Morphometric analysis of Cartesian coordinates of the human skull

A method for locating the three dimensional coordinates of cranial landmarks with respect to the Frankfort, midsagittal, and coronal planes is presented. Sliding calipers were used to obtain the distances from left and right porion and apex to each landmark, except for a few points where spreading calipers are required. In the present example, 35 landmarks (for a total of 105 measurements) were located for each of 35 Peruvian precolumbian skulls. These distances were entered into a program (SKULL) which calculates the Cartesian coordinates of each landmark. The XYZ coordinates of each landmark contain all the information necessary for calculation of the distances between any two landmarks, and these distances may also be obtained as output from program SKULL, if desired (595 distances if all 35 landmarks are used). Reliability of the location of coordinates was determined by comparing computed distances among selected landmarks from program SKULL with traditional anthropometric measurements. Satisfactory agreements were found. Direct multivariate analysis of the coordinates of the landmarks produced insights not available in traditional multivariate analysis of conventional anthropometric measurements.     

Is the instrumented-pointer method of calibrating anatomical landmarks in 3D motion analysis reliable?

Instrumented-pointers are often used to calibrate anatomical landmarks in biomechanical analyses. However, little is known about the effect of altering the orientation of the pointer during calibration on the co-ordinates recorded. Incorrect positioning of a landmark influences the axes created, and thus the kinematic data recorded. This study aimed to investigate the reliability of the pointer method for anatomical calibration. Two points were drawn onto a fixed box to resemble knee joint epicondyles, then a custom-made pointer was used to define the positions of these landmarks in three-dimensions. Twenty different pointer-orientations were chosen, and the position of the pointer in each of these orientations was recorded 8 times. Euclidean distances between single points were calculated for both landmarks and compared statistically (α = 0.05). Average Euclidean distances between all reconstructed points were 3.2±1.4 mm (range: 0.3–7.1 mm) for one landmark and 3.3±1.5 mm (range: 0.3–7.9mm) for the other. The x- and y-co-ordinates recorded differed statistically when the pointer was moved about the X and Y axes (anterior/posterior and superior/inferior to landmark) (p < 0.05). No statistical differences were found between co-ordinates recorded when the pointer was moved around the Z axes (p > 0.05). ICC values for all co-ordinates were excellent, highlighting the reliability of the method (ICC > 0.90). These results support this method of anatomical calibration; however, we recommend that pointers be consistently held in a neutral oriented position (where the handle is not anterior, posterior, superior or inferior to the landmark) during calibration, to reduce the likelihood of calibration errors.     

Movement-Based Estimation and Visualization of Space Use in 3D for Wildlife Ecology and Conservation

Advances in digital biotelemetry technologies are enabling the collection of bigger and more accurate data on the movements of free-ranging wildlife in space and time. Although many biotelemetry devices record 3D location data with x, y, and z coordinates from tracked animals, the third z coordinate is typically not integrated into studies of animal spatial use. Disregarding the vertical component may seriously limit understanding of animal habitat use and niche separation. We present novel movement-based kernel density estimators and computer visualization tools for generating and exploring 3D home ranges based on location data. We use case studies of three wildlife species – giant panda, dugong, and California condor – to demonstrate the ecological insights and conservation management benefits provided by 3D home range estimation and visualization for terrestrial, aquatic, and avian wildlife research.     

Craniometric variation of some Mediterranean and Atlantic populations of Stenella coeruleoalba (Mammalia,Delphinidae): A three‐dimensional geometric morphometric analysis

The variability of cranial features of Atlantic and Mediterranean samples of Stenella coeruleoalba was examined using a three‐dimensional geometric morphometric approach. Data were collected on 79 skulls from the upper and middle Mediterranean Sea, the Atlantic French coasts, and Scotland. Three‐dimensional x, y, and z coordinates of 27 landmarks were recorded on each left half skull using a Microscribe 3‐D digitizer. All configurations were rotated, centered, and scaled, and residuals from the mean configuration were analyzed through multivariate analyses of variance. Mahalanobis distances among populations were used to evaluate phenetic relationships. Consensus configurations were compared to visualize shape differences among samples. Analyses revealed significant differences among populations, a clear distinction of the Scottish coasts dolphins from the other samples, and a closer relationship of the dolphins from the French coasts to the Mediterranean populations than to the Scottish one. Shape differences are mainly concentrated in the rostral and in the occipital regions of the skull. Phylogenetic and adaptive factors were invoked as possible causes of the variation patterns.     

Method for calculating 3-D coordinates from molecular stereograms

The three-dimensional coordinates for the -carbon atoms of crambin and basic pancreatic trypsin inhibitor (BPTI) were determined from the respective -carbon trace stereograms using an improved Simplex algorithm. This algorithm was used in a two-step process to estimate thez-coordinate values. In one approach, an average interatomic distance value, an approximate viewing angle, and a table of digitized values forx _left,y _left andx _right,y _right are provided in the first step. In the second step, thez-coordinate values are derived by varyingz to minimize the bond distance error (Rossmann and Argos, 1980). In another approach, only a reference bond distance table is provided along with the table ofx _left,y _left andx _right,y _right digitized values. In the first step, the viewing angle (), a combined scale and viewing distance parameter (q), a rotational angular distortion from digitizing and/or photocopying (z), and translational distortion factors (x _err andy _err) are calculated. In the second step, thez-coordinate values are varied to minimize the bond distance error. RMS difference values of less than 1.5 Å were obtained for both crambin and BPTI -carbon atoms.     

TNT version 1.5, including a full implementation of phylogenetic morphometrics

Version 1.5 of the computer program TNT completely integrates landmark data into phylogenetic analysis. Landmark data consist of coordinates (in two or three dimensions) for the terminal taxa; TNT reconstructs shapes for the internal nodes such that the difference between ancestor and descendant shapes for all tree branches sums up to a minimum; this sum is used as tree score. Landmark data can be analysed alone or in combination with standard characters; all the applicable commands and options in TNT can be used transparently after reading a landmark data set. The program continues implementing all the types of analyses in former versions, including discrete and continuous characters (which can now be read at any scale, and automatically rescaled by TNT). Using algorithms described in this paper, searches for landmark data can be made tens to hundreds of times faster than it was possible before (from T to 3T times faster, where T is the number of taxa), thus making phylogenetic analysis of landmarks feasible even on standard personal computers.     

秃病蚤蒙冀亚种与长爪沙鼠密度的状态空间模型

 给出了一个描述秃病蚤蒙冀亚种Nosopsyllus laeviceps kuzenkovi与长爪沙鼠M eriones unguiculatus密度的状态空间模型,模型为x_t+1=-0.336x_t+0057y _t+0107z_t, y_t+1=0.586x_t-0369y_t-0274z_t, z_t+1=0.189x _t+0247y_t-0309z_t, 其中x_t,y_t和z_t分别为t月份的沙鼠密度, 巢秃病蚤 和体秃病蚤指数。结果表明,模型能够较好地描述野外秃病蚤蒙 冀亚种与长爪沙鼠间的关系,并发现沙鼠密度显著地影响巢秃病蚤指数。     

Phylogeny,landmark analysis and the use of wing venation to study the evolution of social wasps (Hymenoptera: Vespidae: Vespinae)

Wing venation provides useful characters with which to classify extant and fossil insects. Recently, quantification of its shape using landmarks has increased the potential of wing venation to distinguish taxa. However, the use of wing landmarks in phylogenetic analyses remains largely unexplored. Here, we tested landmark analysis under parsimony (LAUP) to include wing shape data in a phylogenetic analysis of hornets and yellow jackets. Using 68 morphological characters, nine genes and wing landmarks, we produced the first total‐evidence phylogeny of Vespinae. We also tested the influence of LAUP parameters using simulated landmarks. Our data confirmed that optimization parameters, alignment method, landmark number and, under low optimization parameters, the initial orientation of aligned shapes can influence LAUP results. Furthermore, single landmark configurations never accurately reflected the topology used for data simulation, but results were significantly close when compared to random topologies. Thus, wing landmark configurations were unreliable phylogenetic characters when treated independently, but provided some useful insights when combined with other data. Our phylogeny corroborated the monophyly of most groups proposed on the basis of morphology and showed the fossil Palaeovespa is distantly related to extant genera. Unstable relationships among genera suggest that rapid radiations occurred in the early history of the Vespinae.     

Airborne-pollen map for Olea europaea L. in eastern Andalusia (Spain) using GIS: Estimation models

Estimations based upon geostatistics and mapping have enabled the construction of a spatial model to predict the presence of biological particles in a particular region. This methodological proposal has been tested in a case study, at a regional scale, of airborne Olea pollen, using the data acquired from␣various sampling stations that are designed for the aerobiological monitoring of pollen levels. These sampling stations have been set up in cities throughout the region of Andalusia (southern Spain) at sites with very different characteristics in terms of biogeography, bioclimate, topography and vegetation. Pollen counts were made daily at all sites during 2003 using a volumetric spore-trap. Data were comparatively analysed in classical diagrams and by means of spatial-temporal maps. Space-time models were constructed using three coordinates, x, y (the UTM coordinates of each sampling station) and z, (the aerobiological data compiled for a specific period). The aerobiological data were interpolated by applying the traditional geostatistical method of Kriging. The introduction of the variable “space” into the model allowed us to predict pollen levels in different areas throughout the region. The interpolation method was used to make weekly estimations of Olea pollen values in areas where there was no aerobiological sampling station. In addition, the maps generated present a two-dimensional vision of the study area, showing that bioclimatic diversity of this region promotes a step-wise flowering of Olea.     

DELAYED‐RESPONSE PHYLOGENETIC CORRELATION: AN OPTIMIZATION‐BASED METHOD TO TEST COVARIATION OF CONTINUOUS CHARACTERS

A new phylogenetic comparative method is proposed, based on mapping two continuous characters on a tree to generate data pairs for regression or correlation analysis, which resolves problems of multiple character reconstructions, phylogenetic dependence, and asynchronous responses (evolutionary lags). Data pairs are formed in two ways (tree‐down and tree‐up) by matching corresponding changes, Δx and Δy. Delayed responses (Δy occurring later in the tree than Δx) are penalized by weighting pairs using nodal or branch‐length distance between Δx and Δy; immediate (same‐node) responses are given maximum weight. All combinations of character reconstructions (or a random sample thereof) are used to find the observed range of the weighted coefficient of correlation r (or weighted slope b). This range is used as test statistic, and the null distribution is generated by randomly reallocating changes (Δx and Δy) in the topology. Unlike randomization of terminal values, this procedure complies with Generalized Monte Carlo requirements while saving considerable computation time. Phylogenetic dependence is avoided by randomization without data transformations, yielding acceptable type‐I error rates and statistical power. We show that ignoring delayed responses can lead to falsely nonsignificant results. Issues that arise from considering delayed responses based on optimization are discussed.     

Sr2ZnWO6:Eu3+,Bi3+,Li+: a potential white‐emitting phosphor for near‐ultraviolet white light‐emitting diodes

A series of Sr₂ZnWO₆ phosphors co‐doped with Eu³⁺, Bi³⁺ and Li⁺ were prepared using the Pechini method. The samples were tested using X‐ray diffraction and luminescence spectroscopy. The results show that the samples can be effectively excited by near‐ultraviolet (UV) and UV light. The introduction of Bi³⁺ and Li⁺ significantly enhances the fluorescence emission of Sr₂ZnWO₆:Eu³⁺ and changes the light emitted by the phosphors from bluish‐green to white. When excited at 371 nm, Sr_2–x–zZn_1–yWO₆:xEu³⁺,yBi³⁺,zLi⁺ (x = 0.05, y = 0.05, z = 0.05, 0.1 and 0.15) samples emit high‐performance white light. Intense red–orange emission is also observed when excited by UV light. The obtained phosphor is a potential white‐emitting phosphor that could meet the needs of excitation sources with near‐UV chips. In addition, this phosphor might have promising application as a red–orange emitting phosphor for white light‐emitting diodes based on UV light‐emitting diodes. Copyright © 2015 John Wiley & Sons, Ltd.     

Multidimensional profiling of components in complex mixtures of natural products for metabolic analysis,proof of concept: Application to Quillaja saponins

A method for separation and detection of major and minor components in complex mixtures has been developed, utilising two-dimensional high-performance liquid chromatography (2D-HPLC) combined with electrospray ionisation ion-trap multiple-stage mass spectrometry (ESI-ITMSⁿ). Chromatographic conditions were matched with mass spectrometric detection to maximise the number of components that could be separated. The described procedure has proven useful to discern several hundreds of saponin components when applied to Quillaja saponaria Molina bark extracts. The discrimination of each saponin component relies on the fact that three coordinates (x, y, z) for each component can be derived from the retention time of the two chromatographic steps (x, y) and the m/z-values from the multiple-stage mass spectrometry (z_n, n = 1, 2, …). Thus an improved graphical representation was obtained by combining retention times from the two-stage separation with +MS¹ (z₁) and the additional structural information from the second mass stage +MS² (z₂, z₃) corresponding to the main fragment ions. By this approach three-dimensional plots can be made that reveal both the chromatographic and structural properties of a specific mixture which can be useful in fingerprinting of complex mixtures.     

Force treadmill for measuring vertical and horizontal ground reaction forces

Weconstructed a force treadmill to measure the vertical, horizontal andlateral components of the ground-reaction forces (F_z,F_y,F_x, respectively) and the ground-reaction force moments(M_z,M_y,M_x), respectively exerted bywalking and running humans. The chassis of a custom-built, lightweight(90 kg), mechanically stiff treadmill was supported along its length bya large commercial force platform. The natural frequencies of vibrationwere >178 Hz for F_z and >87Hz for F_y, i.e., well above thesignal content of these ground-reaction forces. Mechanical tests andcomparisons with data obtained from a force platform runway indicatedthat the force treadmill recordedF_z,F_y,M_x andM_y ground-reaction forces andmoments accurately. Although the lowest natural frequency of vibrationwas 88 Hz for F_x, thesignal-to-noise ratios for F_x andM_z were unacceptable. This devicegreatly decreases the time and laboratory space required for locomotionexperiments and clinical evaluations. The modular design allows forindependent use of both treadmill and force platform.

     

Adaptive walks by the fittest among finite random mutants on a Mt. Fuji-type fitness landscape II. Effect of small non-additivity

We examined properties of adaptive walks by the fittest on “rough Mt. Fuji-type” fitness landscapes, which are modeled by superposing small uncorrelated random component on an additive fitness landscape. A single adaptive walk is carried out by repetition of the evolution cycle composed of (1) mutagenesis process that produces random d-fold point mutants of population size N and (2) selection process that picks out the fittest mutant among them. To comprehend trajectories of the walkers, the fitness landscape is mapped into a (x, y, z)-space, where x, y and z represent, respectively, normalized Hamming distance from the peak on the additive fitness landscape, scaled additive fitness and scaled non-additive fitness. Thus a single adaptive walk is expressed as the dynamics of a particle in this space. We drew the “hill-climbing” vector field, where each vector represents the most probable step for a walker in a single step. Almost all of the walkers are expected to move along streams of vectors existing on a particular surface that overlies the (x, y)-plane, toward the neighborhood of a characteristic point at which a mutation-selection-random drift balance is reached. We could theoretically predict this reachable point in the case of random sampling search strategy. Received: 1 March 2000 / Published online: 3 August 2000     

Kinetic models of current sheets with a sheared magnetic field

Thin current sheets, whose existence in the Earth’s magnetotail is confirmed by numerous spacecraft measurements, are studied analytically and numerically. The thickness of such sheets is on the order of the ion Larmor radius, and the normal component of the magnetic field (B _z ) in the sheet is almost constant, while the tangential (B _x ) and shear (B _y ) components depend on the transverse coordinate z. The current density in the sheet also has two self-consistent components (j _x and j _y , respectively), and the magnetic field lines are deformed and do not lie in a single plane. To study such quasi-one-dimensional current configurations, two kinetic models are used, in particular, a numerical model based on the particle-in-cell method and an analytical model. The calculated results show that two different modes of the self-consistent shear magnetic field B _y and, accordingly, two thin current sheet configurations can exist for the same input parameters. For the mode with an antisymmetric z profile of the B _y component, the magnetic field lines within the sheet are twisted, whereas the profiles of the plasma density, current density component j _y , and magnetic field component B _x differ slightly from those in the case of a shearless magnetic field (B _y = 0). For the symmetric B _y mode, the magnetic field lines lie in a curved surface. In this case, the plasma density in the sheet varies slightly and the current sheet is two times thicker. Analysis of the dependence of the current sheet structure on the flow anisotropy shows that the sheet thickness decreases significantly with decreasing ratio between the thermal and drift plasma velocities, which is caused by the dynamics of quasi-adiabatic ions. It is shown that the results of the analytical and numerical models are in good agreement. The problems of application of these models to describe current sheets at the magnetopause and near magnetic reconnection regions are discussed.     

Multisubstrate kinetics of PAH mixture biodegradation: analysis in the double-logarithmic plot

The proposed method of kinetic analysis of aqueous-phase biodegradation of polycyclic aromatic hydrocarbons (PAH) mixture presupposes representation of kinetic curves for each pair of mixture components, S _x and S _y , in double-logarithmic coordinates (ln S _x ; ln S _y ). If PAH mixture conversion corresponds to the multisubstrate model with a common active site, then the graphs in double-logarithmic coordinates are straight lines with the angular coefficients equal to the ratio of respective first-order rate constants k_x^y = \fracV_y K_x K_y V_x k_{x}^{y} = {\frac{{V_{y} K_{x} }}{{K_{y} V_{x} }}} , where K _x and K _y are half-saturation constants, V _x and V _y are the maximum conversion rates for substrates S _x and S _y ; the graph slope does not depend on any concentrations and remains constant during the change of reaction rates as a result of inhibition, induction/inactivation of enzymes or biomass growth. The formulated method has been used to analyze PAH mixture conversion by the culture of Sphingomonas sp. VKM B-2434. It has been shown that this process does not satisfy the multisubstrate model with a single active site. The results suggest that the strain VKM B-2434 contains at least two dioxygenases of different substrate specificity: one enzyme converts phenanthrene and fluoranthene and the other converts acenaphthene and acenaphthylene. The ratios of first-order rate constants have been obtained for these pairs of substrates.     

Estimating nest locations of bumblebee <Emphasis Type="Italic">Bombus ardens</Emphasis> from flower quality and distribution

The central-place forager in a social-insect colony, e.g., the bumblebee, has been expected to maximize its net rate of energy gain to increase the success of its colony. In addition to foraging behavior, the nest location is an important factor for the success of the colony. The bumblebee’s nest location would be affected by the spatial distribution of flowers and their food quality. In this study, we constructed a model to estimate bumblebee nest sites, using the net energy intake rate at available food sites for workers foraging from the nest site. We hypothesized that the probability of colony establishment at a site in coordinates (x, y) was high as the sum of the net energy intake rate I(x, y) increased. To obtain I(x, y), nectar standing crop, sugar concentration, and foraging time were measured for ten plant species in the study site covering 6.25 km². As available flowers changed seasonally, I(x, y) was calculated for three periods: the end of April, the beginning of May, and the middle of May. To verify our hypothesis, we compared the estimations in our model with the actual nest sites of Bombus ardens found in the beginning of May and June by means of tracking bumblebees. From the results, we considered that the net energy intake rate at mid-May might represent the probability of colony establishment, because it could affect colony persistence and reproductive success.     

Quantification of Orofacial Phenotypes in Xenopus

Xenopus has become an important tool for dissecting the mechanisms governing craniofacial development and defects. A method to quantify orofacial development will allow for more rigorous analysis of orofacial phenotypes upon abrogation with substances that can genetically or molecularly manipulate gene expression or protein function. Using two dimensional images of the embryonic heads, traditional size dimensions-such as orofacial width, height and area- are measured. In addition, a roundness measure of the embryonic mouth opening is used to describe the shape of the mouth. Geometric morphometrics of these two dimensional images is also performed to provide a more sophisticated view of changes in the shape of the orofacial region. Landmarks are assigned to specific points in the orofacial region and coordinates are created. A principle component analysis is used to reduce landmark coordinates to principle components that then discriminate the treatment groups. These results are displayed as a scatter plot in which individuals with similar orofacial shapes cluster together. It is also useful to perform a discriminant function analysis, which statistically compares the positions of the landmarks between two treatment groups. This analysis is displayed on a transformation grid where changes in landmark position are viewed as vectors. A grid is superimposed on these vectors so that a warping pattern is displayed to show where significant landmark positions have changed. Shape changes in the discriminant function analysis are based on a statistical measure, and therefore can be evaluated by a p-value. This analysis is simple and accessible, requiring only a stereoscope and freeware software, and thus will be a valuable research and teaching resource.