Unique Spatial Patterns Research Articles

Pattern Recognition Analysis of Age-Related Retinal Ganglion Cell Signatures in the Human Eye.

PurposeTo characterize macular ganglion cell layer (GCL) changes with age and provide a framework to assess changes in ocular disease. This study used data clustering to analyze macular GCL patterns from optical coherence tomography (OCT) in a large cohort of subjects without ocular disease.MethodsSingle eyes of 201 patients evaluated at the Centre for Eye Health (Sydney, Australia) were retrospectively enrolled (age range, 20–85); 8 × 8 grid locations obtained from Spectralis OCT macular scans were analyzed with unsupervised classification into statistically separable classes sharing common GCL thickness and change with age. The resulting classes and gridwise data were fitted with linear and segmented linear regression curves. Additionally, normalized data were analyzed to determine regression as a percentage. Accuracy of each model was examined through comparison of predicted 50-year-old equivalent macular GCL thickness for the entire cohort to a true 50-year-old reference cohort.ResultsPattern recognition clustered GCL thickness across the macula into five to eight spatially concentric classes. F-test demonstrated segmented linear regression to be the most appropriate model for macular GCL change. The pattern recognition–derived and normalized model revealed less difference between the predicted macular GCL thickness and the reference cohort (average ± SD 0.19 ± 0.92 and −0.30 ± 0.61 μm) than a gridwise model (average ± SD 0.62 ± 1.43 μm).ConclusionsPattern recognition successfully identified statistically separable macular areas that undergo a segmented linear reduction with age. This regression model better predicted macular GCL thickness. The various unique spatial patterns revealed by pattern recognition combined with core GCL thickness data provide a framework to analyze GCL loss in ocular disease.

Spatial relationships and movement patterns of the air cargo industry in airport regions

Background: During the past few years, with the increase in air traffic and the expansion of airports, very few industries had such a large spatial development and movement impact as that of airport-related clusters or airport regions. Although much research was done on the various impacts of the airport industry, very little research was done on the air cargo industry in airport regions.Objectives: This article specifically explored the unique spatial relationships, impacts, trends and movement patterns of the air cargo industry within a typical airport region.Method: The article focused on the OR Tambo International Airport in Gauteng, South Africa, as a case study and was informed by an extensive quantitative spatial and land use analysis and modelling of the study area.Results: The article presented findings and insights on the movement patterns and relationships between (1) the airport facility and (2) the spatial configuration of air cargo industries in the particular airport region. These findings also provided some framework for a possible spatial model and guideline that could assist in steering and managing development and movement patterns in airport regions.Conclusion: The article provided new insights and understanding on the spatial dynamics of airport regions and the air cargo industry, ultimately addressing some gaps in this knowledge field. The article in the end highlighted the need for a different and novel approach to the planning and management of the air cargo industry in airport regions and a basis for further research.

Simultaneous In Vivo Fluorescent Markers for Perfusion, Protoporphyrin Metabolism, and EGFR Expression for Optically Guided Identification of Orthotopic Glioma.

Purpose: While extent of tumor resection is an important predictor of outcome in glioma, margin delineation remains challenging due to lack of inherent contrast between tumor and normal parenchyma. Fluorescence-guided surgery is promising for its ability to enhance contrast through exogenous fluorophores; however, the specificity and sensitivity of the underlying contrast mechanism and tumor delivery and uptake vary widely across approved and emerging agents.Experimental Design: Rats with orthotopic F98 wild-type and F98 EGFR-positive (EGFR+) gliomas received in vivo administration of IRDye680RD, 5-aminioleuvulinic acid, and ABY-029-markers of perfusion, protoporphyrin metabolism, and EGFR expression, respectively. Ex vivo imaging demonstrates the contrast mechanism-dependent spatial heterogeneity and enables within-animal comparisons of tumor-to-background ratio (TBR).Results: Generally, ABY-029 outperformed PpIX in F98EGFR orthotopic tumor margins and core (50% and 60% higher TBR, respectively). PpIX outperformed ABY-029 in F98wt margins by 60% but provided equivalent contrast in the bulk tumor. IRDye680RD provided little contrast, having an average TBR of 1.7 ± 0.2. The unique spatial patterns of each agent were combined into a single metric, the multimechanistic fluorescence-contrast index (MFCI). ABY-029 performed best in EGFR+ tumors (91% accuracy), while PpIX performed best in wild-type tumors (87% accuracy). Across all groups, ABY-029 and PpIX performed similarly (80% and 84%, respectively) but MFCI was 91% accurate, supporting multiagent imaging when tumor genotype was unknown.Conclusions: Human use of ABY-029 for glioma resection should enhance excision of EGFR+ tumors and could be incorporated into current PpIX strategies to further enhance treatment in the general glioma case. Clin Cancer Res; 23(9); 2203-12. ©2016 AACR.

Equity in neighbourhood walkability? A comparative analysis of three large U.S. cities

ABSTRACTThis study examines the spatial and statistical relationships between social vulnerability (SV) and neighbourhood walkability across three large U.S. cities with different urban typologies and development patterns: Charlotte, NC (a low-density, fast-growing “Sunbelt” city); Pittsburgh, PA (a moderate density, shrinking “Rust Belt” city); and Portland, OR (a progressive West Coast city known for its sprawl-containment policies). Binary logistic regression, independent-samples t-tests, and mapping techniques are employed to determine whether neighbourhoods with high SV (i.e. older populations, higher poverty rates, more service occupations, lower educational attainment, and a higher proportion of minorities) are as likely as those with low SV to exhibit a high degree of walkability. The publically available Walk Score® metric, based on proximity to amenities, street network connectivity, and density, was used as a proxy for neighbourhood walkability. The results indicate significant variability among cities, with Charlotte exhibiting the greatest potential for inequitable access to walkable urban environments and the most prominent concentration of “walk-vulnerable” block groups (BGs) with high SV and low walkability. Both Portland and Pittsburgh exhibited more equitable access when comparing BGs with high and low SV; however, they each presented unique spatial patterns, visualised using a series of maps.

Spatial Upscaling of Soil Respiration under a Complex Canopy Structure in an Old‐Growth Deciduous Forest, Central Japan

The structural complexity, especially canopy and gap structure, of old‐growth forests affects the spatial variation of soil respiration (Rs). Without considering this variation, the upscaling of Rs from field measurements to the forest site will be biased. The present study examined responses of Rs to soil temperature (Ts) and water content (W) in canopy and gap areas, developed the best fit modelof Rs and used the unique spatial patterns of Rs and crown closure to upscale chamber measurements to the site scale in an old‐growth beech‐oak forest. Rs increased with an increase in Ts in both gap and canopy areas, but the effect of W on Rs was different between the two areas. The generalized linear model (GLM) analysis identified that an empirical model of Rs with thecoupling of Ts and W was better than an exponential model of Rs with only Ts. Moreover, because of different responses of Rs to W between canopy and gap areas, it was necessary to estimate Rs in these areas separately. Consequently, combining the spatial patterns of Rs and the crown closure could allow upscaling of Rs from chamber‐based measurements to the whole site in the present study.

2012년 전국 지역사회 건강조사 자료를 이용한 시·군·구 단위 질병 유병률의 공간 자기상관도에 관한 연구

As a basic research to investigate geographical variations of diseases, this study analyzes and compares spatial patterns of 24 different diseases in South Korea using prevalence rate data provided by Community Health Survey in 2012. Descriptive statistical analysis, global Morans I computation, and disease mapping were conducted to examine spatial associations and patterns of each disease. After the unique spatial patterns and distinctive spatial associations of each disease were observed, we concluded that 12 diseases displayed statistically significant spatial autocorrelation while the other 12 showed no spatial associations. This study suggests that diseases are caused by different risk factors and possess different etiological mechanisms. Furthermore, the study may lay foundation for future studies of geographical variations of disease prevalence in South Korea.

Spatial and Temporal Variation of Water Temperature Regimes on the Snoqualmie River Network

AbstractAlthough mean temperatures change annually and are highly correlated with elevation, the entire thermal regime on the Snoqualmie River, Washington, USA does not simply shift with elevation or season. Particular facets of the thermal regime have unique spatial patterns on the river network and at particular times of the year. We used a spatially and temporally dense temperature dataset to generate 13 temperature metrics representing popular summary measures (e.g., minimum, mean, or maximum temperature) and wavelet variances over each of seven time windows. Spatial stream‐network models which account for within‐network dependence were fit using three commonly used predictors of riverine thermal regime (elevation, mean annual discharge, and percent commercial area) to each temperature metric in each time window. Predictors were strongly related (r2 > 0.6) to common summaries of the thermal regime but were less effective at describing other facets of the thermal regime. Relationships shifted with season and across facets. Summer mean temperatures decreased strongly with increasing elevation but this relationship was weaker for winter mean temperatures and winter minimum temperatures; it was reversed for mean daily range and there was no relationship between elevation and wavelet variances. We provide examples of how enriched information about the spatial and temporal complexities of natural thermal regimes can improve management and monitoring of aquatic resources.

The role of connectivity and stochastic osteocyte behavior in the distribution of perilabyrinthine bone degeneration. A Monte Carlo based simulation study

Previous studies of undecalcified temporal bones labeled with fluorescent tissue time markers and basic fuchsine have documented the unique spatial and temporal patterns underlying inner ear bone development, morphology and degeneration, and has led to the identification of inner ear OPG as the candidate inhibiter of perilabyrinthine bone resorption. Resulting age related excessive matrix microdamage, osteocyte death and degeneration of the OPG signaling pathway is expected to trigger bone remodeling in the otic capsule, but when this happens the morphology of the remodeling bone is abnormal and the distribution is not entirely smooth and predictable, but rather multifocal and chaotic with a centripetal predilection at the window regions, as in otosclerosis.Based on the observed histological patterns, the fundamental preconditions of perilabyrinthine bone cell behavior can be deduced. When this information is used to generate a virtual computer representation of the cellular signaling network, the fate of the aging network can be studied by ‘virtual histology’ in any number of simulated ‘individuals’.We demonstrate how a combination of simple osteocyte survival functions derived from histological observations and the effect of connectivity may account for gradual centripetal degeneration as well as occasional focal degeneration of the cellular anti resorptive signaling pathway around the fluid space of the inner ear and create a permissive environment for otosclerosis.

Abstract C108: Quantifying PD-L1 spatial distribution signatures for patient selection approaches

Abstract Inhibitors of inflammatory checkpoints, such as PD-L1 inhibitors, have demonstrated great promise in preclinical and clinical studies. This therapeutic paradigm focuses on controlling natural inflammatory checkpoints to stimulate an elevated inflammatory response against the tumor to increase anti-tumor inflammatory cell infiltrates in the tumor microenvironment or decrease inflammatory suppressor infiltrates. The proteins which control these processes can be found in the tumor cells, cells in the tumor micro-environment (TME), or in both locales. Positive cells are often assessed in a qualitative or semi-quantitative manner using immunohistochemistry and evaluation of a limited number of representative microscopy fields across a particular tissue compartment (tumor vs stroma) or the whole tissue area. However, the locale of the inflammatory suppressors such as PD-L1 may be more revealing than estimating the tumor-wide dispersion of an inflammatory cell type. Unfortunately, the intricate spatial relationships and the often complex distribution of inflammatory cells in tissues pose significant challenges for a meaningful evaluation. We have developed an approach which can quantify these spatial relationship in a contextual, biologically meaningful score. Immunohistochemistry staining for PD-L1 in whole lung cancer tissue sections was performed, and our CellMap software was used to assess inflammatory cell distribution in the whole tissue sections. PD-L1 positive cells were quantified relative to: 1) the total number of cells in the tumor and stromal tissue compartments, and 2) the number of cells within a distance from the tumor/stroma interface. Interestingly, several unique PD-L1 distribution patterns relative to the tumor/stroma interface were observed in the sample cohort analyzed. Quantifying the distribution of PD-L1 positive cells as a function of distance from the tumor/stroma interface revealed distribution signatures, which could be used to differentiate between samples. In contrast, this differentiation of the same samples was not possible when PD-L1 cells were assessed relative to the total number of cells. This study provided a novel method for assessing inflammatory cell type spatial distribution relative to a tissue feature, the tumor/stroma interface. The data suggested that unique spatial patterns of inflammatory cell type distribution could be used to uniquely stratify patients compared to existing quantitative methods. Taken together, this proof-of-concept study demonstrates a unique quantitative assessment of inflammatory cell infiltrates in tumors that could be used to gain new insights into inflammatory cell type distributions and interactions in tumors, inflammatory cell spatial responses to oncology therapies, and novel patient selection criteria for traditional and immuno-oncology therapeutics. Citation Format: Joseph S. Krueger, Nathan Martin, Anthony Milici, Famke Aeffner. Quantifying PD-L1 spatial distribution signatures for patient selection approaches. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2015 Nov 5-9; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2015;14(12 Suppl 2):Abstract nr C108.

Death by Segregation: Does the Dimension of Racial Segregation Matter?

The county-level geographic mortality differentials have persisted in the past four decades in the United States (US). Though several socioeconomic factors (e.g., inequality) partially explain this phenomenon, the role of race/ethnic segregation, in general, and the different dimensions of segregation, more specifically, has been underexplored. Focusing on all-cause age-sex standardized US county-level mortality (2004–2008), this study has two substantive goals: (1) to understand whether segregation is a determinant of mortality and if yes, how the relationship between segregation and mortality varies by racial/ethnic dyads (e.g., white/black), and (2) to explore whether different dimensions of segregation (i.e., evenness, exposure, concentration, centralization, and clustering) are associated with mortality. A third goal is methodological: to assess whether spatial autocorrelation influences our understanding of the associations between the dimensions of segregation and mortality. Race/ethnic segregation was found to contribute to the geographic mortality disparities. Moreover, the relationship with mortality differed by both race/ethnic group and the dimension of segregation. Specifically, white/black segregation is positively related to mortality, whereas the segregation between whites and non-black minorities is negatively associated with mortality. Among the five dimensions of segregation, evenness and exposure are more strongly related to mortality than other dimensions. Spatial filtering approaches also identified six unique spatial patterns that significantly affect the spatial distribution of mortality. These patterns offer possible insights that help identify omitted variables related to the persistent patterning of mortality in the US.

Abstract 2358: Quantifying PD-L1 spatial distribution signatures for patient selection approaches

Abstract Inhibitors of inflammatory checkpoints, such as PD-L1 inhibitors, have demonstrated great promise in preclinical and clinical studies. This therapeutic paradigm focuses on controlling natural inflammatory checkpoints to stimulate an elevated inflammatory response against the tumor to increase anti-tumor inflammatory cell infiltrates in the tumor microenvironment or decrease inflammatory suppressor infiltrates. The proteins which control these processes can be found in the tumor cells, cells in the tumor micro-environment (TME), or in both locales. Positive cells are often assessed in a qualitative or semi-quantitative manner using immunohistochemistry and evaluation of a limited number of representative microscopy fields across a particular tissue compartment (tumor vs stroma) or the whole tissue area. However, the locale of the inflammatory suppressors such as PD-L1 may be more revealing than estimating the tumor-wide dispersion of an inflammatory cell type. Unfortunately, the intricate spatial relationships and the often complex distribution of inflammatory cells in tissues pose significant challenges for a meaningful evaluation. We have developed an approach which can quantify these spatial relationships in a contextual, biologically meaningful score. Immunohistochemistry staining for PD-L1 in whole lung cancer tissue sections was performed, and our CellMap software was used to assess inflammatory cell distribution in the whole tissue sections. PD-L1 positive cells were quantified relative to: 1) the total number of cells in the tumor and stromal tissue compartments, and 2) the number of cells within a distance from the tumor/stroma interface. Interestingly, several unique PD-L1 distribution patterns relative to the tumor/stroma interface were observed in the sample cohort analyzed. Quantifying the distribution of PD-L1 positive cells as a function of distance from the tumor/stroma interface revealed distribution signatures, which could be used to differentiate between samples. In contrast, this differentiation of the same samples was not possible when PD-L1 cells were assessed relative to the total number of cells. This study provided a novel method for assessing inflammatory cell type spatial distribution relative to a tissue feature, the tumor/stroma interface. The data suggested that unique spatial patterns of inflammatory cell type distribution could be used to uniquely stratify patients compared to existing quantitative methods. Taken together, this proof-of-concept study demonstrates a unique quantitative assessment of inflammatory cell infiltrates in tumors that could be used to gain new insights into inflammatory cell type distributions and interactions in tumors, inflammatory cell spatial responses to oncology therapies, and novel patient selection criteria for traditional and immuno-oncology therapeutics. Citation Format: Joseph S. Krueger, Nathan Martin, Anthony Milici, Holger Lange. Quantifying PD-L1 spatial distribution signatures for patient selection approaches. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2358. doi:10.1158/1538-7445.AM2015-2358

Dendritic connectivity shapes spatial patterns of genetic diversity: a simulation-based study.

Landscape features notoriously affect spatial patterns of biodiversity. For instance, in dendritic ecological networks (such as river basins), dendritic connectivity has been proposed to create unique spatial patterns of biodiversity. Here, we compared genetic datasets simulated under a lattice-like, a dendritic and a circular landscape to test the influence of dendritic connectivity on neutral genetic diversity. The circular landscape had a level of connectivity similar to that of the dendritic landscape, so as to isolate the influence of dendricity on genetic diversity. We found that genetic diversity and differentiation varied strikingly among the three landscapes. For instance, the dendritic landscape generated higher total number of alleles and higher global Fst than the lattice-like landscape, and these indices also varied between the dendritic and the circular landscapes, suggesting an effect of dendricity. Furthermore, in the dendritic landscape, allelic richness was higher in highly connected demes (e.g. confluences in rivers) than in low-connected demes (e.g. upstream and downstream populations), which was not the case in the circular landscape, hence confirming the major role of dendricity. This led to bell-shaped distributions of allelic richness along an upstream-downstream gradient. Conversely, genetic differentiation (Fst ) was lower in highly than in low-connected demes (which was not observed in circular landscape), and significant patterns of isolation by distance (IBD) were also observed in the dendritic landscape. We conclude that in dendritic networks, the combined influence of dendricity and connectivity generates unique spatial patterns of neutral genetic diversity, which has implications for population geneticists and conservationists.

MELK-a conserved kinase: functions, signaling, cancer, and controversy.

Maternal embryonic leucine zipper kinase (MELK) is a highly conserved serine/threonine kinase initially found to be expressed in a wide range of early embryonic cellular stages, and as a result has been implicated in embryogenesis and cell cycle control. Recent evidence has identified a broader spectrum of tissue expression pattern for this kinase than previously appreciated. MELK is expressed in several human cancers and stem cell populations. Unique spatial and temporal patterns of expression within these tissues suggest that MELK plays a prominent role in cell cycle control, cell proliferation, apoptosis, cell migration, cell renewal, embryogenesis, oncogenesis, and cancer treatment resistance and recurrence. These findings have important implications for our understanding of development, disease, and cancer therapeutics. Furthermore understanding MELK signaling may elucidate an added dimension of stem cell control.

Spatial Patterns of Nutrient Distribution in Dalingshan Forest Soil of Guangdong Province China

Spatial nutrients that includes OM, Avail.K, Avail.P and TN distribution and the influences on vegetation patterns in Dalingshan was the cardinal focus of this study. Ecological data (moisture content, bulk density and topography) were considered. One way ANOVA was statistically tested of spatial distribution of major nutrients across 4 plots which indicated non significant at p = 0.05 level, TN (p = 0.0216), OM (p = 0.00004), Avail.K (p = 0.00216) respectively. Furthermore one way ANOVA was tested on acidity level (pH) measured against the nutrients distribution TN (p = 0.0031), OM (p = 0.0004), Avail.K (p = 0.0216) respectively at non significance level but available phosphorous was significantly different (p = 0.6412). The study revealed unique spatial patterns of soil nutrient distribution in Dalingshan and species abundance while vegetation census posed a new direction of study that may be adapted for a broad range of regional vegetation and floristic modeling. This paper suggests that forest soil nutrients and vegetation interaction can be utilized for further studies on multifactor ecosystem responses towards regional ecological restoration.

Differential expression of sirtuin family members in the developing, adult, and aged rat brain.

The sirtuins are NAD+-dependent protein deacetylases and/or ADP-ribosyltransferases that play roles in metabolic homeostasis, stress response and potentially aging. This enzyme family resides in different subcellular compartments, and acts on a number of different targets in the nucleus, cytoplasm and in the mitochondria. Despite their recognized ability to regulate metabolic processes, the roles played by specific sirtuins in the brain—the most energy demanding tissue in the body—remains less well investigated and understood. In the present study, we examined the regional mRNA and protein expression patterns of individual sirtuin family members in the developing, adult, and aged rat brain. Our results show that while each sirtuin is expressed in the brain at each of these different stages, they display unique spatial and temporal expression patterns within the brain. Further, for specific members of the family, the protein expression profile did not coincide with their respective mRNA expression profile. Moreover, using primary cultures enriched for neurons and astrocytes respectively, we found that specific sirtuin members display preferential neural lineage expression. Collectively, these results provide the first composite illustration that sirtuin family members display differential expression patterns in the brain, and provide evidence that specific sirtuins could potentially be targeted to achieve cell-type selective effects within the brain.

Brain network markers of abnormal cerebral glucose metabolism and blood flow in Parkinson's disease.

Neuroimaging of cerebral glucose metabolism and blood flow is ideally suited to assay widely-distributed brain circuits as a result of local molecular events and behavioral modulation in the central nervous system. With the progress in novel analytical methodology, this endeavor has succeeded in unraveling the mechanisms underlying a wide spectrum of neurodegenerative diseases. In particular, statistical brain mapping studies have made significant strides in describing the pathophysiology of Parkinson's disease (PD) and related disorders by providing signature biomarkers to determine the systemic abnormalities in brain function and evaluate disease progression, therapeutic responses, and clinical correlates in patients. In this article, we review the relevant clinical applications in patients in relation to healthy volunteers with a focus on the generation of unique spatial covariance patterns associated with the motor and cognitive symptoms underlying PD. These characteristic biomarkers can be potentially used not only to improve patient recruitment but also to predict outcomes in clinical trials.

Unique temporal and spatial expression patterns of IL-33 in ovaries during ovulation and estrous cycle are associated with ovarian tissue homeostasis.

Ovaries are among the most active organs. Frequently occurring events such as ovulation and ovarian atresia are accompanied with tissue destruction and repairing. Critical roles of immune cells or molecules in those events have been well recognized. IL-33 is a new member of the IL-1 cytokine gene family. Recent studies suggest its roles beyond immune responses. We systemically examined its expression in ovaries for its potential roles in ovarian functions. During ovulation, a high level of IL-33 was transiently expressed, making it the most significantly upregulated immune gene. During estrous cycle, IL-33 expression levels fluctuated along with numbers of ovarian macrophages and atresia wave. Cells with nuclear form of IL-33 (nIL-33(+) cells) were mostly endothelial cells of veins, either in the inner layer of theca of ovulating follicles during ovulation, or surrounding follicles during estrous cycle. Changes in number of nIL-33(+) cells showed a tendency similar to that in IL-33 mRNA level during estrous cycle. However, the cell number sharply declined before a rapid increase of macrophages and a surge of atresia. The decline in nIL-33(+) cell number was coincident with detection of higher level of the cytokine form of IL-33 by Western blot, suggesting a release of cytokine form of IL-33 before the surge of macrophage migration and atresia. However, IL-33 Ab, either by passive transfer or immunization, showed a limited effect on ovulation or atresia. It raises a possibility of IL-33's role in tissue homeostasis after ovarian events, instead of a direct involvement in ovarian functions.

Polarization Anisotropy of Multiple Localized Plasmon Resonance Modes in Noble Metal Nanocrescents

Multiple localized surface plasmon resonance (LSPR) modes induced in gold and silver nanocrescents exhibit anisotropic behavior with respect to polarization of incident light. Extinction spectroscopy with polarization control was used to characterize the optical properties of asymmetric nanocrescents with diameters ranging from 100 to 500 nm. The analysis shows that selective induction of distinct dipole and quadrupole LSPR modes can be accomplished through polarization of incident light. Finite-difference time-domain calculations of the LSPR responses of the nanocrescent corroborate the polarization-dependent optical behavior. Simulations reveal optical near field enhancements with unique spatial patterns associated with the individual resonance modes depending on the polarization and wavelength of incident light. Quantitative analysis of the anisotropic LSPR behavior supports the potential for controlling the near field through selective induction of specific resonance modes with particular near field d...

Combining Geo‐SOM and Hierarchical Clustering to Explore Geospatial Data

AbstractGeo‐SOM is a useful geovisualization technique for revealing patterns in spatial data, but is ineffective in supporting interactive exploration of patterns hidden in different Geo‐SOM sizes. Based on the divide and group principle in geovisualization, the article proposes a new methodology that combines Geo‐SOM and hierarchical clustering to tackle this problem. Geo‐SOM was used to “divide” the dataset into several homogeneous subsets; hierarchical clustering was then used to “group” neighboring homogeneous subsets for pattern exploration in different levels of granularity, thus permitting exploration of patterns at multiple scales. An artificial dataset was used for validating the method's effectiveness. As a case study, the rush hour motorcycle flow data in Taipei City, Taiwan were analyzed. Compared with the best result generated solely by Geo‐SOM, the proposed method performed better in capturing the homogeneous zones in the artificial dataset. For the case study, the proposed method discovered six clusters with unique data and spatial patterns at different levels of granularity, while the original Geo‐SOM only identified two. Among the four hierarchical clustering methods, Ward's clustering performed the best in pattern discovery. The results demonstrated the effectiveness of the approach in visually and interactively exploring data and spatial patterns in geospatial data.

Genome-wide characterization of the pectate lyase-like (PLL) genes in Brassica rapa

Pectate lyases (PL) depolymerize demethylated pectin (pectate, EC 4.2.2.2) by catalyzing the eliminative cleavage of α-1,4-glycosidic linked galacturonan. Pectate Lyase-like (PLL) genes are one of the largest and most complex families in plants. However, studies on the phylogeny, gene structure, and expression of PLL genes are limited. To understand the potential functions of PLL genes in plants, we characterized their intron-exon structure, phylogenetic relationships, and protein structures, and measured their expression patterns in various tissues, specifically the reproductive tissues in Brassica rapa. Sequence alignments revealed two characteristic motifs in PLL genes. The chromosome location analysis indicated that 18 of the 46 PLL genes were located in the least fractionated sub-genome (LF) of B. rapa, while 16 were located in the medium fractionated sub-genome (MF1) and 12 in the more fractionated sub-genome (MF2). Quantitative RT-PCR analysis showed that BrPLL genes were expressed in various tissues, with most of them being expressed in flowers. Detailed qRT-PCR analysis identified 11 pollen specific PLL genes and several other genes with unique spatial expression patterns. In addition, some duplicated genes showed similar expression patterns. The phylogenetic analysis identified three PLL gene subfamilies in plants, among which subfamily II might have evolved from gene neofunctionalization or subfunctionalization. Therefore, this study opens the possibility for exploring the roles of PLL genes during plant development.