Separable Dual Space Gaussian Pseudo-potentials

We present pseudo-potential coefficients for the first two rows of the periodic table. The pseudo potential is of a novel analytic form, that gives optimal efficiency in numerical calculations using plane waves as basis set. At most 7 coefficients are necessary to specify its analytic form. It is separable and has optimal decay properties in both real and Fourier space. Because of this property, the application of the nonlocal part of the pseudo-potential to a wave-function can be done in an efficient way on a grid in real space. Real space integration is much faster for large systems than ordinary multiplication in Fourier space since it shows only quadratic scaling with respect to the size of the system. We systematically verify the high accuracy of these pseudo-potentials by extensive atomic and molecular test calculations.Comment: 16 pages, 4 postscript figure

Close companions around young stars

Multiplicity is a fundamental property that is set early during stellar lifetimes, and it is a stringent probe of the physics of star formation. The distribution of close companions around young stars is still poorly constrained by observations. We present an analysis of stellar multiplicity derived from APOGEE-2 spectra obtained in targeted observations of nearby star-forming regions. This is the largest homogeneously observed sample of high-resolution spectra of young stars. We developed an autonomous method to identify double lined spectroscopic binaries (SB2s). Out of 5007 sources spanning the mass range of $\sim$0.05--1.5 \msun, we find 399 binaries, including both RV variables and SB2s. The mass ratio distribution of SB2s is consistent with a uniform for $q0.95$. The period distribution is consistent with what has been observed in close binaries ($<10$ AU) in the evolved populations. Three systems are found to have $q\sim$0.1, with a companion located within the brown dwarf desert. There are not any strong trends in the multiplicity fraction (MF) as a function of cluster age from 1 to 100 Myr. There is a weak dependence on stellar density, with companions being most numerous at $\Sigma_*\sim30$ stars/pc$^{-2}$, and decreasing in more diffuse regions. Finally, disk-bearing sources are deficient in SB2s (but not RV variables) by a factor of $\sim$2; this deficit is recovered by the systems without disks. This may indicate a quick dispersal of disk material in short-period equal mass systems that is less effective in binaries with lower $q$.Comment: 25 pages, 20 figures. Accepted to A

The APOGEE-2 Survey of the Orion Star Forming Complex: I. Target Selection and Validation with early observations

The Orion Star Forming Complex (OSFC) is a central target for the APOGEE-2 Young Cluster Survey. Existing membership catalogs span limited portions of the OSFC, reflecting the difficulty of selecting targets homogeneously across this extended, highly structured region. We have used data from wide field photometric surveys to produce a less biased parent sample of young stellar objects (YSOs) with infrared (IR) excesses indicative of warm circumstellar material or photometric variability at optical wavelengths across the full 420 square degrees extent of the OSFC. When restricted to YSO candidates with H < 12.4, to ensure S/N ~100 for a six visit source, this uniformly selected sample includes 1307 IR excess sources selected using criteria vetted by Koenig & Liesawitz and 990 optical variables identified in the Pan-STARRS1 3$\pi$ survey: 319 sources exhibit both optical variability and evidence of circumstellar disks through IR excess. Objects from this uniformly selected sample received the highest priority for targeting, but required fewer than half of the fibers on each APOGEE-2 plate. We fill the remaining fibers with previously confirmed and new color-magnitude selected candidate OSFC members. Radial velocity measurements from APOGEE-1 and new APOGEE-2 observations taken in the survey's first year indicate that ~90% of the uniformly selected targets have radial velocities consistent with Orion membership.The APOGEE-2 Orion survey will include >1100 bona fide YSOs whose uniform selection function will provide a robust sample for comparative analyses of the stellar populations and properties across all sub-regions of Orion.Comment: Accepted for publication in ApJ

Social interaction, noise and antibiotic-mediated switches in the intestinal microbiota

The intestinal microbiota plays important roles in digestion and resistance against entero-pathogens. As with other ecosystems, its species composition is resilient against small disturbances but strong perturbations such as antibiotics can affect the consortium dramatically. Antibiotic cessation does not necessarily restore pre-treatment conditions and disturbed microbiota are often susceptible to pathogen invasion. Here we propose a mathematical model to explain how antibiotic-mediated switches in the microbiota composition can result from simple social interactions between antibiotic-tolerant and antibiotic-sensitive bacterial groups. We build a two-species (e.g. two functional-groups) model and identify regions of domination by antibiotic-sensitive or antibiotic-tolerant bacteria, as well as a region of multistability where domination by either group is possible. Using a new framework that we derived from statistical physics, we calculate the duration of each microbiota composition state. This is shown to depend on the balance between random fluctuations in the bacterial densities and the strength of microbial interactions. The singular value decomposition of recent metagenomic data confirms our assumption of grouping microbes as antibiotic-tolerant or antibiotic-sensitive in response to a single antibiotic. Our methodology can be extended to multiple bacterial groups and thus it provides an ecological formalism to help interpret the present surge in microbiome data.Comment: 20 pages, 5 figures accepted for publication in Plos Comp Bio. Supplementary video and information availabl

Raltegravir Cerebrospinal Fluid Concentrations in HIV-1 Infection

Raltegravir is an HIV-1 integrase inhibitor currently used in treatment-experienced HIV-1-infected patients resistant to other drug classes. In order to assess its central nervous system penetration, we measured raltegravir concentrations in cerebrospinal fluid (CSF) and plasma in subjects receiving antiretroviral treatment regimens containing this drug.Raltegravir concentrations were determined by liquid chromatography tandem mass spectrometry in 25 paired CSF and plasma samples from 16 HIV-1-infected individuals. The lower limit of quantitation was 2.0 ng/ml for CSF and 10 ng/ml for plasma.Twenty-four of the 25 CSF samples had detectable raltegravir concentrations with a median raltegravir concentration of 18.4 ng/ml (range, <2.0-126.0). The median plasma raltegravir concentration was 448 ng/ml (range, 37-5180). CSF raltegravir concentrations correlated with CSF:plasma albumin ratios and CSF albumin concentrations.Approximately 50% of the CSF specimens exceeded the IC(95) levels reported to inhibit HIV-1 strains without resistance to integrase inhibitors. In addition to contributing to control of systemic HIV-1 infection, raltegravir achieves local inhibitory concentrations in CSF in most, but not all, patients. Blood-brain and blood-CSF barriers likely restrict drug entry, while enhanced permeability of these barriers enhances drug entry

Outer-Sphere Contributions to the Electronic Structure of Type Zero Copper Proteins

Bioinorganic canon states that active-site thiolate coordination promotes rapid electron transfer (ET) to and from type 1 copper proteins. In recent work, we have found that copper ET sites in proteins also can be constructed without thiolate ligation (called “type zero” sites). Here we report multifrequency electron paramagnetic resonance (EPR), magnetic circular dichroism (MCD), and nuclear magnetic resonance (NMR) spectroscopic data together with density functional theory (DFT) and spectroscopy-oriented configuration interaction (SORCI) calculations for type zero Pseudomonas aeruginosa azurin variants. Wild-type (type 1) and type zero copper centers experience virtually identical ligand fields. Moreover, O-donor covalency is enhanced in type zero centers relative that in the C112D (type 2) protein. At the same time, N-donor covalency is reduced in a similar fashion to type 1 centers. QM/MM and SORCI calculations show that the electronic structures of type zero and type 2 are intimately linked to the orientation and coordination mode of the carboxylate ligand, which in turn is influenced by outer-sphere hydrogen bonding

X-ray absorption spectroscopy systematics at the tungsten L-edge

A series of mononuclear six-coordinate tungsten compounds spanning formal oxidation states from 0 to +VI, largely in a ligand environment of inert chloride and/or phosphine, has been interrogated by tungsten L-edge X-ray absorption spectroscopy. The L-edge spectra of this compound set, comprised of [W&lt;sup&gt;0&lt;/sup&gt;(PMe&lt;sub&gt;3&lt;/sub&gt;)&lt;sub&gt;6&lt;/sub&gt;], [W&lt;sup&gt;II&lt;/sup&gt;Cl&lt;sub&gt;2&lt;/sub&gt;(PMePh&lt;sub&gt;2&lt;/sub&gt;)&lt;sub&gt;4&lt;/sub&gt;], [W&lt;sup&gt;III&lt;/sup&gt;Cl&lt;sub&gt;2&lt;/sub&gt;(dppe)&lt;sub&gt;2&lt;/sub&gt;][PF&lt;sub&gt;6&lt;/sub&gt;] (dppe = 1,2-bis(diphenylphosphino)ethane), [W&lt;sup&gt;IV&lt;/sup&gt;Cl&lt;sub&gt;4&lt;/sub&gt;(PMePh&lt;sub&gt;2&lt;/sub&gt;)&lt;sub&gt;2&lt;/sub&gt;], [W&lt;sup&gt;V&lt;/sup&gt;(NPh)Cl&lt;sub&gt;3&lt;/sub&gt;(PMe&lt;sub&gt;3&lt;/sub&gt;)&lt;sub&gt;2&lt;/sub&gt;], and [W&lt;sup&gt;VI&lt;/sup&gt;Cl&lt;sub&gt;6&lt;/sub&gt;] correlate with formal oxidation state and have usefulness as references for the interpretation of the L-edge spectra of tungsten compounds with redox-active ligands and ambiguous electronic structure descriptions. The utility of these spectra arises from the combined correlation of the estimated branching ratio (EBR) of the L&lt;sub&gt;3,2&lt;/sub&gt;-edges and the L&lt;sub&gt;1&lt;/sub&gt; rising-edge energy with metal Z&lt;sub&gt;eff&lt;/sub&gt;, thereby permitting an assessment of effective metal oxidation state. An application of these reference spectra is illustrated by their use as backdrop for the L-edge X-ray absorption spectra of [W&lt;sup&gt;IV&lt;/sup&gt;(mdt)&lt;sub&gt;2&lt;/sub&gt;(CO)&lt;sub&gt;2&lt;/sub&gt;] and [W&lt;sup&gt;IV&lt;/sup&gt;(mdt)&lt;sub&gt;2&lt;/sub&gt;(CN)&lt;sub&gt;2&lt;/sub&gt;]&lt;sup&gt;2–&lt;/sup&gt; (mdt&lt;sup&gt;2–&lt;/sup&gt; = 1,2-dimethylethene-1,2-dithiolate), which shows that both compounds are effectively W&lt;sup&gt;IV&lt;/sup&gt; species. Use of metal L-edge XAS to assess a compound of uncertain formulation requires: 1) Placement of that data within the context of spectra offered by unambiguous calibrant compounds, preferably with the same coordination number and similar metal ligand distances. Such spectra assist in defining upper and/or lower limits for metal Z&lt;sub&gt;eff&lt;/sub&gt; in the species of interest; 2) Evaluation of that data in conjunction with information from other physical methods, especially ligand K-edge XAS; 3) Increased care in interpretation if strong π-acceptor ligands, particularly CO, or π-donor ligands are present. The electron-withdrawing/donating nature of these ligand types, combined with relatively short metal-ligand distances, exaggerate the difference between formal oxidation state and metal Z&lt;sub&gt;eff&lt;/sub&gt; or, as in the case of [W&lt;sup&gt;IV&lt;/sup&gt;(mdt)&lt;sub&gt;2&lt;/sub&gt;(CO)&lt;sub&gt;2&lt;/sub&gt;], add other subtlety by modulating the redox level of other ligands in the coordination sphere

Notes on Amanita section Validae in Hainan Island, China

Hainan is the second largest island in China with the most extensive and well-preserved tropical forests and is also the largest island of the Indo Burma Biodiversity Hotspot. It provides in situ conservation for the unique ecosystem of the island. Recent studies have shown that there are diverse fungal species in Hainan. In this study, about 40 collections of the genus Amanita have been studied based on the morphology and molecular systematics, including 35 Chinese specimens (24 from Hainan, and eleven from other regions) and three specimens from other countries (Singapore and Malaysia). In total, five new species belonging to Amanita section Validae are described: A. cacaina, A. parvigrisea, A. pseudofritillaria, A. pseudosculpta, and A. yangii. Amanita parvifritillaria is recorded for the first time in Hainan. It is also the first report of this fungus occurring, outside Yunnan Province, China. Among the five new species, two are unique in this section because of the appendiculate pileus margin and the absence of an annulus. Based on these new findings, the diagnosis of the section Validae should be slightly modified to include a few species with appendiculate margin and the lack of annulus

Biological, clinical and population relevance of 95 loci for blood lipids.

Plasma concentrations of total cholesterol, low-density lipoprotein cholesterol, high-density lipoprotein cholesterol and triglycerides are among the most important risk factors for coronary artery disease (CAD) and are targets for therapeutic intervention. We screened the genome for common variants associated with plasma lipids in &gt;100,000 individuals of European ancestry. Here we report 95 significantly associated loci (P &lt; 5 x 10(-8)), with 59 showing genome-wide significant association with lipid traits for the first time. The newly reported associations include single nucleotide polymorphisms (SNPs) near known lipid regulators (for example, CYP7A1, NPC1L1 and SCARB1) as well as in scores of loci not previously implicated in lipoprotein metabolism. The 95 loci contribute not only to normal variation in lipid traits but also to extreme lipid phenotypes and have an impact on lipid traits in three non-European populations (East Asians, South Asians and African Americans). Our results identify several novel loci associated with plasma lipids that are also associated with CAD. Finally, we validated three of the novel genes-GALNT2, PPP1R3B and TTC39B-with experiments in mouse models. Taken together, our findings provide the foundation to develop a broader biological understanding of lipoprotein metabolism and to identify new therapeutic opportunities for the prevention of CAD

Hundreds of variants clustered in genomic loci and biological pathways affect human height

Most common human traits and diseases have a polygenic pattern of inheritance: DNA sequence variants at many genetic loci influence the phenotype. Genome-wide association (GWA) studies have identified more than 600 variants associated with human traits, but these typically explain small fractions of phenotypic variation, raising questions about the use of further studies. Here, using 183,727 individuals, we show that hundreds of genetic variants, in at least 180 loci, influence adult height, a highly heritable and classic polygenic trait. The large number of loci reveals patterns with important implications for genetic studies of common human diseases and traits. First, the 180 loci are not random, but instead are enriched for genes that are connected in biological pathways (P = 0.016) and that underlie skeletal growth defects (P < 0.001). Second, the likely causal gene is often located near the most strongly associated variant: in 13 of 21 loci containing a known skeletal growth gene, that gene was closest to the associated variant. Third, at least 19 loci have multiple independently associated variants, suggesting that allelic heterogeneity is a frequent feature of polygenic traits, that comprehensive explorations of already-discovered loci should discover additional variants and that an appreciable fraction of associated loci may have been identified. Fourth, associated variants are enriched for likely functional effects on genes, being over-represented among variants that alter amino-acid structure of proteins and expression levels of nearby genes. Our data explain approximately 10% of the phenotypic variation in height, and we estimate that unidentified common variants of similar effect sizes would increase this figure to approximately 16% of phenotypic variation (approximately 20% of heritable variation). Although additional approaches are needed to dissect the genetic architecture of polygenic human traits fully, our findings indicate that GWA studies can identify large numbers of loci that implicate biologically relevant genes and pathways.