. Ce4, Po2, Gal alpha-3-(Gal alpha-6)(Fuc alpha-2)Gal beta-6Man alpha-, whereas A. virosa, Av-3, has a more complex, highly alpha-fucosylated terminus, Gal alpha-3 (Fuc alpha-2)(Fuc alpha-6)Gal alpha-2(Gal alpha-3)Gal beta-6Man alpha-. L. edodes basidiolipids show further elongation by alpha-mannoside, e.g. Le3, Man alpha-2Man alpha-6Gal alpha-3(Fuc alpha-2)Gal beta-6Man alpha-, C. exipuliformis glycolipid by alpha-glucoside, i.e. Ce3, Glc alpha-6Gal beta-6Man alpha-. Basidiolipid Ls1 from L. scabrum, notably, has a 3-alpha-mannosylated alpha-fucose, i.e. Gal alpha-6(Man alpha-3Fuc alpha-2)Gal alpha-6Gal beta-6Man alpha-. In conclusion, basidiolipids, though identical in their ceramide constitution, display wide and systematic mushroom species dependent variabilities of their chemical structures.

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A new multi-quantum version of the HBHA(CBCACO)NH experiment for partially deuterated protein samples is presented. The method is based on the significant reduction of the proton and carbon relaxation rates due to multi-quantum delays in highly deuterated proteins recently published by our group. The introduction of a multi-quantum period in the coherence transfer pathway of the HBHA(CBCACO)NH experiment yields a dramatic increase of sensitivity-on average 46% with a 75% deuterated sample of the homodimeric 31 kDa E. coli IIAMan domain. Additional resolution in the proton dimension can be achieved by a double time shared approach keeping the 1H single-quantum period at a minimum.

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From the edible mushroom, the basidiomycetes Agaricus bisporus and Agaricus campestris, a novel carbohydrate-homologous series of four glyco-inositol-phospho-sphingolipids, designated basidiolipids, was isolated and the constituents purified. The chemical structures of the basidiolipids were elucidated to be: Manpbeta1-2inositol1-phospho-ceramide, Galpalpha-6[Fucpalpha-2]Galpbeta-6Manpbeta-2i nositol1-phospho-ceramide, Galpalpha-6Galpalpha-6[Fucpalpha-2]Galpbeta- 6Manpbeta-2inositol1-phospho-ceramide and Galpalpha-6Galpalpha-6Galpalpha-6[Fucpalpha-2] Galpbeta-6Manpbeta-2ino sitol1-phospho-ceramide. All four glycolipids contained a ceramide which was composed of phytosphingosine and predominantly alpha-hydroxy-behenic and alpha-hydroxy-lignoceric acid.

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Renal cell carcinomas (RCCs) with sarcomatoid transformation show the most malignant behaviour of all renal carcinoma types. In this study, comparative genomic hybridization was used to screen for losses and gains of DNA sequences along all chromosome arms in 12 sarcomatoid (S) RCCs. On average, there were 8.6 aberrations per tumour. DNA sequence losses (5.2 +/- 4.4) were slightly more frequent than gains (3.4 +/- 2.6). DNA gains most often involved chromosomes 17 (33 per cent), 7, and 8q (25 per cent each). High-level co-amplification involving 11q22-23 and 7p21-22 in one SRCC was not present in adjacent non-sarcomatous tumour areas, raising the possibility of oncogene involvement at these loci for sarcomatoid transformation. DNA losses were most prevalent at 13q (75 per cent) and 4q (50 per cent), suggesting that inactivation of tumour suppressor genes at chromosomes 13q and 4q may be linked to sarcomatoid growth of RCC. It is concluded that SRCCs are genetically highly complex. Chromosomes 13q, 4q, 7p21-22, and 11q22-23 may carry genes with relevance for sarcomatoid growth in RCC.

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The NusB protein of Escherichia coli is involved in the regulation of rRNA biosynthesis by transcriptional antitermination. In cooperation with several other proteins, it binds to a dodecamer motif designated rrn boxA on the nascent rRNA. The antitermination proteins of E.coli are recruited in the replication cycle of bacteriophage lambda, where they play an important role in switching from the lysogenic to the lytic cycle. Multidimensional heteronuclear NMR experiments were performed with recombinant NusB protein labelled with 13C, 15N and 2H. The three-dimensional structure of the protein was solved from 1926 NMR-derived distances and 80 torsion angle restraints. The protein folds into an alpha/alpha-helical topology consisting of six helices; the arginine-rich N-terminus appears to be disordered. Complexation of the protein with an RNA dodecamer equivalent to the rrn boxA site results in chemical shift changes of numerous amide signals. The overall packing of the protein appears to be conserved, but the flexible N-terminus adopts a more rigid structure upon RNA binding, indicating that the N-terminus functions as an arginine-rich RNA-binding motif (ARM).

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The sequential assignment of backbone resonances is the first step in the structure determination of proteins by heteronuclear NMR. For larger proteins, an assignment strategy based on proton side-chain information is no longer suitable for the use in an automated procedure. Our program PASTA (Protein ASsignment by Threshold Accepting) is therefore designed to partially or fully automate the sequential assignment of proteins, based on the analysis of NMR backbone resonances plus C beta information. In order to overcome the problems caused by peak overlap and missing signals in an automated assignment process, PASTA uses threshold accepting, a combinatorial optimization strategy, which is superior to simulated annealing due to generally faster convergence and better solutions. The reliability of this algorithm is shown by reproducing the complete sequential backbone assignment of several proteins from published NMR data. The robustness of the algorithm against misassigned signals, noise, spectral overlap and missing peaks is shown by repeating the assignment with reduced sequential information and increased chemical shift tolerances. The performance of the program on real data is finally demonstrated with automatically picked peak lists of human nonpancreatic synovial phospholipase A2, a protein with 124 residues.

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The introduction of deuterated and partially deuterated protein samples has greatly facilitated the 13C assignment of larger proteins. Here we present a new version of the HC(CO)NH-TOCSY experiment, the ed-H(CCO)NH-TOCSY experiment for partially deuterated samples, introducing a multi-quantum proton evolution period. This approach removes the main relaxation source (the dipolar coupling to the directly bound 13C spin) and leads to a significant reduction of the proton and carbon relaxation rates. Thus, the indirect proton dimension can be acquired with high resolution, combined with a phase labeling of the proton resonances according to the C-C spin system topology. This editing scheme, independent of the CHn multiplicity, allows to distinguish between proton side-chain positions occurring within a narrow chemical shift range. Therefore this new experiment facilitates the assignment of the proton chemical shifts of partially deuterated samples even of high molecular weights, as demonstrated on a 31 kDa protein.

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The product of the nusB gene of Escherichia coli modulates the efficiency of transcription termination at nut (N utilization) sites of various bacterial and bacteriophage lambda genes. Similar control mechanisms operate in eukaryotic viruses (e.g. human immunodeficiency virus). A recombinant strain of E. coli producing relatively large amounts of NusB protein (about 10% of cell protein) was constructed. The protein could be purified with high yield by anion-exchange chromatography followed by gel-permeation chromatography. The protein is a monomer of 15.6 kDa as shown by analytical ultracentrifugation. Structural studies were performed using protein samples labelled with 15N, 13C and 2H in various combinations. Heteronuclear three-dimensional triple-resonance NMR experiments combined with a semi-automatic assignment procedure yielded the sequential assignment of the 1H, 13C and 15N backbone resonances. Based on experimentally derived scalar couplings, chemical-shift values, amide-exchange data, and a semiquantitative interpretation of NOE data, the secondary structure of NusB has classified as alpha helical, comprising seven alpha helices.

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