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Pattern Analysis (pattern + analysis)
Kinds of Pattern Analysis Selected AbstractsWavelet Packet-Autocorrelation Function Method for Traffic Flow Pattern AnalysisCOMPUTER-AIDED CIVIL AND INFRASTRUCTURE ENGINEERING, Issue 5 2004Xiaomo Jiang A detailed understanding of the properties of traffic flow is essential for building a reliable forecasting model. The discrete wavelet packet transform (DWPT) provides more coefficients than the conventional discrete wavelet transform (DWT), representing additional subtle details of a signal. In wavelet multiresolution analysis, an important decision is the selection of the decomposition level. In this research, the statistical autocorrelation function (ACF) is proposed for the selection of the decomposition level in wavelet multiresolution analysis of traffic flow time series. A hybrid wavelet packet-ACF method is proposed for analysis of traffic flow time series and determining its self-similar, singular, and fractal properties. A DWPT-based approach combined with a wavelet coefficients penalization scheme and soft thresholding is presented for denoising the traffic flow. The proposed methodology provides a powerful tool in removing the noise and identifying singularities in the traffic flow. The methods created in this research are of value in developing accurate traffic-forecasting models. [source] Neccesity for Standardization in Fluorescence Pattern AnalysisIMAGING & MICROSCOPY (ELECTRONIC), Issue 1 2009Petra Perner Dr. Fluorescent pattern analysis is used in cellular and molecular biology as well as in medicine, agriculture or other applications. To make it feasible in daily practice, standardization is necessary to obtain authentically and reproducible results. Standardization has many aspects (fig. 1). It has to do with sample preparation, imaging techniques, knowledge acquisition, and image interpretation. It is an iterative process and cannot be solved from scratch. [source] Structural flyby characterization of nanoporosityPHYSICA STATUS SOLIDI (C) - CURRENT TOPICS IN SOLID STATE PHYSICS, Issue S2 2004R. R. Rosa Abstract Recently, Ferreira da Silva et al. [3] have performed a gradient pattern analysis of a canonical sample set (CSS) of scanning force microscopy (SFM) images of ,-Si. They applied the so-called Gradient Pattern Analysis to images of three typical ,-Si samples distinguished by different absorption energy levels and aspect ratios. Taking into account the measures of spatial asymmetric fluctuations they interpreted the global porosity not only in terms of the amount of roughness, but rather in terms of the structural complexity (e.g., walls and fine structures as slots). This analysis has been adapted in order to operate in a OpenGL flyby environment (the StrFB code), whose application give the numerical characterization of the structure during the flyby real time. Using this analysis we compare the levels of asymmetric fragmentation of active porosity related to different materials as ,-Si and "porous diamond-like" carbon. In summary we have shown that the gradient pattern analysis technique in a flyby environment is a reliable sensitive method to investigate, qualitatively and quantitatively, the complex morphology of active nanostructures. (© 2004 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Dermoscopy is a suitable method for the observation of the pregnancy-related changes in melanocytic neviJOURNAL OF THE EUROPEAN ACADEMY OF DERMATOLOGY & VENEREOLOGY, Issue 8 2007AS Aktürk Summary Background, It is a common opinion that expansion and darkening in melanocytic nevi may occur during pregnancy. The main problem is that whether it is a usual finding, or it is a condition that requires suspicion about melanoma. Objectives, It was aimed to find the changes that might occur in the sizes and structures of melanocytic nevi during pregnancy. Methods, Ninety-seven nevi of the 56 pregnant women in the first trimester were evaluated in the study. The localization and size of the nevi were recorded on a standard body diagram. After clinical examination, dermoscopic analyses were applied. Pattern analyses were done, and total dermoscopy scores (TDS) were calculated by applying ABCD scoring system. All subjects were seen again during the third trimester. Results, There was a statistically significant difference between the mean diameters of nevi in the first and third trimester (P = 0.001). Of nevi whose diameters increased, 10 (50.00%) were localized on the front of body, 6 (30.00%) on the face and neck, 3 (15.00%) on the legs, and 1 (5.00%) on the back. The enlargement in diameters was more significant on the front of the body, but there was no statistically significant difference. Compared according to the pattern analysis, new dot formation was observed only on the structure of six nevi during the last trimester. Four of them were localized on the front of the body. There was statistically significant increase in mean TDS in comparison between the first and third trimesters (P = 0008). Conclusions, During the pregnancy, widening in diameters and structure changes of nevi may be seen especially on the front of the body. We also think that these findings might be connected with expansion of the skin during pregnancy. Dermoscopic controls are the first choice of method to analyse the nevi since the patient may not recognize these changes. [source] Timing and connectivity in the human somatosensory cortex from single trial mass electrical activityHUMAN BRAIN MAPPING, Issue 4 2002Andreas A. Ioannides Abstract Parallel-distributed processing is ubiquitous in the brain but often ignored by experimental designs and methods of analysis, which presuppose sequential and stereotypical brain activations. We introduce here a methodology that can effectively deal with sequential and distributed activity. Regional brain activations elicited by electrical median nerve stimulation are identified in tomographic estimates extracted from single trial magnetoencephalographic signals. Habituation is identified in both primary somatosensory cortex (SI) and secondary somatosensory cortex (SII), often interrupted by resurgence of strong activations. Pattern analysis is used to identify single trials with homogeneous regional brain activations. Common activity patterns with well-defined connectivity are identified within each homogeneous group of single trials across the subjects studied. On the contralateral side one encounters distinct sets of single trials following identical stimuli. We observe in one set of trials sequential activation from SI to SII and insula with onset of SII at 60 msec, whereas in the other set simultaneous early co-activations of the same two areas. Hum. Brain Mapping 15:231,246, 2002. © 2002 Wiley-Liss, Inc. [source] Differences in cognitive factors between "true drug" versus "placebo pattern" response to fluoxetine as defined by pattern analysisHUMAN PSYCHOPHARMACOLOGY: CLINICAL AND EXPERIMENTAL, Issue 4 2006Amy H. Farabaugh Abstract Objective Pattern analysis has identified two types of response patterns to antidepressants: "true drug" response (TDR) and "placebo pattern" response (PPR). This study examines the relationship between cognitive factors and TDR and PPR to fluoxetine. Methods We assessed 310 outpatients meeting DSM-III-R criteria for major depressive disorder (MDD) who were enrolled in an 8-week open trial of fluoxetine 20,mg/day. Response patterns were determined using the clinical global impressions-improvement (CGI-I). We administered the following self-rated scales to all patients at the baseline visit and at endpoint: perceived stress scale (PSS), cognitions questionnaire (CQ), Beck hopelessness scale (BHS) and dysfunctional attitudes scale (DAS). Results One hundred and thirty-four patients had TDR, 66 patients had PPR, and 110 patients were non-responders (NR). Demographic variables and severity of depression at baseline (HAMD-17) were not significantly different between the two response pattern groups. We compared cognitive factors before and after treatment across patients with TDR and PPR, and there were no significant differences at baseline in CQ, PSS, BHS, and DAS scores. At endpoint, outpatients with PPR had significantly lower scores on the PSS (p,<,0.001) compared to the patients with TDR, even after adjusting for multiple comparisons and severity of depression at endpoint. Conclusions Significant differences in cognitive/psychological factors, specifically lower post-treatment perceived stress, accompany "placebo" pattern of response to antidepressant treatment and differentiate it from "true drug" response pattern, as defined by pattern analysis. Copyright © 2006 John Wiley & Sons, Ltd. [source] Pattern analysis, not simplified algorithms, is the most reliable method for teaching dermoscopy for melanoma diagnosis to residents in dermatologyBRITISH JOURNAL OF DERMATOLOGY, Issue 2 2004A. Blum No abstract is available for this article. [source] Spatial pattern of adult trees and the mammal-generated seed rain in the Iberian pearECOGRAPHY, Issue 3 2010Jose M. Fedriani The degree to which plant individuals are aggregated or dispersed co-determines how a species uses resources, how it is used as a resource, and how it reproduces. Quantifying such spatial patterns, however, presents several methodological issues that can be overcome by using spatial point pattern analyses (SPPA). We used SPPA to assess the distribution of P. bourgaeana adult trees and their seeds (within fecal samples) dispersed by three mammals (badger, fox, and wild boar) within a 72-ha plot across a range of spatial scales. Pyrus bourgaeana trees in our study plot (n=75) were clearly aggregated with a critical spatial scale of ca 25,m, and approximately nine randomly distributed tree clusters were identified. As expected from their marking behaviors, the spatial patterns of fecal deposition varied widely among mammal species. Whereas badger feces and dispersed seeds were clearly clustered at small spatial scales (<10,m), boar and fox feces were relatively scattered across the plot. A toroidal shift null model testing for independence indicated that boars tended to deliver seeds to the vicinity of adult trees and thus could contribute to the maintenance and enlargement of existing tree clusters. Badgers delivered feces and seeds in a highly clumped pattern but unlike boars, away from P. bourgaeana neighborhoods; thus, they are more likely to create new tree clusters than boars. The strong tree aggregation is likely to be the result of one or several non-exclusive processes, such as the spatial patterning of seed delivery by dispersers and seedling establishment beneath mother trees. In turn, the distinctive distribution of P. bourgaeana in Doñana appeared to interact with the foraging behavior of its mammalian seed dispersers, leading to neighbourhood-specific dispersal patterns and fruit-removal rates. Our study exemplifies how a detailed description of patterns generates testable hypotheses concerning the ecology of zoochorous. Pyrus bourgaeana dispersers were unique and complementary in their spatial patterning of seed delivery, which likely confers resilience to their overall service and suggests lack of redundancy and expendability of any one species. [source] Spatial analysis of an invasion front of Acer platanoides: dynamic inferences from static dataECOGRAPHY, Issue 3 2005Wei Fang It is an open question whether the invading tree species Acer platanoides is invading and displacing native trees within pre-existing forest stands, or merely preferentially occupying new stands of secondary forest growth at the edges of existing forests. Several threads of spatial pattern analyses were used to assess the invasibility of A. platanoides, and to link the invasion to the structure of a plant community in the deciduous forest of the northeastern United States. The analyses were based on maps of a contiguous 100×50 m area along an A. platanoides infestation gradient. The distribution of A. platanoides was highly aggregated and the population importance value increased from 28.1 to 38.5% according to mortality estimated from standing dead trees, while the distribution of native tree species was close to random and importance value of Quercus spp. decreased from 33.4 to 26.9% over time. The size distributions of each tree species across distance indicated that A. platanoides was progressively invading the interior of the forest while the native species (including A. rubrum) were not spreading back towards the A. platanoides monospecific patch. The null hypothesis of no invasibility was rejected based on quantile regressions. There were negative correlations between A. platanoides density and the densities of native species in different functional groups, and negative correlation of A. platanoides density and the species diversity in forest understory. The null hypothesis that A. platanoides invasion did not suppress native trees or understory was rejected based on Dutilleul's modified t-test for correlation, consistent with experimental results in the same study site. The combination of multiple spatial analyses of static data can be used to infer historical dynamical processes that shape a plant community structure. The concept of "envelop effects" was discussed and further developed. [source] Multigenerational analysis of spatial structure in the terrestrial, food-deceptive orchid Orchis masculaJOURNAL OF ECOLOGY, Issue 2 2009Hans Jacquemyn Summary 1In long-lived, terrestrial orchids, strong aggregation of adults and recruits within populations and pronounced spatial association between recruits and adults can be expected when seed dispersal is limited, probabilities of seed germination decrease with increasing distance from mother plants and/or not all mother plants contribute to future generations. When individuals are distributed evenly across life-history stages, these processes can also be expected to result in a significant fine-scale spatial genetic structure in recruits that will persist into the adult-stage class. 2We combined detailed spatial genetic and point pattern analyses across different generations with parentage analyses to elucidate the role of the diverse processes that might determine spatial structure in Orchis mascula. 3Analyses of spatial point patterns showed a significant association between adults and recruits and similar clustering patterns for both. Weak, but highly significant spatial genetic structure was observed in adults and recruits, but no significant differences were observed across life stages, indicating that the spatial genetic structure present in recruits persists into the adult stage. 4Parentage analyses highlighted relatively short seed dispersal distances (median offspring-recruitment distance: 1.55 and 1.70 m) and differential contribution of mother plants to future generations. 5Persistence of fine-scale spatial genetic structure from seedlings into the adult stage class is consistent with the life history of O. mascula, whereas relatively large dispersal distances of both pollen and seeds compared to the fine-scale clustering of adults and seedlings suggest overlapping seed shadows and mixing of genotypes within populations as the major factors explaining the observed weak spatial genetic structure. 6Nonetheless, comparison of the spatial association between recruits and adults with the genetic analysis of offspring-parent distances suggests that the tight clustering of recruits around adults was probably caused by decreasing probabilities of seed germination with increasing distance from mother plants. 7Synthesis. This study shows that the approach presented here, which combines spatial genetic and spatial pattern analyses with parentage analyses, may be broadly applied to other plant species to elucidate the processes that determine spatial structure within their populations. [source] Tree spacing and area of competitive influence do not scale with tree size in an African rain forestJOURNAL OF VEGETATION SCIENCE, Issue 5 2008Michael J. Lawes Abstract Questions: Is the area of influence of individual trees determined by tree size? Does competition, inferred from spatial pattern between neighbouring trees, affect adult tree spacing patterns in an tropical forest? At what size-class or stage is competition between neighbours most likely to affect adult tree spacing patterns? Location: Kibale National Park, western Uganda. Methods: Relationships between focal tree size and nearest neighbour distance, size, density, and species in a 4-ha permanent plot, using point pattern analyses. Results: We found non-random patterns of distribution of nearest tree neighbours (stems > 10 cm DBH). Independent of identity, tree density was highest and neighbours were regularly spaced within 3,5m of an individual. Tree densities were lower and relatively constant at distances >5m and neighbours were typically randomly spaced. In general, conspecific patterns conformed to the latter trends. Thus, individual area of influence was small (within a radius of 3,5 m). Rarer species were more clumped than common species. Weak competitive thinning occurred among more densely packed small trees (<20 cm DBH), and rapidly disappeared with increasing tree size and distance from an individual. The clumping and density of individuals was not significantly affected by tree size. Conclusions: Negative effects of competition among trees are weak, occur within the crown radius of most individuals, and are independent of adult tree size and identity. The density of neighbouring trees (aggregation) did not decline with increasing focal tree size at either the conspecific or the community level and tree diameter (tree size) was not a good estimator of the implied competitive influence of a tree. Mechanisms operating at the recruitment stage may be important determinants of adult tree community diversity and spacing patterns. [source] Spatial pattern and neighbour effects on Helianthemum squamatum seedlings in a Mediterranean gypsum communityJOURNAL OF VEGETATION SCIENCE, Issue 4 2005Adrián Escudero Abstract Question: Do, in a semi-arid gypsum environment, neighbours condition the spatial patterns of emergence, survival and height of Helianthemum squamatum seedlings? Location: Vicinity of Chinchón, province of Madrid, Spain (40°11,N, 3° 35,W, 550 m a.s.l.) Methods: We evaluated the effects of neighbours on the survival and growth of naturally emerging Helianthemum seedlings in a semi-arid area during a two-year period. We followed a two-fold approach based on the use of neighbour models for seedling survival and growth and spatial point pattern analyses for seedling emergence, taking into account the germination date. Results: Seedlings appeared clumped in the vicinity of mature Helianthemum individuals. The neighbour models fitted showed that interactions with neighbours were extremely important for the survival and growth of Helianthemum seedlings. These models also suggest that the effects of neighbours on these variables vary with changes in spatial scale and in the abiotic conditions. Some species exerted negative or positive effects on Helianthemum seedlings only at certain spatial scales, and others exerted negative or positive effects at earlier stages of seedling development, but none later and vice versa. Conclusions: We suggest that the observed patterns are mainly influenced by small-scale modifications in soil conditions and microclimate created by neighbours, which change in time and space. [source] Biotransformation of the triketone herbicide mesotrione by a Bacillus strain.RAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 17 2006Metabolite profiling using liquid chromatography/electrospray ionization quadrupole time-of-flight mass spectrometry The metabolic pathway involved in the biotransformation of the herbicide mesotrione by the bacterial strain Bacillus sp. 3B6 was investigated by a reliable liquid chromatography/electrospray ionization quadrupole time-of-flight mass spectrometry (LC/ESI-QTOF-MS) method. The LC/ESI-MS method, both in positive and negative mode, with the assistance of MS2 fragments and isotopic pattern analyses, allowed us to identify five metabolites. This work constitutes the first complete monitoring of mesotrione degradation kinetics. Among the transformation products found by both techniques, one was formed by intramolecular cyclization between a hydroxylamine and a keto function, which is quite a rare biological reactivity process. For each identified metabolite, a fragmentation pathway is proposed for negative and positive mode. Copyright © 2006 John Wiley & Sons, Ltd. [source] Cellular patterns in the inner retina of adult zebrafish: Quantitative analyses and a computational model of their formationTHE JOURNAL OF COMPARATIVE NEUROLOGY, Issue 1 2004David A. Cameron Abstract The mechanisms that control cellular pattern formation in the growing vertebrate central nervous system are poorly understood. In an effort to reveal mechanistic rules of cellular pattern formation in the central nervous system, quantitative spatial analysis and computational modeling techniques were applied to cellular patterns in the inner retina of the adult zebrafish. All the analyzed cell types were arrayed in nonrandom patterns tending toward regularity; specifically, they were locally anticlustered. Over relatively large spatial scales, only one cell type exhibited consistent evidence for pattern regularity, suggesting that cellular pattern formation in the inner retina is dominated by local anticlustering mechanisms. Cross-correlation analyses revealed independence between the patterns of different cell types, suggesting that cellular pattern formation may involve multiple, independent, homotypic anticlustering mechanisms. A computational model of cellular pattern formation in the growing zebrafish retina was developed, which featured an inhibitory, homotypic signaling mechanism, arising from differentiated cells, that controlled the spatial profile of cell fate decisions. By adjusting the spatial profile of this decaying-exponential signal, the model provided good estimates of all the cellular patterns that were observed in vivo, as objectively judged by quantitative spatial pattern analyses. The results support the hypothesis that cellular pattern formation in the inner retina of zebrafish is dominated by a set of anticlustering mechanisms that may control events at, or near, the spatiotemporal point of cell fate decision. J. Comp. Neurol. 471:11,25, 2004. © 2004 Wiley-Liss, Inc. [source] Proliferative remodeling of the spatial organization of human superficial chondrocytes distant from focal early osteoarthritisARTHRITIS & RHEUMATISM, Issue 2 2010Bernd Rolauffs Objective Human superficial chondrocytes show distinct spatial organizations, and they commonly aggregate near osteoarthritic (OA) fissures. The aim of this study was to determine whether remodeling or destruction of the spatial chondrocyte organization might occur at a distance from focal (early) lesions in patients with OA. Methods Samples of intact cartilage (condyles, patellofemoral groove, and proximal tibia) lying distant from focal lesions of OA in grade 2 joints were compared with location-matched nondegenerative (grade 0,1) cartilage samples. Chondrocyte nuclei were stained with propidium iodide, examined by fluorescence microscopy, and the findings were recorded in a top-down view. Chondrocyte arrangements were tested for randomness or significant grouping via point pattern analyses (Clark and Evans Aggregation Index) and were correlated with the OA grade and the surface cell densities. Results In grade 2 cartilage samples, superficial chondrocytes were situated in horizontal patterns, such as strings, clusters, pairs, and singles, comparable to the patterns in nondegenerative cartilage. In intact cartilage samples from grade 2 joints, the spatial organization included a novel pattern, consisting of chondrocytes that were aligned in 2 parallel lines, building double strings. These double strings correlated significantly with an increased number of chondrocytes per group and an increased corresponding superficial zone cell density. They were observed in all grade 2 condyles and some grade 2 tibiae, but never in grade 0,1 cartilage. Conclusion This study is the first to identify a distinct spatial reorganization of human superficial chondrocytes in response to distant early OA lesions, suggesting that proliferation had occurred distant from focal early OA lesions. This spatial reorganization may serve to recruit metabolically active units as an attempt to repair focal damage. [source] Disturbance affects spatial patterning and stand structure of a tropical rainforest treeAUSTRAL ECOLOGY, Issue 4 2010BRUCE L. WEBBER Abstract The distribution and spatial patterns of plant populations in natural ecosystems have recently received much attention; yet the impacts of human-induced disturbances on these patterns and underlying processes remain poorly understood. We used the sub-canopy tree, Ryparosa kurrangii (Achariaceae), to explore the possible effects of such disturbances on stand structure and spatial patterning in an Australian tropical rainforest. We studied three populations that differed in their extent of habitat modification: anthropogenic disturbance (proximate settlement and roads) and internal damage by an invasive alien species, the feral pig (Sus scrofa). Populations were mapped, characterized, and three size cohorts (seedlings, saplings, trees) were analysed using a suite of spatial point pattern analyses (univariate: Diggle's G and F and Ripley's K; bivariate: Diggle's G and Ripley's K). Ryparosa kurrangii has a typical stand structure for a sub-canopy tree species, but occurs at high densities locally (>400 stems ha,1). At all sites, the tree cohort were randomly distributed and saplings were spatially aggregated at distances of up to 2,3 m. Between sites there were distinct differences in the size structure and spatial pattern of seedlings, the cohort most affected by recent habitat modification. That is, the least disturbed site had no aggregation among seedlings, the site with the greatest anthropogenic disturbance had many small, clustered seedlings that were spatially associated with trees, and the site with pig damage had clustered seedlings that had no spatial relationship with trees. We propose that habitat modification by anthropogenic and pig disturbance disrupts seed dispersal and establishment regimes, which leads to altered seedling spatial patterns. These disturbances could have long-term implications for the population structure and health of R. Kurrangii. [source] Comparative expression pattern analysis of the highly conserved chemokines SDF1 and CXCL14 during amniote embryonic developmentDEVELOPMENTAL DYNAMICS, Issue 10 2010Clara García-Andrés Abstract Chemokines are secreted proteins with essential roles in leukocyte trafficking and cell migration during embryogenesis. CXCL14 displays a degree of evolutionary conservation unmatched by any other chemokine except for SDF1(CXCL12). However, its role during embryogenesis has not been studied. Here we describe the expression pattern of mouse and chicken CXCL14 during embryogenesis and compare it with that of SDF1. CXCL14 is widely expressed in embryonic ectoderm and shows a restricted and dynamic expression pattern in paraxial mesoderm, mesonephros, neural tube, and limbs. During limb development, CXCL14 marks a unique connective tissue subset that surrounds developing tendons. Comparison of CXCL14 and SDF1 reveals mostly non-overlapping or complementary expression patterns, suggesting an interactive regulation of developmental processes by these two chemokines. Our study identifies CXCL14 as a novel marker of tendon connective tissue and provides a conceptual framework for the coordinated action of two highly conserved chemokines in embryonic development. Developmental Dynamics 239:2769,2777, 2010. © 2010 Wiley-Liss, Inc. [source] Expression of qBrn-1, a new member of the POU gene family, in the early developing nervous system and embryonic kidneyDEVELOPMENTAL DYNAMICS, Issue 4 2006Lei Lan Abstract It has been shown that POU domain genes play critical roles in the development of the nervous system. We have obtained a new member of the class III POU domain genes, qBrn-1, from the cDNA library of embryonic day 5 quail and have made an extensive expression pattern analysis of qBrn-1 and qBrn-2 throughout the early embryonic development by in situ hybridization. With a specific antibody we prepared, further analysis by immunohistochemistry showed that the location of qBrn-1 protein was consistent with that of the transcripts in the early developing quail. Our results showed that both qBrn-1 and qBrn-2 were preferentially expressed in the developing central nervous system, and their transcripts were initially detected in the neural plate and later in the distinct regions of the neural tube with a stage-dependent pattern. Moreover, their expression was also detected in both notochord and neural crests. However, qBrn-1 signal, different from qBrn-2, was more widely found in the auditory pits, branchial arches, and in the mesodermal components of the developing kidney. And the expression of qBrn-1 in nephric region was earlier and wider than that of mouse Brn-1, suggesting the characteristic function of qBrn-1 in the kidney formation. The distinct dynamic expression patterns of qBrn-1 and qBrn-2 indicate multiple roles of the class III POU genes in quail neurogenesis and organogenesis. Developmental Dynamics 235:1107,1114, 2006. © 2006 Wiley-Liss, Inc. [source] Diagnosis of invasion depth in early colorectal carcinoma by pit pattern analysis with magnifying endoscopyDIGESTIVE ENDOSCOPY, Issue 2001Shinji Tanaka Background: The aim of this study was to clarify whether various pit patterns on the surface of colorectal tumors are associated with various levels of submucosal invasion. Methods: We examined pathologic features of the pit pattern of the tumor surface in 457 colorectal adenomas and early carcinomas. The examinations involved the use of magnifying endoscopy with indigocarmine dye spraying or crystal violet staining methods. Regarding the pit pattern classification, we used the types I, II, IIIL, IIIS, IV, VA and VN. We subclassified the VN pit pattern according to the area of the tumor surface covered into grades A (small), B (medium) and C (large). Results: Magnifying colonoscopic observation revealed the rates of submucosal invasion associated with specific pit patterns to be 1% (3/213) for IIIL, 5% (2/42) for IIIS, 8% (4/57) for IV, 14% (13/93) for VA and 80% (42/52) for VN. The rates of submucosal massive invasion (> 400 ,m) associated with specific pit patterns was 0% (0/213) for IIIL, 0% (0/42) for IIIS, 4% (2/57) for IV, 5% (5/93) for VA and 72% (38/52) for VN. Within the VN pit pattern subclassification, the incidence of submucosal invasion , 1500 ,m was found each grade (A, B & C): 5% (1/19) for grade A, 64% (14/22) for grade B and 93% (13/14) for grade C. Conclusion: Determination of pit pattern is useful for prediction of submucosal invasion depth and for decisions concerning treatment in colorectal tumors. Lesions with VA and non-grade C VN pit patterns are candidates for total endoscopic resection. A grade C VN pit pattern is a definite indicator of severely invasive submucosal carcinoma, which is unresectable by endoscopic resection. [source] Using neutral landscapes to identify patterns of aggregation across resource pointsECOGRAPHY, Issue 3 2006Jill Lancaster Many organisms are aggregated within resource patches and aggregated spatially across landscapes with multiple resources. Such patchy distributions underpin models of population regulation and species coexistence, so ecologists require methods to analyse spatially-explicit data of resource distribution and use. I describe a method for analysing maps of resources and testing hypotheses about how resource distribution influences the distribution of organisms, where resource patches can be described as points in a landscape and the number of organisms on each resource point is known. Using a mark correlation function and the linearised form of Ripley's K-function, this version of marked point pattern analysis can characterise and test hypotheses about the spatial distribution of organisms (marks) on resource patches (points). The method extends a version of point pattern analysis that has wide ecological applicability, it can describe patterns over a range of scales, and can detect mixed patterns. Statistically, Monte Carlo permutations are used to estimate the difference between the observed and expected values of the mark correlation function. Hypothesis testing employs a flexible neutral landscape approach in which spatial characteristics of point patterns are preserved to some extent, and marks are randomised across points. I describe the steps required to identify the appropriate neutral landscape and apply the analysis. Simulated data sets illustrate how the choice of neutral landscape can influence ecological interpretations, and how this spatially-explicit method and traditional dispersion indices can yield different interpretations. Interpretations may be general or context-sensitive, depending on information available about the underlying point pattern and the neutral landscape. An empirical example of caterpillars exploiting food plants illustrates how this technique might be used to test hypotheses about adult oviposition and larval dispersal. This approach can increase the value of survey data, by making it possible to quantify the distribution of resource points in the landscape and the pattern of resource use by species. [source] Applicability of spraints for monitoring organic contaminants in free-ranging otters (Lutra lutra)ENVIRONMENTAL TOXICOLOGY & CHEMISTRY, Issue 11 2006Nico W. van den Brink Abstract In the current study, the use of spraints for monitoring levels of polychlorinated biphenyls (PCBs) in individual otters was experimentally validated. On the basis of a detailed pattern analysis, it is concluded that in the current study, PCB concentrations in spraints that contain relatively high concentrations of nonmetabolizable PCB congeners (PCB 138 and 153>42.5% of total PCB concentrations) reflect the internal PCB concentrations of the otter that produced the spraint. In general, however, spraints should be selected that contain relative concentrations of PCB 138 and PCB 153>95th percentile of these congeners in samples from local food items of otters. On the basis of relationships between levels in spraints and internal levels and on earlier reported effect concentrations, a threshold level range of 1.0 to 2.3 ,g/g (lipid normalized) in such spraints is proposed. The validated methods to monitor PCBs in otters may be combined with genetic marker techniques that can assess the identity of the otter that produced the spraints. In such a design, it is feasible to monitor PCB levels in individual free-ranging otters in a truly animal friendly way. [source] Spatial point-process statistics: concepts and application to the analysis of lead contamination in urban soil,ENVIRONMETRICS, Issue 4 2005Christian Walter Abstract This article explores the use of spatial point-process analysis as an aid to describe topsoil lead distribution in urban environments. The data used were collected in Glebe, an inner suburb of Sydney. The approach focuses on the locations of punctual events defining a point pattern, which can be statistically described through local intensity estimates and between-point distance functions. F -, G - and K -surfaces of a marked spatial point pattern were described and used to estimate nearest distance functions over a sliding band of quantiles belonging to the marking variable. This provided a continuous view of the point pattern properties as a function of the marking variable. Several random fields were simulated by selecting points from random, clustered or regular point processes and diffusing them. Recognition of the underlying point process using variograms derived from dense sampling was difficult because, structurally, the variograms were very similar. Point-event distance functions were useful complimentary tools that, in most cases, enabled clear recognition of the clustered processes. Spatial sampling quantile point pattern analysis was defined and applied to the Glebe data set. The analysis showed that the highest lead concentrations were strongly clustered. The comparison of this data set with the simulation confidence limits of a Poisson process, a short-radius clustered point process and a geostatistical simulation showed a random process for the third quartile of lead concentrations but strong clustering for the data in the upper quartile. Thus the distribution of topsoil lead concentrations over Glebe may have resulted from several contamination processes, mainly from regular or random processes with large diffusion ranges and short-range clustered processes for the hot spots. Point patterns with the same characteristics as the Glebe experimental pattern could be generated by separate additive geostatistical simulation. Spatial sampling quantile point patterns statistics can, in an easy and accurate way, be used complementarily with geostatistical methods. Copyright © 2005 John Wiley & Sons, Ltd. [source] Prediction of coenzyme specificity in dehydrogenases/ reductasesFEBS JOURNAL, Issue 6 2006A hidden Markov model-based method, its application on complete genomes Dehydrogenases and reductases are enzymes of fundamental metabolic importance that often adopt a specific structure known as the Rossmann fold. This fold, consisting of a six-stranded ,-sheet surrounded by ,-helices, is responsible for coenzyme binding. We have developed a method to identify Rossmann folds and predict their coenzyme specificity (NAD, NADP or FAD) using only the amino acid sequence as input. The method is based upon hidden Markov models and sequence pattern analysis. The prediction sensitivity is 79% and the selectivity close to 100%. The method was applied on a set of 68 genomes, representing the three kingdoms archaea, bacteria and eukaryota. In prokaryotes, 3% of the genes were found to code for Rossmann-fold proteins, while the corresponding ratio in eukaryotes is only around 1%. In all genomes, NAD is the most preferred cofactor (41,49%), followed by NADP with 30,38%, while FAD is the least preferred cofactor (21%). However, the NAD preponderance over NADP is most pronounced in archaea, and least in eukaryotes. In all three kingdoms, only 3,8% of the Rossmann proteins are predicted to have more than one membrane-spanning segment, which is much lower than the frequency of membrane proteins in general. Analysis of the major protein types in eukaryotes reveals that the most common type (26%) of the Rossmann proteins are short-chain dehydrogenases/reductases. In addition, the identified Rossmann proteins were analyzed with respect to further protein types, enzyme classes and redundancy. The described method is available at http://www.ifm.liu.se/bioinfo, where the preferred coenzyme and its binding region are predicted given an amino acid sequence as input. [source] Local Indicators of Network-Constrained Clusters in Spatial Point PatternsGEOGRAPHICAL ANALYSIS, Issue 3 2007Ikuho Yamada The detection of clustering in a spatial phenomenon of interest is an important issue in spatial pattern analysis. While traditional methods mostly rely on the planar space assumption, many spatial phenomena defy the logic of this assumption. For instance, certain spatial phenomena related to human activities are inherently constrained by a transportation network because of our strong dependence on the transportation system. This article thus introduces an exploratory spatial data analysis method named local indicators of network-constrained clusters (LINCS), for detecting local-scale clustering in a spatial phenomenon that is constrained by a network space. The LINCS method presented here applies to a set of point events distributed over the network space. It is based on the network K -function, which is designed to determine whether an event distribution has a significant clustering tendency with respect to the network space. First, an incremental K -function is developed so as to identify cluster size more explicitly than the original K -function does. Second, to enable identification of cluster locations, a local K -function is derived by decomposing and modifying the original network K -function. The local K -function LINCS, which is referred to as KLINCS, is tested on the distribution of 1997 highway vehicle crashes in the Buffalo, NY area. Also discussed is an adjustment of the KLINCS method for the nonuniformity of the population at risk over the network. As traffic volume can be seen as a surrogate of the population exposed to a risk of vehicle crashes, the spatial distribution of vehicle crashes is examined in relation to that of traffic volumes on the network. The results of the KLINCS analysis are validated through a comparison with priority investigation locations (PILs) designated by the New York State Department of Transportation. [source] Comparison of High Resolution Magnifying Endoscopy and Standard Videoendoscopy for the Diagnosis of Helicobacter pylori Gastritis in Routine Clinical Practice: A Prospective StudyHELICOBACTER, Issue 1 2009Can Gonen Abstract Background:, It has been shown that standard endoscopic features often labeled as gastritis has a poor correlation with histopathology. Recently, high resolution magnifying endoscopy has been reported to be an effective method to diagnose gastritis. The aim of the present study was to compare standard endoscopy with magnifying endoscopy for the diagnosis of Helicobacter pylori gastritis, and to determine whether gastritis can be diagnosed based on findings at magnification endoscopy. Materials and Methods:, A total of 129 patients were enrolled into the study. Erythema, erosions, prominent area gastrica, nodularity, and regular arrangement of collecting venules (RAC) were investigated by standard endoscopy. Standard endoscopy was followed by magnifying endoscopy in all patients, and repeated in 55 patients after indigo carmine spraying. Results:, None of the standard endoscopic features showed a sensitivity of more than 70% for H. pylori gastritis, except RAC pattern analysis. Absence of a corporal RAC pattern had 85.7% sensitivity and 82.8% specificity for predicting H. pylori infection. Under magnification, the sensitivity and specificity of regular corporal pattern (regular collecting and capillary vascular structures with gastric pits resembling pinholes) for predicting normal histology were 90.3% and 93.9%, respectively. Loss of collecting venules, or both collecting and capillary structures was correlated with chronic inflammation and activity. With the progression of mucosal atrophy, irregular collecting venules became visible. The values for irregularly arranged antral ridge pattern for the prediction of antral gastritis were 89.3% and 65.2%, respectively. Indigo carmine staining increased sensitivity and specificity up to 97.6% and 100% for corporal gastritis, and up to 88.4% and 75.0% for antral gastritis, respectively. Indigo carmine staining significantly increases the detection of intestinal metaplasia. Conclusions:, High resolution magnifying is superior to standard endoscopy for the diagnosis of H. pylori gastritis, and identification of specific histopathologic features such as atrophy and intestinal metaplasia seems possible. [source] High-resolution multi-voxel pattern analysis of category selectivity in the medial temporal lobesHIPPOCAMPUS, Issue 6 2008Rachel A. Diana Abstract Although the parahippocampal cortex (PHc) is known to be critical for memory formation, little is known about what is encoded by this area. Using multi-voxel pattern analysis of high-resolution functional magnetic resonance imaging (MRI) data, we examined responses to blocks of categorically coherent stimuli and found that patterns of activity in PHc were selective for not only scenes, but also for other nonspatial object categories (e.g., faces and toys). This pattern of results was also found in the parahippocampal place area (PPA), indicating that this region is not sensitive exclusively to scenes. In contrast, neither the hippocampus nor perirhinal cortex (PRc) were found to be selective for category information. The results indicate that regions within the medial temporal lobe may support distinct functions, and that the PHc appears to be particularly sensitive to category-level information. © 2008 Wiley-Liss, Inc. [source] Differences in cognitive factors between "true drug" versus "placebo pattern" response to fluoxetine as defined by pattern analysisHUMAN PSYCHOPHARMACOLOGY: CLINICAL AND EXPERIMENTAL, Issue 4 2006Amy H. Farabaugh Abstract Objective Pattern analysis has identified two types of response patterns to antidepressants: "true drug" response (TDR) and "placebo pattern" response (PPR). This study examines the relationship between cognitive factors and TDR and PPR to fluoxetine. Methods We assessed 310 outpatients meeting DSM-III-R criteria for major depressive disorder (MDD) who were enrolled in an 8-week open trial of fluoxetine 20,mg/day. Response patterns were determined using the clinical global impressions-improvement (CGI-I). We administered the following self-rated scales to all patients at the baseline visit and at endpoint: perceived stress scale (PSS), cognitions questionnaire (CQ), Beck hopelessness scale (BHS) and dysfunctional attitudes scale (DAS). Results One hundred and thirty-four patients had TDR, 66 patients had PPR, and 110 patients were non-responders (NR). Demographic variables and severity of depression at baseline (HAMD-17) were not significantly different between the two response pattern groups. We compared cognitive factors before and after treatment across patients with TDR and PPR, and there were no significant differences at baseline in CQ, PSS, BHS, and DAS scores. At endpoint, outpatients with PPR had significantly lower scores on the PSS (p,<,0.001) compared to the patients with TDR, even after adjusting for multiple comparisons and severity of depression at endpoint. Conclusions Significant differences in cognitive/psychological factors, specifically lower post-treatment perceived stress, accompany "placebo" pattern of response to antidepressant treatment and differentiate it from "true drug" response pattern, as defined by pattern analysis. Copyright © 2006 John Wiley & Sons, Ltd. [source] Onset of action of antidepressants: results of different analysesHUMAN PSYCHOPHARMACOLOGY: CLINICAL AND EXPERIMENTAL, Issue S1 2002Chris Thompson Abstract Because the value of antidepressants is hampered by their delay in onset of action, considerable attention has been focused on developing a drug that acts more rapidly. However, although specific studies are now ongoing, there have been no peer-reviewed prospective onset of action trials published in the literature to date. Some data are currently available from post-hoc pooled analyses and numerous methods have been developed for evaluating the onset of action; these include the time to response, the time to onset of therapeutic effect, pattern analysis and survival analyses. Such an analysis of four large-scale, double-blind studies has provided evidence for an earlier onset of action with mirtazapine than with the SSRIs (fluoxetine, paroxetine and citalopram). Significant differences were seen between mirtazapine and the SSRIs after 1 week of treatment. This effect was consistent across the four different methodologies and appears to be due to a specific antidepressant effect rather than an early effect on, for example, sleep. These findings await confirmation from specifically designed prospective onset of action studies. Copyright © 2002 John Wiley & Sons, Ltd. [source] Neccesity for Standardization in Fluorescence Pattern AnalysisIMAGING & MICROSCOPY (ELECTRONIC), Issue 1 2009Petra Perner Dr. Fluorescent pattern analysis is used in cellular and molecular biology as well as in medicine, agriculture or other applications. To make it feasible in daily practice, standardization is necessary to obtain authentically and reproducible results. Standardization has many aspects (fig. 1). It has to do with sample preparation, imaging techniques, knowledge acquisition, and image interpretation. It is an iterative process and cannot be solved from scratch. [source] The contribution of limb bone fracture patterns to reconstructing early hominid behaviour at Swartkrans cave (South Africa): archaeological application of a new analytical methodINTERNATIONAL JOURNAL OF OSTEOARCHAEOLOGY, Issue 4 2005T. R. Pickering Abstract Recently, Alcántara García et al. (in press) presented a new method and criteria for distinguishing between fractures imparted by hominid hammerstone percussion and carnivores chewing on ,green' limb bones of ungulates. The method uses a combination of fracture plane and fracture angle data that are useful for elucidating the relative role of hominids in the accumulation of prehistoric archaeofaunas, especially when employed in concert with other classes of taphonomic data. We briefly summarise the method and apply it to the ungulate limb bone subassemblage from Swartkrans Member 3, a c. 1.0 million year old site from South Africa that preserves Early Stone Age lithic artefacts, hominid fossils, and an abundant mammalian fauna with cutmarked, hammerstone-percussed and burned bone specimens. Results of the fracture pattern analysis corroborate indications from other lines of taphonomic data that there was minimal carnivore,hominid interdependence in the formation of the fauna, and that carnivores were probably responsible for the majority of the bone collection in Member 3. However, we also document a significant hominid influence on assemblage formation, a finding that expands and refines our understanding of large animal carcass foraging by hominids in southern Africa during the early Pleistocene. Copyright © 2004 John Wiley & Sons, Ltd. [source] | ||||||||||||||||||||||||||||