Microbial controls on metal mobility under the low nutrient fluxes found throughout the subsurface

Laboratory simulations and field studies of the shallow subsurface have shown that microbes and their extracellular products can influence the mobility of toxic metals from waste disposal sites. Modelling the transport of contaminants in groundwater may, therefore, require the input of microbial ecology data in addition to geochemical data, thus increasing the costs and the uncertainty of predictions. However, whether microbial effects on contaminant mobility occur extensively in the natural subsurface is unknown because the conditions under which they have been observed hitherto are generally unrepresentative of the average subsurface environment. Here, we show that microbial activity affects the mobility of a toxic trace metal (Cu) under the relatively low nutrient fluxes that dominate subsurface systems. More particularly, we show that under these low nutrient conditions, microbes and microbial products can immobilize metal but may themselves be subject to subsequent mobilization, thus complicating the pattern of metal storage and release. Our results show that the capability of microbes in the subsurface to change both the capacity of porous media to store metal, and the behaviour of metal that is released, is not restricted to the well researched environments close to sites of waste disposal. We anticipate our simulations will be a starting point for generating input data for transport models, and specifying the mechanism of metal remobilisation in environments more representative of the subsurface generally.     

Statistical analysis of manual segmentations of structures in medical images

The problem of extracting anatomical structures from medical images is both very important and difficult. In this paper we are motivated by a new paradigm in medical image segmentation, termed Citizen Science, which involves a volunteer effort from multiple, possibly non-expert, human participants. These contributors observe 2D images and generate their estimates of anatomical boundaries in the form of planar closed curves. The challenge, of course, is to combine these different estimates in a coherent fashion and to develop an overall estimate of the underlying structure. Treating these curves as random samples, we use statistical shape theory to generate joint inferences and analyze this data generated by the citizen scientists. The specific goals in this analysis are: (1) to find a robust estimate of the representative curve that provides an overall segmentation, (2) to quantify the level of agreement between segmentations, both globally (full contours) and locally (parts of contours), and (3) to automatically detect outliers and help reduce their influence in the estimation. We demonstrate these ideas using a number of artificial examples and real applications in medical imaging, and summarize their potential use in future scenarios.     

Simultaneous reconstruction of evolutionary history and epidemiological dynamics from viral sequences with the birth–death SIR model

The evolution of RNA viruses, such as human immunodeficiency virus (HIV), hepatitis C virus and influenza virus, occurs so rapidly that the viruses'' genomes contain information on past ecological dynamics. Hence, we develop a phylodynamic method that enables the joint estimation of epidemiological parameters and phylogenetic history. Based on a compartmental susceptible–infected–removed (SIR) model, this method provides separate information on incidence and prevalence of infections. Detailed information on the interaction of host population dynamics and evolutionary history can inform decisions on how to contain or entirely avoid disease outbreaks. We apply our birth–death SIR method to two viral datasets. First, five HIV type 1 clusters sampled in the UK between 1999 and 2003 are analysed. The estimated basic reproduction ratios range from 1.9 to 3.2 among the clusters. All clusters show a decline in the growth rate of the local epidemic in the middle or end of the 1990s. The analysis of a hepatitis C virus genotype 2c dataset shows that the local epidemic in the Córdoban city Cruz del Eje originated around 1906 (median), coinciding with an immigration wave from Europe to central Argentina that dates from 1880 to 1920. The estimated time of epidemic peak is around 1970.     

Find the firn line! The suitability of ERS-1 and ERS-2 SAR data for the analysis of glacier facies on Icelandic icecaps

Icelandic Icecaps are sensitive indicators of climatic fluctuations. Glacier facies boundaries can be identified using remote sensing techniques; SAR data represents the first real opportunity to monitor glacier facies, without cloud attenuation at regular or inter-annual intervals. This study assesses the overall suitability of the data for the monitoring of glacier facies and in particular the firn line altitude (FLA) on Icelandic Icecaps. The results show that the firn line can be identified and located to within +/- 20-40m (vertically). These results were validated using aerial photograph and ground data. RAIDS (Rapid Information Dissemination System) processed data were found to compare favourably with other satellite data for this type of application.     

Exploring Web keyword analysis as an alternative to link analysis: a multi-industry case

The study explored the feasibility of using Web keyword analysis as an alternative to link analysis and tested the feasibility in a multi-industry environment. The keyword is the organization??s name, in this case the company name. American companies from five industries were included in the study. The study found that the Web visibility of a company as measured by the number of Webpages on which the company name appears correlates with the company??s business measures (revenue, profits, and assets). The correlation coefficients are similar to that between the inlink counts and the business measures. This suggests that the keyword count (searched by the company name) could replace inlink count as an alternative indicator of some commonly used business measures. The co-word (the co-occurrence of the names of two companies on Webpages) count was used as a measure of the relatedness of the two companies. Multidimensional scaling (MDS) analysis was applied to the co-word matrices and generated MDS maps that showed relationships among companies in a multi-industry context. Keyword data were collected from three different types of Websites (general Websites, blog sites, and Web news sites) and results were compared. The study found blog sites to be the better source to collect data for this type of study. The comparison of MDS maps generated from co-link data and the blog co-word data showed that the co-word analysis is as effective as co-link analysis in mapping business relationships. The value of the study is not limited to the business sector as the co-word method could be applied to analysing relationships among other types of organizations.     

Cell morphology and focal adhesion location alters internal cell stress

Extracellular mechanical cues have been shown to have a profound effect on osteogenic cell behaviour. However, it is not known precisely how these cues alter intracellular mechanics to initiate changes in cell behaviour. In this study, a combination of in vitro culture of MC3T3-E1 cells and finite-element modelling was used to investigate the effects of passive differences in substrate stiffness on intracellular mechanics. Cells on collagen-based substrates were classified based on the presence of cell processes and the dimensions of various cellular features were quantified. Focal adhesion (FA) density was quantified from immunohistochemical staining, while cell and substrate stiffnesses were measured using a live-cell atomic force microscope. Computational models of cell morphologies were developed using an applied contraction of the cell body to simulate active cell contraction. The results showed that FA density is directly related to cell morphology, while the effect of substrate stiffness on internal cell tension was modulated by both cell morphology and FA density, as investigated by varying the number of adhesion sites present in each morphological model. We propose that the cells desire to achieve a homeostatic stress state may play a role in osteogenic cell differentiation in response to extracellular mechanical cues.     

Noise Reduction Methods for Weighing Lysimeters

Mechanical vibration of the grass and crop weighing lysimeters, located at the University of California West Side Field Research and Extension Station at Five Points, Calif. generated noise in lysimeter mass measurements and reduced the quality of evapotranspiration (ET) data. The estimated power spectral density (PSD) for grass lysimeter mass data acquired at 1.3?ms intervals contained a large peak at 11?Hz. Crop lysimeter data produced similar peaks at frequencies greater than 1?Hz. An effective method for eliminating this noise source is arithmetic averaging of the data, which should be acquired sufficiently rapidly to avoid aliasing. The PSD also increased with decreasing frequency in the range 1.0–0.1?Hz. This noise was addressed by Savitsky–Golay (SG) filtering using 7-, 11-, and 15-point filters. Each filter was applied to the same data set consisting of 2,560 measurements taken during a 1-min interval every 10?min over a 26.3-h period. Noise reduction factors, defined as the ratio of standard deviation of filtered lysimeter mass to standard deviation of unfiltered mean values of lysimeter mass for subsequences of the same data, were 0.90, 0.88, and 0.86 for the 7-, 11-, and 15-point filters, respectively. For the daytime data only, the factors were 0.88, 0.85, and 0.83. The SG filters were more effective during daytime when most of the lysimeter ET occurs. These methods are simple enough to be programmed into commercially available dataloggers for real time filtering. Hourly averages of the standard deviations of lysimeter mass measurements bear a distinct nonlinear relationship to hourly mean wind speed confirming earlier suppositions that wind loading causes noise in counterbalanced weighing lysimeters.     

Diversity gain from a single-port adaptive antenna using switchedparasitic elements illustrated with a wire and monopole prototype

A new concept in single-port adaptive antennas using parasitic elements with switched terminating impedances is presented including results from a concept prototype. Each parasitic element can be effectively terminated in three impedance values. The antenna concept provides multiple radiation patterns with a single RF signal port without the need for RF switches or phase shifters in the direct RF signal path. Impedance variations in the active antenna element are minimized by use of only rotationally symmetric configurations. Measured patterns are used to demonstrate the performance improvement expected using switched diversity combining in a simulated uniform scattering scenario. The concept prototype having one active element and four parasitic elements, is shown to have equivalent diversity performance to between three and four uncorrelated branches     

Molecular approaches to study probiotic bacteria

Functional foods comprising probiotic bacteria are receiving increasing attention from the scientific community and science funding agencies [1]. An essential aspect relating to the functionality of probiotic-based foods is to develop molecular methods to determine the presence, activity and viability of probiotic bacteria in the human gastrointestinal (GI) tract [2]. The GI tract is composed of a complex ecosystem of various microbial habitats colonized by numerous different commensal micro-organisms. This indigenous gut microbiota is essential to the overall health of the host by performing important physiological functions. In particular, they protect against pathogenic bacteria and drive the development of the immune system during neonatal life. Further metabolic activities of the GI microbiota that beneficially affect the host include continued degradation of food components, vitamin production, and production of short chain fatty acids that feed the colonic mucosa. It is clear that factors such as diet, sickness, stress, or medication can result in loss of well-being of the host, and it is assumed that some of these symptoms are due to perturbation of what is termed the normal balance of the gut microbiota. Knowledge of the structure and function of the standard microbiota, and its response to diet, genetic background and lifetime of the host must be taken into account when designing probiotic-based functional foods. The application of molecular techniques for detection and identification of microbes has provided a major breakthrough in the analysis of microbial ecosystems and their function [3]. The successful application and further potential of these molecular methods to study probiotic bacteria and their impact on the standard GI microbiota is discussed below.     

Recovery of Metal Working Fluids Using Chelation-Ultrafiltration Process

Metal working (MW) fluids are used to control friction and temperature, improve workpiece surface quality, and reduce tool wear. The batch-life of the MW fluid investigated was controlled primarily by the concentration of metallic soaps (complexes between the oil emulsifier and Al∕Mg. Ethylenediaminetetraacetic acid, a strong metal chelator, was added to the MW fluid to break the oil-Al∕Mg complexes. The aqueous-phase ethylenediaminetetraacetic acid-Al∕Mg complexes were then separated from the oil phase by ultrafiltration (UF). Al levels were reduced between 39 and 49%, and Mg levels were reduced between 67 and 77%. Al transfer from the oil phase to the aqueous phase was slow and increased during UF concentration. Rinsing the concentrated MW fluid with deionized water decreased the ash content but had a lesser impact on Al∕Mg removal. Al mass balances produced errors of 2.8% for run 3 and 6.2% for run 4. The UF system (0.11-μm ceramic membrane) effectively separated the oil and aqueous phases. Permeate turbidity was generally <1 nephelometric turbidity unit and permeate flux ranged from 390 to 220 L∕m2-h (230 to 130 gal.∕ft2-day) depending on the degree of concentration.