Dust distribution in protoplanetary disks - Vertical settling and radial migration

We present the results of a three dimensional, locally isothermal, non-self-gravitating SPH code which models protoplanetary disks with two fluids: gas and dust. We ran simulations of a 1 Msun star surrounded by a 0.01 Msun disk comprising 99% gas and 1% dust in mass and extending from 0.5 to ~300 AU. The grain size ranges from 0.001 mm to 10 m for the low resolution (~25 000 SPH particles) simulations and from 0.1 mm to 10 cm for the high resolution (~160 000 SPH particles) simulations. Dust grains are slowed down by the sub-Keplerian gas and lose angular momentum, forcing them to migrate towards the central star and settle to the midplane. The gas drag efficiency varies according to the grain size, with the larger bodies being weakly influenced and following marginally perturbed Keplerian orbits, while smaller grains are strongly coupled to the gas. For intermediate sized grains, the drag force decouples the dust and gas, allowing the dust to preferentially migrate radially and efficiently settle to the midplane. The resulting dust distributions for each grain size will indicate, when grain growth is added, the regions when planets are likely to form.Comment: Accepted for publication in Astronomy & Astrophysics. 11 pages, 6 figure

Estimates of measles case fatality ratios: a comprehensive review of community-based studies.

BACKGROUND: Global deaths from measles have decreased notably in past decades, due to both increases in immunization rates and decreases in measles case fatality ratios (CFRs). While some aspects of the reduction in measles mortality can be monitored through increases in immunization coverage, estimating the level of measles deaths (in absolute terms) is problematic, particularly since incidence-based methods of estimation rely on accurate measures of measles CFRs. These ratios vary widely by geographic and epidemiologic context and even within the same community from year-to-year. METHODS: To understand better the variations in CFRs, we reviewed community-based studies published between 1980 and 2008 reporting age-specific measles CFRs. RESULTS: The results of the search consistently document that measles CFRs are highest in unvaccinated children under age 5 years; in outbreaks; the lowest CFRs occur in vaccinated children regardless of setting. The broad range of case and death definitions, study populations and geography highlight the complexities in extrapolating results for global public health planning. CONCLUSIONS: Values for measles CFRs remain imprecise, resulting in continued uncertainty about the actual toll measles exacts

Imputation of Missing Data When Measuring Physical Activity by Accelerometry

We consider the issue of summarizing accelerometer activity count data accumulated over multiple days when the time interval in which the monitor is worn is not uniform for every subject on every day. The fact that counts are not being recorded during periods in which the monitor is not worn means that many common estimators of daily physical activity are biased downward

Bioclipse: an open source workbench for chemo- and bioinformatics

BACKGROUND: There is a need for software applications that provide users with a complete and extensible toolkit for chemo- and bioinformatics accessible from a single workbench. Commercial packages are expensive and closed source, hence they do not allow end users to modify algorithms and add custom functionality. Existing open source projects are more focused on providing a framework for integrating existing, separately installed bioinformatics packages, rather than providing user-friendly interfaces. No open source chemoinformatics workbench has previously been published, and no sucessful attempts have been made to integrate chemo- and bioinformatics into a single framework. RESULTS: Bioclipse is an advanced workbench for resources in chemo- and bioinformatics, such as molecules, proteins, sequences, spectra, and scripts. It provides 2D-editing, 3D-visualization, file format conversion, calculation of chemical properties, and much more; all fully integrated into a user-friendly desktop application. Editing supports standard functions such as cut and paste, drag and drop, and undo/redo. Bioclipse is written in Java and based on the Eclipse Rich Client Platform with a state-of-the-art plugin architecture. This gives Bioclipse an advantage over other systems as it can easily be extended with functionality in any desired direction. CONCLUSION: Bioclipse is a powerful workbench for bio- and chemoinformatics as well as an advanced integration platform. The rich functionality, intuitive user interface, and powerful plugin architecture make Bioclipse the most advanced and user-friendly open source workbench for chemo- and bioinformatics. Bioclipse is released under Eclipse Public License (EPL), an open source license which sets no constraints on external plugin licensing; it is totally open for both open source plugins as well as commercial ones. Bioclipse is freely available at

Quantum Monte Carlo study of the one-dimensional Holstein model of spinless fermions

The Holstein model of spinless fermions interacting with dispersionless phonons in one dimension is studied by a Green's function Monte Carlo technique. The ground state energy, first fermionic excited state, density wave correlations, and mean lattice displacement are calculated for lattices of up to 16 sites, for one fermion per two sites, i.e., a half-filled band. Results are obtained for values of the fermion hopping parameter of $t=0.1 \omega$, $\omega$, and $10 \omega$ where $\omega$ is the phonon frequency. At a finite fermion-phonon coupling $g$ there is a transition from a metallic phase to an insulating phase in which there is charge-density-wave order. Finite size scaling is found to hold in the metallic phase and is used to extract the coupling dependence of the Luttinger liquid parameters, $u_\rho$ and $K_\rho$, the velocity of charge excitations and the correlation exponent, respectively. For free fermions ($g=0$) and for strong coupling ($g^2 \gg t \omega$) our results agree well with known analytic results. For $t=\omega$ and $t=10\omega$ our results are inconsistent with the metal-insulator transition being a Kosterlitz-Thouless transition.\\Comment: 16 pages of ReVTeX, 11 figures in uuencoded compressed tar file. Minor changes to text. Our results are inconsistent with the metal-insulator transition studied being a Kosterlitz-Thouless transition. The figures are now in the correct order. To appear in Physical Review B, April 15, 199

Home and Online Management and Evaluation of Blood Pressure (HOME BP) using a digital intervention in poorly controlled hypertension: randomised controlled trial

Objective: The HOME BP (Home and Online Management and Evaluation of Blood Pressure) trial aimed to test a digital intervention for hypertension management in primary care by combining self-monitoring of blood pressure with guided self-management. Design: Unmasked randomised controlled trial with automated ascertainment of primary endpoint. Setting: 76 general practices in the United Kingdom. Participants: 622 people with treated but poorly controlled hypertension (>140/90 mm Hg) and access to the internet. Interventions: Participants were randomised by using a minimisation algorithm to self-monitoring of blood pressure with a digital intervention (305 participants) or usual care (routine hypertension care, with appointments and drug changes made at the discretion of the general practitioner; 317 participants). The digital intervention provided feedback of blood pressure results to patients and professionals with optional lifestyle advice and motivational support. Target blood pressure for hypertension, diabetes, and people aged 80 or older followed UK national guidelines. Main outcome measures: The primary outcome was the difference in systolic blood pressure (mean of second and third readings) after one year, adjusted for baseline blood pressure, blood pressure target, age, and practice, with multiple imputation for missing values. Results: After one year, data were available from 552 participants (88.6%) with imputation for the remaining 70 participants (11.4%). Mean blood pressure dropped from 151.7/86.4 to 138.4/80.2 mm Hg in the intervention group and from 151.6/85.3 to 141.8/79.8 mm Hg in the usual care group, giving a mean difference in systolic blood pressure of −3.4 mm Hg (95% confidence interval −6.1 to −0.8 mm Hg) and a mean difference in diastolic blood pressure of −0.5 mm Hg (−1.9 to 0.9 mm Hg). Results were comparable in the complete case analysis and adverse effects were similar between groups. Within trial costs showed an incremental cost effectiveness ratio of £11 ($15, €12; 95% confidence interval £6 to £29) per mm Hg reduction. Conclusions: The HOME BP digital intervention for the management of hypertension by using self-monitored blood pressure led to better control of systolic blood pressure after one year than usual care, with low incremental costs. Implementation in primary care will require integration into clinical workflows and consideration of people who are digitally excluded. Trial registration: ISRCTN13790648

Saturation Diving Alters Folate Status and Biomarkers of DNA Damage and Repair

Exposure to oxygen-rich environments can lead to oxidative damage, increased body iron stores, and changes in status of some vitamins, including folate. Assessing the type of oxidative damage in these environments and determining its relationships with changes in folate status are important for defining nutrient requirements and designing countermeasures to mitigate these effects. Responses of humans to oxidative stressors were examined in participants undergoing a saturation dive in an environment with increased partial pressure of oxygen, a NASA Extreme Environment Mission Operations mission. Six participants completed a 13-d saturation dive in a habitat 19 m below the ocean surface near Key Largo, FL. Fasting blood samples were collected before, twice during, and twice after the dive and analyzed for biochemical markers of iron status, oxidative damage, and vitamin status. Body iron stores and ferritin increased during the dive (P<0.001), with a concomitant decrease in RBC folate (P<0.001) and superoxide dismutase activity (P<0.001). Folate status was correlated with serum ferritin (Pearson r = −0.34, P<0.05). Peripheral blood mononuclear cell poly(ADP-ribose) increased during the dive and the increase was significant by the end of the dive (P<0.001); γ-H2AX did not change during the mission. Together, the data provide evidence that when body iron stores were elevated in a hyperoxic environment, a DNA damage repair response occurred in peripheral blood mononuclear cells, but double-stranded DNA damage did not. In addition, folate status decreases quickly in this environment, and this study provides evidence that folate requirements may be greater when body iron stores and DNA damage repair responses are elevated

School-Level Intraclass Correlation for Physical Activity in Sixth Grade Girls

The Trial for Activity in Adolescent Girls (TAAG) is a group-randomized trial (GRT) to reduce the usual decline in moderate to vigorous physical activity (MVPA) among middle school girls. We report the school-level intraclass correlation (ICC) for MVPA from the TAAG baseline survey of sixth grade girls and describe the relationship between the schedule of data collection and the ICC