Modelling Grassland Ecosystems

In this contribution a view of the promise and difficulties of modelling grassland is given. This is largely centred around work with a grassland ecosystem simulator known as the Hurley Pasture Model. A brief introduction sets forth possible reasons for building a large ecosystem model, and stresses the importance of modelling objectives. It is suggested that a model is de rigeur for any research programme which aims to take a firm grasp of the complex responses of grassland. Mechanistic models are required to provide the understanding needed for intelligent and flexible management of grassland, whatever the prevailing environmental or economic objectives. The models are necessarily large, reflecting the complexity of the ‘real’ system, and, in a sense, are ‘big’ science. The challenge is to develop models of ‘engineering strength’. This requires an appropriate research environment, which should be reasonably stable, multidisciplinary, well-connected to experimental programmes, and permit adequate support for the three essential legs of an ecosystem model: development, documentation, and application. Some modelling researchers are dismayed by the wasteful fragmentation of many plant ecosystem modelling research programmes. Next an outline account of the Hurley Pasture Model (HPM) is given. Most plant ecosystem models are now quite similar at the qualitative level, and few would dispute the statement that a reasonable level of consensus is emerging. The HPM is a standard model of the genre. It comprises plant, animal, soil and water submodels. To-date there is no phenology submodel. There are environmental and management drivers, the former accepting monthly, daily or diurnal data, the latter permitting the simulation of fertilizer, grazing, and cutting scenarios, more or less ad libitum. Recent developments of the HPM include a submodel to take account of acclimation of photosynthesis to light, nitrogen, carbon dioxide (‘down-regulation’) and temperature; and a simple method of using the HPM to simulate legume dynamics in a grass-legume pasture. Finally, some applications of the model are presented, relating to fertilizer application, grazing, harvesting, and climate change. These are to illustrate the scope of the model, for both application and understanding. The last application shows that in grassland ecosystems climate change responses can be greatly affected by (i) a variable legume content; (ii) management, e.g. how the crop is grazed or cut; and (iii) water stress, as occurs in southern Britain. The impact of climate change on grassland ecosystems is of particular interest. It is known that, in a constant climate, a grassland ecosystem can take hundreds of years to come to equilibrium. Experiments cannot address the problem directly. Short-term experiments can give very variable responses, depending on conditions, which are often misleading, even opposite in sign from long-term responses. Mechanistic models provide a clear framework for unifying these variable results, understanding why they arise, and making predictions about the future time course of plant ecosystems. There seems to be no other way of doing this work

How to Measure Subdiffusion Parameters

We propose a method to measure the subdiffusion parameter $\alpha$ and subdiffusion coefficient $D_{\alpha}$ which are defined by means of the relation $=\frac{2D_\alpha} {\Gamma(1+\alpha)} t^\alpha$ where $$ denotes a mean square displacement of a random walker starting from $x=0$ at the initial time $t=0$. The method exploits a membrane system where a substance of interest is transported in a solvent from one vessel to another across a thin membrane which plays here only an auxiliary role. We experimentally study a diffusion of glucose and sucrose in a gel solvent, and we precisely determine the parameters $\alpha$ and $D_{\alpha}$, using a fully analytic solution of the fractional subdiffusion equation.Comment: short version of cond-mat/0309072, to appear in Phys. Rev. Let

Uncovering Spiral Structure in Flocculent Galaxies

We present K'(2.1 micron) observations of four nearby flocculent spirals, which clearly show low-level spiral structure and suggest that kiloparsec-scale spiral structure is more prevalent in flocculent spirals than previously supposed. In particular, the prototypical flocculent spiral NGC 5055 is shown to have regular, two-arm spiral structure to a radius of 4 kpc in the near infrared, with an arm-interarm contrast of 1.3. The spiral structure in all four galaxies is weaker than that in grand design galaxies. Taken in unbarred galaxies with no large, nearby companions, these data are consistent with the modal theory of spiral density waves, which maintains that density waves are intrinsic to the disk. As an alternative, mechanisms for driving spiral structure with non-axisymmetric perturbers are also discussed. These observations highlight the importance of near infrared imaging for exploring the range of physical environments in which large-scale dynamical processes, such as density waves, are important.Comment: 12 pages AASTeX; 3 compressed PS figures can be retrieved from ftp://ftp.astro.umd.edu/pub/michele as file thornley.tar (1.6Mbytes). Accepted to Ap.J. Letters.(Figures now also available here, and from ftp://ftp.astro.umd.edu/pub/michele , in GIF format.

The inter-rater reliability of the diagnosis of surgical site infection in the context of a clinical trial.

ObjectivesThe diagnosis of surgical site infection following endoprosthetic reconstruction for bone tumours is frequently a subjective diagnosis. Large clinical trials use blinded Central Adjudication Committees (CACs) to minimise the variability and bias associated with assessing a clinical outcome. The aim of this study was to determine the level of inter-rater and intra-rater agreement in the diagnosis of surgical site infection in the context of a clinical trial.Materials and methodsThe Prophylactic Antibiotic Regimens in Tumour Surgery (PARITY) trial CAC adjudicated 29 non-PARITY cases of lower extremity endoprosthetic reconstruction. The CAC members classified each case according to the Centers for Disease Control (CDC) criteria for surgical site infection (superficial, deep, or organ space). Combinatorial analysis was used to calculate the smallest CAC panel size required to maximise agreement. A final meeting was held to establish a consensus.ResultsFull or near consensus was reached in 20 of the 29 cases. The Fleiss kappa value was calculated as 0.44 (95% confidence interval (CI) 0.35 to 0.53), or moderate agreement. The greatest statistical agreement was observed in the outcome of no infection, 0.61 (95% CI 0.49 to 0.72, substantial agreement). Panelists reached a full consensus in 12 of 29 cases and near consensus in five of 29 cases when CDC criteria were used (superficial, deep or organ space). A stable maximum Fleiss kappa of 0.46 (95% CI 0.50 to 0.35) at CAC sizes greater than three members was obtained.ConclusionsThere is substantial agreement among the members of the PARITY CAC regarding the presence or absence of surgical site infection. Agreement on the level of infection, however, is more challenging. Additional clinical information routinely collected by the prospective PARITY trial may improve the discriminatory capacity of the CAC in the parent study for the diagnosis of infection.Cite this article: J. Nuttall, N. Evaniew, P. Thornley, A. Griffin, B. Deheshi, T. O'Shea, J. Wunder, P. Ferguson, R. L. Randall, R. Turcotte, P. Schneider, P. McKay, M. Bhandari, M. Ghert. The inter-rater reliability of the diagnosis of surgical site infection in the context of a clinical trial. Bone Joint Res 2016;5:347-352. DOI: 10.1302/2046-3758.58.BJR-2016-0036.R1

Measuring subdiffusion parameters

We propose a method to extract from experimental data the subdiffusion parameter $\alpha$ and subdiffusion coefficient $D_\alpha$ which are defined by means of the relation $=2D_\alpha/\Gamma(1+\alpha) t^\alpha$ where $$ denotes a mean square displacement of a random walker starting from $x=0$ at the initial time $t=0$. The method exploits a membrane system where a substance of interest is transported in a solvent from one vessel to another across a thin membrane which plays here only an auxiliary role. Using such a system, we experimentally study a diffusion of glucose and sucrose in a gel solvent. We find a fully analytic solution of the fractional subdiffusion equation with the initial and boundary conditions representing the system under study. Confronting the experimental data with the derived formulas, we show a subdiffusive character of the sugar transport in gel solvent. We precisely determine the parameter $\alpha$, which is smaller than 1, and the subdiffusion coefficient $D_\alpha$.Comment: 17 pages, 9 figures, revised, to appear in Phys. Rev.

The Opacity of Spiral Galaxy Disks VIII: Structure of the Cold ISM

The quantity of dust in a spiral disk can be estimated using the dust's typical emission or the extinction of a known source. In this paper, we compare two techniques, one based on emission and one on absorption, applied on sections of fourteen disk galaxies. The two measurements reflect, respectively the average and apparent optical depth of a disk section. Hence, they depend differently on the average number and optical depth of ISM structures in the disk. The small scale geometry of the cold ISM is critical for accurate models of the overall energy budget of spiral disks. ISM geometry, relative contributions of different stellar populations and dust emissivity are all free parameters in galaxy Spectral Energy Distribution (SED) models; they are also sometimes degenerate, depending on wavelength coverage. Our aim is to constrain typical ISM geometry. The apparent optical depth measurement comes from the number of distant galaxies seen in HST images through the foreground disk. We measure the IR flux in images from the {\it Spitzer} Infrared Nearby Galaxy Survey in the same section of the disk that was covered by HST. A physical model of the dust is fit to the SED to estimate the dust surface density, mean temperature, and brightness in these disk sections. The surface density is subsequently converted into the average optical depth estimate. The two measurements generally agree. The ratios between the measured average and apparent optical depths of the disk sections imply optically thin clouds in these disks. Optically thick disks, are likely to have more than a single cloud along the line-of-sight.Comment: 31 pages, 5 figures, 4 tables, accepted for publication in A

Mid-Infrared IRS Spectroscopy of NGC 7331: A First Look at the SINGS Legacy

The nearby spiral galaxy NGC 7331 was spectrally mapped from 5-38um using all modules of Spitzer's IRS spectrograph. A strong new dust emission feature, presumed due to PAHs, was discovered at 17.1um. The feature's intensity is nearly half that of the ubiquitous 11.3um band. The 7-14um spectral maps revealed significant variation in the 7.7 and 11.3um PAH features between the stellar ring and nucleus. Weak [OIV] 25.9um line emission was found to be centrally concentrated in the nucleus, with an observed strength over 10% of the combined neon line flux, indicating an AGN or unusually active massive star photo-ionization. Two [SIII] lines fix the characteristic electron density in the HII regions at n_e < ~200 cm^-3. Three detected H_2 rotational lines, tracing warm molecular gas, together with the observed IR continuum, are difficult to match with standard PDR models. Either additional PDR heating or shocks are required to simultaneously match lines and continuum.Comment: 6 pages, 5 figures, accepted for publication in ApJS Spitzer Special Issu

Infrared Spectral Energy Distributions of Nearby Galaxies

The Spitzer Infrared Nearby Galaxies Survey (SINGS) is carrying out a comprehensive multi-wavelength survey on a sample of 75 nearby galaxies. The 1-850um spectral energy distributions are presented using broadband imaging data from Spitzer, 2MASS, ISO, IRAS, and SCUBA. The infrared colors derived from the globally-integrated Spitzer data are generally consistent with the previous generation of models that were developed based on global data for normal star-forming galaxies, though significant deviations are observed. Spitzer's excellent sensitivity and resolution also allow a detailed investigation of the infrared spectral energy distributions for various locations within the three large, nearby galaxies NGC3031 (M81), NGC5194 (M51), and NGC7331. Strong correlations exist between the local star formation rate and the infrared colors f_nu(70um)/f_nu(160um) and f_nu(24um)/f_nu(160um), suggesting that the 24 and 70um emission are useful tracers of the local star formation activity level. Preliminary evidence indicates that variations in the 24um emission, and not variations in the emission from polycyclic aromatic hydrocarbons at 8um, drive the variations in the f_nu(8.0um)/f_nu(24um) colors within NGC3031, NGC5194, and NGC7331. If the galaxy-to-galaxy variations in spectral energy distributions seen in our sample are representative of the range present at high redshift then extrapolations of total infrared luminosities and star formation rates from the observed 24um flux will be uncertain at the factor-of-five level (total range). The corresponding uncertainties using the redshifted 8.0um flux (e.g. observed 24um flux for a z=2 source) are factors of 10-20. Considerable caution should be used when interpreting such extrapolated infrared luminosities.Comment: 32 pages including 16 figures; accepted for publication in the Astrophysical Journa

The Calibration of Mid-Infrared Star Formation Rate Indicators

With the goal of investigating the degree to which the mid-infrared emission traces the star formation rate (SFR), we analyze Spitzer 8 um and 24 um data of star-forming regions in a sample of 33 nearby galaxies with available HST/NICMOS images in the Paschen-alpha (1.8756 um) emission line. The galaxies are drawn from the Spitzer Infrared Nearby Galaxies Survey (SINGS) sample, and cover a range of morphologies and a factor ~10 in oxygen abundance. Published data on local low-metallicity starburst galaxies and Luminous Infrared Galaxies are also included in the analysis. Both the stellar-continuum-subtracted 8 um emission and the 24 um emission correlate with the extinction-corrected Pa-alpha line emission, although neither relationship is linear. Simple models of stellar populations and dust extinction and emission are able to reproduce the observed non-linear trend of the 24 um emission versus number of ionizing photons, including the modest deficiency of 24 um emission in the low metallicity regions, which results from a combination of decreasing dust opacity and dust temperature at low luminosities. Conversely, the trend of the 8 um emission as a function of the number of ionizing photons is not well reproduced by the same models. The 8 um emission is contributed, in larger measure than the 24 um emission, by dust heated by non-ionizing stellar populations, in agreement with previous findings. Two SFR calibrations, one using the 24 um emission and the other using a combination of the 24 um and H-alpha luminosities (Kennicutt et al. 2007), are presented. No calibration is presented for the 8 um emission, because of its significant dependence on both metallicity and environment. The calibrations presented here should be directly applicable to systems dominated by on-going star formation.Comment: 67 pages, 15 figures, accepted for publication on the Astrophysical Journal; replacement contains: correction to equation 8; important tweaks to equation 9; various typos correcte