Comparing semantically-blind and semantically-aware landscape similarity measures with application to query-by-content and regionalization

Local landscapes can be assessed for a degree of mutual similarity between their patterns using a methodology pioneered in the domain of Content-Based Image Retrieval (CBIR). They are represented by multivariate histograms of selected pattern features and their similarity is calculated as the similarity between those histograms. Potential similarity functions include semantically-blind measures — designed to compare only the patterns without taking into account intrinsic similarities between the features, and semantically-aware measures — that also take into account intrinsic (semantic) alikeness between landscape features. In this paper we compare the performance of these two types of landscape similarity measures. Two measures are evaluated, the semantically-blind Jensen–Shanon (JS) and the semantically-aware Earth Mover's Distance (EMD). The performance of these two measures is evaluated empirically by running tests pertaining to their potential practical applications: a query-by-content and regionalization into landscape types. Variants of the JS and EMD corresponding to 1D and 2D histograms are applied to the two test sites taken from the NLCD 2006. Each test site is divided into 400 3 × 3 km areal units serving as local landscapes. For each test site extensive query-by-content and regionalization calculations are run using different variants of JS and EMD. The results are compared using statistics and visual assessment. The EMD has been found to perform better than the JS, but the difference in performance is not pronounced, especially if a 1D histogram representation of landscapes is used. For the 2D histogram representation of landscapes the EMD consistently yields better results than the JS but suffers from high computational cost. The EMD also enables the comparison of landscapes having different legends.     

Homeomorphy between Devonian brachiopod communities in France and Iowa

The diverse brachiopod faunas from the Calcaire de Ferques of north France and the Lime Creek Formation of Iowa show a remarkable homeomorphy. They are both of Frasnian age and occupied similar mid-shelf muddy carbonate environments. It is possible to match species in the two faunas on external form; this similarity can also be seen in the population histograms. The two areas originated in different faunal provinces, however, and serial sections show that homeomorphic forms were not genetically related. Thus it seems possible that the similarity between the two faunas is entirely a result of adaptation to similar environments.     

Correlation of fine structures of distributions of amplitudes of a photomultiplier dark current fluctuations with the Earth rotations about its axis

The fine structures of distributions of photomultiplier dark current fluctuations measured in two laboratories 2000 km distant from other: in the international Institute of Biophysics (Neuss, Germany) and in the Moscow State University (Moscow, Russia) were compared. It is shown that similar forms of appropriate histograms are apparently more often realized at both locations at the same local time. This confirms the previous conclusion that the fine structure of distributions correlates with rotation of the Earth about its axis.     

Dependence of 'macroscopic fluctuations" on geographic coordinates (from materials of Arctic (2000) and Antarctic (2001) expeditions

The detailed structure of histograms constructed from the results of synchronous measurements of the alpha-activity of 239Pu microsamples, conducted in Pushchino (Moscow Region, Russia) and on board the ship "Academician Fedorov" during the Arctic and Antarctic expeditions (2000 and 2001) was analyzed. It was shown that, if the histograms were constructed over a total period of 15 min and more, the "local zone effect" and the circadian periodicity in the similarity of histogram structure, observed during measurements in Pushchino, are not found in measurements on board the ship near the North Pole (latitude 82 degrees). If the histograms were constructed over a total time of 1 min, a strict periodicity ("stellar day" 23 h 56 min) in the appearance of similar histograms in Pushchino and the Arctic and a strict synchronicity of the appearance of similar histograms of measurements in Pushchino and on board the ship at the same local geographical time were observed. During the Antarctic expedition, the effect of synchronicity of the appearance of similar histograms in Pushchino and on board the ship decreased as the ship moved towards the South Pole and the difference in latitude between the points of measurements increased.     

Dry mass, DNA and non-histone protein determinations in lung cancer cells

Summary Cell nuclei from two biopsies of bronchial mucosa, seven squamous-cell carcinomas and six small-cell carcinomas of the lung were investigated. DNA and non-histone protein (NHP) content were simultaneously determined in Feulgen—Naphthol Yellow S-stained smears by means of multiple plug cytophotometry. In addition, the nuclear dry mass of cells originating from the same populations was measured by interference microscopy.DNA histograms of carcinomas were characterized by DNA stemlines being situated in the diploid range in four out of six small-cell carcinomas and in the hyperdiploid to hypertetraploid range in six out of seven squamous-cell carcinomas.Polyploid values (up to 8 c) were seldom found in small-cell carcinomas whereas squamous-cell carcinomas showed a broader dispersion approaching the 16 c level.The similarity of the NHP distributions with the DNA histograms was more marked in small-cell carcinomas than in the squamous-cell carcinomas. In comparison with the NHP distributions of normal bronchial epithelial cells, those of carcinomas were shifted to higher values. The increased NHP content was found to be a more prominent sign of malignancy in small-cell carcinomas than the DNA mass. The increase in nuclear dry mass in carcinomas was mainly caused by the accumulation of NHP in tumour cell nuclei.     

Cubic phases of lipid-containing systems. The structure of phase Q223 (space group Pm3n). An X-ray scattering study.

The hexagonal (H) and the cubic (Q223) phases of the systems dodecyltrimethylammonium chloride-water and palmitoyllysophosphatidy choline-water have been studied by X-ray scattering techniques. The signs of the reflections of phase H were determined by a systematic study as a function of the water content, those of phase Q223 were assessed using a pattern recognition approach based upon the axiom that the histograms of the electron density maps of phases Q223 and H, extrapolated to the same concentration and properly normalized in scale and shape, are very similar to each other. In the case of phase Q223, all the sign combinations (the phi-sets) compatible with the observed reflections were generated, and each of the corresponding histograms was compared with the histogram of the map of phase H. One novelty of this work is the use of a highly sensitive criterion to estimate the similarity of the histograms, namely the distance in the six-dimensional space of the moments [mean value of (delta rho)n]1/n, for 3 greater than or equal to n greater than or equal to 8. In the two systems, the use of this criterion has led to the unambiguous choice of one electron density map. The maps show that the structure of phase Q223 consists of disjointed micelles (of type I), belonging to two different classes: those of one class are quasi-spherical in shape and are centered at the points a, those of the other class are disc-shaped and are centred at the points c. The results of this work rule out a structure formed by a cage-like distribution of rods enclosing a set of quasi-spherical micelles and is consistent with previous proposals. This is the second example, after that of phase Q227, of a micellar cubic phases in lipid-containing systems; all the known examples of phase Q223 are of type I, those of phase Q227 of type II.     

Periodic forcing of a K+ channel at various temperatures.

The random sequence of openings and closings of single ion channels and the channel conductances have been the object of intense study over the past two decades with a view toward illuminating the underlying kinetics of the channel protein molecules. Channels that are sensitive to voltage, such as many K(+)-selective channels, have been particularly useful, because the kinetic rates can be manipulated by changing the membrane voltage. Most such studies have been performed under stationary conditions and usually at a single temperature. Here we report the results of experiments with sinusoidal modulation of the membrane potential performed at several temperatures. Dwell time and cycle histograms, objects not normally associated with ion channel experiments, are herein reported. From the last, the transition probability densities for channel opening and closing events are obtained. A new and unusual phase anticipation is observed in the cycle histograms, and its temperature dependence is measured.     

Evidence for multiple open states of sodium channels in neuroblastoma cells

Summary Open times of voltage-gated sodium channels in neuroblastoma cells were measured during repolarization (following a short depolarizing conditioning pulse) and during moderate depolarization. Conditional and unconditional channel open-time histograms were best fitted by the sum of two exponentials. (The conditional open time was measured from the end of the conditioning pulse until an open channel shuts provided it was open att=0). Time constants of both histograms depended on the postpulse and were shifted to more positive potentials with increasing conditioning pulse potential. This shift could be explained by assuming more than two time constants in the histograms, which could not be separated. Channel open-time histograms from single-pulse experiments showed a maximum att>0. These histograms could be best fitted by an exponential function with three time constants. One term of this function included the difference of two exponentials resulting in a maximum att>0. Open-time histograms showed a definite time dependence. At 2 to 6.5 msec after the beginning of the depolarization the best fit could be obtained by the difference of two exponentials. To these components another term had to be added at 0 to 2 msec. Between 6.5 and 14.0 msec the sum of two exponentials, and after 14.0 msec a single exponential resulted in a good fit. The results support the hypothesis that sodium channels in neuroblastoma cells may have multiple open states. Two of these states are irreversibly coupled.     

Statistical analysis and biological interpretation of the flow cytometric heterogeneity observed in bacterial axenic cultures

Histogram comparison and meaningful statistics in flow cytometry is probably the most widely encountered mathematical problem in flow cytometry. Ideally, a test for determining the statistical equality or difference of flow cytometric distributions will identify the significant differences or similarities of the obtained histograms. This situation is of particular interest when flow cytometry is used to study the heterogeneity of axenic bacterial populations. We have statistically measured the heterogeneity of successive cytometric measures, the modifications produced after 20 transfers from the same culture, and the differences between 20 subcultures of identical origin. The heterogeneity of the bacterial populations and the similarity of the obtained 360 histograms were analysed by standard statistical methods. We have studied bacterial axenic cultures in order to detect, quantify and interpret their cytometric heterogeneity, and to assess intrinsic differences and differences produced by laboratory manipulations. We concluded that the standard axenic cultures have a considerable intrinsic cellular and molecular heterogeneity. We suggest that the heterogeneity we have detected basically has two origins: cell size diversity and cell cycle variations.     

Macronuclear chromatin structure dynamics in Colpoda inflata (Protista, Ciliophora) resting encystment.

The chromatin structure dynamics of the Colpoda inflata macronucleus have been investigated in relation to its functional condition, concerning chromatin body extrusion regulating activity. Samples of 2- and 25-day-old resting cysts derived from a standard culture, and of 1-year-old resting cysts derived from a senescent culture, were examined by means of histogram analysis performed on acquired optical microscopy images. Three groups of histograms were detected in each sample. Histogram classification, clustering and matching were assessed in order to obtain the mean histogram of each group. Comparative analysis of the mean histogram showed a similarity in the grey level range of 25-day- and 1-year-old cysts, unlike the wider grey level range found in 2-day-old cysts. Moreover, the respective mean histograms of the three cyst samples appeared rather similar in shape. All this implies that macronuclear chromatin structural features of 1-year-old cysts are common to both cyst standard cultures. The evaluation of the acquired images and their respective histograms evidenced a dynamic state of the macronuclear chromatin, appearing differently condensed in relation to the chromatin body extrusion regulating activity of the macronucleus. The coexistence of a chromatin-decondensed macronucleus with a pycnotic extrusion body suggests that chromatin unable to decondense, thus inactive, is extruded. This finding, along with the presence of chromatin structural features common to standard and senescent cyst populations, supports the occurrence of 'rejuvenated' cell lines from 1-year-old encysted senescent cells, a phenomenon which could be a result of accomplished macronuclear renewal.     

Comparison of gaussian and t-distribution densities for modeling fluorescence dispersion in flow cytometric DNA histograms

In this paper, we have analyzed, on an experimental basis, the behaviour of the standardized t-distribution with three degrees of freedom versus the gaussian model, when employed for describing the fluorescence dispersion effect in flow cytometric DNA measurements. The comparison has been performed by employing two different objective criteria based on a computer analysis for fitting DNA histograms and on a parameter related to the peak distribution shape. The results indicate that, when the peak variance is not particularly small, the two models are substantially equivalent. In the case of experimental data with very sharp peaks, the t-distribution performs better than the gaussian density.     

Comparison of automated and manual techniques for analysis of DNA frequency distributions in bladder washings

Quantitative methods for interpretation of flow cytometry DNA histograms are required for the widespread clinical use of this technology. The usefulness of a histogram analysis technique in this setting requires that it be operator independent, easy to implement in a clinical laboratory, and provide high sensitivity to the desired information. Additionally, the technique must be tolerant of the relatively low signal-to-noise ratios often found in DNA distributions obtained from clinical samples. Among the factors that have been used to assess the malignant potential of tumors are the presence of an aneuploid population, the proportion of hyperdiploid cells, the width of the G1 peak, the DNA index, and the fraction of cells in S. A computer-based method has been developed for extraction of the above-mentioned features from DNA histograms. The program detects peaks in the histogram and uses straight-line fits to the cumulative frequency distribution to define cell population bounds. A test set of 44 histograms compiled from bladder irrigation specimens obtained from patients with a present or past history of transitional cell carcinoma (TCC) was analyzed by five collaborating laboratories forming a Network sponsored by the National Cancer Institute (NCI). This test set was used to evaluate the performance of the computer-based method by comparing results with those of four expert observers. In this preliminary analysis, perfect agreement was found in the detection of aneuploid cell populations by all observers and the computer-based method. Correlation of percent hyperdiploid cell fraction was also excellent.(ABSTRACT TRUNCATED AT 250 WORDS)     

On using landscape metrics for landscape similarity search

Landscape similarity search involves finding landscapes from among a large collection that are similar to a query landscape. An example of such collection is a large land cover map subdivided into a grid of smaller local landscapes, a query is a local landscape of interest, and the task is to find other local landscapes within a map which are perceptually similar to the query. Landscape search and the related task of pattern-based regionalization, requires a measure of similarity – a function which quantifies the level of likeness between two landscapes. The standard approach is to use the Euclidean distance between vectors of landscape metrics derived from the two landscapes, but no in-depth analysis of this approach has been conducted. In this paper we investigate the performance of different implementations of the standard similarity measure. Five different implementations are tested against each other and against a control similarity measure based on histograms of class co-occurrence features and the Jensen–Shannon divergence. Testing consists of a series of numerical experiments combined with visual assessments on a set of 400 3 km-scale landscapes. Based on the cases where visual assessment provides definitive answer, we have determined that the standard similarity measure is sensitive to the way landscape metrics are normalized and, additionally, to whether weights aimed at controlling the relative contribution of landscape composition vs. configuration are used. The standard measure achieves the best performance when metrics are normalized using their extreme values extracted from all possible landscapes, not just the landscapes in the given collection, and when weights are assigned so the combined influence of composition metrics on the similarity value equals the combined influence of configuration metrics. We have also determined that the control similarity measure outperforms all implementations of the standard measure.     

Comparison of microscopic imaging strategies for evaluating immunocytochemical (PAP) steroid receptor heterogeneity

Receptogram analysis was compared with three other imaging strategies for immunocytochemical assay of estrogen receptors. These included nuclear-specific methods for analysis of nuclear integrated optical density (IOD) or mean optical density (MOD) histograms, and field-specific methods, where the pixel optical density (POD) histogram was evaluated for the composite nuclear phase. Measurements in culture and in breast cancer cryosections were treated separately to isolate geometric considerations. In culture receptograms the modality of IOD and MOD histograms and their bivariate contour maps revealed one, two, or more subpopulations with discrete receptor content and concentration. However, when the field of nuclei was imaged as a whole, regardless of the number of subpopulations, POD histograms showed two minima, defining three intranuclear phases. This was due to mottling and variegation of intranuclear chromatin and nucleolar immunostaining and not to differences between nuclei. These limitations were also revealed in breast cancer sections. In POD histograms, % unstained pixels did not provide a reliable estimate of % receptor negative nuclei, as determined by their enumeration. In sections, correction of IOD for nuclear volume variability was essential to suppress artifactual peaks not representing differences in receptor content. This was achieved by multiplying nuclear IOD by the spherical nuclear radius (S) of individual slab sections. Peaks of IOD(S) then reflected receptor content on a true ratio scale. Only receptogram analysis, which incorporates these strategies, permitted objective evaluation of receptor heterogeneity at the level of tumor subpopulations.     

Response of frog midbrain neurons to tones amplitude-modulated by pseudorandom noise

Spike response in torus semicircularis units to the effects of uninterrupted characteristic frequency tones amplitude-modulated by pseudorandom noise were investigated during experiments on immobilizedRana ridibunda. Period histograms of modulating waveform of 512 msec duration (both modulating polarities) were produced for 32 units. Almost all neurons investigated responded exclusively to the positive half of the modulating signal. Difference histograms obtained by calculating period histograms for different polarities of the envelope faithfully reproduced the dynamics of signal amplitude in four units. The remainder responded only to envelope maxima, without reproducing amplitude dynamics among these; over half the units represented only some of the envelope maxima, moreover. Certain cells were found which retained their specific pattern of response to pseudorandom noise over a wide range of carrier intensities.N. N. Andreev Acoustical Institute, Moscow. Translated from Neirofiziologiya, Vol. 22, No. 2, pp. 227–235, March–April, 1990.     

Changes in the functional organization of the lateral geniculate body after tetanus toxin injection

Changes in unit activity in the lateral geniculate body during formation of a generator of pathologically enhanced excitation as a result of local injection of tetanus toxin into this nucleus were investigated in unanesthetized cats. To assess changes taking place a classification of geniculate neurons in normal animals obtained by analysis of interspike interval histograms of spontaneous activity and poststimulus histograms of unit activity evoked by photic stimulation was used. As a result of the action of the toxin substantial changes were observed in the quantitative distribution of the neurons by groups. A new group of neurons with a considerably increased duration of the first spike volley also was identified. The appearance of these neurons is connected with disappearance of the inhibitory pause in the overwhelming majority of relay neurons of the nucleus.Institute of General Pathology and Pathological Physiology, Academy of Medical Sciences of the USSR, Moscow. Translated from Neirofiziologiya, Vol. 10, No. 1, pp. 38–43, January–February, 1978.     

Autolysis is a potential source of false aneuploid peaks in flow cytometric DNA histograms

Serial flow cytometric nuclear DNA content analyses were performed from normal human spleen, thyroid, liver, and pancreas removed from ten patients at autopsy and stored for up to 8 d without any preservative to study the effect of autolysis on DNA histograms. Fine needle aspiration biopsy (FNAB) samples were taken in diluted ethanol and tissue biopsies from the same area in formalin for embedding into paraffin at the time of autopsy and serially thereafter. Histograms obtained from samples taken within 10 h after death had a symmetrical G1 peak with a small coefficient of variance (CV) except histograms produced from paraffin-embedded pancreatic tissue, but bimodal distributions similar to those seen in aneuploid tumors were obtained from many samples stored longer than for 20 h. The DNA indices of the bimodal histograms were usually less than 1.3. The false peaks were more prominent in FNAB samples than in paraffin-embedded samples. The time of appearance of the false aneuploid peaks varied individually, and they were usually first seen in samples taken from the pancreas, followed by the liver, the thyroid and the spleen. Because neoplasms may become necrotic in vivo and fixation of fresh surgical samples may be slow and incomplete, increased DNA staining caused by autolysis may be a source of false aneuploid peaks in DNA content analysis.     

Analysis of Gliadin Polymorphism in aTriticum speltaL. Collection

Using gliadins, endorperm storage proteins of kernels, as markers, the genetic diversity of 170 samples from the Triticum speltaL. collection of the Vavilov Institute of Plant Industry was studied. High intraspecific polymorphism of the gliadin electrophoretic patterns was revealed. On the basis of similarity of the gliadin electrophoretic patterns, groups of samples were isolated, and the genetic stucturization of the collection was performed.     

DNA flow cytometric analysis of mouse seminiferous epithelium

In order to provide a basis for quantitative studies of murine spermatogenesis, we performed a DNA flow cytometric analysis on the mouse seminiferous tubules isolated at defined stages of the epithelial cycle by transillumination-assisted microdissection. Accurate stage identification was performed by examining spermatids in the adjacent tubule segments by phase-contrast microscopy. For flow cytometry, suspension of nuclei of spermatogenic cells was obtained by detergent treatment of isolated seminiferous tubules, and fresh samples were stained with propidium iodide. DNA histograms of the 12 stages of the mouse seminiferous epithelial cycle varied in a stage-specific manner. DNA histograms of stages I-VIII of the cycle were characterized by a hypofluorescent haploid peak, the location of which changed with the decreasing DNA dye (propidium iodide)-binding capacity of elongated spermatids. The absence of the hypohaploid peak and the high ratio of the cells with 4C amount of DNA to the cells with 1C amount of DNA characterized stages IX-XI of the cycle. Stage XII showed a high 2C peak, owing to a large population of secondary spermatocytes arisen from the first meiotic division. By using fluorescent beads as an internal volume standard cell numbers in defined stages were determined. These data provide a basis for quantitative studies of mouse spermatogenesis.