Impact and collisional processes in the solar system

As impact cratered terrains have been successively recognized on certain planets and planetary satellites, it has become clear that impact processes are important to the understanding of the accretion and evolution of all solid planets. The noble gases in the normalized atmospheric inventories of the planets and the normalized gas content of meteorites are grossly similar, but demonstrate differences from each other which are not understood. In order to study shock devolatilization of the candidate carrier phases which are principally thought to be carbonaceous or hydrocarbons in planetesimals, experiments were conducted on noble gase implantation in various carbons: carbon black, activated charcoal, graphite, and carbon glass. These were candidate starting materials for impact devolatilization experiments. Initial experiments were conducted on vitreous amorphous carbon samples which were synthesized under vapor saturated conditions using argon as the pressurizing medium. An amino acid and surface analysis by laser ionization analyses were performed on three samples of shocked Murchison meteorite. A first study was completed in which a series of shock loading experiments on a porous limestone and on a non-porous gabbro in one and three dimensions were performed. Also a series of recovery experiments were conducted in which shocked molten basalt a 1700 C is encapsulated in molybdenum containers and shock recovered from up to 6 GPa pressures

Dissemination of the nurse-administered Tobacco Tactics intervention versus usual care in six Trinity community hospitals: study protocol for a comparative effectiveness trial

Abstract Background The objectives of this smoking cessation study among hospitalized smokers are to: 1) determine provider and patient receptivity, barriers, and facilitators to implementing the nurse-administered, inpatient Tobacco Tactics intervention versus usual care using face-to-face feedback and surveys; 2) compare the effectiveness of the nurse-administered, inpatient Tobacco Tactics intervention versus usual care across hospitals, units, and patient characteristics using thirty-day point prevalence abstinence at thirty days and six months (primary outcome) post-recruitment; and 3) determine the cost-effectiveness of the nurse-administered, inpatient Tobacco Tactics intervention relative to usual care including cost per quitter, cost per life-year saved, and cost per quality-adjusted life-year saved. Methods/Design This effectiveness study will be a quasi-experimental design of six Michigan community hospitals of which three will get the nurse-administered Tobacco Tactics intervention and three will provide their usual care. In both the intervention and usual care sites, research assistants will collect data from patients on their smoking habits and related variables while in the hospital and at thirty days and six months post-recruitment. The intervention will be integrated into the experimental sites by a research nurse who will train Master Trainers at each intervention site. The Master Trainers, in turn, will teach the intervention to all staff nurses. Research nurses will also conduct formative evaluation with nurses to identify barriers and facilitators to dissemination. Descriptive statistics will be used to summarize the results of surveys administered to nurses, nurses’ participation rates, smokers’ receipt of specific cessation services, and satisfaction with services. General estimating equation analyses will be used to determine differences between intervention groups on satisfaction and quit rates, respectively, with adjustment for the clustering of patients within hospital units. Regression analyses will test the moderation of the effects of the interventions by patient characteristics. Cost-effectiveness will be assessed by constructing three ratios including cost per quitter, cost per life-year saved, and cost per quality-adjusted life-year saved. Discussion Given that nurses represent the largest group of front-line providers, this intervention, if proven effective, has the potential for having a wide reach and thus decrease smoking, morbidity and mortality among inpatient smokers. Trial registration Dissemination of Tobacco Tactics for Hospitalized Smokers NCT01309217http://deepblue.lib.umich.edu/bitstream/2027.42/109462/1/13063_2011_Article_1134.pd

Recombination rate and selection strength in HIV intra-patient evolution

The evolutionary dynamics of HIV during the chronic phase of infection is driven by the host immune response and by selective pressures exerted through drug treatment. To understand and model the evolution of HIV quantitatively, the parameters governing genetic diversification and the strength of selection need to be known. While mutation rates can be measured in single replication cycles, the relevant effective recombination rate depends on the probability of coinfection of a cell with more than one virus and can only be inferred from population data. However, most population genetic estimators for recombination rates assume absence of selection and are hence of limited applicability to HIV, since positive and purifying selection are important in HIV evolution. Here, we estimate the rate of recombination and the distribution of selection coefficients from time-resolved sequence data tracking the evolution of HIV within single patients. By examining temporal changes in the genetic composition of the population, we estimate the effective recombination to be r=1.4e-5 recombinations per site and generation. Furthermore, we provide evidence that selection coefficients of at least 15% of the observed non-synonymous polymorphisms exceed 0.8% per generation. These results provide a basis for a more detailed understanding of the evolution of HIV. A particularly interesting case is evolution in response to drug treatment, where recombination can facilitate the rapid acquisition of multiple resistance mutations. With the methods developed here, more precise and more detailed studies will be possible, as soon as data with higher time resolution and greater sample sizes is available.Comment: to appear in PLoS Computational Biolog

Schizont transcriptome variation among clinical isolates and laboratory-adapted clones of the malaria parasite Plasmodium falciparum

Background: Malaria parasites are genetically polymorphic and phenotypically plastic. In studying transcriptome variation among parasites from different infections, it is challenging to overcome potentially confounding technical and biological variation between samples. We investigate variation in the major human parasite Plasmodium falciparum, generating RNA-seq data on multiple independent replicate sample preparations of merozoite-containing intra-erythrocytic schizonts from a panel of clinical isolates and from long-term laboratory-adapted clones, with a goal of robustly identifying differentially expressed genes. Results: Analysis of biological sample replicates shows that increased numbers improve the true discovery rate of differentially expressed genes, and that six independent replicates of each parasite line allowed identification of most differences that could be detected with larger numbers. For highly expressed genes, focusing on the top quartile at schizont stages, there was more power to detect differences. Comparing cultured clinical isolates and laboratory-adapted clones, genes more highly expressed in the laboratory-adapted clones include those encoding an AP2 transcription factor (PF3D7_0420300), a ubiquitin-binding protein and two putative methyl transferases. In contrast, higher expression in clinical isolates was seen for the merozoite surface protein gene dblmsp2, proposed to be a marker of schizonts forming merozoites committed to sexual differentiation. Variable expression was extremely strongly, but not exclusively, associated with genes known to be targeted by Heterochromatin Protein 1. Clinical isolates show variable expression of several known merozoite invasion ligands, as well as other genes for which new RT-qPCR assays validate the quantitation and allow characterisation in samples with more limited material. Expression levels of these genes vary among schizont preparations of different clinical isolates in the first ex vivo cycle in patient erythrocytes, but mean levels are similar to those in continuously cultured clinical isolates. Conclusions: Analysis of multiple biological sample replicates greatly improves identification of genes variably expressed between different cultured parasite lines. Clinical isolates recently established in culture show differences from long-term adapted clones in transcript levels of particular genes, and are suitable for analyses requiring biological replicates to understand parasite phenotypes and variable expression likely to be relevant in nature

Extreme Fermi surface smearing in a maximally disordered concentrated solid solution

We show that the Fermi surface can survive the presence of extreme compositional disorder in the equiatomic alloy Ni0.25Fe0.25Co0.25Cr0.25. Our high-resolution Compton scattering experiments reveal a Fermi surface which is smeared across a significant fraction of the Brillouin zone (up to 40% of 2π/a). The extent of this smearing and its variation on and between different sheets of the Fermi surface have been determined, and estimates of the electron mean free path and residual resistivity have been made by connecting this smearing with the coherence length of the quasiparticle states

A systematic variation of the stellar initial mass function in early-type galaxies

Much of our knowledge of galaxies comes from analysing the radiation emitted by their stars. It depends on the stellar initial mass function (IMF) describing the distribution of stellar masses when the population formed. Consequently knowledge of the IMF is critical to virtually every aspect of galaxy evolution. More than half a century after the first IMF determination, no consensus has emerged on whether it is universal in different galaxies. Previous studies indicated that the IMF and the dark matter fraction in galaxy centres cannot be both universal, but they could not break the degeneracy between the two effects. Only recently indications were found that massive elliptical galaxies may not have the same IMF as our Milky Way. Here we report unambiguous evidence for a strong systematic variation of the IMF in early-type galaxies as a function of their stellar mass-to-light ratio, producing differences up to a factor of three in mass. This was inferred from detailed dynamical models of the two-dimensional stellar kinematics for the large Atlas3D representative sample of nearby early-type galaxies spanning two orders of magnitude in stellar mass. Our finding indicates that the IMF depends intimately on a galaxy's formation history.Comment: 4 pages, 2 figures, LaTeX. Accepted for publication as a Nature Letter. More information about our Atlas3D project is available at http://purl.org/atlas3

Reducing the Social Gradient in Uptake of the NHS Colorectal Cancer Screening Programme Using a Narrative-Based Information Leaflet: A Cluster-Randomised Trial

Objective: To test the effectiveness of adding a narrative leaflet to the current information material delivered by the NHS English colorectal cancer (CRC) screening programme on reducing socioeconomic inequalities in uptake. / Participants: 150,417 adults (59-74 years) routinely invited to complete the guaiac Faecal Occult Blood test (gFOBt) in March 2013. / Design: A cluster randomised controlled trial (ISRCTN74121020) to compare uptake between two arms. The control arm received the standard NHS CRC screening information material (SI) and the intervention arm received the standard information plus a supplementary narrative leaflet, which had previously been shown to increase screening intentions (SI+N). Between group comparisons were made for uptake overall and across socioeconomic status (SES). Results: Uptake was 57.7% and did not differ significantly between the two trial arms (SI: 58.5%; SI+N: 56.7%; Odds Ratio = 0.93, 95% confidence interval: 0.81-1.06, p = 0.27). There was no interaction between group and SES quintile (p = 0.44). / Conclusions: Adding a narrative leaflet to existing information materials does not reduce the SES gradient in uptake. Despite the benefits of using a pragmatic trial design, the need to add to, rather than replace existing information may have limited the true value of an evidence-based intervention on behaviour

Pretreatment dietary intake is associated with tumor suppressor DNA methylation in head and neck squamous cell carcinomas

Diet is associated with cancer prognosis, including head and neck cancer (HNC), and has been hypothesized to influence epigenetic state by determining the availability of functional groups involved in the modification of DNA and histone proteins. The goal of this study was to describe the association between pretreatment diet and HNC tumor DNA methylation. Information on usual pretreatment food and nutrient intake was estimated via food frequency questionnaire (FFQ) on 49 HNC cases. Tumor DNA methylation patterns were assessed using the Illumina Goldengate Methylation Cancer Panel. First, a methylation score, the sum of individual hypermethylated tumor suppressor associated CpG sites, was calculated and associated with dietary intake of micronutrients involved in one-carbon metabolism and antioxidant activity, and food groups abundant in these nutrients. Second, gene specific analyses using linear modeling with empirical Bayesian variance estimation were conducted to identify if methylation at individual CpG sites was associated with diet. All models were controlled for age, sex, smoking, alcohol and HPV status. Individuals reporting in the highest quartile of folate, vitamin B12 and vitamin A intake, compared with those in the lowest quartile, showed significantly less tumor suppressor gene methylation, as did patients reporting the highest cruciferous vegetable intake. Gene specific analyses identified differential associations between DNA methylation and vitamin B12 and vitamin A intake when stratifying by HPV status. These preliminary results suggest that intake of folate, vitamin A and vitamin B12 may be associated with the tumor DNA methylation profile in HNC and enhance tumor suppression

Pretreatment dietary intake is associated with tumor suppressor DNA methylation in head and neck squamous cell carcinomas

Diet is associated with cancer prognosis, including head and neck cancer (HNC), and has been hypothesized to influence epigenetic state by determining the availability of functional groups involved in the modification of DNA and histone proteins. The goal of this study was to describe the association between pretreatment diet and HNC tumor DNA methylation. Information on usual pretreatment food and nutrient intake was estimated via food frequency questionnaire (FFQ) on 49 HNC cases. Tumor DNA methylation patterns were assessed using the Illumina Goldengate Methylation Cancer Panel. First, a methylation score, the sum of individual hypermethylated tumor suppressor associated CpG sites, was calculated and associated with dietary intake of micronutrients involved in one-carbon metabolism and antioxidant activity, and food groups abundant in these nutrients. Second, gene specific analyses using linear modeling with empirical Bayesian variance estimation were conducted to identify if methylation at individual CpG sites was associated with diet. All models were controlled for age, sex, smoking, alcohol and HPV status. Individuals reporting in the highest quartile of folate, vitamin B12 and vitamin A intake, compared with those in the lowest quartile, showed significantly less tumor suppressor gene methylation, as did patients reporting the highest cruciferous vegetable intake. Gene specific analyses identified differential associations between DNA methylation and vitamin B12 and vitamin A intake when stratifying by HPV status. These preliminary results suggest that intake of folate, vitamin A and vitamin B12 may be associated with the tumor DNA methylation profile in HNC and enhance tumor suppression