BENCHMARKING AND IMPLEMENTATION OF A NEW INDEPENDENT MONTE CARLO DOSE CALCULATION QUALITY ASSURANCE AUDIT TOOL FOR CLINICAL TRIALS

Introduction Commercial treatment planning systems employ a variety of dose calculation algorithms to plan and predict the dose distributions a patient receives during external beam radiation therapy. Traditionally, the Radiological Physics Center has relied on measurements to assure that institutions participating in the National Cancer Institute sponsored clinical trials administer radiation in doses that are clinically comparable to those of other participating institutions. To complement the effort of the RPC, an independent dose calculation tool needs to be developed that will enable a generic method to determine patient dose distributions in three dimensions and to perform retrospective analysis of radiation delivered to patients who enrolled in past clinical trials. Methods A multi-source model representing output for Varian 6 MV and 10 MV photon beams was developed and evaluated. The Monte Carlo algorithm, know as the Dose Planning Method (DPM), was used to perform the dose calculations. The dose calculations were compared to measurements made in a water phantom and in anthropomorphic phantoms. Intensity modulated radiation therapy and stereotactic body radiation therapy techniques were used with the anthropomorphic phantoms. Finally, past patient treatment plans were selected and recalculated using DPM and contrasted against a commercial dose calculation algorithm. Results The multi-source model was validated for the Varian 6 MV and 10 MV photon beams. The benchmark evaluations demonstrated the ability of the model to accurately calculate dose for the Varian 6 MV and the Varian 10 MV source models. The patient calculations proved that the model was reproducible in determining dose under similar conditions described by the benchmark tests. Conclusions The dose calculation tool that relied on a multi-source model approach and used the DPM code to calculate dose was developed, validated, and benchmarked for the Varian 6 MV and 10 MV photon beams. Several patient dose distributions were contrasted against a commercial algorithm to provide a proof of principal to use as an application in monitoring clinical trial activity.

Independent variations of CH₄ emissions and isotopic composition over the past 160,000 years

During the last glacial cycle, greenhouse gas concentrations fluctuated on decadal and longer timescales. Concentrations of methane, as measured in polar ice cores, show a close connection with Northern Hemisphere temperature variability, but the contribution of the various methane sources and sinks to changes in concentration is still a matter of debate. Here we assess changes in methane cycling over the past 160,000 years by measurements of the carbon isotopic composition delta C-13 of methane in Antarctic ice cores from Dronning Maud Land and Vostok. We find that variations in the delta C-13 of methane are not generally correlated with changes in atmospheric methane concentration, but instead more closely correlated to atmospheric CO2 concentrations. We interpret this to reflect a climatic and CO2-related control on the isotopic signature of methane source material, such as ecosystem shifts in the seasonally inundated tropical wetlands that produce methane. In contrast, relatively stable delta C-13 values occurred during intervals of large changes in the atmospheric loading of methane. We suggest that most methane sources-most notably tropical wetlands-must have responded simultaneously to climate changes across these periods.

Naive B-cell trafficking is shaped by local chemokine availability and LFA-1-independent stromal interactions.

It is not known how naive B cells compute divergent chemoattractant signals of the T-cell area and B-cell follicles during in vivo migration. Here, we used two-photon microscopy of peripheral lymph nodes (PLNs) to analyze the prototype G-protein-coupled receptors (GPCRs) CXCR4, CXCR5, and CCR7 during B-cell migration, as well as the integrin LFA-1 for stromal guidance. CXCR4 and CCR7 did not influence parenchymal B-cell motility and distribution, despite their role during B-cell arrest in venules. In contrast, CXCR5 played a nonredundant role in B-cell motility in follicles and in the T-cell area. B-cell migration in the T-cell area followed a random guided walk model, arguing against directed migration in vivo. LFA-1, but not α4 integrins, contributed to B-cell motility in PLNs. However, stromal network guidance was LFA-1 independent, uncoupling integrin-dependent migration from stromal attachment. Finally, we observed that despite a 20-fold reduction of chemokine expression in virus-challenged PLNs, CXCR5 remained essential for B-cell screening of antigen-presenting cells. Our data provide an overview of the contribution of prototype GPCRs and integrins during naive B-cell migration and shed light on the local chemokine availability that these cells compute.

A study of the impact of cigarette advertising on adolescent susceptibility to smoking among 5th-, 8th-, and 12th-grade students in Hempstead and Hitchcock Independent School Districts

This study assessed the impact of cigarette advertising on adolescent susceptibility to smoking in the Hempstead and Hitchcock Independent School Districts. A convenience sample of 217 youths, 10-19 years of age was recruited in the study. Students completed both a paper-and-pencil and a computer-aided questionnaire in April 1996. Adolescents were defined as susceptible to smoking if they could not definitely rule out the possibility of future smoking. For the analysis, an index was devised: a 5-point index of an individual's receptivity to cigarette advertising. The index is determined by the number of positive responses to five survey items (recognizing cigarette brand logos, recognizing cigarette advertisement's pictures, recognizing cigarette brand slogans, evaluating adolescent attitudes toward cigarette advertising, and the degree to which adolescents were exposed to cigarette advertisements). Using logistic regression, we assessed the independent importance of the index in predicting susceptibility to smoking and ever smoking after adjusting for sociodemographic variables, perceived school performance and family composition. Of students surveyed, 54.4% of students appeared to have started the smoking uptake process as measured by susceptibility to smoking. Camel was recognized by the majority of students (88%), followed by Marlboro (41.5%) and Newport (40.1%). The pattern for recognition of the cigarette advertisements was the same as the pattern of market for cigarette. Advertisement featuring the cartoon character Joe Camel was significantly more appealing to adolescents than were advertisements with human models, with animal models, and with text only (p $<$ 0.001). Text only advertisement was significantly less appealing than other types of advertisements. The cigarette advertisement with White models (Marlboro) had significantly higher appeal to White students than to African-American students (p $<$ 0.001). The cigarette advertisement featuring African-American models (Virginia Slims) was significantly more appealing to African-American students than other ethnic groups (p $<$ 0.001). Receptivity to cigarette advertising was to be an important concurrent predictor of past smoking experience and intention to smoke in the future. Adolescents who scored in the fourth quartile of the Index of Receptivity to Cigarette Advertising were 7.54 (95% confidence interval (CI) = 1.92-29.56) times as likely to be susceptible to smoking, and were 4.56 (95% CI = 1.55-13.38) times as likely to have tried smoking, as those who scored in the first quartile of the Index. The findings confirmed the hypothesis that cigarette advertising may be a strong current influence in encouraging adolescents to initiate the smoking uptake process than sociodemographic variables, perceived school performance and family composition. ^

Having your cake and eating it too: Can regulatory agencies be both independent and accountable?

Independent regulatory agencies (IRAs) were created in various sectors and on different governmental levels to implement liberalization policies. This paper investigates the link between IRAs' independence, which is said to promote regulatory credibility and the use of technical expertise, and their accountability, which is related to the need for controlling and legitimizing independent regulators. The literature on the regulatory state anticipates a positive relation between the independence and accountability of IRAs, but systematic empirical evidence is still lacking. To tackle this question, this paper measures and compares the independence and the accountability of IRAs in three differentially liberalized sectors in Switzerland (telecommunications, electricity and railways). With the application of Social Network Analysis, this piece of research shows that IRAs can be de facto independent and accountable at the same time, but the two features do not necessarily co-evolve in the same direction.

The Quiet Eye and motor performance – Introducing fixation duration as an independent variable

Evidence suggests a strong relation between superior motor performance and the duration of the last fixation before movement initiation (called Quiet Eye, QE). Although this phenomenon proves to be quite robust, to date, only little is known about its functional role. Therefore, in two experiments, a novel paradigm is introduced, testing the QE as independent variable by experimentally manipulating the duration of the last fixation in a throwing task. In addition, this paradigm allowed for the manipulation of the predictability of the target position. Results of the first study revealed an increase in throwing accuracy as function of experimentally prolonged QE durations. Thus, the assumption that the QE does not surface as a mere by-product of superior performance could be confirmed. In the second study, this dependency was found only under high task-demand conditions in which the target position was not predictable. This finding confirms the hypothesis that it is the optimization of information processing which serves as the crucial mechanisms behind QE effects.

U7 snRNP-specific Lsm11 protein: dual binding contacts with the 100 kDa zinc finger processing factor (ZFP100) and a ZFP100-independent function in histone RNA 3' end processing

The 3' cleavage generating non-polyadenylated animal histone mRNAs depends on the base pairing between U7 snRNA and a conserved histone pre-mRNA downstream element. This interaction is enhanced by a 100 kDa zinc finger protein (ZFP100) that forms a bridge between an RNA hairpin element upstream of the processing site and the U7 small nuclear ribonucleoprotein (snRNP). The N-terminus of Lsm11, a U7-specific Sm-like protein, was shown to be crucial for histone RNA processing and to bind ZFP100. By further analysing these two functions of Lsm11, we find that Lsm11 and ZFP100 can undergo two interactions, i.e. between the Lsm11 N-terminus and the zinc finger repeats of ZFP100, and between the N-terminus of ZFP100 and the Sm domain of Lsm11, respectively. Both interactions are not specific for the two proteins in vitro, but the second interaction is sufficient for a specific recognition of the U7 snRNP by ZFP100 in cell extracts. Furthermore, clustered point mutations in three phylogenetically conserved regions of the Lsm11 N-terminus impair or abolish histone RNA processing. As these mutations have no effect on the two interactions with ZFP100, these protein regions must play other roles in histone RNA processing, e.g. by contacting the pre-mRNA or additional processing factors.

Acoustic Detection of Organic Enrichment in Sediments at a Salmon Farm Is Confirmed by Independent Groundtruthing Methods

Acoustic backscatter contrast in depositional sediments under salmon farm cages in the Bay of Fundy, Canada, was correlated with localized changes in (unknown) sediment geotechnical properties, as indicated by 4 independent measures of organic enrichment. Sediment total sulfides and redox potentials, enzyme hydrolyzable amino acids, sediment profile imaging and macrofaunal samples, taken at mid-cage positions, each rejected the null hypothesis that salmon cage footprints, defined acoustically as high backscatter areas, were indistinguishable from nearby reference areas. Acoustic backscatter imaging appears capable of mapping organic enrichment in depositional sediments caused by excessive inputs of salmon farm wastes associated with intensive aquaculture.

Hypertrophy of infected Peyer’s patches arises from global, interferon-receptor, and CD69-independent shutdown of lymphocyte egress

Lymphoid organ hypertrophy is a hallmark of localized infection. During the inflammatory response, massive changes in lymphocyte recirculation and turnover boost lymphoid organ cellularity. Intriguingly, the exact nature of these changes remains undefined to date. Here, we report that hypertrophy of Salmonella-infected Peyer's patches (PPs) ensues from a global "shutdown" of lymphocyte egress, which traps recirculating lymphocytes in PPs. Surprisingly, infection-induced lymphocyte sequestration did not require previously proposed mediators of lymphoid organ shutdown including type I interferon receptor and CD69. In contrast, following T-cell receptor-mediated priming, CD69 was essential to selectively block CD4+ effector T-cell egress. Our findings segregate two distinct lymphocyte sequestration mechanisms, which differentially rely on intrinsic modulation of lymphocyte egress capacity and inflammation-induced changes in the lymphoid organ environment.

NADPH oxidase-independent formation of extracellular DNA traps by basophils

Basophils are primarily associated with a proinflammatory and immunoregulatory role in allergic diseases and parasitic infections. Recent studies have shown that basophils can also bind various bacteria both in the presence and the absence of opsonizing Abs. In this report, we show that both human and mouse basophils are able to produce mitochondrial reactive oxygen species and to form extracellular DNA traps upon IL-3 priming and subsequent activation of the complement factor 5 a receptor or FcεRI. Such basophil extracellular traps (BETs) contain mitochondrial, but not nuclear DNA, as well as the granule proteins basogranulin and mouse mast cell protease 8. BET formation occurs despite the absence of any functional NADPH oxidase in basophils. BETs can be found in both human and mouse inflamed tissues, suggesting that they also play a role under in vivo inflammatory conditions. Taken together, these findings suggest that basophils exert direct innate immune effector functions in the extracellular space.

A novel phosphorylation-independent interaction between SMG6 and UPF1 is essential for human NMD

Eukaryotic mRNAs with premature translation-termination codons (PTCs) are recognized and eliminated by nonsense-mediated mRNA decay (NMD). NMD substrates can be degraded by different routes that all require phosphorylated UPF1 (P-UPF1) as a starting point. The endonuclease SMG6, which cleaves mRNA near the PTC, is one of the three known NMD factors thought to be recruited to nonsense mRNAs via an interaction with P-UPF1, leading to eventual mRNA degradation. By artificial tethering of SMG6 and mutants thereof to a reporter mRNA combined with knockdowns of various NMD factors, we demonstrate that besides its endonucleolytic activity, SMG6 also requires UPF1 and SMG1 to reduce reporter mRNA levels. Using in vivo and in vitro approaches, we further document that SMG6 and the unique stalk region of the UPF1 helicase domain, along with a contribution from the SQ domain, form a novel interaction and we also show that this region of the UPF1 helicase domain is critical for SMG6 function and NMD. Our results show that this interaction is required for NMD and for the capability of tethered SMG6 to degrade its bound RNA, suggesting that it contributes to the intricate regulation of UPF1 and SMG6 enzymatic activities.

Independent measurement of biogenic silica in sediments by FTIR spectroscopy and PLS regression

We present an independent calibration model for the determination of biogenic silica (BSi) in sediments, developed from analysis of synthetic sediment mixtures and application of Fourier transform infrared spectroscopy (FTIRS) and partial least squares regression (PLSR) modeling. In contrast to current FTIRS applications for quantifying BSi, this new calibration is independent from conventional wet-chemical techniques and their associated measurement uncertainties. This approach also removes the need for developing internal calibrations between the two methods for individual sediments records. For the independent calibration, we produced six series of different synthetic sediment mixtures using two purified diatom extracts, with one extract mixed with quartz sand, calcite, 60/40 quartz/calcite and two different natural sediments, and a second extract mixed with one of the natural sediments. A total of 306 samples—51 samples per series—yielded BSi contents ranging from 0 to 100 %. The resulting PLSR calibration model between the FTIR spectral information and the defined BSi concentration of the synthetic sediment mixtures exhibits a strong cross-validated correlation ( R2cv = 0.97) and a low root-mean square error of cross-validation (RMSECV = 4.7 %). Application of the independent calibration to natural lacustrine and marine sediments yields robust BSi reconstructions. At present, the synthetic mixtures do not include the variation in organic matter that occurs in natural samples, which may explain the somewhat lower prediction accuracy of the calibration model for organic-rich samples.