Trunk density profile estimates from dual X-ray absorptiometry

Accurate body segment parameters are necessary to estimate joint loads when using biomechanical models. Geometric methods can provide individualized data for these models but the accuracy of the geometric methods depends on accurate segment density estimates. The trunk, which is important in many biomechanical models, has the largest variability in density along its length. Therefore, the objectives of this study were to: (1) develop a new method for modeling trunk density profiles based on dual X-ray absorptiometry (DXA) and (2) develop a trunk density function for college-aged females and males that can be used in geometric methods. To this end, the density profiles of 25 females and 24 males were determined by combining the measurements from a photogrammetric method and DXA readings. A discrete Fourier transformation was then used to develop the density functions for each sex. The individual density and average density profiles compare well with the literature. There were distinct differences between the profiles of two of participants (one female and one male), and the average for their sex. It is believed that the variations in these two participants' density profiles were a result of the amount and distribution of fat they possessed. Further studies are needed to support this possibility. The new density functions eliminate the uniform density assumption associated with some geometric models thus providing more accurate trunk segment parameter estimates. In turn, more accurate moments and forces can be estimated for the kinetic analyses of certain human movements.     

A simple and sensitive method for lipoprotein and lipids profiles analysis of individual micro-liter scale serum samples

A simple and sensitive method to determine lipoprotein and lipids profiles in micro-liter scale individual serum sample is not presently available. Traditional lipoprotein separation techniques either by ultra-centrifugation or by liquid chromatography methods have their disadvantages in both lipoprotein separation and lipids component quantification. In this study we used small volume needing size-exclusion fast protein liquid chromatography to separate different lipoprotein subclasses in 50μL serum. And lipids contents, such as cholesterol, cholesterol ester and triacylglycerol, were measured by using two different fluorescence-based lipid detection methods. With this method, very low density lipoprotein, low density lipoprotein and high density lipoprotein could be easily separated, and follow-up lipid detection was completed by simple kinds of reactions. Serum lipoprotein and lipids profiling from C57BL/6 mice (n=5) and human (n=5) were analyzed. The elution profiles of five individuals were highly reproducible, and there were lipoprotein and lipids distribution variations between C57BL/6 mice and human beings. In conclusion, this method which combined small volume needing size-exclusion fast protein liquid chromatography and fluorescence-based lipids measurement, provided a simple, efficient, integrity and reproducible procedure for determining serum lipoprotein and lipids profiles in micro-liter scale levels. It becomes possible that determination of lipoprotein profiles and gaining information of lipids in different lipoproteins can be accomplished simultaneously.     

Isopycnic density values for lysosomes and mitochondria in rat adrenal cortex

Adrenocortical tissues of male adult Wistar rats were fractionated by isopycnic density gradient centrifugation. Fractions were analyzed for density, protein and marker enzymes for lysosomes and mitochondria with rat liver being used as a reference tissue for subcellular enzyme distribution. Both lysosomes and mitochondria of adrenal cortex showed unimodal distribution profiles of marker enzymes with their modal isopycnic density values at 1.165. This value was significantly lower than the corresponding ones for lysosomes and mitochondria in rat liver but was very close to those in porcine adrenal cortex. Modal isopycnic density as well as distribution profiles of marker enzymes for lysosomes and mitochondria remained unchanged 24 hr after 0.1 or 10 units of ACTH (Cortrosyn Z) administration. As in porcine adrenal cortex, lysosomes in rat adrenal cortex were characterized by a higher content of cathepsin D than those in rat liver.     

Temporal annotation of high-resolution intra-annual wood density information of Eucalyptus urophylla and its correlation with hydroclimatic conditions

Three different Eucalyptus urophylla clones grown under two different spacing regimes in an experimental site in the state of São Paulo, Brazil, were analyzed to test effects of clone identity, spacing, cambial age and hydroclimatic conditions on high-resolution intra-annual wood density profiles. Since distinct periodic tree-ring boundaries were not visible on the stem cross-sectional surfaces, finding an alternative method for synchronization of density profiles was crucial for the analysis. The challenge was to generate intra- and inter-tree synchronized density profiles that possess high amplitude variation and low phase variation. Thus, we developed a protocol and workflow of how such high-resolution density profiles can be spatially aligned and temporally annotated to enable correlation analyses between trees and with time series of environmental stimuli. Mean wood density was significantly different between clones, but not between the spacings. Wood density increased significantly with increasing cambial age and decreasing growth rate. Principal component analysis showed that the overall variability in the temporally annotated density profiles is dominated by a highly significant common signal. We found significant negative correlation values for precipitation, indicating that water supply is the main driver of stem growth at the site, and providing evidence for the correctness of the method. The developed workflow can easily be adjusted to the analysis of other intra-annual tree-ring features like anatomical xylem cell traits or isotopic signals in the wood. It has a large potential to be used as a general guideline for the synchronization of intra-annual tree-ring traits, especially when distinct tree-ring boundaries are missing, as it is often the case under tropical climatic conditions. The workflow supports the development of spatially aligned and temporally annotated chronologies under non-annual growth rhythms.     

Interpretation of small angle X-ray measurements guided by molecular dynamics simulations of lipid bilayers

Reconstruction and interpretation of lipid bilayer structure from X-ray scattering often rely on assumptions regarding the molecular distributions across the bilayer. It is usually assumed that changes in head-head spacings across the bilayer, as measured from electron density profiles, equal the variations in hydrocarbon thicknesses. One can then determine the structure of a bilayer by comparison to the known structure of a lipid with the same headgroup. Here we examine this procedure using simulated electron density profiles for the benchmark lipids DMPC and DPPC. We compare simulation and experiment in both real and Fourier space to address two main aspects: (i) the measurement of head-head spacings from relative electron density profiles, and (ii) the determination of the absolute scale for these profiles. We find supporting evidence for the experimental procedure, thus explaining the robustness and consistency of experimental structural results derived from electron density profiles. However, we also expose potential pitfalls in the Fourier reconstruction that are due to the limited number of scattering peaks. Volumetric analysis of simulated bilayers allows us to propose an improved, yet simple method for scale determination. In this way we are able to remove some of the restrictions imposed by limited scattering data in constructing reliable electron density profiles.     

Estimating Soil Organic Carbon Stocks and Spatial Patterns with Statistical and GIS-Based Methods

Accurately quantifying soil organic carbon (SOC) is considered fundamental to studying soil quality, modeling the global carbon cycle, and assessing global climate change. This study evaluated the uncertainties caused by up-scaling of soil properties from the county scale to the provincial scale and from lower-level classification of Soil Species to Soil Group, using four methods: the mean, median, Soil Profile Statistics (SPS), and pedological professional knowledge based (PKB) methods. For the SPS method, SOC stock is calculated at the county scale by multiplying the mean SOC density value of each soil type in a county by its corresponding area. For the mean or median method, SOC density value of each soil type is calculated using provincial arithmetic mean or median. For the PKB method, SOC density value of each soil type is calculated at the county scale considering soil parent materials and spatial locations of all soil profiles. A newly constructed 1∶50,000 soil survey geographic database of Zhejiang Province, China, was used for evaluation. Results indicated that with soil classification levels up-scaling from Soil Species to Soil Group, the variation of estimated SOC stocks among different soil classification levels was obviously lower than that among different methods. The difference in the estimated SOC stocks among the four methods was lowest at the Soil Species level. The differences in SOC stocks among the mean, median, and PKB methods for different Soil Groups resulted from the differences in the procedure of aggregating soil profile properties to represent the attributes of one soil type. Compared with the other three estimation methods (i.e., the SPS, mean and median methods), the PKB method holds significant promise for characterizing spatial differences in SOC distribution because spatial locations of all soil profiles are considered during the aggregation procedure.     

Frequency Dependent Topological Patterns of Resting-State Brain Networks

The topological organization underlying brain networks has been extensively investigated using resting-state fMRI, focusing on the low frequency band from 0.01 to 0.1 Hz. However, the frequency specificities regarding the corresponding brain networks remain largely unclear. In the current study, a data-driven method named complementary ensemble empirical mode decomposition (CEEMD) was introduced to separate the time series of each voxel into several intrinsic oscillation rhythms with distinct frequency bands. Our data indicated that the whole brain BOLD signals could be automatically divided into five specific frequency bands. After applying the CEEMD method, the topological patterns of these five temporally correlated networks were analyzed. The results showed that global topological properties, including the network weighted degree, network efficiency, mean characteristic path length and clustering coefficient, were observed to be most prominent in the ultra-low frequency bands from 0 to 0.015 Hz. Moreover, the saliency of small-world architecture demonstrated frequency-density dependency. Compared to the empirical mode decomposition method (EMD), CEEMD could effectively eliminate the mode-mixing effects. Additionally, the robustness of CEEMD was validated by the similar results derived from a split-half analysis and a conventional frequency division method using the rectangular window band-pass filter. Our findings suggest that CEEMD is a more effective method for extracting the intrinsic oscillation rhythms embedded in the BOLD signals than EMD. The application of CEEMD in fMRI data analysis will provide in-depth insight in investigations of frequency specific topological patterns of the dynamic brain networks.     

Microstructure alignment of wood density profiles: an approach to equalize radial differences in growth rate

We studied intra-annual wood density profiles of Douglas-fir tree rings (Pseudotsuga menziesii [Mirb.] Franco) in southwestern Germany. Growth rates are variable around the tree circumference. This leads to differences in wood formation, which can be observed in the shape of the density profiles of the same tree ring measured in different radial directions. Due to this spatial variation in density profiles, we need a reliable method to determine an average profile, which preserves the common characteristics of the data. To this end, we developed a multiple interval-based curve alignment (MICA) procedure. It identifies characteristic points within the profiles such as minima, maxima and inflection points. These reference points are shifted gradually against each other within a proportionally defined baseline interval. Using our progressive alignment approach, we are able to calculate an average profile that represents very well the characteristics of all measured curves of a specific tree ring. We applied the procedure to get year-specific average profiles using various trees. This results in representative mean density profiles that preserve the density variations common to all aligned profiles. Individual noise is reduced, thereby enabling the analysis of the impact of weather variations on wood density.     

Density and bonding profiles of interbilayer water as functions of bilayer separation: a Monte Carlo study

We have used the Monte Carlo method to calculate the equilibrium properties of water between two interfaces consisting of phosphatidylcholine (PC) headgroups. Using the TIPS2 optimized potential for water-water interactions, and 6–12 and coulombic potentials for water-PC interactions, we have determined the density, orientational, and hydrogen bonding profiles of the water as functions of the location of the water relative to the PC groups. We present here our results for several different studies in which we varied the interbilayer separation, the PC group configurations, and the interbilayer aqueous density. We find that very near each surface there is a layer of water strongly bound to the PC groups, and removing this water from the density profiles reveals a region of reduced water density extending 1–2 Å further into the interbilayer space. In addition when bilayers are very close together all the water is affected by the PC groups, as revealed in the hydrogen bonding profiles.     

Presence, distribution, and diversity of iron-oxidizing bacteria at a landfill leachate-impacted groundwater surface water interface

We examined the presence of iron-oxidizing bacteria (IOB) at a groundwater surface water interface (GSI) impacted by reduced groundwater originating as leachate from an upgradient landfill. IOB enrichments and quantifications were obtained, at high vertical resolution, by an iron/oxygen opposing gradient cultivation method. The depth-resolved soil distribution profiles of water content, Fe²⁺, and total Fe indicated sharp gradients within the top 10 cm sediments of the GSI, where the IOB density was the highest. In addition, the vertical distribution of iron-reducing bacteria at the same sampling site mirrored the IOB distribution. Clone libraries from two separate IOB enrichments indicated a stratified IOB community with clear differences at short vertical distances. Alpha- and Betaproteobacteria were the dominant phylotypes. Clones from the near-surface sediment (1–2 cm below ground surface) were dominated by members of the Bradyrhizobiaceae and Comamonadaceae ; clones from the deeper sediments were phylogenetically more diverse, dominated by members of the Rhodocyclaceae . The iron deposition profiles indicated that active iron oxidation occurred only within the near-to-surface GSI sediments. The match between the iron deposition profiles and the IOB abundance profiles strongly hints at the contribution of the IOB community to Fe oxidation in this Fe-rich GSI ecosystem.     

Estimation of hydrophobic effects using the fundamental measure theory

A method is developed on the basis of the fundamental measure model of the density functional theory for calculating solvation of hydrophobic particles. This method allows one to calculate density and solvation energy profiles for hydrophobic molecules. An additional merit of the method is the possibility to calculate the interaction forces and mean force potential for hydrophobic nanoparticles. Solvation parameters for spherical solutes with sizes from one angstrom to several nanometers have been calculated using this method.     

Apparent densities of spermatozoa of various mammalian species

The apparent densities of sperm cells in several mammalian species were determined by means of Percoll density-gradient centrifugation. Semen samples were obtained from (1) ejaculates from the bull, human, and rabbit, and (2) from the cauda epididymis of the goat, golden hamster, house musk shrew, mastomys, and mouse. The profiles of sperm distribution showed a single peak after the centrifugation in the first group and goat, whereas two separate main peaks in the second group (except goat). This disparity in sperm distribution profiles may be due mainly to differences in the degree of maturity of the sperm. Highly motile and mature sperm were obtained at higher densities, whereas immotile or immature sperm were found at the apparent densities. Thus, in mammals, the profiles of sperm distribution in the Percoll density gradient are classified into two types, those with a single peak and those with two separate peaks. The apparent density of sperm cells may be of importance in sperm physiology.     

Optimum kinetic energy dissipation in blood flow in glass capillaries by flow field determination: Analysis of curvature effect by axial tomographic and image velocimetry techniques

Based on the variation in the optical density due to erythrocyte concentration and movement, the axial tomographic and image velocimetry techniques are respectively applied to determine the flow field, i.e., the distribution of erythrocytes and axial and radial velocity components, in steady blood flow through a curved glass capillary with a diameter of 180 μm. The data at four positions (two straight and two curved segments of the capillary) are recorded by a video-microscopic system on a video cassette. The erythrocyte and velocity distribution profiles change from symmetric at the straight position to an asymmetric shape at the curved sections. These profiles become symmetric again at the straight section of the capillary. The increase in the radial velocity component at curved portions is attributed to the secondary flow. The tomograms obtained by concentration profiles show respective changes in the cellular population at various cross-sectional positions. The kinetic energy dissipation, as calculated based on a determination of the flow field, is the minimum for the observed profiles. Any deviation towards parabolic form leads to the dissipation of a higher amount of energy.     

Contribution of solvent water to the solution X-ray scattering profile of proteins

A theoretical framework is presented to analyze how solvent water contributes to the X-ray scattering profile of protein solution. Molecular dynamics simulations were carried out on pure water and an aqueous solution of myoglobin to determine the spatial distribution of water molecules in each of them. Their solution X-ray scattering (SXS) profiles were numerically evaluated with obtained atomic-coordinate data. It is shown that two kinds of contributions from solvent water must be considered to predict the SXS profile of a solution accurately. One is the excluded solvent scattering originating in exclusion of water molecules from the space occupied by solutes. The other is the hydration effect resulting from formation of a specific distribution of water around solutes. Explicit consideration of only two molecular layers of water is practically enough to incorporate the hydration effect. Care should be given to using an approximation in which an averaged electron density distribution is assumed for the structure factor because it may predict profiles considerably deviating from the correct profile at large K.     

Orientation and conformation of a lipase at an interface studied by molecular dynamics simulations

Electron density profiles calculated from molecular dynamics trajectories are used to deduce the orientation and conformation of Thermomyces lanuginosa lipase and a mutant adsorbed at an air-water interface. It is demonstrated that the profiles display distinct fine structures, which uniquely characterize enzyme orientation and conformation. The density profiles are, on the nanosecond timescale, determined by the average enzyme conformation. We outline a computational scheme that from a single molecular dynamics trajectory allows for extraction of electron density profiles referring to different orientations of the lipase relative to an implicit interface. Profiles calculated for the inactive and active conformations of the lipase are compared with experimental electron density profiles measured by x-ray reflectivity for the lipase adsorbed at an air-water interface. The experimental profiles contain less fine structural information than the calculated profiles because the resolution of the experiment is limited by the intrinsic surface roughness of water. Least squares fits of the calculated profiles to the experimental profiles provide areas per adsorbed enzyme and suggest that Thermomyces lanuginosa lipase adsorbs to the air-water interface in a semiopen conformation with the lid oriented away from the interface.     

Using hydropathy features for function prediction of membrane proteins

A novel alignment-free method for computing functional similarity of membrane proteins based on features of hydropathy distribution is presented. The features of hydropathy distribution are used to represent protein families as hydropathy profiles. The profiles statistically summarize the hydropathy distribution of member proteins. The summation is made by using hydropathy features that numerically represent structurally/functionally significant portions of protein sequences. The hydropathy profiles are numerical vectors that are points in a high dimensional 'hydropathy' space. Their similarities are identified by projection of the space onto principal axes. Here, the approach is applied to the secondary transporters. The analysis using the presented approach is validated by the standard classification of the secondary transporters. The presented analysis allows for prediction of function attributes for proteins of uncharacterized families of secondary transporters. The results obtained using the presented analysis may help to characterize unknown function attributes of secondary transporters. They also show that analysis of hydropathy distribution can be used for function prediction of membrane proteins.     

Using hydropathy features for function prediction of membrane proteins

A novel alignment-free method for computing functional similarity of membrane proteins based on features of hydropathy distribution is presented. The features of hydropathy distribution are used to represent protein families as hydropathy profiles. The profiles statistically summarize the hydropathy distribution of member proteins. The summation is made by using hydropathy features that numerically represent structurally/functionally significant portions of protein sequences. The hydropathy profiles are numerical vectors that are points in a high dimensional ‘hydropathy’ space. Their similarities are identified by projection of the space onto principal axes. Here, the approach is applied to the secondary transporters. The analysis using the presented approach is validated by the standard classification of the secondary transporters. The presented analysis allows for prediction of function attributes for proteins of uncharacterized families of secondary transporters. The results obtained using the presented analysis may help to characterize unknown function attributes of secondary transporters. They also show that analysis of hydropathy distribution can be used for function prediction of membrane proteins.     

Filtration-fluorescence determination of DNA sedimentation profiles

A method for determination of DNA sedimentation profiles in density gradients of sucrose or salts is proposed. The method consists in isolation and purification of DNA from the fractions by molecular filtration and a subsequent determination of DNA content by the fluorescence of the DNA-ethidium bromide complex.     

Studies on a fractionated murine fibrosarcoma: proliferative potential of the separated cells.

A transplantable methylcholanthrene-induced fibrosarcoma of female BALB/c mice (the MC-2 fibrosarcoma) was dissociated by combined mechanical and enzymatic means, then fractionated by isopycnic centrifugation in linear albumin gradients. In some experiments recovered cells were both cultured in soft nutrietn agar and inoculated subcutaneously into syngeneic recipients. In these experiments a highly significant correlation was observed between subsequtnt colony number and rapid growth phase tumor size suggesting identity of clonigenic and tumorigenic cells. It was consistently found that clonigenic cells were markedly depleted from the low density extremes of the cell density distribution profiles suggesting that the low density neoplastic cells had irreversibly left the growth fraction. With increasing tumor age, sequential studies showed that both total and clonigenic cell density distribution profiles were variable, showing no obvious trend, suggesting that in the age (13-35 days) and size (2-8 g) range studied growth fraction changes had little selective effect on cells of any specific density. These results imply that a marked selective depletion of low density clonigenic cells (or selective accumulation of low density non-proliferative cells) must mainly occur during an earlier phase of tumor growth. Studies on several other murine solid tumors also showed maximal depletion of clonigenic cells from the least dense fractions, suggesting that this situation may be common.