OLD family nuclease function across diverse anti-phage defense systems

Bacteriophages constitute a ubiquitous threat to bacteria, and bacteria have evolved numerous anti-phage defense systems to protect themselves. These systems include well-studied phenomena such as restriction endonucleases and CRISPR, while emerging studies have identified many new anti-phage defense systems whose mechanisms are unknown or poorly understood. Some of these systems involve overcoming lysogenization defect (OLD) nucleases, a family of proteins comprising an ABC ATPase domain linked to a Toprim nuclease domain. Despite being discovered over 50 years ago, OLD nuclease function remained mysterious until recent biochemical, structural, and bioinformatic studies revealed that OLD nucleases protect bacteria by functioning in diverse anti-phage defense systems including the Gabija system and retrons. In this review we will highlight recent discoveries in OLD protein function and their involvement in multiple discrete anti-phage defense systems

The Star Formation History of LGS 3

We have determined the distance and star formation history of the Local Group dwarf galaxy LGS 3 from deep Hubble Space Telescope WFPC2 observations. LGS 3 is intriguing because ground-based observations showed that, while its stellar population is dominated by old, metal-poor stars, there is a handful of young, blue stars. Also, the presence of HI gas makes this a possible ``transition object'' between dwarf spheroidal and dwarf irregular galaxies. The HST data are deep enough to detect the horizontal branch and young main sequence for the first time. A new distance of D=620+/-20 kpc has been measured from the positions of the TRGB, the red clump, and the horizontal branch. The mean metallicity of the stars older than 8 Gyr is Fe/H = -1.5 +/- 0.3. The most recent generation of stars has Fe/H ~ -1. For the first few Gyr the global star formation rate was several times higher than the historical average and has been fairly constant since then. However, we do see significant changes in stellar populations and star formation history with radial position in the galaxy. Most of the young stars are found in the central 63 pc (21''), where the star formation rate has been relatively constant, while the outer parts have had a declining star formation rate.Comment: To appear in The Astrophysical Journal, 26 pages, 14 figures, uses AASTe

Geometrically-controlled twist transitions in nematic cells

We study geometrically-controlled twist transitions of a nematic confined between a sinusoidal grating and a flat substrate. In these cells the transition to the twisted state is driven by surface effects. We have identified the mechanisms responsible for the transition analytically and used exact numerical calculations to study the range of surface parameters where the twist instability occurs. Close to these values the cell operates under minimal external fields or temperature variations

Turbulent Mixing in the Interstellar Medium -- an application for Lagrangian Tracer Particles

We use 3-dimensional numerical simulations of self-gravitating compressible turbulent gas in combination with Lagrangian tracer particles to investigate the mixing process of molecular hydrogen (H2) in interstellar clouds. Tracer particles are used to represent shock-compressed dense gas, which is associated with H2. We deposit tracer particles in regions of density contrast in excess of ten times the mean density. Following their trajectories and using probability distribution functions, we find an upper limit for the mixing timescale of H2, which is of order 0.3 Myr. This is significantly smaller than the lifetime of molecular clouds, which demonstrates the importance of the turbulent mixing of H2 as a preliminary stage to star formation.Comment: 10 pages, 5 figures, conference proceedings "Turbulent Mixing and Beyond 2007

The Observed Growth of Massive Galaxy Clusters I: Statistical Methods and Cosmological Constraints

(Abridged) This is the first of a series of papers in which we derive simultaneous constraints on cosmological parameters and X-ray scaling relations using observations of the growth of massive, X-ray flux-selected galaxy clusters. Our data set consists of 238 clusters drawn from the ROSAT All-Sky Survey, and incorporates extensive follow-up observations using the Chandra X-ray Observatory. Here we describe and implement a new statistical framework required to self-consistently produce simultaneous constraints on cosmology and scaling relations from such data, and present results on models of dark energy. In spatially flat models with a constant dark energy equation of state, w, the cluster data yield Omega_m=0.23 +- 0.04, sigma_8=0.82 +- 0.05, and w=-1.01 +- 0.20, marginalizing over conservative allowances for systematic uncertainties. These constraints agree well and are competitive with independent data in the form of cosmic microwave background (CMB) anisotropies, type Ia supernovae (SNIa), cluster gas mass fractions (fgas), baryon acoustic oscillations (BAO), galaxy redshift surveys, and cosmic shear. The combination of our data with current CMB, SNIa, fgas, and BAO data yields Omega_m=0.27 +- 0.02, sigma_8=0.79 +- 0.03, and w=-0.96 +- 0.06 for flat, constant w models. For evolving w models, marginalizing over transition redshifts in the range 0.05-1, we constrain the equation of state at late and early times to be respectively w_0=-0.88 +- 0.21 and w_et=-1.05 +0.20 -0.36. The combined data provide constraints equivalent to a DETF FoM of 15.5. Our results highlight the power of X-ray studies to constrain cosmology. However, the new statistical framework we apply to this task is equally applicable to cluster studies at other wavelengths.Comment: 16 pages, 7 figures. v4: final version (typographic corrections). Results can be downloaded at https://www.stanford.edu/group/xoc/papers/xlf2009.htm

Survival probability of Baltic larval cod in relation to spatial overlap paterns with their prey obtained from drift model studies

Temporal mismatch between the occurrence of larvae and their prey potentially affects the spatial overlap and thus the contact rates between predator and prey. This might have important consequences for growth and survival. We performed a case study investigating the influence of circulation patterns on the overlap of Baltic cod larvae with their prey. A three-dimensional hydrodynamic model was used to analyse spatio-temporally resolved drift patterns of larval Baltic cod. A coefficient of overlap between modelled larval and idealized prey distributions indicated the probability of predator–prey overlap, dependent on the hatching time of cod larvae. By performing model runs for the years 1979–1998 investigated the intra- and interannual variability of potential spatial overlap between predator and prey. Assuming uniform prey distributions, we generally found the overlap to have decreased since the mid-1980s, but with the highest variability during the 1990s. Seasonally, predator–prey overlap on the Baltic cod spawning grounds was highest in summer and lowest at the end of the cod spawning season. Horizontally variable prey distributions generally resulted in decreased overlap coefficients. Finally, we related variations in overlap patterns to the variability of Baltic cod recruitment success

News from Lattice QCD on Heavy Quark Potentials and Spectral Functions of Heavy Quark States

We discuss recent lattice results on in-medium properties of hadrons and focus on thermal properties of heavy quark bound states. We will clarify the relation between heavy quark free energies and potentials used to analyze the melting of heavy quark bound states. Furthermore, we present calculations of meson spectral functions which indicate that the charmonium ground states, J/psi and eta_c, persist in the quark gluon plasma as well defined resonances with no significant change of their zero temperature masses at least up to T ~ 1.5 T_c. We also briefly comment on the current status of lattice calculations at non-vanishing baryon number density.Comment: Plenary talk at the 17th International Conference on Ultra Relativistic Nucleus-Nucleus Collisions (Quark Matter 2004), Oakland, California, 11-17 Jan 2004. Submitted to J.Phys.

The usefulness of rapid diagnostic tests in the new context of low malaria transmission in zanzibar.

BACKGROUND\ud \ud We assessed if histidine-rich-protein-2 (HRP2) based rapid diagnostic test (RDT) remains an efficient tool for Plasmodium falciparum case detection among fever patients in Zanzibar and if primary health care workers continue to adhere to RDT results in the new epidemiological context of low malaria transmission. Further, we evaluated the performance of RDT within the newly adopted integrated management of childhood illness (IMCI) algorithm in Zanzibar.\ud \ud METHODS AND FINDINGS\ud \ud We enrolled 3890 patients aged ≥2 months with uncomplicated febrile illness in this health facility based observational study conducted in 12 primary health care facilities in Zanzibar, between May-July 2010. One patient had an inconclusive RDT result. Overall 121/3889 (3.1%) patients were RDT positive. The highest RDT positivity rate, 32/528 (6.1%), was found in children aged 5-14 years. RDT sensitivity and specificity against PCR was 76.5% (95% CI 69.0-83.9%) and 99.9% (95% CI 99.7-100%), and against blood smear microscopy 78.6% (95% CI 70.8-85.1%) and 99.7% (95% CI 99.6-99.9%), respectively. All RDT positive, but only 3/3768 RDT negative patients received anti-malarial treatment. Adherence to RDT results was thus 3887/3889 (99.9%). RDT performed well in the IMCI algorithm with equally high adherence among children <5 years as compared with other age groups.\ud \ud CONCLUSIONS\ud \ud The sensitivity of HRP-2 based RDT in the hands of health care workers compared with both PCR and microscopy for P. falciparum case detection was relatively low, whereas adherence to test results with anti-malarial treatment was excellent. Moreover, the results provide evidence that RDT can be reliably integrated in IMCI as a tool for improved childhood fever management. However, the relatively low RDT sensitivity highlights the need for improved quality control of RDT use in primary health care facilities, but also for more sensitive point-of-care malaria diagnostic tools in the new epidemiological context of low malaria transmission in Zanzibar.\ud \ud TRIAL REGISTRATION\ud \ud ClinicalTrials.gov NCT01002066

New constraints on dark energy from the observed growth of the most X-ray luminous galaxy clusters

We present constraints on the mean matter density, Omega_m, the normalization of the density fluctuation power spectrum, sigma_8, and the dark-energy equation-of-state parameter, w, obtained from measurements of the X-ray luminosity function of the largest known galaxy clusters at redshifts z<0.7, as compiled in the Massive Cluster Survey (MACS) and the local BCS and REFLEX galaxy cluster samples. Our analysis employs an observed mass-luminosity relation, calibrated by hydrodynamical simulations, including corrections for non-thermal pressure support and accounting for the presence of intrinsic scatter. Conservative allowances for all known systematic uncertainties are included, as are standard priors on the Hubble constant and mean baryon density. We find Omega_m=0.28 +0.11 -0.07 and sigma_8=0.78 +0.11 -0.13 for a spatially flat, cosmological-constant model, and Omega_m=0.24 +0.15 -0.07, sigma_8=0.85 +0.13 -0.20 and w=-1.4 +0.4 -0.7 for a flat, constant-w model. Future work improving our understanding of redshift evolution and observational biases affecting the mass--X-ray luminosity relation have the potential to significantly tighten these constraints. Our results are consistent with those from recent analyses of type Ia supernovae, cosmic microwave background anisotropies, the X-ray gas mass fraction of relaxed galaxy clusters, baryon acoustic oscillations and cosmic shear. Combining the new X-ray luminosity function data with current supernova, cosmic microwave background and cluster gas fraction data yields the improved constraints Omega_m=0.269 +- 0.016, sigma_8=0.82 +- 0.03 and w=-1.02 +- 0.06. (Abridged)Comment: Submitted to MNRAS. 15 pages, 15 figures. v2: Improved modeling of the mass-luminosity relation, including additional systematic allowances for evolution in the scatter and non-thermal pressure support. Constraints are somewhat weaker, but overall conclusions are unchanged