Quantized Lattice Dynamic Effects on the Spin-Peierls Transition

The density matrix renormalization group method is used to investigate the spin-Peierls transition for Heisenberg spins coupled to quantized phonons. We use a phonon spectrum that interpolates between a gapped, dispersionless (Einstein) limit to a gapless, dispersive (Debye) limit. A variety of theoretical probes are used to determine the quantum phase transition, including energy gap crossing, a finite size scaling analysis, bond order auto-correlation functions, and bipartite quantum entanglement. All these probes indicate that in the antiadiabatic phonon limit a quantum phase transition of the Berezinskii-Kosterlitz-Thouless type is observed at a non-zero spin-phonon coupling, $g_{\text c}$. An extrapolation from the Einstein limit to the Debye limit is accompanied by an increase in $g_{\text c}$ for a fixed optical ($q=\pi$) phonon gap. We therefore conclude that the dimerized ground state is more unstable with respect to Debye phonons, with the introduction of phonon dispersion renormalizing the effective spin-lattice coupling for the Peierls-active mode. We also show that the staggered spin-spin and phonon displacement order parameters are unreliable means of determining the transition.Comment: To be published in Phys. Rev.

Quantifying microbial utilization of petroleum hydrocarbons in salt-marsh sediments using the ^(13)C content of bacterial rRNA

Natural remediation of oil spills is catalyzed by complex microbial consortia. Here we take a whole-community approach to investigate bacterial incorporation of petroleum hydrocarbons from a simulated oil spill. We utilized the natural difference in carbon-isotopic abundance between a salt marsh ecosystem supported by the ^(13)C-enriched C4 grass, Spartina alterniflora, and the ^(13)C-depleted composition of petroleum to monitor changes in the ^(13)C content of biomass. Magnetic-bead capture methods for the selective recovery of bacterial RNA were used to monitor the ^(13)C content of bacterial biomass during a two-week experiment. The data show that by the end of the experiment, up to 26% of bacterial biomass derived from consumption of the freshly-spilled oil. The results contrast with the inertness of a nearby relict spill, which occurred in 1969 in West Falmouth, MA. Sequences of 16S rRNA genes from our experimental samples also were consistent with previous reports suggesting the importance of {gamma}- and {delta}-Proteobacteria and Firmicutes in the remineralization of hydrocarbons. The magnetic-bead capture approach makes it possible to quantify uptake of petroleum hydrocarbons by microbes in-situ. Although employed here at the Domain level, RNA-capture procedures can be highly specific. The same strategy could be used with genus-level specificity, something which is not currently possible using the ^(13)C content of biomarker lipids

Homologous over-extension: a challenge for iterative similarity searches

We have characterized a novel type of PSI-BLAST error, homologous over-extension (HOE), using embedded PFAM domain queries on searches against a reference library containing Pfam-annotated UniProt sequences and random synthetic sequences. PSI-BLAST makes two types of errors: alignments to non-homologous regions and HOE alignments that begin in a homologous region, but extend beyond the homology into neighboring sequence regions. When the neighboring sequence region contains a non-homologous domain, PSI-BLAST can incorporate the unrelated sequence into its position specific scoring matrix, which then finds non-homologous proteins with significant expectation values. HOE accounts for the largest fraction of the initial false positive (FP) errors, and the largest fraction of FPs at iteration 5. In searches against complete protein sequences, 5–9% of alignments at iteration 5 are non-homologous. HOE frequently begins in a partial protein domain; when partial domains are removed from the library, HOE errors decrease from 16 to 3% of weighted coverage (hard queries; 35–5% for sampled queries) and no-error searches increase from 2 to 58% weighed coverage (hard; 16–78% sampled). When HOE is reduced by not extending previously found sequences, PSI-BLAST specificity improves 4–8-fold, with little loss in sensitivity

Feasibility of National Surveillance of Health-Care-Associated Infections in Home-Care Settings

This article examines the rationale and strategies for surveillance of health-care-associated infections in home-care settings, the challenges of nonhospital-based surveillance, and the feasibility of developing a national surveillance system

The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues identified in enzymes.

Understanding which are the catalytic residues in an enzyme and what function they perform is crucial to many biology studies, particularly those leading to new therapeutics and enzyme design. The original version of the Catalytic Site Atlas (CSA) (http://www.ebi.ac.uk/thornton-srv/databases/CSA) published in 2004, which catalogs the residues involved in enzyme catalysis in experimentally determined protein structures, had only 177 curated entries and employed a simplistic approach to expanding these annotations to homologous enzyme structures. Here we present a new version of the CSA (CSA 2.0), which greatly expands the number of both curated (968) and automatically annotated catalytic sites in enzyme structures, utilizing a new method for annotation transfer. The curated entries are used, along with the variation in residue type from the sequence comparison, to generate 3D templates of the catalytic sites, which in turn can be used to find catalytic sites in new structures. To ease the transfer of CSA annotations to other resources a new ontology has been developed: the Enzyme Mechanism Ontology, which has permitted the transfer of annotations to Mechanism, Annotation and Classification in Enzymes (MACiE) and UniProt Knowledge Base (UniProtKB) resources. The CSA database schema has been re-designed and both the CSA data and search capabilities are presented in a new modern web interface

Onset of Surface-Tension-Driven Benard Convection

Experiments with shadowgraph visualization reveal a subcritical transition to a hexagonal convection pattern in thin liquid layers that have a free upper surface and are heated from below. The measured critical Marangoni number (84) and observation of hysteresis (3%) agree with theory. In some experiments, imperfect bifurcation is observed and is attributed to deterministic forcing caused in part by the lateral boundaries in the experiment.Comment: 4 pages. The RevTeX file has a macro allowing various styles. The appropriate style is "mypprint" which is the defaul

Determining the Cosmic Distance Scale from Interferometric Measurements of the Sunyaev-Zel'dovich Effect

We determine the distances to 18 galaxy clusters with redshifts ranging from z~0.14 to z~0.78 from a maximum likelihood joint analysis of 30 GHz interferometric Sunyaev-Zel'dovich effect (SZE) and X-ray observations. We model the intracluster medium (ICM) using a spherical isothermal beta model. We quantify the statistical and systematic uncertainties inherent to these direct distance measurements, and we determine constraints on the Hubble parameter for three different cosmologies. These distances imply a Hubble constant of 60 (+4, -4) (+13, -18) km s-1 Mpc-1 for an Omega_M = 0.3, Omega_Lambda = 0.7 cosmology, where the uncertainties correspond to statistical followed by systematic at 68% confidence. With a sample of 18 clusters, systematic uncertainties clearly dominate. The systematics are observationally approachable and will be addressed in the coming years through the current generation of X-ray satellites (Chandra & XMM-Newton) and radio observatories (OVRO, BIMA, & VLA). Analysis of high redshift clusters detected in future SZE and X-ray surveys will allow a determination of the geometry of the universe from SZE determined distances.Comment: ApJ Submitted; 40 pages, 9 figures (fig 3 B&W for size constraint), 13 tables, uses emulateapj5 styl

Searching for Planets in the Hyades II: Some Implications of Stellar Magnetic Activity

The Hyades constitute a homogeneous sample of stars ideal for investigating the dependence of planet formation on the mass of the central star. Due to their youth, Hyades members are much more chromospherically active than stars traditionally surveyed for planets using high precision radial velocity (RV) techniques. Therefore, we have conducted a detailed investigation of whether magnetic activity of our Hyades target stars will interfere with our ability to make precise RV searches for substellar companions. We measure chromospheric activity (which we take as a proxy for magnetic activity) by computing the equivalent of the R'HK activity index from the Ca II K line. is not constant in the Hyades: we confirm that it decreases with increasing temperature in the F stars, and also find it decreases for stars cooler than mid-K. We examine correlations between simultaneously measured R'HK and RV using both a classical statistical test and a Bayesian odds ratio test. We find that there is a significant correlation between R'HK and the RV in only 5 of the 82 stars in this sample. Thus, simple Rprime HK-RV correlations will generally not be effective in correcting the measured RV values for the effects of magnetic activity in the Hyades. We argue that this implies long timescale activity variations (of order a few years; i.e., magnetic cycles or growth and decay of plage regions) will not significantly hinder our search for planets in the Hyades if the stars are closely monitored for chromospheric activity. The trends in the RV scatter (sigma'_v) with , vsini, and P_rot for our stars is generally consistent with those found in field stars in the Lick planet search data, with the notable exception of a shallower dependence of sigma'_v on for F stars.Comment: 15 pages, 7 figures, 3 tables; To appear in the July 2002 issue of The Astronomical Journa

Time trends in prescribing of type 2 diabetes drugs, glycaemic response and risk factors:a retrospective analysis of primary care data, 2010-2017

This is the author accepted manuscript. The final version is available on open access from Wiley via the DOI in this recordAim: Prescribing in type 2 diabetes has changed markedly in recent years, with increasing use of newer, more expensive glucose-lowering drugs. We aimed to describe population-level time trends in both prescribing patterns and short-term patient outcomes (HbA1c, weight, blood pressure, hypoglycemia and treatment discontinuation) after initiating new therapy. Materials and methods: We studied 81,532 UK patients with type 2 diabetes initiating a first to fourth line drug in primary care between 2010-2017 inclusive (Clinical Practice Research Datalink). Trends in new prescriptions and subsequent six and twelve-month adjusted changes in glycemic response (reduction in HbA1c), weight, blood pressure, and rates of hypoglycemia and treatment discontinuation were examined. Results: DPP4-inhibitor use second-line near doubled (41% of new prescriptions in 2017 vs. 22% 2010), replacing sulfonylureas as the most common second-line drug (29% 2017 vs. 53% 2010). SGLT2-inhibitors, introduced in 2013, comprised 17% of new first-fourth line prescriptions by 2017. First-line use of metformin remained stable (91% of new prescriptions in 2017 vs. 91% 2010). Over the study period there was little change in average glycemic response and treatment discontinuation. There was a modest reduction in weight second and third-line (second line 2017 vs. 2010: -1.5 kg (95%CI -1.9;-1.1), p<0.001), and a slight reduction in systolic blood pressure first to third-line (2017 vs. 2010 difference range -1.7 to -2.1 mmHg, all p<0.001). Hypoglycemia rates decreased second-line (incidence rate ratio 0.94 per-year (95%CI 0.88;1.00, p=0.04)), mirroring the decline in use of sulfonylureas. 4 Conclusions: Recent changes in prescribing of therapy in type 2 diabetes have not led to a change in glycemic response and have resulted in modest improvements in other population-level short-term patient outcomes.Medical Research Council (MRC)National Institute for Health Research (NIHR)Wellcome Trus