Symbolic vector/dyadic multibody formalism for tree-topology systems

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/76159/1/AIAA-20780-671.pd

Is the Hexacyanoferrate(II) Anion Stable in Aqueous Solution? A Combined Theoretical and Experimental Study

A combined theoretical and experimental study was performed to elucidate the structural and dynamical properties of the isolated aqueous hexacyanoferrate(II) ion as well as in the presence of potassium counterions. It is shown that in absence of counterions, the highly negatively charged hexacyanoferrate(II) complex is not stable in aqueous solution. However, if the high negative charge is compensated by potassium counterions, a stable complex is observed, which is proven by theoretical simulations as well as by extended X-ray absorption fine structure (EXAFS) experiments. From the simulation it is found that potassium ions surrounding the complex are highly mobile and thus cannot be observed via EXAFS experiments. The structure of aqueous hexacyanoferrate(II) in the presence of potassium ions is identical to that of the solid-state structure, but the mobility of potassium ions is significantly increased in the liquid. These highly mobile potassium ions circulating the complex are the reason for the very short lifetime of hydrogen bonds between solvent water molecules and cyanide ligands being on the femtosecond scale

The MUSIC of CLASH: predictions on the concentration-mass relation

We present the results of a numerical study based on the analysis of the MUSIC-2 simulations, aimed at estimating the expected concentration-mass relation for the CLASH cluster sample. We study nearly 1400 halos simulated at high spatial and mass resolution, which were projected along many lines-of-sight each. We study the shape of both their density and surface-density profiles and fit them with a variety of radial functions, including the Navarro-Frenk-White, the generalised Navarro-Frenk-White, and the Einasto density profiles. We derive concentrations and masses from these fits and investigate their distributions as a function of redshift and halo relaxation. We use the X-ray image simulator X-MAS to produce simulated Chandra observations of the halos and we use them to identify objects resembling the X-ray morphologies and masses of the clusters in the CLASH X-ray selected sample. We also derive a concentration-mass relation for strong-lensing clusters. We find that the sample of simulated halos which resemble the X-ray morphology of the CLASH clusters is composed mainly by relaxed halos, but it also contains a significant fraction of un-relaxed systems. For such a sample we measure an average 2D concentration which is ~11% higher than found for the full sample of simulated halos. After accounting for projection and selection effects, the average NFW concentrations of CLASH clusters are expected to be intermediate between those predicted in 3D for relaxed and super-relaxed halos. Matching the simulations to the individual CLASH clusters on the basis of the X-ray morphology, we expect that the NFW concentrations recovered from the lensing analysis of the CLASH clusters are in the range [3-6], with an average value of 3.87 and a standard deviation of 0.61. Simulated halos with X-ray morphologies similar to those of the CLASH clusters are affected by a modest orientation bias.Comment: 21 pages, 16 figures, 3 tables, submitted to Ap

Transcriptional Regulation of Multi-Drug Tolerance and Antibiotic-Induced Responses by the Histone-Like Protein Lsr2 in M. tuberculosis

Multi-drug tolerance is a key phenotypic property that complicates the sterilization of mammals infected with Mycobacterium tuberculosis. Previous studies have established that iniBAC, an operon that confers multi-drug tolerance to M. bovis BCG through an associated pump-like activity, is induced by the antibiotics isoniazid (INH) and ethambutol (EMB). An improved understanding of the functional role of antibiotic-induced genes and the regulation of drug tolerance may be gained by studying the factors that regulate antibiotic-mediated gene expression. An M. smegmatis strain containing a lacZ gene fused to the promoter of M. tuberculosis iniBAC (PiniBAC) was subjected to transposon mutagenesis. Mutants with constitutive expression and increased EMB-mediated induction of PiniBAC::lacZ mapped to the lsr2 gene (MSMEG6065), a small basic protein of unknown function that is highly conserved among mycobacteria. These mutants had a marked change in colony morphology and generated a new polar lipid. Complementation with multi-copy M. tuberculosis lsr2 (Rv3597c) returned PiniBAC expression to baseline, reversed the observed morphological and lipid changes, and repressed PiniBAC induction by EMB to below that of the control M. smegmatis strain. Microarray analysis of an lsr2 knockout confirmed upregulation of M. smegmatis iniA and demonstrated upregulation of genes involved in cell wall and metabolic functions. Fully 121 of 584 genes induced by EMB treatment in wild-type M. smegmatis were upregulated (“hyperinduced”) to even higher levels by EMB in the M. smegmatis lsr2 knockout. The most highly upregulated genes and gene clusters had adenine-thymine (AT)–rich 5-prime untranslated regions. In M. tuberculosis, overexpression of lsr2 repressed INH-mediated induction of all three iniBAC genes, as well as another annotated pump, efpA. The low molecular weight and basic properties of Lsr2 (pI 10.69) suggested that it was a histone-like protein, although it did not exhibit sequence homology with other proteins in this class. Consistent with other histone-like proteins, Lsr2 bound DNA with a preference for circular DNA, forming large oligomers, inhibited DNase I activity, and introduced a modest degree of supercoiling into relaxed plasmids. Lsr2 also inhibited in vitro transcription and topoisomerase I activity. Lsr2 represents a novel class of histone-like proteins that inhibit a wide variety of DNA-interacting enzymes. Lsr2 appears to regulate several important pathways in mycobacteria by preferentially binding to AT-rich sequences, including genes induced by antibiotics and those associated with inducible multi-drug tolerance. An improved understanding of the role of lsr2 may provide important insights into the mechanisms of action of antibiotics and the way that mycobacteria adapt to stresses such as antibiotic treatment

Symbolic computer language for multibody systems

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/76245/1/AIAA-20770-590.pd

Galaxy clusters discovered with a Sunyaev-Zel'dovich effect survey

The South Pole Telescope (SPT) is conducting a Sunyaev-Zel'dovich (SZ) effect survey over large areas of the southern sky, searching for massive galaxy clusters to high redshift. In this preliminary study, we focus on a 40 square-degree area targeted by the Blanco Cosmology Survey (BCS), which is centered roughly at right ascension 5h30m, declination -53 degrees. Over two seasons of observations, this entire region has been mapped by the SPT at 95 GHz, 150 GHz, and 225 GHz. We report the four most significant SPT detections of SZ clusters in this field, three of which were previously unknown and, therefore, represent the first galaxy clusters discovered with an SZ survey. The SZ clusters are detected as decrements with greater than 5-sigma significance in the high-sensitivity 150 GHz SPT map. The SZ spectrum of these sources is confirmed by detections of decrements at the corresponding locations in the 95 GHz SPT map and non-detections at those locations in the 225 GHz SPT map. Multiband optical images from the BCS survey demonstrate significant concentrations of similarly colored galaxies at the positions of the SZ detections. Photometric redshift estimates from the BCS data indicate that two of the clusters lie at moderate redshift (z ~ 0.4) and two at high redshift (z >~ 0.8). One of the SZ detections was previously identified as a galaxy cluster using X-ray data from the ROSAT All-Sky Survey (RASS). Potential RASS counterparts (not previously identified as clusters) are also found for two of the new discoveries. These first four galaxy clusters are the most significant SZ detections from a subset of the ongoing SPT survey. As such, they serve as a demonstration that SZ surveys, and the SPT in particular, can be an effective means for finding galaxy clusters.Comment: 11 pages, 3 figures, revised to match published version, uses emulateap

Measurements of Secondary Cosmic Microwave Background Anisotropies with the South Pole Telescope

We report cosmic microwave background (CMB) power spectrum measurements from the first 100 sq. deg. field observed by the South Pole Telescope (SPT) at 150 and 220 GHz. On angular scales where the primary CMB anisotropy is dominant, ell ~< 3000, the SPT power spectrum is consistent with the standard LambdaCDM cosmology. On smaller scales, we see strong evidence for a point source contribution, consistent with a population of dusty, star-forming galaxies. After we mask bright point sources, anisotropy power on angular scales of 3000 50 at both frequencies. We combine the 150 and 220 GHz data to remove the majority of the point source power, and use the point source subtracted spectrum to detect Sunyaev-Zel'dovich (SZ) power at 2.6 sigma. At ell=3000, the SZ power in the subtracted bandpowers is 4.2 +/- 1.5 uK^2, which is significantly lower than the power predicted by a fiducial model using WMAP5 cosmological parameters. This discrepancy may suggest that contemporary galaxy cluster models overestimate the thermal pressure of intracluster gas. Alternatively, this result can be interpreted as evidence for lower values of sigma8. When combined with an estimate of the kinetic SZ contribution, the measured SZ amplitude shifts sigma8 from the primary CMB anisotropy derived constraint of 0.794 +/- 0.028 down to 0.773 +/- 0.025. The uncertainty in the constraint on sigma8 from this analysis is dominated by uncertainties in the theoretical modeling required to predict the amplitude of the SZ power spectrum for a given set of cosmological parameters.Comment: 28 pages, 11 figures, submitted to Ap

Risk-adjusted CUSUM control charts for shared frailty survival models with application to hip replacement outcomes: a study using the NJR dataset

Background:  Continuous monitoring of surgical outcomes after joint replacement is needed to detect which brands’ components have a higher than expected failure rate and are therefore no longer recommended to be used in surgical practice. We developed a monitoring method based on cumulative sum (CUSUM) chart specifically for this application.  Methods:  Our method entails the use of the competing risks model with the Weibull and the Gompertz hazard functions adjusted for observed covariates to approximate the baseline time-to-revision and time-to-death distributions, respectively. The correlated shared frailty terms for competing risks, corresponding to the operating unit, are also included in the model. A bootstrap-based boundary adjustment is then required for risk-adjusted CUSUM charts to guarantee a given probability of the false alarm rates. We propose a method to evaluate the CUSUM scores and the adjusted boundary for a survival model with the shared frailty terms. We also introduce a unit performance quality score based on the posterior frailty distribution. This method is illustrated using the 2003-2012 hip replacement data from the UK National Joint Registry (NJR). Results:  We found that the best model included the shared frailty for revision but not for death. This means that the competing risks of revision and death are independent in NJR data. Our method was superior to the standard NJR methodology. For one of the two monitored components, it produced alarms four years before the increased failure rate came to the attention of the UK regulatory authorities. The hazard ratios of revision across the units varied from 0.38 to 2.28. Conclusions:  An earlier detection of failure signal by our method in comparison to the standard method used by the NJR may be explained by proper risk-adjustment and the ability to accommodate time-dependent hazards. The continuous monitoring of hip replacement outcomes should include risk adjustment at both the individual and unit level

SSWAP: A Simple Semantic Web Architecture and Protocol for semantic web services

<p>Abstract</p> <p>Background</p> <p>SSWAP (<b>S</b>imple <b>S</b>emantic <b>W</b>eb <b>A</b>rchitecture and <b>P</b>rotocol; pronounced "swap") is an architecture, protocol, and platform for using reasoning to semantically integrate heterogeneous disparate data and services on the web. SSWAP was developed as a hybrid semantic web services technology to overcome limitations found in both pure web service technologies and pure semantic web technologies.</p> <p>Results</p> <p>There are currently over 2400 resources published in SSWAP. Approximately two dozen are custom-written services for QTL (Quantitative Trait Loci) and mapping data for legumes and grasses (grains). The remaining are wrappers to Nucleic Acids Research Database and Web Server entries. As an architecture, SSWAP establishes how clients (users of data, services, and ontologies), providers (suppliers of data, services, and ontologies), and discovery servers (semantic search engines) interact to allow for the description, querying, discovery, invocation, and response of semantic web services. As a protocol, SSWAP provides the vocabulary and semantics to allow clients, providers, and discovery servers to engage in semantic web services. The protocol is based on the W3C-sanctioned first-order description logic language OWL DL. As an open source platform, a discovery server running at <url>http://sswap.info</url> (as in to "swap info") uses the description logic reasoner Pellet to integrate semantic resources. The platform hosts an interactive guide to the protocol at <url>http://sswap.info/protocol.jsp</url>, developer tools at <url>http://sswap.info/developer.jsp</url>, and a portal to third-party ontologies at <url>http://sswapmeet.sswap.info</url> (a "swap meet").</p> <p>Conclusion</p> <p>SSWAP addresses the three basic requirements of a semantic web services architecture (<it>i.e</it>., a common syntax, shared semantic, and semantic discovery) while addressing three technology limitations common in distributed service systems: <it>i.e</it>., <it>i</it>) the fatal mutability of traditional interfaces, <it>ii</it>) the rigidity and fragility of static subsumption hierarchies, and <it>iii</it>) the confounding of content, structure, and presentation. SSWAP is novel by establishing the concept of a canonical yet mutable OWL DL graph that allows data and service providers to describe their resources, to allow discovery servers to offer semantically rich search engines, to allow clients to discover and invoke those resources, and to allow providers to respond with semantically tagged data. SSWAP allows for a mix-and-match of terms from both new and legacy third-party ontologies in these graphs.</p