Concepts of aggregation and their quantification: A critical review with some new results and applications

Various indices of spatial patterns based on plot counts are reviewed for theoretical population models appropriate to ecological studies. It is seen that many of the indices proposed in the literature are essentially equivalent to either the index ω= σ²/μ or to the index γ= (σ²-μ)/μ², thus providing a variety of motiviations and interpretations of these two indices as measures of spatial patterns. A vector approach to measuring spatial patterns which suggests both a unifying relationship between these indices and an extension of them is proposed. This leads to an interpretation of the measures of spatial patterns in terms of the transition probabilities of a pure birth process.     

Further Study on the Statistical Test to Detect Spatial Pattern

In the study of spatial patterns, the statistic I' = (n — 1)s²/x was commonly used. In this paper, we found that x — s² has an approximated normal distribution with zero mean if the x_i's (i = 1 to n) are independent identically distributed Poisson variables. Based on this conclusion, the hypothesis that a point pattern is completely random can be tested directly. And a method for the test of spatial patterns was proposed which can be sued as an alternative to the Chi-square based dispersion index test.     

Spatial scale dependence of the species diversityin Tianmu Mountain and its relationship with spatial patterns by using multifractal analysis

This study took the Tianmu Mountain National Natural Preservation Area in western Zhejiang Province as an example 1) to quantify the species diversity with selected species indices including Shannon-Wiener index (H), Margalef index (K) and Evenness index (E) at different spatial scales, 2) to analyze the spatial distribution patterns of the species diversity by multifractal parameters such as the singularity index α, its fractal dimension f(α), the f(α)–α spectrum range (SR) and its symmetry (Dist) using the multifractal theory, and 3) to determine their relationships. Results of nonlinear regression analysis with power functions showed that increasing spatial scale resulted in increasing H but decreasing E and K, indicating that the scale dependence of species diversity existed. By using the multifractal method, it was indicated that species spatial distribution had multifractal features. Moreover, strong linear relationships of the diversity indices H, E and K with α_min and clear nonlinear associations of the diversity indices H, E and K with power functions for SR and Dist were found. Since interactions of the species diversity and the spatial characteristics are very complex, the above mentioned relationships need further validation along with precise explanations of any correlations among their ecological processes.     

Detecting spatial aggregation from distance sampling: a probability distribution model of nearest neighbor distance

Spatial point pattern is an important tool for describing the spatial distribution of species in ecology. Negative binomial distribution (NBD) is widely used to model spatial aggregation. In this paper, we derive the probability distribution model of event-to-event nearest neighbor distance (distance from a focal individual to its n-th nearest individual). Compared with the probability distribution model of point-to-event nearest neighbor distance (distance from a randomly distributed sampling point to the n-th nearest individual), the new probability distribution model is more flexible. We propose that spatial aggregation can be detected by fitting this probability distribution model to event-to-event nearest neighbor distances. The performance is evaluated using both simulated and empirical spatial point patterns.     

The oxidation-reduction potentials of the hemes and copper of cytochrome oxidase from beef heart

The oxidation-reduction potentials of the heme and copper components of isolated beef heart cytochrome oxidase have been studied by potentiometric techniques. In highly purified preparations the two heme components give a single titration curve with a midpoint potential at pH 7.0 (E_m^7.0) of +285 mV and an n value of 0.5. In partially purified preparations the heme components could be resolved into a high potential cytochrome (a₃) (E_m^7.0 = +375 mV, an n value of 1.0) and a low potential cytochrome (a) (E_m^7.0 = +225 mV, an n value of 1.0). In general, with decrease in enzymatic activity the E_m^7.0 of the high potential component becomes more negative.     

A new eigenfunction spatial analysis describing population genetic structure

Several methods of spatial analyses have been proposed to infer the relative importance of evolutionary processes on genetic population structure. Here we show how a new eigenfunction spatial analysis can be used to model spatial patterns in genetic data. Considering a sample of n local populations, the method starts by modeling the response variable (allele frequencies or phenotypic variation) against the eigenvectors sequentially extracted from a geographic distance matrix (n × n). The relationship between the coefficient of determination (R ²) of the models and the cumulative eigenvalues, which we named the spatial signal-representation (SSR) curve, can be more efficient than Moran’s I correlograms in describing different patterns. The SSR curve was also applied to simulated data (under distinct scenarios of population differentiation) and to analyze spatial patterns in alleles from microsatellite data for 25 local populations of Dipteryx alata, a tree species endemic to the Brazilian Cerrado. The SSR curves are consistent with previous phylogeographical patterns of the species, revealing combined effects of isolation-by-distance and range expansion. Our analyses demonstrate that the SSR curve is a useful exploratory tool for describing spatial patterns of genetic variability and for selecting spatial eigenvectors for models aiming to explain spatial responses to environmental variables and landscape features.     

Genetics of the apolipoprotein E-system in man

The polymorphism of apolipoprotein E (Apo E) in man is controlled by two codominant alleles, Apo Eⁿ and Apo E^d, at the Apo E-N/D locus and by two alleles, the dominant, Apo E4⁺, and the recessive, Apo E4^o, at the Apo E4 locus.

Frequency distribution analysis of Apo E phenotypes demonstrated a highly significant association between both systems (P ~ 1%). The Apo E4-(+) variant was about twice as frequent in phenotype Apo E-N (30.1%) than in phenotype Apo E-ND (16.4%). The phenotypic combination Apo E-D/-E4(+) was not observed. The segregation of Apo E phenotypes in informative matings is consistent with a close linkage of both loci.

The results may be explained by different models. On the basis of the present data, these models cannot be distinguished by formal genetic criteria. (1) Haplotypes Apo Eⁿ/E4⁺, Apo Eⁿ/E4^o, and Apo E^d/E4^o determine the different phenotypes, and a linkage disequilibrium exists of Δ = .0147 between the E-N/D and E4 loci. (2) The fourth haplotype, Apo E^d/E4⁺, exists, but the gene E4⁺ is not expressed in coupling with Apo E^d. The four-haplotype model seems more attractive in view of Apo E-N/D polymorphism's quantitative character and of biochemical results, which show that phenotypes Apo E-N and Apo E-D differ in the apparent molecular weight (M_r) of the respective major Apo E polymorphic form. Hence, the Apo E-N/D locus may control structural genes involved in the posttranslational modification of Apo E. (3) Finally, there may exist only one Apo E structural gene locus but with mutations at two sites susceptible to posttranslational modification.

     

Further notes on the behavior of induced asymmetric dyads in the male of Drosophila melanogaster

The present study confirms the findings of Zimmering and Bendbow [28], that there is preferential recovery of the shorter elements of asymmetric dyads following induced exchanges in irradiated T(2;3)bw^V4 males. Deletion studies giving rough estimates of contaminations of phenotypic crossovers by deletions (or point mutations) have now provided more accurate estimates of the degrees of non-randomness (c) in the regions studied. The significance of the V4 studies and their implications on the mechanisms of meiotic drive are discussed.     

Calculation of the energy confinement time and power threshold for L-H transitions in a tokamak with allowance for the parameters of the transport barrier

The ASTRA-ETL code is used to simulate L-H transition scenarios and calculate the energy confinement time and the threshold power of the L-H transition as functions of the averaged electron density 〈n〉, the averaged magnetic field B, the neutral density n _n , and the neutral temperature T _n , as well as the values of T _Se , T _Si , and n _S at the separatrix. It is shown that the linear dependence of the threshold power of the L-H transition on the averaged electron density, Q _L-H∝〈n〉, is associated with an increase in the viscosity of a poloidally rotating plasma due to charge exchange and is governed exclusively by an increase in the neutral density n _n . When the averaged electron density 〈n〉 is low, the threshold power rises because T _Si and T _Se increase. The accuracy of predictions for the power threshold of the L-H transition can be improved if the scaling of Q _L-H versus 〈n〉 and B is derived by processing experimental data from discharges with close parameter values at the separatrix. The hysteresis effect during an L-H-L transition triggered by varying the input power is modeled. The global energy confinement time τ_E is shown to increase linearly with 〈n〉 in the range 〈n〉<3.6×10¹⁹ m^?3 and to saturate at higher electron densities; this behavior is found to be characteristic of the Ohmic, L-, and H-modes. The saturation is associated with the fact that losses via the ion channel (when the transport coefficients are density-independent) dominate over losses via the electron channel. The dependence of τ _E on the input power is determined from the calculated database and is found to be τ _E =0.12Q _L-H ^?0.46 at a fixed averaged electron density 〈n〉. In the simulations of the L-H transition, the energy confinement time τ _E increases by a factor of 2 only if the thermal diffusivity inside the transport barrier is lower than that in the central plasma by a factor of more than 6.     

Measurement of non-randomness in spatial distributions

The measurement of departure from randomness in spatial distributions has widespread application in ecological work. Several “indices of non-randomness” are compared with regard to their dependence on sample number, sample size and density. Criteria for the best choice of index for specific situations are discussed. A new coefficient C_x is proposed for use with positively contagious distributions and tests of significance are given. When C_x and another index (S²/m−1) are used for positive and negative contagion respectively, values ranging from −1 through 0 (random) to +1 are obtained, regardless of sample number, sample size or density.     

A Standardized Method for the Construction of Tracer Specific PET and SPECT Rat Brain Templates: Validation and Implementation of a Toolbox

High-resolution anatomical image data in preclinical brain PET and SPECT studies is often not available, and inter-modality spatial normalization to an MRI brain template is frequently performed. However, this procedure can be challenging for tracers where substantial anatomical structures present limited tracer uptake. Therefore, we constructed and validated strain- and tracer-specific rat brain templates in Paxinos space to allow intra-modal registration. PET [¹⁸F]FDG, [¹¹C]flumazenil, [¹¹C]MeDAS, [¹¹C]PK11195 and [¹¹C]raclopride, and SPECT [^99mTc]HMPAO brain scans were acquired from healthy male rats. Tracer-specific templates were constructed by averaging the scans, and by spatial normalization to a widely used MRI-based template. The added value of tracer-specific templates was evaluated by quantification of the residual error between original and realigned voxels after random misalignments of the data set. Additionally, the impact of strain differences, disease uptake patterns (focal and diffuse lesion), and the effect of image and template size on the registration errors were explored. Mean registration errors were 0.70±0.32mm for [¹⁸F]FDG (n = 25), 0.23±0.10mm for [¹¹C]flumazenil (n = 13), 0.88±0.20 mm for [¹¹C]MeDAS (n = 15), 0.64±0.28mm for [¹¹C]PK11195 (n = 19), 0.34±0.15mm for [¹¹C]raclopride (n = 6), and 0.40±0.13mm for [^99mTc]HMPAO (n = 15). These values were smallest with tracer-specific templates, when compared to the use of [¹⁸F]FDG as reference template (p&0.001). Additionally, registration errors were smallest with strain-specific templates (p&0.05), and when images and templates had the same size (p≤0.001). Moreover, highest registration errors were found for the focal lesion group (p&0.005) and the diffuse lesion group (p = n.s.). In the voxel-based analysis, the reported coordinates of the focal lesion model are consistent with the stereotaxic injection procedure. The use of PET/SPECT strain- and tracer-specific templates allows accurate registration of functional rat brain data, independent of disease specific uptake patterns and with registration error below spatial resolution of the cameras. The templates and the SAMIT package will be freely available for the research community.     

A homeotic mutation influences the wing vibration patterns during mating in males of the silkworm moth Bombyx mori

An abnormality in the wing vibration pattern in males of the E^Nc homeotic mutant of Bombyx mori was investigated. The wild-type (+/+) males show a switching of the rhythmic wing vibrations from a sequential pattern to an intermittent pattern during mating, whereas the E^Nc mutants show a sequential pattern both before and during mating. Wing motions in +/+ males became small during mating, but those in +/E^Nc males did not. Ablation of the head ganglia of +/+ and +/E^Nc males during mating caused no change in the motor patterns of wing vibrations. Ablation or cooling of the posterior abdomen in the +/+ males during mating caused sequential wing vibrations, suggesting that the change in wing vibrations is induced by signals from the posterior abdomen. The pterothoracic ganglion in the +/E^Nc males is separated into two ganglia, in contrast to the complete ganglionic fusion in the +/+ males. The neurons in the pterothoracic ganglion stained from abdominal nerve cords are homologus in +/+ and +/E^Nc males, but many of these in +/E^Nc males are elongated along the anteroposterior axis. These results suggest that the wing vibration pattern is restricted by genetic factors through reconstruction of the thoracic nervous system during metamorphosis.     

Herbivore-Alga Interaction Strength Influences Spatial Heterogeneity in a Kelp-Dominated Intertidal Community

There is a general consensus that marine herbivores can affect algal species composition and abundance, but little empirical work exists on the role of herbivores as modifiers of the spatial structure of resource assemblages. Here, we test the consumption/bulldozing effects of the molluscan grazer Enoplochiton niger and its influence on the spatial structure of a low intertidal community dominated by the bull kelp Durvillaea antarctica and the kelp Lessonia spicata. Through field experiments conducted at a rocky intertidal shore in north-central Chile (~30°-32°S), the edge of the grazer and algae geographic distributions, we estimated the strength and variability of consumptive effects of the grazer on different functional group of algae. We also used data from abundance field surveys to evaluate spatial co-occurrence patterns of the study species. Exclusion-enclosure experiments showed that E. niger maintained primary space available by preventing algal colonization, even of large brown algae species. The grazing activity of E. niger also reduced spatial heterogeneity of the ephemeral algal species, increasing bare space availability and variability through time in similar ways to those observed for the collective effect with other grazers. Overall, our result suggests that E. niger can be considered an important modifier of the spatial structure of the large brown algae-dominated community. Effects of E. niger on resource variability seem to be directly related to its foraging patterns, large body size, and population densities, which are all relevant factors for management and conservation of the large brown algae community. Our study thus highlights the importance of considering functional roles and identity of generalist consumers on spatial structure of the entire landscape.     

Biochemical Characterization of the Oxygenation of Unsaturated Fatty Acids by the Dioxygenase and Hydroperoxide Isomerase of Pseudomonas aeruginosa 42A2

We have studied oxygenation of fatty acids by cell extract of Pseudomonas aeruginosa 42A2. Oleic acid ((9Z)-18:1) was transformed to (10S)-hydroperoxy-(8E)-octadecenoic acid ((10S)-HPOME) and to (7S,10S)-dihydroxy-(8E)-octadecenoic acid (7,10-DiHOME). Experiments under oxygen-18 showed that 7,10-DiHOME contained oxygen from air and was formed sequentially from (10S)-HPOME by isomerization. (10R)-HPOME was not isomerized. The (10S)-dioxygenase and hydroperoxide isomerase activities co-eluted on ion exchange chromatography and on gel filtration with an apparent molecular size of ∼50 kDa. 16:1n-7, 18:2n-6, and 20:1n-11 were also oxygenated to 7,10-dihydroxy fatty acids, and (8Z)-18:1 was oxygenated to 6,9-dihydroxy-(7E)-octadecenoic acid. A series of fatty acids with the double bond positioned closer to ((6Z)-18:1, (5Z,9Z)-18:2) or more distant from the carboxyl group ((11Z)-, (13Z)-, and (15Z)-18:1) were poor substrates. The oxygenation mechanism was studied with [7S-²H]18:1n-9, [7R-²H]18:2n-6, and [8R-²H]18:2n-6 as substrates. The pro-R hydrogen at C-8 was lost in the biosynthesis of (10S)-HPODE, whereas the pro-S hydrogen was lost and the pro-R hydrogen was retained at C-7 during biosynthesis of the 7,10-dihydroxy metabolites. Analysis of the fatty acid composition of P. aeruginosa revealed relatively large amounts of (9E/Z)-16:1 and (11E/Z)-18:1 and only traces of 18:1n-9. We found that (11Z)-18:1 (vaccenic acid) was transformed to (11S,14S)-dihydroxy-(12E)-octadecenoic acid and to a mixture of 11- and 12-HPOME, possibly due to reverse orientation of (11Z)-18:1 at the active site compared with oleic acid. The reaction mechanism of the hydroperoxide isomerase suggests catalytic similarities to cytochrome P450.     

Assembly of a Tyr122 Hydrophobic Cluster in Sarcoplasmic Reticulum Ca2+-ATPase Synchronizes Ca2+ Affinity Reduction and Release with Phosphoenzyme Isomerization

The mechanism whereby events in and around the catalytic site/head of Ca²⁺-ATPase effect Ca²⁺ release to the lumen from the transmembrane helices remains elusive. We developed a method to determine deoccluded bound Ca²⁺ by taking advantage of its rapid occlusion upon formation of E1PCa₂ and of stabilization afforded by a high concentration of Ca²⁺. The assay is applicable to minute amounts of Ca²⁺-ATPase expressed in COS-1 cells. It was validated by measuring the Ca²⁺ binding properties of unphosphorylated Ca²⁺-ATPase. The method was then applied to the isomerization of the phosphorylated intermediate associated with the Ca²⁺ release process E1PCa₂ → E2PCa₂ → E2P + 2Ca²⁺. In the wild type, Ca²⁺ release occurs concomitantly with EP isomerization fitting with rate-limiting isomerization (E1PCa₂ → E2PCa₂) followed by very rapid Ca²⁺ release. In contrast, with alanine mutants of Leu¹¹⁹ and Tyr¹²² on the cytoplasmic part of the second transmembrane helix (M2) and Ile¹⁷⁹ on the A domain, Ca²⁺ release in 10 μm Ca²⁺ lags EP isomerization, indicating the presence of a transient E2P state with bound Ca²⁺. The results suggest that these residues function in Ca²⁺ affinity reduction in E2P, likely via a structural rearrangement at the cytoplasmic part of M2 and a resulting association with the A and P domains, therefore leading to Ca²⁺ release.     

Modeling Spatial Patterns of Soil Respiration in Maize Fields from Vegetation and Soil Property Factors with the Use of Remote Sensing and Geographical Information System

To examine the method for estimating the spatial patterns of soil respiration (R_s) in agricultural ecosystems using remote sensing and geographical information system (GIS), R_s rates were measured at 53 sites during the peak growing season of maize in three counties in North China. Through Pearson''s correlation analysis, leaf area index (LAI), canopy chlorophyll content, aboveground biomass, soil organic carbon (SOC) content, and soil total nitrogen content were selected as the factors that affected spatial variability in R_s during the peak growing season of maize. The use of a structural equation modeling approach revealed that only LAI and SOC content directly affected R_s. Meanwhile, other factors indirectly affected R_s through LAI and SOC content. When three greenness vegetation indices were extracted from an optical image of an environmental and disaster mitigation satellite in China, enhanced vegetation index (EVI) showed the best correlation with LAI and was thus used as a proxy for LAI to estimate R_s at the regional scale. The spatial distribution of SOC content was obtained by extrapolating the SOC content at the plot scale based on the kriging interpolation method in GIS. When data were pooled for 38 plots, a first-order exponential analysis indicated that approximately 73% of the spatial variability in R_s during the peak growing season of maize can be explained by EVI and SOC content. Further test analysis based on independent data from 15 plots showed that the simple exponential model had acceptable accuracy in estimating the spatial patterns of R_s in maize fields on the basis of remotely sensed EVI and GIS-interpolated SOC content, with R² of 0.69 and root-mean-square error of 0.51 µmol CO₂ m⁻² s⁻¹. The conclusions from this study provide valuable information for estimates of R_s during the peak growing season of maize in three counties in North China.     

Characterization of a dominant-active STAT that promotes tumorigenesis in Drosophila

Little is known about the molecular mechanisms by which STAT proteins promote tumorigenesis. Drosophila is an ideal system for investigating this issue, as there is a single STAT (Stat92E), and its hyperactivation causes overgrowths resembling human tumors. Here we report the first identification of a dominant-active Stat92E protein, Stat92E^ΔNΔC, which lacks both N- and C-termini. Mis-expression of Stat92E^ΔNΔCin vivo causes melanotic tumors, while in vitro it transactivates a Stat92E-luciferase reporter in the absence of stimulation. These gain-of-function phenotypes require phosphorylation of Y⁷¹¹ and dimer formation with full-length Stat92E. Furthermore, a single point mutation, an R^442P substitution in the DNA-binding domain, abolishes Stat92E function. Recombinant Stat92E^R442P translocates to the nucleus following activation but fails to function in all assays tested. Interestingly, R⁴⁴² is conserved in most STATs in higher organisms, suggesting conservation of function. Modeling of Stat92E indicates that R⁴⁴² may contact the minor groove of DNA via invariant TC bases in the consensus binding element bound by all STAT proteins. We conclude that the N- and C- termini function unexpectedly in negatively regulating Stat92E activity, possibly by decreasing dimer dephosphorylation or increasing stability of DNA interaction, and that Stat92E^R442 has a nuclear function by altering dimer:DNA binding.     

Charge and energy spectra of fast multicharged ions in a laser plasma

In measuring the charge and energy spectra of the ions of a single-element laser plasma, in addition to thermal ions, fast multicharged ions are recorded that are accelerated by the electric field of laser radiation in the region of the critical plasma density. The charge and energy spectra of Co ions with the charge numbers z=1–3 are measured at laser intensities of q=5×10¹¹–10¹² W/cm². The energy spectra of these ions are broad and are located on the high-energy side (z _max=3, E>5.0 keV) with respect to the thermal ions (z _max=9, E<4.0 keV). The increase in q to 10¹⁴ W/cm² results in an increase in the charge number of both thermal and fast ions.     

Thermoelectric (seebeck) effect of the cuticle of social wasps

The thermoelectric (Seebeck) coefficient ($\text{S =}\text{ΔV}\text{ΔT}$) in various cuticular areas of the Oriental hornet (Vespa orientalis) fluctuates from 0·3 to 2·4 mV deg^?1 within a temperature range of 27–36°C and when the temperature difference between the two measuring electrodes (ΔT) is 0·6–8·0°C. The values measured on the brown-colored cuticle suggest an n-type conduction, while those measured on the yellow-colored cuticle point to a p-type conduction. It is suggested hornets use this phenomenon for temperature detection.