Indirect effects of invasive species affecting the population structure of an ecosystem engineer

Species invasion is of increasing concern as non-native species often have negative impacts on ecosystems that they were introduced to. Invaders negatively affect the abundance of native species due to direct interactions like predation and competition. Additionally, invaders may benefit native biota by imposing indirect effects on resident species interactions. Invaders indirectly affect resident species via both density-mediated indirect interactions (DMIIs) and trait-mediated indirect interactions (TMIIs). Previous studies on these different indirect interactions have largely examined the effects on structuring ecological systems, with paying little attention to the role of body size. Here, we experimentally demonstrate that an invasive habitat modifier of European coastal waters, the Pacific oyster (Crassostrea gigas), alters the population structure of native mussels (Mytilus edulis) by modifying the size specific predator-prey interaction between the mussels and the shore crab (Carcinus maenas). In laboratory split-plot experiments, the presence of Pacific oysters reduced the mortality of unconditioned mussels as well as mussels that were acclimatized in presence of predatory cues, while being exposed to predation by crabs of two different size classes. The reduction in mortality was size-dependent both in terms of the predators and the prey. The presence of oysters notably reduced mussel mortality in presence of small crabs, while the mortality rate in presence of big crabs was less affected. Mussels that benefited the most by the presence of oysters were those of recruitment stages, smaller than 20 mm in shell length. Our results suggest that oysters cause a strong shift in the population structure of M. edulis, reducing particularly the mortality of smaller sized mussels

Academic dismissal policy for medical students:effect on study progress and help-seeking behaviour

CONTEXT Medical students often fail to finish medical school within the designated time. An academic dismissal (AD) policy aims to enforce satisfactory progress and to enable early identification and timely support or referral of struggling students. In this study, we assessed whether the implementation of an AD policy improved study progress in the first 2 years of medical school. Additionally, we analysed its effect on the help-seeking behaviour of struggling students. METHODS We compared two AD cohorts (entering in 2005 and 2006, respectively) and two non-AD cohorts (entering in 2003 and 2004, respectively) on dropout rates, Year 1 curriculum completion rates and the percentage of students with an optimal study rate (i.e. all modules completed) at 1 and 2 years after enrolment. We also measured the effect on study progress of attending the support meetings offered. RESULTS The AD (n = 809) and non-AD cohorts (n = 809) did not differ significantly in dropout rate at 5 months, in Year 1 completion rate at 2 years and in the percentage of optimally performing students at 1 year after enrolment. At 2 years after enrolment, more students from the AD cohorts had left and more non-AD students demonstrated optimal performance, but effect sizes (ESs) for these differences were small. Voluntary support at 4 months was attended by AD students more often than by non-AD students (68.9% versus 39.8%; chi(2)((1)) = 43.95, p <0.001, ES = 0.29). The AD students who attended the support meetings completed the Year 1 curriculum more often than those who did not (73.4% versus 52.5%; chi(2)((1)) = 10.92, p <0.001, ES = 0.20). Attending the obligatory support meeting at 7 months had a similar effect (70.5% versus 33.3%; chi(2)((1)) = 13.60, p <0.001, ES = 0.23). CONCLUSIONS The presence of an AD policy did not lead to earlier dropout, higher completion rates or an improved study rate during the first 2 years at medical school. However, uptake of the support offered increased to almost 70%. Although support participants finished the Year 1 curriculum more often than non-participants, the current support system was not sufficient to improve overall study progress

Computational Simulations of the NASA Langley HyMETS Arc-Jet Facility

The Hypersonic Materials Environmental Test System (HyMETS) arc-jet facility located at the NASA Langley Research Center in Hampton, Virginia, is primarily used for the research, development, and evaluation of high-temperature thermal protection systems for hypersonic vehicles and reentry systems. In order to improve testing capabilities and knowledge of the test article environment, an effort is underway to computationally simulate the flow-field using computational fluid dynamics (CFD). A detailed three-dimensional model of the arc-jet nozzle and free-jet portion of the flow-field has been developed and compared to calibration probe Pitot pressure and stagnation-point heat flux for three test conditions at low, medium, and high enthalpy. The CFD model takes into account uniform pressure and non-uniform enthalpy profiles at the nozzle inlet as well as catalytic recombination efficiency effects at the probe surface. Comparing the CFD results and test data indicates an effectively fully-catalytic copper surface on the heat flux probe of about 10% efficiency and a 2-3 kpa pressure drop from the arc heater bore, where the pressure is measured, to the plenum section, prior to the nozzle. With these assumptions, the CFD results are well within the uncertainty of the stagnation pressure and heat flux measurements. The conditions at the nozzle exit were also compared with radial and axial velocimetry. This simulation capability will be used to evaluate various three-dimensional models that are tested in the HyMETS facility. An end-to-end aerothermal and thermal simulation of HyMETS test articles will follow this work to provide a better understanding of the test environment, test results, and to aid in test planning. Additional flow-field diagnostic measurements will also be considered to improve the modeling capability

The Ellipticity and Orientation of Clusters of Galaxies from N-Body Experiments

In this study we use simulations of 128$^3$ particles to study the ellipticity and orientation of clusters of galaxies in N-body simulations of differing power-law initial spectra (P(k) \propto k^n ,n = +1, 0, -1, -2$), and density parameters ($\Omega_0 = 0.2$to 1.0). Furthermore, unlike most theoretical studies we mimic most observers by removing all particles which lie at distances greater than 2 1/h Mpc from the cluster center of mass. We computed the axial ratio and the principal axes using the inertia tensor of each cluster. The mean ellipticity of clusters increases strongly with increasing$n$. We also find that clusters tend to become more spherical at smaller radii. We compared the orientation of a cluster to the orientation of neighboring clusters as a function of distance (correlation). In addition, we considered whether a cluster's major axis tends to lie along the line connecting it to a neighboring cluster, as a function of distance (alignment). Both alignments and correlations were computed in three dimensions and in projection to mimic observational surveys. Our results show that significant alignments exist for all spectra at small separations ($D < 15 h^{-1}$Mpc) but drops off at larger distance in a strongly$n-$dependent way.Comment: 22 pages, requires aaspp4.sty, flushrt.sty, and epsf.sty Revised manuscript, accepted for publication in Ap

Remote Infrared Imaging of the Space Shuttle During Hypersonic Flight: HYTHIRM Mission Operations and Coordination

The Hypersonic Thermodynamic Infrared Measurements (HYTHIRM) project has been responsible for obtaining spatially resolved, scientifically calibrated in-flight thermal imagery of the Space Shuttle Orbiter during reentry. Starting with STS-119 in March of 2009 and continuing through to the majority of final flights of the Space Shuttle, the HYTHIRM team has to date deployed during seven Shuttle missions with a mix of airborne and ground based imaging platforms. Each deployment of the HYTHIRM team has resulted in obtaining imagery suitable for processing and comparison with computational models and wind tunnel data at Mach numbers ranging from over 18 to under Mach 5. This paper will discuss the detailed mission planning and coordination with the NASA Johnson Space Center Mission Control Center that the HYTHIRM team undergoes to prepare for and execute each mission

Initial conditions, Discreteness and non-linear structure formation in cosmology

In this lecture we address three different but related aspects of the initial continuous fluctuation field in standard cosmological models. Firstly we discuss the properties of the so-called Harrison-Zeldovich like spectra. This power spectrum is a fundamental feature of all current standard cosmological models. In a simple classification of all stationary stochastic processes into three categories, we highlight with the name ``super-homogeneous'' the properties of the class to which models like this, with $P(0)=0$, belong. In statistical physics language they are well described as glass-like. Secondly, the initial continuous density field with such small amplitude correlated Gaussian fluctuations must be discretised in order to set up the initial particle distribution used in gravitational N-body simulations. We discuss the main issues related to the effects of discretisation, particularly concerning the effect of particle induced fluctuations on the statistical properties of the initial conditions and on the dynamical evolution of gravitational clustering.Comment: 28 pages, 1 figure, to appear in Proceedings of 9th Course on Astrofundamental Physics, International School D. Chalonge, Kluwer, eds N.G. Sanchez and Y.M. Pariiski, uses crckapb.st pages, 3 figure, ro appear in Proceedings of 9th Course on Astrofundamental Physics, International School D. Chalonge, Kluwer, Eds. N.G. Sanchez and Y.M. Pariiski, uses crckapb.st

Quantitative analysis of chromatin interaction changes upon a 4.3 Mb deletion at mouse 4E2

BACKGROUND: Circular chromosome conformation capture (4C) has provided important insights into three dimensional (3D) genome organization and its critical impact on the regulation of gene expression. We developed a new quantitative framework based on polymer physics for the analysis of paired-end sequencing 4C (PE-4Cseq) data. We applied this strategy to the study of chromatin interaction changes upon a 4.3 Mb DNA deletion in mouse region 4E2. RESULTS: A significant number of differentially interacting regions (DIRs) and chromatin compaction changes were detected in the deletion chromosome compared to a wild-type (WT) control. Selected DIRs were validated by 3D DNA FISH experiments, demonstrating the robustness of our pipeline. Interestingly, significant overlaps of DIRs with CTCF/Smc1 binding sites and differentially expressed genes were observed. CONCLUSIONS: Altogether, our PE-4Cseq analysis pipeline provides a comprehensive characterization of DNA deletion effects on chromatin structure and function

Doxorubicin versus doxorubicin and cisplatin in endometrial carcinoma: definitive results of a randomised study (55872) by the EORTC Gynaecological Cancer Group

Background: Combination chemotherapy yields better response rates which do not always lead to a survival advantage. The aim of this study was to investigate whether the reported differences in the efficacy and toxicity of monotherapy with doxorubicin (DOX) versus combination therapy with cisplatin (CDDP) in endometrial adenocarcinoma lead to significant advantage in favour of the combination. Patients and methods: Eligible patients had histologically-proven advanced and/or recurrent endometrial adenocarcinoma and were chemo-naïve. Treatment consisted of either DOX 60 mg/m2 alone or CDDP 50 mg/m2 added to DOX 60 mg/m2, every 4 weeks. Results: A total of 177 patients were entered and median follow-up is 7.1 years. The combination DOX-CDDP was more toxic than DOX alone. Haematological toxicity consisted mainly of white blood cell toxicity grade 3 and 4 (55% versus 30%). Non-haematological toxicity consisted mainly of grade 3 and 4 alopecia (72% versus 65%) and nausea/vomiting (36 % versus 12%). The combination DOX-CDDP provided a significantly higher response rate than single agent DOX (P <0.001). Thirty-nine patients (43%) responded on DOX-CDDP [13 complete responses (CRs) and 26 partial responses (PRs)], versus 15 patients (17%) on DOX alone (8 CR and 7 PR). The median overall survival (OS) was 9 months in the DOX-CDDP arm versus 7 months in the DOX alone arm (Wilcoxon P = 0.0654). Regression analysis showed that WHO performance status was statistically significant as a prognostic factor for survival, and stratifying for this factor, treatment effect reaches significance (hazard ratio = 1.46, 95% confidence interval 1.05-2.03, P = 0.024). Conclusions: In comparison to single agent DOX, the combination of DOX-CDDP results in higher but acceptable toxicity. The response rate produced is significantly higher, and a modest survival benefit is achieved with this combination regimen, especially in patients with a good performance statu

Targeted Locus Amplification and Haplotyping

Targeted locus amplification (TLA) allows for the detection of all genetic variation (including structural variation) in a genomic region of interest. As TLA is based on proximity ligation, variants can be linked to each other, thereby enabling allelic phasing and the generation of haplotypes. This allows for the study of genetic variants in an allele-specific manner. Here, we provide a step-by-step protocol for TLA sample preparation and a complete bioinformatics pipeline for the allelic phasing of TLA data. Additionally, to illustrate the protocol, we show the ability of TLA to re-sequence and haplotype the complete cystic fibrosis transmembrane (CFTR) gene (&amp;gt; 200 kb in size) from patient-derived intestinal organoids.</p