The relative importance of local phase and local amplitude in patchwise image reconstruction

Natural images were subjected to patchwise Fourier analysis, and the local amplitude and phase spectra were swapped between different images. When the patches were large relative to the image size, the appearance of the reconstructed image was similar to that of the image from which the phase information had been derived, in agreement with previous reports of phase-dominance in the global Fourier Transform. However, when the patch size was made sufficiently small, the appearance of reconstructed images was dominated by amplitude rather than phase. This was not simply due to the DC component of the amplitude spectrum. Prior low-pass filtering of the images enhanced the dominance of amplitude information in the patchwise transform. We conclude that patchwise-reconstructed images contain two quite distinct kinds of information for the human observer. The first is the positional information (local sign) of the patches themselves; the second is the textural information within patches, which is dominated by amplitude rather than phase. The reason why the global Fourier Transform is dominated by phase is that in the absence of any other information about local sign, phase is necessary to reconstruct localised features such as edges.     

What shapes local density? The importance of migration rates and local growth for density‐patch size relationships in two Cionus weevils

1. The relative effect of migration and local growth on the spatio‐temporal density‐distribution of two co‐existing herbivorous weevils, Cionus scrophulariae L. and C. tuberculosus Scop., in 32 host plant Scrophularia nodosa L. patches of varying sizes was investigated. 2. Predictions of the temporal development of the slope in the density‐patch size relationships were derived from a basic population model with scale‐dependent migration rates. The model indicated that the slopes in the density‐patch size relationships during the early season should be reflected by the net scaling of immigration and emigration rates, whereas the slopes during the later season should increase as a result of local growth. 3. Emigration rates of the weevils were estimated in a field experiment, were the weevils coexisted in space and time. These results were then combined with a previous estimate of immigration rates in order to determine the net scaling of migration rates. 4. The emigration rate differed between species, caused by different movement rates in small patches, which could explain differences in the general slope of the density‐patch size relationships of the weevils in the natural figwort patches throughout the summer. The slopes in the relationships in the early season were largely predicted by the net scaling of migration rates. The slope also increased in the later season for C. tuberculosus, whereas the slope decreased for C. scrophulariae. 5. It was concluded that the understanding of both inter‐ and intra‐specific variations in density‐patch size relationships of insect herbivores can be improved using population models incorporating scale‐dependent migration and local growth.     

Expanding the understanding of local community assembly in adaptive radiations

Communities are thought to be assembled by two types of filters: by the environment relating to the fundamental niche and by biotic interactions relating to the realized niche. Both filters include parameters related to functional traits and their variation along environmental gradients. Here, we infer the general importance of environmental filtering of a functional trait determining local community assembly within insular adaptive radiations on the example of Caribbean Anolis lizards. We constructed maps for the probability of presence of Anolis ecomorphs (ecology‐morphology‐behavior specialists) on the Greater Antilles and overlaid these to estimate ecomorph community completeness (ECC) over the landscape. We then tested for differences in environmental parameter spaces among islands for real and cross‐fitted ECC values to see whether the underlying assembly filters are deterministic (i.e., similar among islands). We then compared information‐theoretic models of climatic and landscape parameters among Greater Antillean islands and inferred whether body mass as functional trait determines ECC. We found areas with high ECC to be strongly correlated with environmental filters, partly related to elevation. The environmental parameters influencing high ECC differed among islands. With the exception of the Jamaican twig ecomorph (which we suspect to be misclassified), smaller ecomorphs were more restricted to higher elevations than larger ones which might reflect filtering on the basis of differential physiological restrictions of ecomorphs. Our results in Anolis show that local community assembly within adaptive island radiations of animals can be determined by environmental filtering of functional traits, independently from species composition and realized environmental niche space.     

Image Quality Assessment Based on Inter-Patch and Intra-Patch Similarity

In this paper, we propose a full-reference (FR) image quality assessment (IQA) scheme, which evaluates image fidelity from two aspects: the inter-patch similarity and the intra-patch similarity. The scheme is performed in a patch-wise fashion so that a quality map can be obtained. On one hand, we investigate the disparity between one image patch and its adjacent ones. This disparity is visually described by an inter-patch feature, where the hybrid effect of luminance masking and contrast masking is taken into account. The inter-patch similarity is further measured by modifying the normalized correlation coefficient (NCC). On the other hand, we also attach importance to the impact of image contents within one patch on the IQA problem. For the intra-patch feature, we consider image curvature as an important complement of image gradient. According to local image contents, the intra-patch similarity is measured by adaptively comparing image curvature and gradient. Besides, a nonlinear integration of the inter-patch and intra-patch similarity is presented to obtain an overall score of image quality. The experiments conducted on six publicly available image databases show that our scheme achieves better performance in comparison with several state-of-the-art schemes.     

Pharmacophore modeling and structure-based virtual screening to identify potent inhibitors targeting LuxP of Vibrio harveyi

The main aim of the study is to identify molecules that can disrupt quorum sensing (QS) system of Vibrio harveyi and therefore perhaps the production of toxins. Recently, a novel class of dioxazaborocane derivatives has been found to block AI-2 QS by targeting LuxPQ, but the mechanism of protein inhibition is still unclear. In order to investigate the possible binding modes, all the derivatives were docked into the binding site of LuxP using induced fit docking (IFD). The computed binding affinity is in good agreement with the experimental data. Resultant protein–ligand complexes were simulated using Desmond module and the result revealed better binding of ligands in the binding site of LuxP. Both pharmacophore- and structure-based virtual screening was performed to identify novel hits against LuxP. A filtering protocol, including lipinski filters, number of rotatable bonds and three levels of docking precisions were used for the selection of hits with specific properties. The virtual screening results were then combined and analyzed, which retrieved six hits with significant Glide score, binding affinity toward LuxP. The pharmacokinetic properties of the retrieved hits are in the acceptable range. Enrichment calculation was performed to validate the final hits, to discriminate the active compounds from the inactive compounds. The identified hits could serve as a base for further drug development against LuxP of Vibrio harveyi.     

Local floral composition and the behaviour of pollinators: attraction to and foraging within experimental patches

1. Understanding how foraging decisions take place at the local scale is relevant because they may directly affect the fitness of individual plants. However, little is known about how local diversity and density affect the foraging behaviour of most pollinator groups. 2. By introducing two potted plant species (Salvia farinacae and Tagetes bonanza) into two populations of Taraxacum officinale, we investigated how plant identity, the mixtures of these plant species, and total plant density affected the attraction to and the foraging within a patch for six pollinator groups. 3. The foraging behaviour was mainly driven by the availability of the preferred plant species, and secondly by patch diversity and density. In general, dense patches and those containing the three‐species mixture were preferred by all insect groups for arrival, although muscoid and hover flies responded less to local floral composition than bees. Local diversity and density had, however, a weaker effect on foraging behaviour within patches. Site dependence in response to floral treatments could be attributable to differences between sites in pollinator assemblage and Taraxacum density. 4. Studies like ours will help to understand how foraging decisions occur at the local scale and how foraging patterns may differ between pollinators and sites.     

EFFECT OF THE SINKING RATE OF TWO DIATOMS (THALASSIOSIRA SPP.) ON UPTAKE FROM LOW CONCENTRATIONS OF PHOSPHATE1

The effect of the sinking rate, or rate of medium flow (φ) on the rate of phosphate incorporation (V) by the planktonic diatoms Thalassiosira fluviatilis Hust. and T. pseudonana Hasle & Heimdal in batch and chemostat cultures was determined by passing medium at defined flow rates (0.5–25.0 mm·min^?1) over algae on membrane filters. At concentrations from 1 to 100 μg phosphorus·l^?1 V, increases with increasing velocity of flow, approaching a maximum value (V_m) as described by the empirical relationship: where K_φ is the sinking rate value when V = 1/2 V_m+ V_o and V_o is the uptake at 0 rate of flow. By comparing uptake at controlled flow with uptake in a vigorously stirred medium, the phosphate concentration in the cell boundary layer can be determined. The sinking rate that reduces the phosphate concentration in the boundary layer to half of nominal concentration in the medium is much lower for the larger T. fluviatilis than for T. pseudonana. For both diatoms, it is inversely related to the nominal concentration.     

Relative importance of host plant patch geometry and habitat quality on the patterns of occupancy,extinction and density of the monophagous butterfly <Emphasis Type="Italic">Iolana iolas</Emphasis>

Habitat fragmentation is a major cause of species rarity and decline because it increases local population extinctions and reduces recolonisation rates of remnant patches. Although two major patch characteristics (area and connectivity) have been used to predict distribution patterns in fragmented landscapes, other factors can affect the occurrence of a species as well as the probability of it becoming extinct. In this paper, we study the spatial structure and dynamics of the butterfly Iolana iolas in a 75-patch network of its host plant (Colutea hispanica) to determine the relative importance of patch area, connectivity and habitat quality characteristics on occupancy, extinction and density over the period 2003–2006. Occupancy in 2003, incidence (proportion of years occupied) and probability of extinction were mostly affected by patch area. Smaller patches were less likely to be occupied because they had a higher probability of extinction, partly due to environmental stochasticity. The density of I. iolas was negatively related to patch area in all study years. Only in 2004 was the density of I. iolas positively influenced by fruit production per plant. Our results suggest that for I. iolas, and probably for other specialist butterflies with clearly delimited resource requirements, metapopulation dynamics can be satisfactorily predicted using only geometric variables because most habitat characteristics are subsumed in patch area. However, this hypothesis should be subject to further testing under diverse environmental conditions to evaluate the extent of its generalisation.     

Determination of the filamentous cyanobacteria Planktothrix rubescens in environmental water samples using an image processing system

Cyanobacteria occur in surface waters worldwide. Many of these produce peptides and/or alkaloids, which can present a risk for animal and human health. Effective risk assessment and management requires continuous and precise observation and quantification of cyanobacterial cell densities. In this respect, quantification of filamentous Planktothrix species is problematic. The aim of this study was to develop an automated system to count filamentous Planktothrix rubescens using image processing. Furthermore, this study aimed to assess optimum sample volumes and filament density for measurement precision and to validate image processing measurement of P. rubescens for an effective risk assessment.Three environmental samples and one cultured sample of P. rubescens were collected by filtration onto nitrocellulose filters. Filament lengths were determined using fluorescence microscopy combined with an image processor. Cell density could be calculated from the resulting images. Cyanobacteria could easily be discriminated from algae via their fluorescence properties. The results were found to be independent of the mode of image acquisition. The precision of total filament length determination was dependent on the total filament length on the filter, i.e. analyses of highest precision could be expected for filters containing 2000–20,000 μm filaments per mm². When using suitable filtration volumes, the detection limits of the described method are sufficient for an effective risk assessment. To summarise, this procedure is a fast, easy and accurate method to determine cell densities of filamentous P. rubescens in water samples without costly and tedious manual handling.     

Filtering of temporal parameters of the calling song by cricket females of two closely related species: a behavioral analysis

The phonotactic response of cricket females was investigated on a locomotion compensator to determine the temporal parameters of the male's calling song which are important for species recognition. Two sympatric species (Teleogryllus commodus, T. oceanicus) that show different syllable periods in the chirp and trill parts of their calling songs were used. By their responses T. commodus females exhibited two temporal filters for syllable periods, which were tuned to the species-specific syllable periods occurring during chirp and trill. For song recognition both filters had to be activated and for both a minimum number of three to five consecutive syllable periods was necessary. In contrast, T. oceanicus females showed only one sharply tuned filter corresponding to the chirp part of the male's calling song. This filter was sufficient for calling song recognition. Syllable periods of the trill part also influenced calling song recognition, but these played only a minor role. Carrier frequency was also important for positive phonotaxis. Calling song recognition by T. commodus females is largely based on central nervous processing, while for T. oceanicus both peripheral frequency filtering and central temporal filtering is important. Accepted: 17 January 1997     

Untangling associations between chironomid taxa in Neotropical streams using local and landscape filters

1. Analyses of species association have major implications for selecting indicators for freshwater biomonitoring and conservation, because they allow for the elimination of redundant information and focus on taxa that can be easily handled and identified. These analyses are particularly relevant in the debate about using speciose groups (such as the Chironomidae) as indicators in the tropics, because they require difficult and time‐consuming analysis, and their responses to environmental gradients, including anthropogenic stressors, are poorly known. 2. Our objective was to show whether chironomid assemblages in Neotropical streams include clear associations of taxa and, if so, how well these associations could be explained by a set of models containing information from different spatial scales. For this, we formulated a priori models that allowed for the influence of local, landscape and spatial factors on chironomid taxon associations (CTA). These models represented biological hypotheses capable of explaining associations between chironomid taxa. For instance, CTA could be best explained by local variables (e.g. pH, conductivity and water temperature) or by processes acting at wider landscape scales (e.g. percentage of forest cover). 3. Biological data were taken from 61 streams in Southeastern Brazil, 47 of which were in well‐preserved regions, and 14 of which drained areas severely affected by anthropogenic activities. We adopted a model selection procedure using Akaike’s information criterion to determine the most parsimonious models for explaining CTA. 4. Applying Kendall’s coefficient of concordance, seven genera (Tanytarsus/Caladomyia, Ablabesmyia, Parametriocnemus, Pentaneura, Nanocladius, Polypedilum and Rheotanytarsus) were identified as associated taxa. The best‐supported model explained 42.6% of the total variance in the abundance of associated taxa. This model combined local and landscape environmental filters and spatial variables (which were derived from eigenfunction analysis). However, the model with local filters and spatial variables also had a good chance of being selected as the best model. 5. Standardised partial regression coefficients of local and landscape filters, including spatial variables, derived from model averaging allowed an estimation of which variables were best correlated with the abundance of associated taxa. In general, the abundance of the associated genera tended to be lower in streams characterised by a high percentage of forest cover (landscape scale), lower proportion of muddy substrata and high values of pH and conductivity (local scale). 6. Overall, our main result adds to the increasing number of studies that have indicated the importance of local and landscape variables, as well as the spatial relationships among sampling sites, for explaining aquatic insect community patterns in streams. Furthermore, our findings open new possibilities for the elimination of redundant data in the assessment of anthropogenic impacts on tropical streams.     

El Niño,grazers and fisheries interact to greatly elevate extinction risk for Galapagos marine species

Comparisons between historical and recent ecological datasets indicate that shallow reef habitats across the central Galapagos Archipelago underwent major transformation at the time of the severe 1982/1983 El Niño warming event. Heavily grazed reefs with crustose coralline algae (‘urchin barrens’) replaced former macroalgal and coral habitats, resulting in large local and regional declines in biodiversity. Following recent threat assessment workshops, a total of five mammals, six birds, five reptiles, six fishes, one echinoderm, seven corals, six brown algae and nine red algae reported from coastal environments in Galapagos are now recognized as globally threatened. The 2008 International Union for the Conservation of Nature (IUCN) Red List includes 43 of these species, while two additional species (Galapagos damsel Azurina eupalama and 24‐rayed sunstar Heliaster solaris) not seen for > 25 years also fulfil IUCN threatened species criteria. Two endemic species (Galapagos stringweed Bifurcaria galapagensis and the damselfish A. eupalama) are now regarded as probably extinct, while an additional six macroalgal species (Dictyota galapagensis, Spatoglossum schmittii, Desmarestia tropica, Phycodrina elegans, Gracilaria skottsbergii and Galaxaura barbata) and the seastar H. solaris are possibly extinct. The removal of large lobster and fish predators by artisanal fishing probably magnified impacts of the 1982/1983 El Niño through a cascade of indirect effects involving population expansion of grazing sea urchins. Marine protected areas with adequate enforcement are predicted to ameliorate but not eliminate ecosystem impacts caused by increasing thermal anomalies associated with El Niño and global climate change.     

A Generic Approach for Efficient Detection of Vascular Structures

Vascular segmentation is often required in medical image analysis for various imaging modalities. Despite the rich literature in the field, the proposed methods need most of the time adaptation to the particular investigation and may sometimes lack the desired accuracy in terms of true positive and false positive detection rate. This paper proposes a general method for vascular segmentation based on locally connected filtering applied in a multiresolution scheme. The filtering scheme performs progressive detection and removal of the vessels from the image relief at each resolution level, by combining directional 2D-3D locally connected filters (LCF). An important property of the LCF is that it preserves (positive contrasted) structures in the image if they are topologically connected with other similar structures in their local environment. Vessels, which appear as curvilinear structures, can be filtered out by an appropriate LCF set-up which will minimally affect sheet-like structures. The implementation in a multiresolution framework allows dealing with different vessel sizes. The outcome of the proposed approach is illustrated on several image modalities including lung, liver and coronary arteries. It is shown that besides preserving high accuracy in detecting small vessels, the proposed technique is less sensitive with respect to noise and the presence of pathologies of positive-contrast appearance on the images. The detection accuracy is compared with a previously developed approach on the 20 patient database from the VESSEL12 challenge.     

多枝柽柳年轮生长速率测量及TRGR指标优势分析

灌木对生境和气候变化具有高度敏感性,其年轮资料在认识区域环境演变过程、全球气候变化和环境保护中具有重要作用。灌木植株在生长过程中受遗传和极端环境的影响,年轮常出现偏心和不规则生长,这使得专业年轮分析软件测量的年轮宽度数据难以准确反映其整体径向生长信息。为探讨适合于寒旱区灌木年轮学研究的年轮测量指标和测量方法,研究以该区域荒漠常见植物多枝柽柳(Tamarix ramosissima Ledeb.)为研究对象,通过U-net深度学习方法,获得年轮提取训练模型,自动获取扫描轮盘各年早材区域。轮盘扫描及语义分割后的图像经GIS配准赋坐标、ENVI图像处理后,借助GIS编辑和测量工具,完成多枝柽柳各年年轮生长速率(Tree-ring growth rate, TRGR)、年轮宽度(Tree-ring width, TRW)和树木基部断面积生长增量(Basal area increment, BAI)的测量;研究基于Timesat Savitzky-Golay(S-G)滤波时间序列拟合,获取点样尺度归一化植被指数(Normalized difference vegetation index, ND...     

Characterization of Deciliation-Regeneration Process of Tetrahymena Pyriformis for Cellular Robot Fabrication

Artificial magnetotactic Tetrahymena pyriformis GL (T. pyriformis) cells were created by the internalization of iron oxide nano particles and became controllable with a time-varying external magnetic field. Thus, T. pyriformis can be utilized as a cellular robot to conduct micro-scale tasks such as transportation and manipulation. To complete these tasks, loading inorganic or organic materials onto the cell body is essential, but functionalization of the cell membrane is obstructed by their motile organelles, cilia. Dibucaine HCl, a local anesthetic, removes the cilia from the cell body, and the functional group would be absorbed more efficiently during cilia regeneration. In this paper, we characterize the recovery of artificial magnetotactic T. pyriformis after the deciliation process to optimize a cellular robot fabrication process. After sufficient time to recover, the motility rate and the average velocity of the deciliated cells were six and ten percent lower than that of non-deciliated cells, respectively. We showed that the motile cells after recovery can still be controlled using magnetotaxis, making T. pyriformis a good candidate to be used as a cellular robot.     

A spin-state-selective experiment for measuring heteronuclear one-bond and homonuclear two-bond couplings from an HSQC-type spectrum

Recently, a set of selective 1D experiments with spin-state-selective excitation for CH spin systems was introduced by Parella and Belloc (J. Magn. Reson., 148, 78–87 (2001)). We have expanded and generalized this concept further, and demonstrated that a very simple experiment utilizing spin-state-selective filtering can be used for simultaneous measurement of heteronuclear ¹ J _NH (or ¹ J _CH) and geminal ² J _HH couplings from two-dimensional ¹⁵N-¹H (or ¹³C-¹H) correlation spectrum. The experiment has very high sensitivity owing to the preservation of equivalent coherence transfer pathways analogous to the sensitivity and gradient enhanced HSQC experiment. However, overall length of the pulse sequence is 1/(2J) shorter than the gradient selected SE-HSQC experiment. Furthermore, the spin-state-selection can be utilized between NH and NH₂ (or CH and CH₂) moieties by changing the phase of only one pulse. The pulse scheme will be useful for the measurement of scalar and residual dipolar couplings in wide variety of samples, due to its high sensitivity and artifact suppression efficiency. The method is tested on NH₂ and CH₂ moieties in ¹⁵N- and ¹⁵N/¹³C–labeled ubiquitin samples.     

Life and death near a windy oasis

We propose a simple experiment to study delocalization and extinction in inhomogeneous biological systems. The nonlinear steady state for, say, a bacteria colony living on and near a patch of nutrient or favorable illumination (“oasis”) in the presence of a drift term (“wind”) is computed. The bacteria, described by a simple generalization of the Fisher equation, diffuse, divide A→A + A, die A→ 0, and annihilate A + A→ 0. At high wind velocities all bacteria are blown into an unfavorable region (“desert”), and the colony dies out. At low velocity a steady state concentration survives near the oasis. In between these two regimes there is a critical velocity at which bacteria first survive. If the “desert” supports a small nonzero population, this extinction transition is replaced by a delocalization transition with increasing velocity. Predictions for the behavior as a function of wind velocity are made for one and two dimensions. Received: 3 August 1998 / Revised version: 17 July 1999 / Published online: 4 July 2000     

Texture discrimination by Gabor functions

A 2D Gabor filter can be realized as a sinusoidal plane wave of some frequency and orientation within a two dimensional Gaussian envelope. Its spatial extent, frequency and orientation preferences as well as bandwidths are easily controlled by the parameters used in generating the filters. However, there is an uncertainty relation associated with linear filters which limits the resolution simultaneously attainable in space and frequency. Daugman (1985) has determined that 2D Gabor filters are members of a class of functions achieving optimal joint resolution in the 2D space and 2D frequency domains. They have also been found to be a good model for two dimensional receptive fields of simple cells in the striate cortex (Jones 1985; Jones et al. 1985).The characteristic of optimal joint resolution in both space and frequency suggests that these filters are appropriate operators for tasks requiring simultaneous measurement in these domains. Texture discrimination is such a task. Computer application of a set of Gabor filters to a variety of textures found to be preattentively discriminable produces results in which differently textured regions are distinguished by firstorder differences in the values measured by the filters. This ability to reduce the statistical complexity distinguishing differently textured region as well as the sensitivity of these filters to certain types of local features suggest that Gabor functions can act as detectors of certain texton types. The performance of the computer models suggests that cortical neurons with Gabor like receptive fields may be involved in preattentive texture discrimination.