Impact of use of optical surface imaging on initial patient setup for stereotactic body radiotherapy treatments

Purpose To evaluate the effectiveness of surface image guidance (SG) for pre‐imaging setup of stereotactic body radiotherapy (SBRT) patients, and to investigate the impact of SG reference surface selection on this process. Methods and materials 284 SBRT fractions (SG‐SBRT = 113, non‐SG‐SBRT = 171) were retrospectively evaluated. Differences between initial (pre‐imaging) and treatment couch positions were extracted from the record‐and‐verify system and compared for the two groups. Rotational setup discrepancies were also computed. The utility of orthogonal kVs in reducing CBCT shifts in the SG‐SBRT/non‐SG‐SBRT groups was also calculated. Additionally, the number of CBCTs acquired for setup was recorded and the average for each cohort was compared. These data served to evaluate the effectiveness of surface imaging in pre‐imaging patient positioning and its potential impact on the necessity of including orthogonal kVs for setup. Since reference surface selection can affect SG setup, daily surface reproducibility was estimated by comparing camera‐acquired surface references (VRT surface) at each fraction to the external surface of the planning CT (DICOM surface) and to the VRT surface from the previous fraction. Results The reduction in all initial‐to‐treatment translation/rotation differences when using SG‐SBRT was statistically significant (Rank‐Sum test, α = 0.05). Orthogonal kV imaging kept CBCT shifts below reimaging thresholds in 19%/51% of fractions for SG‐SBRT/non‐SG‐SBRT cohorts. Differences in average number of CBCTs acquired were not statistically significant. The reference surface study found no statistically significant differences between the use of DICOM or VRT surfaces. Conclusions SG‐SBRT improved pre‐imaging treatment setup compared to in‐room laser localization alone. It decreased the necessity of orthogonal kV imaging prior to CBCT but did not affect the average number of CBCTs acquired for setup. The selection of reference surface did not have a significant impact on initial patient positioning

Water seepage beneath dams on soluble evaporite deposits: a laboratory and field study (Caspe Dam, Spain)

The paper presents analytical methods and results for assessing the variation in the concentration of sulphate (and other ions) over space and time in groundwater flowing through a soluble evaporite terrain beneath a dam. The influence of effective porosity, groundwater flow velocity and the specific rate of dissolution (K′) are considered. The theoretical analysis was tested in a scale model simulating a dam constructed on heavily karstified bedrock. A simple and useful method for assessing how much material is lost through dissolution and how the rate of dissolution changes over time is considered in the context of the Caspe Dam, Spain

Glycoprotein Ib activation by thrombin stimulates the energy metabolism in human platelets

<div><p>Thrombin-induced platelet activation requires substantial amounts of ATP. However, the specific contribution of each ATP-generating pathway <i>i</i>.<i>e</i>., oxidative phosphorylation (OxPhos) versus glycolysis and the biochemical mechanisms involved in the thrombin-induced activation of energy metabolism remain unclear. Here we report an integral analysis on the role of both energy pathways in human platelets activated by several agonists, and the signal transducing mechanisms associated with such activation. We found that thrombin, Trap-6, arachidonic acid, collagen, A23187, epinephrine and ADP significantly increased glycolytic flux (3–38 times <i>vs</i>. non-activated platelets) whereas ristocetin was ineffective. OxPhos (33 times) and mitochondrial transmembrane potential (88%) were increased only by thrombin. OxPhos was the main source of ATP in thrombin-activated platelets, whereas in platelets activated by any of the other agonists, glycolysis was the principal ATP supplier. In order to establish the biochemical mechanisms involved in the thrombin-induced OxPhos activation in platelets, several signaling pathways associated with mitochondrial activation were analyzed. Wortmannin and LY294002 (PI3K/Akt pathway inhibitors), ristocetin and heparin (GPIb inhibitors) as well as resveratrol, ATP (calcium-release inhibitors) and PP1 (Tyr-phosphorylation inhibitor) prevented the thrombin-induced platelet activation. These results suggest that thrombin activates OxPhos and glycolysis through GPIb-dependent signaling involving PI3K and Akt activation, calcium mobilization and protein phosphorylation.</p></div

Influence of environmental parameters on movements and habitat utilization of humpback whales (Megaptera novaeangliae) in the Madagascar breeding ground

© The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Royal Society Open Science 3 (2016): 160616, doi:10.1098/rsos.160616.Assessing the movement patterns and key habitat features of breeding humpback whales is a prerequisite for the conservation management of this philopatric species. To investigate the interactions between humpback whale movements and environmental conditions off Madagascar, we deployed 25 satellite tags in the northeast and southwest coast of Madagascar. For each recorded position, we collated estimates of environmental variables and computed two behavioural metrics: behavioural state of ‘transiting’ (consistent/directional) versus ‘localized’ (variable/non-directional), and active swimming speed (i.e. speed relative to the current). On coastal habitats (i.e. bathymetry < 200 m and in adjacent areas), females showed localized behaviour in deep waters (191 ± 20 m) and at large distances (14 ± 0.6 km) from shore, suggesting that their breeding habitat extends beyond the shallowest waters available close to the coastline. Males' active swimming speed decreased in shallow waters, but environmental parameters did not influence their likelihood to exhibit localized movements, which was probably dominated by social factors instead. In oceanic habitats, both males and females showed localized behaviours in shallow waters and favoured high chlorophyll-a concentrations. Active swimming speed accounts for a large proportion of observed movement speed; however, breeding humpback whales probably exploit prevailing ocean currents to maximize displacement. This study provides evidence that coastal areas, generally subject to strong human pressure, remain the core habitat of humpback whales off Madagascar. Our results expand the knowledge of humpback whale habitat use in oceanic habitat and response to variability of environmental factors such as oceanic current and chlorophyll level.Funding was provided by Total Foundation to NeuroPSI, and by individuals and foundations to the WCS Ocean Giants Program

Benthic Nitrogen Cycling Traversing the Peruvian Oxygen Minimum Zone

Benthic nitrogen (N) cycling was investigated at six stations along a transect traversing the Peruvian oxygen minimum zone (OMZ) at 11 °S. An extensive dataset including porewater concentration profiles and in situ benthic fluxes of nitrate (NO3–), nitrite (NO2–) and ammonium (NH4+) was used to constrain a 1–D reaction–transport model designed to simulate and interpret the measured data at each station. Simulated rates of nitrification, denitrification, anammox and dissimilatory nitrate reduction to ammonium (DNRA) by filamentous large sulfur bacteria (e.g. Beggiatoa and Thioploca) were highly variable throughout the OMZ yet clear trends were discernible. On the shelf and upper slope (80 – 260 m water depth) where extensive areas of bacterial mats were present, DNRA dominated total N turnover (less-than-or-equals, slant 2.9 mmol N m–2 d–1) and accounted for greater-or-equal, slanted 65 % of NO3– + NO2– uptake by the sediments from the bottom water. Nonetheless, these sediments did not represent a major sink for dissolved inorganic nitrogen (DIN = NO3– + NO2– + NH4+) since DNRA reduces NO3– and, potentially NO2–, to NH4+. Consequently, the shelf and upper slope sediments were recycling sites for DIN due to relatively low rates of denitrification and high rates of ammonium release from DNRA and ammonification of organic matter. This finding contrasts with the current opinion that sediments underlying OMZs are a strong sink for DIN. Only at greater water depths (300 – 1000 m) did the sediments become a net sink for DIN. Here, denitrification was the major process (less-than-or-equals, slant 2 mmol N m–2 d–1) and removed 55 – 73 % of NO3– and NO2– taken up by the sediments, with DNRA and anammox accounting for the remaining fraction. Anammox was of minor importance on the shelf and upper slope yet contributed up to 62 % to total N2 production at the 1000 m station. The results indicate that the partitioning of oxidized N (NO3–, NO2–) into DNRA or denitrification is a key factor determining the role of marine sediments as DIN sinks or recycling sites. Consequently, high measured benthic uptake rates of oxidized N within OMZs do not necessarily indicate a loss of fixed N from the marine environment

Use of AFLP and RAPD molecular genetic markers and cytogenetic analysis to explore relationships among taxa of the Patagonian Bromus setifolius complex

Bromus setifolius var. pictus (Hook) Skottsb., B. setifolius var. setifolius Presl. and B.setifolius var. brevifolius Ness are three native Patagonian taxa in the section Pnigma Dumort of the genus Bromus L. AFLP and RAPD analysis, in conjunction with genetic distance measurements and statistical techniques, revealed variation within this group and indicated that B. setifolius var. brevifolius was closely related to B. setifolius var. pictus, with both taxa being more distantly related to B. setifolius var. setifolius. Cytogenetic analysis confirmed the chromosomal number of B. setifolius var. pictus (2n = 70) and B. setifolius var. setifolius (2n = 28) and showed for the first time that B. setifolius var. brevifolius had 2n = 70. The combination of molecular genetic and cytogenetic evidence supported a species status for two of the three taxa and suggested hypotheses for the evolutionary origin of these complex taxa. Species status was also indicated for B. setifolius var. setifolius. Based on these findings, we suggest that B. setifolius var. pictus be referred to as B. pictus Hook var. pictus, and B. setifolius var brevifolius as B. pictus Hook var brevifolius. The correlation between AFLP diversity and variation in ecological parameters suggested that this marker system could be used to assess breeding progress and to monitor the domestication of Patagonian Bromus species for agronomic use

New Peptides Isolated from Lyngbya Species: A Review

Cyanobacteria of the genus Lyngbya have proven to be prodigious producers of secondary metabolites. Many of these compounds are bioactive and show potential for therapeutic use. This review covers peptides and hybrid polyketide-non-ribosomal peptides isolated from Lyngbya species. The structures and bioactivities of 50 Lyngbya peptides which were reported since 2007 are presented

Multicentre study on the reproducibility of MALDI-TOF MS for nontuberculous mycobacteria identification

The ability of MALDI-TOF for the identification of nontuberculous mycobacteria (NTM) has improved recently thanks to updated databases and optimized protein extraction procedures. Few multicentre studies on the reproducibility of MALDI-TOF have been performed so far, none on mycobacteria. The aim of this study was to evaluate the reproducibility of MALDI-TOF for the identification of NTM in 15 laboratories in 9 European countries. A total of 98 NTM clinical isolates were grown on Lowenstein-Jensen. Biomass was collected in tubes with water and ethanol, anonymized and sent out to the 15 participating laboratories. Isolates were identified using MALDI Biotyper (Bruker Daltonics). Up to 1330 MALDI-TOF identifications were collected in the study. A score >= 1.6 was obtained for 100% of isolates in 5 laboratories (68.2-98.6% in the other). Species-level identification provided by MALDI-TOF was 100% correct in 8 centres and 100% correct to complex-level in 12 laboratories. In most cases, the misidentifications obtained were associated with closely related species. The variability observed for a few isolates could be due to variations in the protein extraction procedure or to MALDI-TOF system status in each centre. In conclusion, MALDI-TOF showed to be a highly reproducible method and suitable for its implementation for NTM identification

Comparative analysis of non-autonomous effects of tasiRNAs and miRNAs in Arabidopsis thaliana

In plants, small interfering RNAs (siRNAs) can trigger a silencing signal that may spread within a tissue to adjacent cells or even systemically to other organs. Movement of the signal is initially limited to a few cells, but in some cases the signal can be amplified and travel over larger distances. How far silencing initiated by other classes of plant small RNAs (sRNAs) than siRNAs can extend has been less clear. Using a system based on the silencing of the CH42 gene, we have tracked the mobility of silencing signals initiated in phloem companion cells by artificial microRNAs (miRNA) and trans-acting siRNA (tasiRNA) that have the same primary sequence. In this system, both the ta-siRNA and the miRNA act at a distance. Non-autonomous effects of the miRNA can be triggered by several different miRNA precursors deployed as backbones. While the tasiRNA also acts non-autonomously, it has a much greater range than the miRNA or hairpin-derived siRNAs directed against CH42, indicating that biogenesis can determine the non-autonomous effects of sRNAs. In agreement with this hypothesis, the silencing signals initiated by different sRNAs differ in their genetic requirements

Propagation of kinetic uncertainties through a canonical topology of the TLR4 signaling network in different regions of biochemical reaction space

<p>Abstract</p> <p>Background</p> <p>Signal transduction networks represent the information processing systems that dictate which dynamical regimes of biochemical activity can be accessible to a cell under certain circumstances. One of the major concerns in molecular systems biology is centered on the elucidation of the robustness properties and information processing capabilities of signal transduction networks. Achieving this goal requires the establishment of causal relations between the design principle of biochemical reaction systems and their emergent dynamical behaviors.</p> <p>Methods</p> <p>In this study, efforts were focused in the construction of a relatively well informed, deterministic, non-linear dynamic model, accounting for reaction mechanisms grounded on standard mass action and Hill saturation kinetics, of the canonical reaction topology underlying Toll-like receptor 4 (TLR4)-mediated signaling events. This signaling mechanism has been shown to be deployed in macrophages during a relatively short time window in response to lypopolysaccharyde (LPS) stimulation, which leads to a rapidly mounted innate immune response. An extensive computational exploration of the biochemical reaction space inhabited by this signal transduction network was performed via local and global perturbation strategies. Importantly, a broad spectrum of biologically plausible dynamical regimes accessible to the network in widely scattered regions of parameter space was reconstructed computationally. Additionally, experimentally reported transcriptional readouts of target pro-inflammatory genes, which are actively modulated by the network in response to LPS stimulation, were also simulated. This was done with the main goal of carrying out an unbiased statistical assessment of the intrinsic robustness properties of this canonical reaction topology.</p> <p>Results</p> <p>Our simulation results provide convincing numerical evidence supporting the idea that a canonical reaction mechanism of the TLR4 signaling network is capable of performing information processing in a robust manner, a functional property that is independent of the signaling task required to be executed. Nevertheless, it was found that the robust performance of the network is not solely determined by its design principle (topology), but this may be heavily dependent on the network's current position in biochemical reaction space. Ultimately, our results enabled us the identification of key rate limiting steps which most effectively control the performance of the system under diverse dynamical regimes.</p> <p>Conclusions</p> <p>Overall, our <it>in silico </it>study suggests that biologically relevant and non-intuitive aspects on the general behavior of a complex biomolecular network can be elucidated only when taking into account a wide spectrum of dynamical regimes attainable by the system. Most importantly, this strategy provides the means for a suitable assessment of the inherent variational constraints imposed by the structure of the system when systematically probing its parameter space.</p