Computation of protein geometry and its applications: Packing and function prediction

This chapter discusses geometric models of biomolecules and geometric constructs, including the union of ball model, the weigthed Voronoi diagram, the weighted Delaunay triangulation, and the alpha shapes. These geometric constructs enable fast and analytical computaton of shapes of biomoleculres (including features such as voids and pockets) and metric properties (such as area and volume). The algorithms of Delaunay triangulation, computation of voids and pockets, as well volume/area computation are also described. In addition, applications in packing analysis of protein structures and protein function prediction are also discussed.Comment: 32 pages, 9 figure

Anatomical subgroup analysis of the MERIDIAN cohort: failed commissuration

Objective: To assess the contribution of in utero magnetic resonance (iuMR) imaging in fetuses diagnosed with either agenesis of the corpus callosum or hypogenesis of the corpus callosum (grouped as failed commissuration) on antenatal ultrasonography (USS) from the MERIDIAN cohort. Methods: We report a sub-group analysis of fetuses with failed commissuration diagnosed on USS (with or without ventriculomegaly) from the MERIDIAN study who had iuMR imaging within 2 weeks of USS and outcome reference data were available. The diagnostic accuracy of USS and iuMR are reported as well as indicators of diagnostic confidence and effects on prognosis/clinical management. Results: 79 fetuses with failed commissuration are reported (55 with agenesis and 24 with hypogenesis as the USS diagnoses). The diagnostic accuracy for detecting ‘failed commissuration’ as a group label was 34.2% for USS and 94.9% for iuMR (difference = 60.7%, 95% confidence interval 47.6% to 73.9%, p < 0.0001). The diagnostic accuracy for detecting hypogenesis of the corpus callosum as a discrete entity was 8.3% for USS and 87.5% for iuMR whilst the diagnostic accuracy for detecting agenesis of the corpus callosum as a distinct entity was 40.0% for USS and 92.7% for iuMR. There was a statistically significant improvement in ‘appropriate’ diagnostic confidence when using iuMR imaging as assessed by a score-based weighted average’ method (p < 0.0001). Prognostic information given to the women changed in 36/79 (45.6%) cases after iuMR imaging and its overall effect on clinical management was ‘significant’, ‘major’ or ‘decisive’ in 35/79 cases (44.3%). Conclusions: Our data suggests that any woman whose fetus has failed commissuration as the only intracranial finding detected on USS should have iuMR imaging for further evaluation

Ecological Invasion, Roughened Fronts, and a Competitor's Extreme Advance: Integrating Stochastic Spatial-Growth Models

Both community ecology and conservation biology seek further understanding of factors governing the advance of an invasive species. We model biological invasion as an individual-based, stochastic process on a two-dimensional landscape. An ecologically superior invader and a resident species compete for space preemptively. Our general model includes the basic contact process and a variant of the Eden model as special cases. We employ the concept of a "roughened" front to quantify effects of discreteness and stochasticity on invasion; we emphasize the probability distribution of the front-runner's relative position. That is, we analyze the location of the most advanced invader as the extreme deviation about the front's mean position. We find that a class of models with different assumptions about neighborhood interactions exhibit universal characteristics. That is, key features of the invasion dynamics span a class of models, independently of locally detailed demographic rules. Our results integrate theories of invasive spatial growth and generate novel hypotheses linking habitat or landscape size (length of the invading front) to invasion velocity, and to the relative position of the most advanced invader.Comment: The original publication is available at www.springerlink.com/content/8528v8563r7u2742

Cosmological parameters from SDSS and WMAP

We measure cosmological parameters using the three-dimensional power spectrum P(k) from over 200,000 galaxies in the Sloan Digital Sky Survey (SDSS) in combination with WMAP and other data. Our results are consistent with a ``vanilla'' flat adiabatic Lambda-CDM model without tilt (n=1), running tilt, tensor modes or massive neutrinos. Adding SDSS information more than halves the WMAP-only error bars on some parameters, tightening 1 sigma constraints on the Hubble parameter from h~0.74+0.18-0.07 to h~0.70+0.04-0.03, on the matter density from Omega_m~0.25+/-0.10 to Omega_m~0.30+/-0.04 (1 sigma) and on neutrino masses from <11 eV to <0.6 eV (95%). SDSS helps even more when dropping prior assumptions about curvature, neutrinos, tensor modes and the equation of state. Our results are in substantial agreement with the joint analysis of WMAP and the 2dF Galaxy Redshift Survey, which is an impressive consistency check with independent redshift survey data and analysis techniques. In this paper, we place particular emphasis on clarifying the physical origin of the constraints, i.e., what we do and do not know when using different data sets and prior assumptions. For instance, dropping the assumption that space is perfectly flat, the WMAP-only constraint on the measured age of the Universe tightens from t0~16.3+2.3-1.8 Gyr to t0~14.1+1.0-0.9 Gyr by adding SDSS and SN Ia data. Including tensors, running tilt, neutrino mass and equation of state in the list of free parameters, many constraints are still quite weak, but future cosmological measurements from SDSS and other sources should allow these to be substantially tightened.Comment: Minor revisions to match accepted PRD version. SDSS data and ppt figures available at http://www.hep.upenn.edu/~max/sdsspars.htm

Fitting the integrated Spectral Energy Distributions of Galaxies

Fitting the spectral energy distributions (SEDs) of galaxies is an almost universally used technique that has matured significantly in the last decade. Model predictions and fitting procedures have improved significantly over this time, attempting to keep up with the vastly increased volume and quality of available data. We review here the field of SED fitting, describing the modelling of ultraviolet to infrared galaxy SEDs, the creation of multiwavelength data sets, and the methods used to fit model SEDs to observed galaxy data sets. We touch upon the achievements and challenges in the major ingredients of SED fitting, with a special emphasis on describing the interplay between the quality of the available data, the quality of the available models, and the best fitting technique to use in order to obtain a realistic measurement as well as realistic uncertainties. We conclude that SED fitting can be used effectively to derive a range of physical properties of galaxies, such as redshift, stellar masses, star formation rates, dust masses, and metallicities, with care taken not to over-interpret the available data. Yet there still exist many issues such as estimating the age of the oldest stars in a galaxy, finer details ofdust properties and dust-star geometry, and the influences of poorly understood, luminous stellar types and phases. The challenge for the coming years will be to improve both the models and the observational data sets to resolve these uncertainties. The present review will be made available on an interactive, moderated web page (sedfitting.org), where the community can access and change the text. The intention is to expand the text and keep it up to date over the coming years.Comment: 54 pages, 26 figures, Accepted for publication in Astrophysics & Space Scienc

Gender differentials in the impact of parental death: Adolescent's sexual behaviour and risk of HIV infection in rural South Africa

Using data from a longitudinal surveillance study from rural South Africa, we investigated the odds of sexual debut, pregnancy and HIV infection of 15- to 19-year-old adolescents by parental survival. Using descriptive statistics and logistic regressions, we examine the relative risk of orphans compared with non-orphans to have ever had sex, being pregnant and being HIV infected, adjusting for age, sex, socio-economic status, education, being employed and residency. Of 8274 adolescents, 42% were orphaned (one or both parents died). Over 80% of adolescents remained in school, but orphans were significantly more likely to lag behind in grade for age. Female adolescent maternal (aOR 1.32, 95% CI 1.071.62), paternal (aOR 1.26, 95% CI 1.061.49) and dual (aOR 1.37, 95% CI 1.051.78) orphans were significantly more likely than non-orphaned females to have ever had sex; among males it was only paternal (aOR 1.27, 95% CI 1.051.53) orphans. Maternal (aOR 1.49, 95% CI 1.032.15) and dual (aOR 1.74, 95% CI 1.112.73) female orphans relative to non-orphaned females were significantly more likely to be HIV infected; male paternal (aOR 3.41, 95% CI 1.378.46) and dual (aOR 3.54, 95% CI 1.0611.86) orphans had over three-fold the odds of being infected. There was strong evidence that death of mother for girls was associated with increased vulnerability to earlier sexual debut and HIV infection, while fathers appeared to play a significant role in both their son's and daughter's lives

The phenotype of Floating-Harbor syndrome: Clinical characterization of 52 individuals with mutations in exon 34 of SRCAP

Background: Floating-Harbor syndrome (FHS) is a rare condition characterized by short stature, delays in expressive language, and a distinctive facial appearance. Recently, heterozygous truncating mutations in SRCAP were determined to be disease-causing. With the availability of a DNA based confirmatory test, we set forth to define the clinical features of this syndrome. Methods and results. Clinical information on fifty-two individuals with SRCAP mutations was collected using standardized questionnaires. Twenty-four males and twenty-eight females were studied with ages ranging from

Search for electroweak production of single top quarks in ppˉp\bar{p} collisions.

We present a search for electroweak production of single top quarks in the electron+jets and muon+jets decay channels. The measurements use ~90 pb^-1 of data from Run 1 of the Fermilab Tevatron collider, collected at 1.8 TeV with the DZero detector between 1992 and 1995. We use events that include a tagging muon, implying the presence of a b jet, to set an upper limit at the 95% confidence level on the cross section for the s-channel process ppbar->tb+X of 39 pb. The upper limit for the t-channel process ppbar->tqb+X is 58 pb. (arXiv

Measurement of the W+W- Production Cross Section in ppbar Collisions at sqrt(s)=1.96 TeV using Dilepton Events

We present a measurement of the W+W- production cross section using 184/pb of ppbar collisions at a center-of-mass energy of 1.96 TeV collected with the Collider Detector at Fermilab. Using the dilepton decay channel W+W- -> l+l-vvbar, where the charged leptons can be either electrons or muons, we find 17 candidate events compared to an expected background of 5.0+2.2-0.8 events. The resulting W+W- production cross section measurement of sigma(ppbar -> W+W-) = 14.6 +5.8 -5.1 (stat) +1.8 -3.0 (syst) +-0.9 (lum) pb agrees well with the Standard Model expectation.Comment: 8 pages, 2 figures, 2 tables. To be submitted to Physical Review Letter