Utilization of tmRNA sequences for bacterial identification

In recent years, molecular approaches based on nucleotide sequences of ribosomal RNA (rRNA) have become widely used tools for identification of bacteria [1-4]. The high degree of evolutionary conservation makes 16S and 23S rRNA molecules very suitable for phylogenetic studies above the species level [3-5]. More than 16,000 sequences of 16S rRNA are presently available in public databases [4,6]. The 16S rRNA sequences are commonly used to design fluorescently labeled oligonucleotide probes. Fluorescence in situ hybridization (FISH) with these probes followed by observation with epifluorescence microscopy allows the identification of a specific microorganism in a mixture with other bacteria [2-4]. By shifting probe target sites from conservative to increasingly variable regions of rRNA, it is possible to adjust the probe specificity from kingdom to species level. Nevertheless, 16S rRNA sequences of closely related strains, subspecies, or even of different species are often identical and therefore can not be used as differentiating markers [3]. Another restriction concerns the accessibility of target sites to the probe in FISH experiments. The presence of secondary structures, or protection of rRNA segments by ribosomal proteins in fixed cells can limit the choice of variable regions as in situ targets for oligonucleotide probes [7,8]. One way to overcome the limitations of in situ identification of bacteria is to use molecules other than rRNA for phylogenetic identification of bacteria, for which nucleotide sequences would be sufficiently divergent to design species specific probes, and which would be more accessible to oligonucleotide probes. For this purpose we investigated the possibility of using tmRNA (also known as 10Sa RNA; [9-11]). This molecule was discovered in E. coli and described as small stable RNA, present at ~1,000 copies per cell [9,11]. The high copy number is an important prerequisite for FISH, which works best with naturally amplified target molecules. In E. coli, tmRNA is encoded by the ssrA gene, is 363 nucleotides long and has properties of tRNA and mRNA [12,13]. tmRNA was shown to be involved in the degradation of truncated proteins: the tmRNA associates with ribosomes stalled on mRNAs lacking stop codons, finally resulting in the addition of a C-terminal peptide tag to the truncated protein. The peptide tag directs the abnormal protein to proteolysis [14,15]. 165 tmRNA sequences have so far (August 2001; The tmRNA Website: http://www.indiana.edu/~tmrna/) been determined [16,17]. The tmRNA is likely to be present in all bacteria and has also been found in algae chloroplasts, the cyanelle of Cyanophora paradoxa and the mitochondrion of the flagellate Reclinomonas americana[10,17,18]

Determination of fragmentation functions and their uncertainties from e+ + e- -> h + X data

Fragmentation functions are determined for pions, kaons, and nucleons by a global analysis of charged-hadron production data in electron-positron annihilation. The optimum functions are obtained in both leading order (LO) and next-to-leading order (NLO) of alpha_s. It is important that uncertainties of the fragmentation functions are estimated in this work by the Hessian method. We found that the uncertainties are large at small Q^2 and that they are generally reduced in the NLO in comparison with the LO ones. We supply a code for calculating the fragmentation functions and their uncertainties for the pions, kaons, and nucleons at given z and Q^2.Comment: 4 pages, LaTeX, 5 eps files, to be published in AIP proceedings of the 17th International Spin Physics Symposium (SPIN2006), Oct. 2-7, 2006, Kyoto, Japa

Photon - Jet Correlations and Constraints on Fragmentation Functions

We study the production of a large-pT photon in association with a jet in proton-proton collisions. We examine the sensitivity of the jet rapidity distribution to the gluon distribution function in the proton. We then assess the sensitivity of various photon + jet correlation observables to the photon fragmentation functions. We argue that RHIC data on photon-jet correlations can be used to constrain the photon fragmentation functions in a region which was barely accessible in LEP experiments.Comment: 23 pages, 9 figure

Retrospective analysis of the impact of respiratory motion in treatment margins for frameless lung SBRT based on respiratory-correlated CBCT data-sets.

To investigate the impact of respiratory motion in the treatment margins for lung SBRT frameless treatments and to validate our treatment margins using 4D CBCT data analysis. Two hundred and twenty nine fractions with early stage NSCLC were retrospectively analyzed. All patients were treated in frameless and free breathing conditions. The treatment margins were calculated according to van Herk equation in Mid-Ventilation. For each fraction, three 4D CBCT scans, pre- and postcorrection, and posttreatment, were acquired to assess target baseline shift, target localization accuracy and intra-fraction motion errors. A bootstrap analysis was performed to assess the minimum number of patients required to define treatment margins. The retrospectively calculated target-baseline shift, target localization accuracy and intra-fraction motion errors agreed with the literature. The best tailored margins to our cohort of patients were retrospectively computed and resulted in agreement with already published data. The bootstrap analysis showed that fifteen patients were enough to assess treatment margins. The treatment margins applied to our patient's cohort resulted in good agreement with the retrospectively calculated margins based on 4D CBCT data. Moreover, the bootstrap analysis revealed to be a promising method to verify the reliability of the applied treatment margins for safe lung SBRT delivery

Measures Matter: Scales for Adaptation, Cultural Distance, and Acculturation Orientation Revisited

Building upon existing measures, four new brief acculturation scales are presented, measuring sociocultural adaptation, psychological adaptation, perceived cultural distance, and acculturation orientation. Following good scale reliability in initial samples, the English scales were translated into nine different languages (Chinese, French, German, Italian, Japanese, Portuguese, Spanish, Thai, and Turkish). The translated scales were administered to a large sample of sojourners (N = 1,929), demonstrating good reliability and adequate structural equivalence across languages. In line with existing theory, sociocultural adaptation and psychological adaptation were positively correlated, and showed a negative association with perceived cultural distance. General measures of well-being were correlated with adaptation and distance, with better adaptation relating to higher well-being, and more distance relating to lower well-being. Acculturation orientation toward the home and host culture were measured separately and a weak negative correlation was found between the two, supporting their independence. Arguing against dichotomization, these subscales were analyzed as continuous variables. Regression analysis showed sojourners to be better adapted, if they were oriented more toward the host culture and less toward the home culture. These new scales are proposed as alternatives to existing measures

Pour en finir avec le Bronze final ? Les haches à douille de type armoricain en France

A discussion about socket armorican bronze axes datation. They are from Ha D period (VII th & VIt h century B.C.)Révision de la datation des haches à douille de type armoricain, au seul Hallstatt D (VIIe-VIe s; av. J.-C.

Clinical implementation of deep learning-based automated left breast simultaneous integrated boost radiotherapy treatment planning.

Automation in radiotherapy treatment planning aims to improve both the quality and the efficiency of the process. The aim of this study was to report on a clinical implementation of a Deep Learning (DL) auto-planning model for left-sided breast cancer. The DL model was developed for left-sided breast simultaneous integrated boost treatments under deep-inspiration breath-hold. Eighty manual dose distributions were revised and used for training. Ten patients were used for model validation. The model was then used to design 17 clinical auto-plans. Manual and auto-plans were scored on a list of clinical goals for both targets and organs-at-risk (OARs). For validation, predicted and mimicked dose (PD and MD, respectively) percent error (PE) was calculated with respect to manual dose. Clinical and validation cohorts were compared in terms of MD only. Median values of both PD and MD validation plans fulfilled the evaluation criteria. PE was < 1% for targets for both PD and MD. PD was well aligned to manual dose while MD left lung mean dose was significantly less (median:5.1 Gy vs 6.1 Gy). The left-anterior-descending artery maximum dose was found out of requirements (median values:+5.9 Gy and + 2.9 Gy, for PD and MD respectively) in three validation cases, while it was reduced for clinical cases (median:-1.9 Gy). No other clinically significant differences were observed between clinical and validation cohorts. Small OAR differences observed during the model validation were not found clinically relevant. The clinical implementation outcomes confirmed the robustness of the model

Commissioning of an ultra-high dose rate pulsed electron beam medical LINAC for FLASH RT preclinical animal experiments and future clinical human protocols.

To present the acceptance and the commissioning, to define the reference dose, and to prepare the reference data for a quality assessment (QA) program of an ultra-high dose rate (UHDR) electron device in order to validate it for preclinical animal FLASH radiotherapy (FLASH RT) experiments and for FLASH RT clinical human protocols. The Mobetron <sup>®</sup> device was evaluated with electron beams of 9 MeV in conventional (CONV) mode and of 6 and 9 MeV in UHDR mode (nominal energy). The acceptance was performed according to the acceptance protocol of the company. The commissioning consisted of determining the short- and long-term stability of the device, the measurement of percent depth dose curves (PDDs) and profiles at two different positions (with two different dose per pulse regimen) and for different collimator sizes, and the evaluation of the variability of these parameters when changing the pulse width and pulse repetition frequency. Measurements were performed using a redundant and validated dosimetric strategy with alanine and radiochromic films, as well as Advanced Markus ionization chamber for some measurements. The acceptance tests were all within the tolerances of the company's acceptance protocol. The linearity with pulse width was within 1.5% in all cases. The pulse repetition frequency did not affect the delivered dose more than 2% in all cases but 90 Hz, for which the larger difference was 3.8%. The reference dosimetry showed a good agreement within the alanine and films with variations of 2.2% or less. The short-term (resp. long-term) stability was less than 1.0% (resp. 1.8%) and was the same in both CONV and UHDR modes. PDDs, profiles, and reference dosimetry were measured at two positions, providing data for two specific dose rates (about 9 Gy/pulse and 3 Gy/pulse). Maximal beam size was 4 and 6 cm at 90% isodose in the two positions tested. There was no difference between CONV and UHDR mode in the beam characteristics tested. The device is commissioned for FLASH RT preclinical biological experiments as well as FLASH RT clinical human protocols

A Next-to-Leading-Order Study of Dihadron Production

The production of pairs of hadrons in hadronic collisions is studied using a next-to-leading-order Monte Carlo program based on the phase space slicing technique. Up-to-date fragmentation functions based on fits to LEP data are employed, together with several versions of current parton distribution functions. Good agreement is found with data for the dihadron mass distribution. A comparison is also made with data for the dihadron angular distribution. The scale dependence of the predictions and the dependence on the choices made for the fragmentation and parton distribution functions are also presented. The good agreement between theory and experiment is contrasted to the case for single $\pi^0$ production where significant deviations between theory and experiment have been observed.Comment: 22 pages, 15 figures; 3 references added, one figure modified for clarit