Computational inference in systems biology

Parameter inference in mathematical models of biological pathways, expressed as coupled ordinary differential equations (ODEs), is a challenging problem. The computational costs associated with repeatedly solving the ODEs are often high. Aimed at reducing this cost, new concepts using gradient matching have been proposed. This paper combines current adaptive gradient matching approaches, using Gaussian processes, with a parallel tempering scheme, and conducts a comparative evaluation with current methods used for parameter inference in ODEs

Building momentum for business school curriculum change: Measurable lessons from a pilot course in real business experience

Curriculum change requires thoughtful planning and a willingness to experiment with different modes of content delivery. While many business schools are experimenting, few measure student outcomes against the traditional courses they replace. One element of Butler University\u27s College of Business Administration curriculum revision was a pilot course, Real Business Experience , in which students developed a professional business plan, sought and received funding from a professional level funding panel, and ran their businesses. To determine whether the pilot course was successful in reaching its goal of teaching students about the messiness of business and developing more adaptable and confident business leaders assessment instruments were used to identify student development in both the pilot and traditional courses. The analysis presented in this article suggests that the pilot course utilizing the constructivist approach was successful in achieving its goal, but not always in the ways expected

Extended Stromgren Photoelectric Photometry in NGC 752

Photoelectric photometry on the extended Stromgren system (uvbyCa) is presented for 7 giants and 21 main sequence stars in the old open cluster, NGC 752. Analysis of the hk data for the turnoff stars yields a new determination of the cluster mean metallicity. From 10 single-star members, [Fe/H] = -0.06 +/- 0.03, where the error quoted is the standard error of the mean and the Hyades abundance is set at [Fe/H] = +0.12. This result is unchanged if all 20 stars within the limits of the hk metallicity calibration are included. The derived [Fe/H] is in excellent agreement with past estimates using properly-zeroed m1 data, transformed moderate-dispersion spectroscopy, and recent high dispersion spectroscopy.Comment: 14 tex'd pages including 2 tables; 2 separate files with eps figures Accepted for PASP March 200

Monitoring the impacts of trade agreements on food environments

The liberalization of international trade and foreign direct investment through multilateral, regional and bilateral agreements has had profound implications for the structure and nature of food systems, and therefore, for the availability, nutritional quality, accessibility, price and promotion of foods in different locations. Public health attention has only relatively recently turned to the links between trade and investment agreements, diets and health, and there is currently no systematic monitoring of this area. This paper reviews the available evidence on the links between trade agreements, food environments and diets from an obesity and non-communicable disease (NCD) perspective. Based on the key issues identified through the review, the paper outlines an approach for monitoring the potential impact of trade agreements on food environments and obesity/NCD risks. The proposed monitoring approach encompasses a set of guiding principles, recommended procedures for data collection and analysis, and quantifiable ‘minimal’, ‘expanded’ and ‘optimal’ measurement indicators to be tailored to national priorities, capacity and resources. Formal risk assessment processes of existing and evolving trade and investment agreements, which focus on their impacts on food environments will help inform the development of healthy trade policy, strengthen domestic nutrition and health policy space and ultimately protect population nutrition.The following organizations provided funding support for the travel of participants to Italy for this meeting and the preparation of background research papers: The Rockefeller Foundation, International Obesity Taskforce (IOTF), University of Auckland, Deakin University, The George Institute, University of Sydney, Queensland University of Technology, University of Oxford, University of Pennsylvania Perelman School of Medicine, World Cancer Research Fund International, University of Toronto, and The Australian National University. The Faculty of Health at Deakin University kindly supported the costs for open access availability of this paper, and the Australian National Health and Medical Research Council Centre for Research Excellence in Obesity Policy and Food Systems (APP1041020) supported the coordination and finalizing of INFORMAS manuscripts

Using diffusion tensor imaging to identify corticospinal tract projection patterns in children with unilateral spastic cerebral palsy.

AIM: To determine whether diffusion tensor imaging (DTI) can be an independent assessment for identifying the corticospinal tract (CST) projecting from the more-affected motor cortex in children with unilateral spastic cerebral palsy (CP). METHOD: Twenty children with unilateral spastic CP participated in this study (16 males, four females; mean age 9y 2mo [standard deviation (SD) 3y 2mo], Manual Ability Classification System [MACS] level I-III). We used DTI tractography to reconstruct the CST projecting from the more-affected motor cortex. We mapped the motor representation of the more-affected hand by stimulating the more- and the less-affected motor cortex measured with single-pulse transcranial magnetic stimulation (TMS). We then verified the presence or absence of the contralateral CST by comparing the TMS map and DTI tractography. Fisher's exact test was used to determine the association between findings of TMS and DTI. RESULTS: DTI tractography successfully identified the CST controlling the more-affected hand (sensitivity=82%, specificity=78%). INTERPRETATION: Contralateral CST projecting from the lesioned motor cortex assessed by DTI is consistent with findings of TMS mapping. Since CST connectivity may be predictive of response to certain upper extremity treatments, DTI-identified CST connectivity may potentially be valuable for determining such connectivity where TMS is unavailable or inadvisable for children with seizures.K08 NS073796 - NINDS NIH HHS; TL1 RR024158 - NCRR NIH HHS; K01 NS062116 - NINDS NIH HHS; UL1 RR024156 - NCRR NIH HHS; KL2 RR024157 - NCRR NIH HHS; R01 HD076436 - NICHD NIH HHSPublished versio

Abundance Gradients and the Formation of the Milky Way

In this paper we adopt a chemical evolution model, which is an improved version of the Chiappini, Matteucci and Gratton (1997) model, assuming two main accretion episodes for the formation of the Galaxy. The present model takes into account in more detail than previously the halo density distribution and explores the effects of a threshold density in the star formation process, during both the halo and disk phases. In the comparison between model predictions and available data, we have focused our attention on abundance gradients as well as gas, stellar and star formation rate distributions along the disk. We suggest that the mechanism for the formation of the halo leaves detectable imprints on the chemical properties of the outer regions of the disk, whereas the evolution of the halo and the inner disk are almost completely disentangled. This is due to the fact that the halo and disk densities are comparable at large Galactocentric distances and therefore the gas lost from the halo can substantially contribute to building up the outer disk. We also show that the existence of a threshold density for the star formation rate, both in the halo and disk phase, is necessary to reproduce the majority of observational data in the solar vicinity and in the whole disk. Moreover, we predict that the abundance gradients along the Galactic disk must have increased with time and that the average [alpha/Fe] ratio in stars (halo plus disk) slightly decrease going from 4 to 10 Kpcs from the Galactic center. We also show that the same ratios increase substantially towards the outermost disk regions and the expected scatter in the stellar ages decreases, because the outermost regions are dominated by halo stars.Comment: 41 pages (including the figures), To be published in Ap

vbyCaHbeta CCD Photometry of Clusters. VI. The Metal-Deficient Open Cluster NGC 2420

CCD photometry on the intermediate-band vbyCaHbeta system is presented for the metal-deficient open cluster, NGC 2420. Restricting the data to probable single members of the cluster using the CMD and the photometric indices alone generates a sample of 106 stars at the cluster turnoff. The average E(b-y) = 0.03 +/- 0.003 (s.e.m.) or E(B-V) = 0.050 +/- 0.004 (s.e.m.), where the errors refer to internal errors alone. With this reddening, [Fe/H] is derived from both m1 and hk, using b-y and Hbeta as the temperature index. The agreement among the four approaches is reasonable, leading to a final weighted average of [Fe/H] = -0.37 +/- 0.05 (s.e.m.) for the cluster, on a scale where the Hyades has [Fe/H] = +0.12. When combined with the abundances from DDO photometry and from recalibrated low-resolution spectroscopy, the mean metallicity becomes [Fe/H] = -0.32 +/- 0.03. It is also demonstrated that the average cluster abundances based upon either DDO data or low-resolution spectroscopy are consistently reliable to 0.05 dex or better, contrary to published attempts to establish an open cluster metallicity scale using simplistic offset corrections among different surveys.Comment: scheduled for Jan. 2006 AJ; 33 pages, latex, includes 7 figures and 2 table

Stellar Evolution in NGC 6791: Mass Loss on the Red Giant Branch and the Formation of Low Mass White Dwarfs

We present the first detailed study of the properties (temperatures, gravities, and masses) of the NGC 6791 white dwarf population. This unique stellar system is both one of the oldest (8 Gyr) and most metal-rich ([Fe/H] ~ 0.4) open clusters in our Galaxy, and has a color-magnitude diagram (CMD) that exhibits both a red giant clump and a much hotter extreme horizontal branch. Fitting the Balmer lines of the white dwarfs in the cluster, using Keck/LRIS spectra, suggests that most of these stars are undermassive, = 0.43 +/- 0.06 Msun, and therefore could not have formed from canonical stellar evolution involving the helium flash at the tip of the red giant branch. We show that at least 40% of NGC 6791's evolved stars must have lost enough mass on the red giant branch to avoid the flash, and therefore did not convert helium into carbon-oxygen in their core. Such increased mass loss in the evolution of the progenitors of these stars is consistent with the presence of the extreme horizontal branch in the CMD. This unique stellar evolutionary channel also naturally explains the recent finding of a very young age (2.4 Gyr) for NGC 6791 from white dwarf cooling theory; helium core white dwarfs in this cluster will cool ~3 times slower than carbon-oxygen core stars and therefore the corrected white dwarf cooling age is in fact ~7 Gyr, consistent with the well measured main-sequence turnoff age. These results provide direct empirical evidence that mass loss is much more efficient in high metallicity environments and therefore may be critical in interpreting the ultraviolet upturn in elliptical galaxies.Comment: 15 pages, 9 figures, 2 tables. Accepted for publication in Astrophys. J. Very minor changes from first versio

vbyCaHbeta CCD Photometry of Clusters. VIII. The Super-Metal Rich, Old Open Cluster NGC 6791

CCD photometry on the intermediate-band vbyCaHbeta system is presented for the metal-rich, old open cluster, NGC 6791. Preliminary analysis led to [Fe/H] above +0.4 with an anomalously high reddening and an age below 5 Gyr. A revised calibration between (b-y)_0 and [Fe/H] at a given temperature shows that the traditional color-metallicity relations underestimate the color of the turnoff stars at high metallicity. With the revised relation, the metallicity from hk and the reddening for NGC 6791 become [Fe/H] = +0.45 +/- 0.04 and E(b-y) = 0.113 +/- 0.012 or E(B-V) = 0.155 +/- 0.016. Using the same technique, reanalysis of the photometry for NGC 6253 produces [Fe/H] = +0.58 +/-0.04 and E(b-y) = 0.120 +/- 0.018 or E(B-V) = 0.160 +/- 0.025. The errors quoted include both the internal and external errors. For NGC 6791, the metallicity from m_1 is a factor of two below that from hk, a result that may be coupled to the consistently low metal abundance from DDO photometry of the cluster and the C-deficiency found from high dispersion spectroscopy. E(B-V) is the same value predicted from Galactic reddening maps. With E(B-V) = 0.15 and [Fe/H] = +0.45, the available isochrones predict an age of 7.0 +/- 1.0 Gyr and an apparent modulus of (m-M) = 13.60 +/- 0.15, with the dominant source of the uncertainty arising from inconsistencies among the isochrones. The reanalysis of NGC 6253 with the revised lower reddening confirms that on both the hk and m_1 metallicity scales, NGC 6253, while less than half the age of NGC 6791, remains at least as metal-rich as NGC 6791, if not richer.Comment: Accepted for Astronomical Journal. 42 p. latex file includes 11 figures and 3 tables, one of which is a short version of a data table to appear in online AJ in its entiret