Japanese-US common-arm analysis of paclitaxel plus carboplatin in advanced non-small-cell lung cancer: a model for assessing population-related pharmacogenomics

PURPOSE To explore whether population-related pharmacogenomics contribute to differences in patient outcomes between clinical trials performed in Japan and the United States, given similar study designs, eligibility criteria, staging, and treatment regimens. METHODS We prospectively designed and conducted three phase III trials (Four-Arm Cooperative Study, LC00-03, and S0003) in advanced-stage, non-small-cell lung cancer, each with a common arm of paclitaxel plus carboplatin. Genomic DNA was collected from patients in LC00-03 and S0003 who received paclitaxel (225 mg/m(2)) and carboplatin (area under the concentration-time curve, 6). Genotypic variants of CYP3A4, CYP3A5, CYP2C8, NR1I2-206, ABCB1, ERCC1, and ERCC2 were analyzed by pyrosequencing or by PCR restriction fragment length polymorphism. Results were assessed by Cox model for survival and by logistic regression for response and toxicity. Results Clinical results were similar in the two Japanese trials, and were significantly different from the US trial, for survival, neutropenia, febrile neutropenia, and anemia. There was a significant difference between Japanese and US patients in genotypic distribution for CYP3A4*1B (P = .01), CYP3A5*3C (P = .03), ERCC1 118 (P < .0001), ERCC2 K751Q (P < .001), and CYP2C8 R139K (P = .01). Genotypic associations were observed between CYP3A4*1B for progression-free survival (hazard ratio [HR], 0.36; 95% CI, 0.14 to 0.94; P = .04) and ERCC2 K751Q for response (HR, 0.33; 95% CI, 0.13 to 0.83; P = .02). For grade 4 neutropenia, the HR for ABCB1 3425C-->T was 1.84 (95% CI, 0.77 to 4.48; P = .19). CONCLUSION Differences in allelic distribution for genes involved in paclitaxel disposition or DNA repair were observed between Japanese and US patients. In an exploratory analysis, genotype-related associations with patient outcomes were observed for CYP3A4*1B and ERCC2 K751Q. This common-arm approach facilitates the prospective study of population-related pharmacogenomics in which ethnic differences in antineoplastic drug disposition are anticipated.

Call for a reference model of chronic hind limb ischemia to investigate therapeutic angiogenesis

A large number of studies utilize animal models to investigate therapeutic angiogenesis. However, the lack of a standardized experimental model leaves the comparison of different studies problematic. To establish a reference model of prolonged moderate tissue ischemia, we created unilateral hind limb ischemia in athymic rnu-rats by surgical excision of the femoral vessels. Blood flow of the limb was monitored for 60 days by laser Doppler imaging. Following a short postoperative period of substantially depressed perfusion, the animals showed a status of moderate hind limb ischemia from day 14 onwards. Thereafter, the perfusion remained at a constant level (55.5% of normal value) until the end of the observation period. Histopathological assessment of the ischemic musculature on postoperative days 28 and 60 showed essentially no inflammatory cell infiltrate or fibrosis. However, the mitochondrial activity and capillary-to-fiber ratio of the muscular tissue was reduced to 52.7% of normal, presenting with a significant weakness of the ischemic limb evidenced by a progressive decline in performance. Intramuscular injection of culture-expanded human endothelial progenitor cells (EPC) resulted in a significant increase in blood flow (82.0+/-3.5% of normal), capillary density (1.60+/-0.08/muscle fiber) and smooth muscle covered arterioles (8.0+/-0.6/high power field) in the ischemic hind limb as compared to controls (55.0+/-3.1%; 0.99+/-0.03; 5.0+/-0.2). In conclusion, chronic, moderate hind limb ischemia with consistently reduced perfusion levels persisting over a prolonged period can be established reliably in rnu athymic nude rats and is responsive to pro-angiogenic treatments such as EPC transplantation. This study provides a detailed protocol of a highly reproducible reference model to test novel therapeutic options for limb ischemia.

Automatic Labeling of Software Components and their Evolution using Log-Likelihood Ratio of Word Frequencies in Source Code

As more and more open-source software components become available on the internet we need automatic ways to label and compare them. For example, a developer who searches for reusable software must be able to quickly gain an understanding of retrieved components. This understanding cannot be gained at the level of source code due to the semantic gap between source code and the domain model. In this paper we present a lexical approach that uses the log-likelihood ratios of word frequencies to automatically provide labels for software components. We present a prototype implementation of our labeling/comparison algorithm and provide examples of its application. In particular, we apply the approach to detect trends in the evolution of a software system.

A Simple Accounting-based Valuation Model for the Debt Tax Shield

This paper describes a simple way to integrate the debt tax shield into an accounting-based valuation model. The market value of equity is determined by forecasting residual operating income, which is calculated by charging operating income for the operating assets at a required return that accounts for the tax benefit that comes from borrowing to raise cash for the operations. The model assumes that the firm maintains a deterministic financial leverage ratio, which tends to converge quickly to typical steady-state levels over time. From a practical point of view, this characteristic is of particular help, because it allows a continuing value calculation at the end of a short forecast period.

Zebrafish (Danio rerio) neuromast: promising biological endpoint linking developmental and toxicological studies

Aquatic toxicology is facing the challenge to assess the impact of complex mixtures of compounds on diverse biological endpoints. So far, ecotoxicology focuses mainly on apical endpoints such as growth, lethality and reproduction, but does not consider sublethal toxic effects that may indirectly cause ecological effects. One such sublethal effect is toxicant-induced impairment of neurosensory functions which will affect important behavioural traits of exposed organisms. Here, we critically review the mechanosensory lateral line (LL) system of zebrafish as a model to screen for chemical effects on neurosensory function of fish in particular and vertebrates in general. The LL system consists of so-called neuromasts, composed of centrally located sensory hair cells, and surrounding supporting cells. The function of neuromasts is the detection of water movements that is essential for the fish's ability to detect prey, to escape predator, to socially interact or to show rheotactic behaviour. Recent advances in the study of these organs provided researchers with a broad area of molecular tools for easy and rapid detection of neuromasts dysfunction and/or disturbed development. Further, genes involved in neuromasts differentiation have been identified using auditory/mechanosensory mutants and morphants. A number of environmental toxicants including metals and pharmaceuticals have been shown to affect neuromasts development and/or function. The use of the LL organ for toxicological studies offers the advantage to integrate the available profound knowledge on developmental biology of the neuromasts with the study of chemical toxicity. This combination may provide a powerful tool in environmental risk assessment.

Flow-R, a model for susceptibility mapping of debris flows and other gravitational hazards at a regional scale

The development of susceptibility maps for debris flows is of primary importance due to population pressure in hazardous zones. However, hazard assessment by process-based modelling at a regional scale is difficult due to the complex nature of the phenomenon, the variability of local controlling factors, and the uncertainty in modelling parameters. A regional assessment must consider a simplified approach that is not highly parameter dependant and that can provide zonation with minimum data requirements. A distributed empirical model has thus been developed for regional susceptibility assessments using essentially a digital elevation model (DEM). The model is called Flow-R for Flow path assessment of gravitational hazards at a Regional scale (available free of charge under http://www.flow-r.org) and has been successfully applied to different case studies in various countries with variable data quality. It provides a substantial basis for a preliminary susceptibility assessment at a regional scale. The model was also found relevant to assess other natural hazards such as rockfall, snow avalanches and floods. The model allows for automatic source area delineation, given user criteria, and for the assessment of the propagation extent based on various spreading algorithms and simple frictional laws. We developed a new spreading algorithm, an improved version of Holmgren's direction algorithm, that is less sensitive to small variations of the DEM and that is avoiding over-channelization, and so produces more realistic extents. The choices of the datasets and the algorithms are open to the user, which makes it compliant for various applications and dataset availability. Amongst the possible datasets, the DEM is the only one that is really needed for both the source area delineation and the propagation assessment; its quality is of major importance for the results accuracy. We consider a 10 m DEM resolution as a good compromise between processing time and quality of results. However, valuable results have still been obtained on the basis of lower quality DEMs with 25 m resolution.

Eco-evolutionary Dynamics of Individual-Based Food Webs

The past decade has seen the rise of high resolution datasets. One of the main surprises of analysing such data has been the discovery of a large genetic, phenotypic and behavioural variation and heterogeneous metabolic rates among individuals within natural populations. A parallel discovery from theory and experiments has shown a strong temporal convergence between evolutionary and ecological dynamics, but a general framework to analyse from individual-level processes the convergence between ecological and evolutionary dynamics and its implications for patterns of biodiversity in food webs has been particularly lacking. Here, as a first approximation to take into account intraspecific variability and the convergence between the ecological and evolutionary dynamics in large food webs, we develop a model from population genomics and microevolutionary processes that uses sexual reproduction, genetic-distance-based speciation and trophic interactions. We confront the model with the prey consumption per individual predator, species-level connectance and prey–predator diversity in several environmental situations using a large food web with approximately 25,000 sampled prey and predator individuals. We show higher than expected diversity of abundant species in heterogeneous environmental conditions and strong deviations from the observed distribution of individual prey consumption (i.e. individual connectivity per predator) in all the environmental conditions. The observed large variance in individual prey consumption regardless of the environmental variability collapsed species-level connectance after small increases in sampling effort. These results suggest (1) intraspecific variance in prey–predator interactions has a strong effect on the macroscopic properties of food webs and (2) intraspecific variance is a potential driver regulating the speed of the convergence between ecological and evolutionary dynamics in species-rich food webs. These results also suggest that genetic–ecological drift driven by sexual reproduction, equal feeding rate among predator individuals, mutations and genetic-distance-based speciation can be used as a neutral food web dynamics test to detect the ecological and microevolutionary processes underlying the observed patterns of individual and species-based food webs at local and macroecological scales.

Chapter Six – Individual Trait Variation and Diversity in Food Webs

In recent years, there has been a renewed interest in the ecological consequences of individual trait variation within populations. Given that individual variability arises from evolutionary dynamics, to fully understand eco-evolutionary feedback loops, we need to pay special attention to how standing trait variability affects ecological dynamics. There is mounting empirical evidence that intra-specific phenotypic variation can exceed species-level means, but theoretical models of multi-trophic species coexistence typically neglect individual-level trait variability. What is needed are multispecies datasets that are resolved at the individual level that can be used to discriminate among alternative models of resource selection and species coexistence in food webs. Here, using one the largest individual-based datasets of a food web compiled to date, along with an individual trait-based stochastic model that incorporates Approximate Bayesian computation methods, we document intra-population variation in the strength of prey selection by different classes or predator phenotypes which could potentially alter the diversity and coexistence patterns of food webs. In particular, we found that strongly connected individual predators preferentially consumed common prey, whereas weakly connected predators preferentially selected rare prey. Such patterns suggest that food web diversity may be governed by the distribution of predator connectivity and individual trait variation in prey selection. We discuss the consequences of intra-specific variation in prey selection to assess fitness differences among predator classes (or phenotypes) and track longer term food web patterns of coexistence accounting for several phenotypes within each prey and predator species.

Model-Based Estimates of Right Whale Habitat Use in the Gulf of Maine

Balancing human uses of the marine environment with the recovery of protected species requires accurate information on when and where species of interest are likely to be present. Here, we describe a system that can produce useful estimates of right whale Eubalaena glacialis presence and abundance on their feeding grounds in the Gulf of Maine. The foundation of our system is a coupled physical-biological model of the copepod Calan us finmarchicus, the preferred prey of right whales. From the modeled prey densities, we can estimate when whales will appear in the Great South Channel feeding ground. Based on our experience with the system, we consider how the relationship between right whales and copepods changes across spatial scales. The scale-dependent relationship between whales and copepods provides insight into how to improve future estimates of the distribution of right whales and other pelagic predators.

Parasite- and predator-induced maternal effects in the great tit (Parus major)

Both predators and parasites can elicit behavioral and physiological responses in prey and hosts, respectively. These responses may involve the reallocation of resources and may thus limit each other. We investigated the effects of concurrent pre-laying exposure of great tit females (Parus major) to both a simulated predation risk and a nest-based ectoparasite, the hen flea (Ceratophyllus gallinae), on nestling growth and development. We manipulated perceived predation risk using models and vocalizations of sparrowhawks (Accipiter nisus). At the start of incubation, we swapped whole clutches between treated and untreated nests to separate pre-laying maternal effects from posthatching effects. Since costs and benefits of maternal responses to parasites need to be assessed under parasite pressure, we infested half of the rearing nests with hen fleas. Parasites had negative effects on mass gain and wing growth, both via maternal effects and via direct exposure of nestlings, whereas maternal predation risk had no significant effect. The interaction between predator and parasite treatments was not significant and, thus, suggests the absence of a trade-off between the 2 stressors operating at the level of maternal effects. Alternatively, the complexity of the design, despite a relatively large sample size, may have limited the power for detection of this expected trade-off.

Daily ozone cycle in the stratosphere: global, regional and seasonal behaviour modelled with the Whole Atmosphere Community Climate Model

The Whole Atmosphere Community Climate Model (WACCM) is utilised to study the daily ozone cycle and underlying photochemical and dynamical processes. The analysis is focused on the daily ozone cycle in the middle stratosphere at 5 hPa where satellite-based trend estimates of stratospheric ozone are most biased by diurnal sampling effects and drifting satellite orbits. The simulated ozone cycle shows a minimum after sunrise and a maximum in the late afternoon. Further, a seasonal variation of the daily ozone cycle in the stratosphere was found. Depending on season and latitude, the peak-to-valley difference of the daily ozone cycle varies mostly between 3 and 5% (0.4 ppmv) with respect to the midnight ozone volume mixing ratio. The maximal variation of 15% (0.8 ppmv) is found at the polar circle in summer. The global pattern of the strength of the daily ozone cycle is mainly governed by the solar zenith angle and the sunshine duration. In addition, we find synoptic-scale variations in the strength of the daily ozone cycle. These variations are often anti-correlated to regional temperature anomalies and are due to the temperature dependence of the rate coefficients k2 and k3 of the Chapman cycle reactions. Further, the NOx catalytic cycle counteracts the accumulation of ozone during daytime and leads to an anti-correlation between anomalies in NOx and the strength of the daily ozone cycle. Similarly, ozone recombines with atomic oxygen which leads to an anti-correlation between anomalies in ozone abundance and the strength of the daily ozone cycle. At higher latitudes, an increase of the westerly (easterly) wind cause a decrease (increase) in the sunshine duration of an air parcel leading to a weaker (stronger) daily ozone cycle.

Signal Processing for the Measurement of the Deuterium/Hydrogen Ratio in the Local Interstellar Medium

We report on a comprehensive signal processing procedure for very low signal levels for the measurement of neutral deuterium in the local interstellar medium from a spacecraft in Earth orbit. The deuterium measurements were performed with the IBEX-Lo camera on NASA’s Interstellar Boundary Explorer (IBEX) satellite. Our analysis technique for these data consists of creating a mass relation in three-dimensional time of flight space to accurately determine the position of the predicted D events, to precisely model the tail of the H events in the region where the H tail events are near the expected D events, and then to separate the H tail from the observations to extract the very faint D signal. This interstellar D signal, which is expected to be a few counts per year, is extracted from a strong terrestrial background signal, consisting of sputter products from the sensor’s conversion surface. As reference we accurately measure the terrestrial D/H ratio in these sputtered products and then discriminate this terrestrial background source. During the three years of the mission time when the deuterium signal was visible to IBEX, the observation geometry and orbit allowed for a total observation time of 115.3 days. Because of the spinning of the spacecraft and the stepping through eight energy channels the actual observing time of the interstellar wind was only 1.44 days. With the optimised data analysis we found three counts that could be attributed to interstellar deuterium. These results update our earlier work.

Reliable prediction of clinical outcome in patients with chronic HCV infection and compensated advanced hepatic fibrosis: a validated model using objective and readily available clinical parameters.

OBJECTIVE Reliable tools to predict long-term outcome among patients with well compensated advanced liver disease due to chronic HCV infection are lacking. DESIGN Risk scores for mortality and for cirrhosis-related complications were constructed with Cox regression analysis in a derivation cohort and evaluated in a validation cohort, both including patients with chronic HCV infection and advanced fibrosis. RESULTS In the derivation cohort, 100/405 patients died during a median 8.1 (IQR 5.7-11.1) years of follow-up. Multivariate Cox analyses showed age (HR=1.06, 95% CI 1.04 to 1.09, p<0.001), male sex (HR=1.91, 95% CI 1.10 to 3.29, p=0.021), platelet count (HR=0.91, 95% CI 0.87 to 0.95, p<0.001) and log10 aspartate aminotransferase/alanine aminotransferase ratio (HR=1.30, 95% CI 1.12 to 1.51, p=0.001) were independently associated with mortality (C statistic=0.78, 95% CI 0.72 to 0.83). In the validation cohort, 58/296 patients with cirrhosis died during a median of 6.6 (IQR 4.4-9.0) years. Among patients with estimated 5-year mortality risks <5%, 5-10% and >10%, the observed 5-year mortality rates in the derivation cohort and validation cohort were 0.9% (95% CI 0.0 to 2.7) and 2.6% (95% CI 0.0 to 6.1), 8.1% (95% CI 1.8 to 14.4) and 8.0% (95% CI 1.3 to 14.7), 21.8% (95% CI 13.2 to 30.4) and 20.9% (95% CI 13.6 to 28.1), respectively (C statistic in validation cohort = 0.76, 95% CI 0.69 to 0.83). The risk score for cirrhosis-related complications also incorporated HCV genotype (C statistic = 0.80, 95% CI 0.76 to 0.83 in the derivation cohort; and 0.74, 95% CI 0.68 to 0.79 in the validation cohort). CONCLUSIONS Prognosis of patients with chronic HCV infection and compensated advanced liver disease can be accurately assessed with risk scores including readily available objective clinical parameters.

Measurement of the TeV atmospheric muon charge ratio with the complete OPERA data set

The OPERA detector, designed to search for νμ → ντ oscillations in the CNGS beam, is located in the underground Gran Sasso laboratory, a privileged location to study TeV-scale cosmic rays. For the analysis here presented, the detector was used to measure the atmospheric muon charge ratio in the TeV region. OPERA collected chargeseparated cosmic ray data between 2008 and 2012. More than 3 million atmospheric muon events were detected and reconstructed, among which about 110000 multiple muon bundles. The charge ratio Rμ ≡ Nμ+/Nμ− was measured separately for single and for multiple muon events. The analysis exploited the inversion of the magnet polarity which was performed on purpose during the 2012 Run. The combination of the two data sets with opposite magnet polarities allowedminimizing systematic uncertainties and reaching an accurate determination of the muon charge ratio. Data were fitted to obtain relevant parameters on the composition of primary cosmic rays and the associated kaon production in the forward fragmentation region. In the surface energy range 1–20 TeV investigated by OPERA, Rμ is well described by a parametric model including only pion and kaon contributions to themuon flux, showing no significant contribution of the prompt component. The energy independence supports the validity of Feynman scaling in the fragmentation region up to 200 TeV/nucleon primary energy.

High-flow venous pouch aneurysm in the rabbit carotid artery: A model for large aneurysms.

BACKGROUND AND PURPOSE Currently one of the most widely used models for the development of endovascular techniques and coiling devices for treatment of aneurysm is the elastase-induced aneurysm model in the rabbit carotid artery. Microsurgical techniques for creating an aneurysm with a venous pouch have also been established, although both techniques usually result in aneurysms less than 1 cm in diameter. We investigated whether an increase in blood flow toward the neck would produce larger aneurysms in a microsurgical venous pouch model. MATERIALS AND METHODS Microsurgical operations were performed on 11 New Zealand white rabbits. Both carotid arteries and the right jugular vein were dissected, and the right carotid artery was temporarily clipped followed by an arteriotomy. The left carotid artery was also clipped proximally, ligated distally, and sutured onto the proximal half of the arteriotomy in the right carotid artery. The venous graft was sutured onto the distal half of the arteriotomy. Digital subtraction angiography was also performed. RESULTS Angiography showed patent anastomosed vessels and aneurysms in the seven surviving rabbits. Mean aneurysm measurements among surviving rabbits with patent vessels were: 13.9 mm length, 9.3 mm width, and neck diameter 4.7 mm. The resulting mean aspect ratio was 3.35 and the mean bottleneck ratio was 3.05. CONCLUSION A large venous graft and increased blood flow toward the base of the aneurysm seem to be key factors in the creation of large venous pouch aneurysms. These large aneurysms allow testing of endovascular devices designed for large and giant aneurysms.