Co-location Patterns Research Articles

Source Apportionment of Soil Heavy Metals Based on Spatial Co-Location Patterns

Source Apportionment of Soil Heavy Metals Based on Spatial Co-Location Patterns

Impacts of Skill Centrality on Regional Economic Productivity and Occupational Income

A well‐developed perspective in the study of urban systems is that cities are complex systems that manifest as networks of interdependent economic units. These units might be occupations, industries, labor skills, patent technologies, etc. Much research has focused on describing the nature of these networks, quantifying their links, and suggesting applications for policymakers. In this paper, we examine the US skill network, focusing on the relationship between network centrality and economic performance. Here, nodes are represented by individual labor skills, and edge weights are derived from the colocation pattern of skill pairs among 384 US metropolitan statistical areas. The centrality of skills, using three centrality measures, is then aggregated to the occupational and metropolitan level. We find that occupations with higher skill centrality are associated with greater annual salaries, and metropolitan areas with higher skill centrality have higher productivity rates. Overall, these results suggest that the application of traditional network metrics to this view of cities as complex networks can offer new insights into the dynamics of regional economies.

An Efficient Group-Based Replica Placement Policy for Large-Scale Geospatial 3D Raster Data on Hadoop.

Geospatial three-dimensional (3D) raster data have been widely used for simple representations and analysis, such as geological models, spatio-temporal satellite data, hyperspectral images, and climate data. With the increasing requirements of resolution and accuracy, the amount of geospatial 3D raster data has grown exponentially. In recent years, the processing of large raster data using Hadoop has gained popularity. However, data uploaded to Hadoop are randomly distributed onto datanodes without consideration of the spatial characteristics. As a result, the direct processing of geospatial 3D raster data produces a massive network data exchange among the datanodes and degrades the performance of the cluster. To address this problem, we propose an efficient group-based replica placement policy for large-scale geospatial 3D raster data, aiming to optimize the locations of the replicas in the cluster to reduce the network overhead. An overlapped group scheme was designed for three replicas of each file. The data in each group were placed in the same datanode, and different colocation patterns for three replicas were implemented to further reduce the communication between groups. The experimental results show that our approach significantly reduces the network overhead during data acquisition for 3D raster data in the Hadoop cluster, and maintains the Hadoop replica placement requirements.

Dietary carbohydrate influences the colocalization pattern of Glucagon-like Peptide-1 with neurotensin in the chicken ileum

Glucagon-like peptide (GLP)-1 colocalizes with neurotensin (NT) in the same enteroendocrine cells (EECs) of the chicken ileum. The present study was designed to clarify the influence of dietary carbohydrate (CHO) on the colocalization pattern of GLP-1 with NT in the chicken distal ileum. Male White Leghorn chickens at 6 weeks of age (n=15) were divided into three groups, a control and two experimental (low-CHO and CHO-free), with five chickens in each, and fed control or experimental diets for 7 d. Distal ileum was collected from each bird as a tissue sample and subjected to double immunofluorescence staining to detect GLP-1 and NT. Three types of EEC, GLP-1+/NT+, GLP-1+/NT- and GLP-1-/NT+, were demonstrated in the chicken ileum. GLP-1+/NT+ cells in the control group had a spindle-like shape with a long cytoplasmic process, but those in the experimental groups were round and lacked a cytoplasmic process. The ratio of GLP-1+/NT+ cells was significantly decreased in the two experimental groups compared with that in the control group. The ratio of GLP-1+/NT+ cells was significantly lower than those of GLP-1+/NT- and GLP-1-/NT+ cells in the two experimental groups. Most cells that were immunoreactive for GLP-1 and NT antisera lacked signals of proglucagon (PG) and NT precursor (NTP) mRNA in the experimental groups. The number of EECs expressing PG and NTP mRNA signals showed tendencies for decreases with a reduction of dietary CHO level. These findings suggest that dietary CHO could be a significant regulator of the pattern of colocalization pattern of GLP-1 with NT in the chicken ileum.

Protein Kinase A in Human Retina: Differential Localization of Cβ, Cα, RIIα, and RIIβ in Photoreceptors Highlights Non-redundancy of Protein Kinase A Subunits.

Protein kinase A (PKA) signaling is essential for numerous processes but the subcellular localization of specific PKA regulatory (R) and catalytic (C) subunits has yet to be explored comprehensively. Additionally, the localization of the Cβ subunit has never been spatially mapped in any tissue even though ∼50% of PKA signaling in neuronal tissues is thought to be mediated by Cβ. Here we used human retina with its highly specialized neurons as a window into PKA signaling in the brain and characterized localization of PKA Cα, Cβ, RIIα, and RIIβ subunits. We found that each subunit presented a distinct localization pattern. Cα and Cβ were localized in all cell layers (photoreceptors, interneurons, retinal ganglion cells), while RIIα and RIIβ were selectively enriched in photoreceptor cells where both showed distinct patterns of co-localization with Cα but not Cβ. Only Cα was observed in photoreceptor outer segments and at the base of the connecting cilium. Cβ in turn, was highly enriched in mitochondria and was especially prominent in the ellipsoid of cone cells. Further investigation of Cβ using RNA BaseScope technology showed that two Cβ splice variants (Cβ4 and Cβ4ab) likely code for the mitochondrial Cβ proteins. Overall, our data indicates that PKA Cα, Cβ, RIIα, and RIIβ subunits are differentially localized and are likely functionally non-redundant in the human retina. Furthermore, Cβ is potentially important for mitochondrial-associated neurodegenerative diseases previously linked to PKA dysfunction.

High-resolution in situ analysis of Cas9 germline transcript distributions in gene-drive Anopheles mosquitoes.

Gene drives are programmable genetic elements that can spread beneficial traits into wild populations to aid in vector-borne pathogen control. Two different drives have been developed for population modification of mosquito vectors. The Reckh drive (vasa-Cas9) in Anopheles stephensi displays efficient allelic conversion through males but generates frequent drive-resistant mutant alleles when passed through females. In contrast, the AgNosCd-1 drive (nos-Cas9) in Anopheles gambiae achieves almost complete allelic conversion through both genders. Here, we examined the subcellular localization of RNA transcripts in the mosquito germline. In both transgenic lines, Cas9 is strictly coexpressed with endogenous genes in stem and premeiotic cells of the testes, where both drives display highly efficient conversion. However, we observed distinct colocalization patterns for the two drives in female reproductive tissues. These studies suggest potential determinants underlying efficient drive through the female germline. We also evaluated expression patterns of alternative germline genes for future gene-drive designs.

MLCPM-UC:A Multi-level Co-location Pattern Mining Algorithm Based on Uniform Coefficient of Pattern Instance Distribution

MLCPM-UC:A Multi-level Co-location Pattern Mining Algorithm Based on Uniform Coefficient of Pattern Instance Distribution

The location of urban healthcare services: Evidence from Phoenix Yelp reviews

AbstractThe U.S. healthcare sector is a large and important industry. However, relatively little is known about the localization and colocalization patterns of healthcare services within an urban area. By using Yelp data from over 3000 healthcare service establishments in the Phoenix area, this paper applies a recent spatial econometric technique to the analysis of healthcare services. The results reveal that spatial concentration varies across distances and types of healthcare services. Localization is more prevalent at closer distances, and general practitioners tend to be more dispersed than specialists. Colocalization with hospitals is most likely for specialists while family practices and dentistry services tend to locate away from hospitals. Different types of location patterns across different types of healthcare services are relevant for informing policies addressing healthcare access and competition in healthcare markets.

High Influencing Pattern Discovery over Time Series Data

A spatial co-location pattern denotes a subset of spatial features whose instances frequently appear nearby. High influence co-location pattern mining is used to find co-location patterns with high influence in specific aspects. Studies of such pattern mining usually rely on spatial distance for measuring nearness between instances, a method that cannot be applied to an influence propagation process concluded from epidemic dispersal scenarios. To discover meaningful patterns by using fruitful results in this field, we extend existing approaches and propose a mining framework. We first defined a new concept of proximity to depict semantic nearness between instances of distinct features, thus applying a star-shaped materialized model to mine influencing patterns. Then, we designed attribute descriptors to perceive attributes of instances and edges from time series data, and we calculated the attribute weights via an analytic hierarchy process, thereby computing the influence between instances and the influence of features in influencing patterns. Next, we constructed influencing metrics and set a threshold to discover high influencing patterns. Since the metrics do not satisfy the downward closure property, we propose two improved algorithms to boost efficiency. Extensive experiments conducted on real and synthetic datasets verified the effectiveness, efficiency, and scalability of our method.

Suppression of PTRF Alleviates Post-Infectious Irritable Bowel Syndrome via Downregulation of the TLR4 Pathway in Rats.

Background: Accumulating evidence suggests that the polymerase I and transcript release factor (PTRF), a key component of the caveolae structure on the plasma membrane, plays a pivotal role in suppressing the progression of colorectal cancers. However, the role of PTRF in the development of functional gastrointestinal (GI) disorders remains unclear. Post-infectious irritable bowel syndrome (PI-IBS) is a common functional GI disorder that occurs after an acute GI infection. Here, we focused on the role of PTRF in the occurrence of PI-IBS and investigated the underlying mechanisms. Methods: Lipopolysaccharide (LPS) (5 μg/ml) was used to induce inflammatory injury in human primary colonic epithelial cells (HCoEpiCs). Furthermore, a rat model of PI-IBS was used to study the role of PTRF. Intestinal sensitivity was assessed based on the fecal water content. A two-bottle sucrose intake test was used to evaluate behavioral changes. Furthermore, shRNA-mediated knockdown of PTRF was performed both in vitro and in vivo. We detected the expression of PTRF in colonic mucosal tissues through immunohistochemistry (IHC), western blotting (WB), and immunofluorescence (IF) analysis. Luciferase activity was quantified using a luciferase assay. Co-localization of PTRF and Toll-like receptor 4 (TLR4) was detected using IF analysis. The activation of the signaling pathways downstream of TLR4, including the iNOs, p38, extracellular signal-regulated kinase (ERK), and c-Jun N-terminal kinase (JNK) pathways, was detected via WB. The levels of NO, IL-1β, IL-6, and TNF-α were measured using enzyme-linked immunosorbent assays. Results: LPS significantly induced PTRF expression and signaling downstream of TLR4, including p38, ERK, and JNK pathways, in HCoEpiCs. Moreover, shRNA-mediated knockdown of PTRF in HCoEpiCs significantly decreased the phosphorylation of JNK, ERK, and p38 and iNOS expression. In PI-IBS rats, the lack of PTRF not only reduced fecal water content and suppressed depressive behavior but also increased the body weight. Furthermore, we found a strong co-localization pattern for PTRF and TLR4. Consistently, the lack of PTRF impaired TLR4 signaling, as shown by the decreased levels of p-JNK, p-ERK, and p-p38, which are upstream factors involved in iNOS expression. Conclusion: PTRF promoted PI-IBS and stimulated TLR4 signaling both in vitro and in vivo. The results of this study not only enlighten the pathogenesis of PI-IBS but also help us understand the biological activity of PTRF and provide an important basis for the clinical treatment of PI-IBS by targeting PTRF.

Divergent connectomic organization delineates genetic evolutionary traits in the human brain

The relationship between human brain connectomics and genetic evolutionary traits remains elusive due to the inherent challenges in combining complex associations within cerebral tissue. In this study, insights are provided about the relationship between connectomics, gene expression and divergent evolutionary pathways from non-human primates to humans. Using in vivo human brain resting-state data, we detected two co-existing idiosyncratic functional systems: the segregation network, in charge of module specialization, and the integration network, responsible for information flow. Their topology was approximated to whole-brain genetic expression (Allen Human Brain Atlas) and the co-localization patterns yielded that neuron communication functionalities—linked to Neuron Projection—were overrepresented cell traits. Homologue-orthologue comparisons using dN/dS-ratios bridged the gap between neurogenetic outcomes and biological data, summarizing the known evolutionary divergent pathways within the Homo Sapiens lineage. Evidence suggests that a crosstalk between functional specialization and information flow reflects putative biological qualities of brain architecture, such as neurite cellular functions like axonal or dendrite processes, hypothesized to have been selectively conserved in the species through positive selection. These findings expand our understanding of human brain function and unveil aspects of our cognitive trajectory in relation to our simian ancestors previously left unexplored.

Nuclear-localized human respiratory syncytial virus NS1 protein modulates host gene transcription.

SUMMARYHuman respiratory syncytial virus (RSV) is a common cause of lower respiratory tract infections in the pediatric, elderly, and immunocompromised individuals. RSV non-structural protein NS1 is a known cytosolic immune antagonist, but how NS1 modulates host responses remains poorly defined. Here, we observe NS1 partitioning into the nucleus of RSV-infected cells, including the human airway epithelium. Nuclear NS1 coimmunoprecipitates with Mediator complex and is chromatin associated. Chromatin-immunoprecipitation demonstrates enrichment of NS1 that overlaps Mediator and transcription factor binding within the promoters and enhancers of differentially expressed genes during RSV infection. Mutation of the NS1 C-terminal helix reduces NS1 impact on host gene expression. These data suggest that nuclear NS1 alters host responses to RSV infection by binding at regulatory elements of immune response genes and modulating host gene transcription. Our study identifies another layer of regulation by virally encoded proteins that shapes host response and impacts immunity to RSV.

SAW1 is increasingly required to recruit Rad10 as SSA flap-length increases from 20 to 50 bases in single-strand annealing in S. cerevisiae

SAW1 is required by the Rad1-Rad10 nuclease for efficient removal of 3′ non-homologous DNA ends (flaps) formed as intermediates during two modes of double-strand break repair in S. cerevisiae, single-strand annealing (SSA) and synthesis-dependent strand annealing (SDSA). Saw1 was shown in vitro to exhibit increasing affinity for flap DNAs as flap lengths varied from 0 to 40 deoxynucleotides (nt) with almost no binding observed when flaps were shorter than 10 nt. Accordingly, our prior in vivo fluorescence microscopy investigation showed that SAW1 was not required for recruitment of Rad10-YFP to DNA double-strand breaks (DSBs) when flaps were ∼10 nt, but it was required when flaps were ∼500 nt in G1 phase of the cell cycle. We were curious whether we would also observe an increased requirement of SAW1 for Rad10 recruitment in vivo as flaps varied from ∼20 to 50 nt, as was shown in vitro. In this investigation, we utilized SSA substrates that generate 20, 30, and 50 nt flaps in vivo in fluorescence microscopy assays and determined that SAW1 becomes increasingly necessary for SSA starting at about ∼20 nt and is completely required at ∼50 nt. Quantitative PCR experiments corroborate these results by demonstrating that repair product formation decreases in the absence of SAW1 as flap length increases. Experiments with strains containing fluorescently labeled Saw1 (Saw1-CFP) show that Saw1 localizes with Rad10 at SSA foci and that about half of the foci containing Rad10 at DSBs do not contain Saw1. Colocalization patterns of Saw1-CFP are consistent regardless of the flap length of the substrate and are roughly similar in all phases of the cell cycle. Together, these data show that Saw1 becomes increasingly important for Rad1-Rad10 recruitment and SSA repair in the ∼20–50 nt flap range, and Saw1 is present at repair sites even when not required and may depart the repair site ahead of Rad1-Rad10.

Discovery of statistically significant regional co-location patterns on urban road networks

ABSTRACT Detecting regional co-location patterns on urban road networks is challenging because it is computationally prohibitive to search all potential co-location patterns and their localities, and effective statistical methods for evaluating the prevalence of regional co-location patterns are lacking. To overcome these challenges, this study developed an adaptive method for detecting network-constrained regional co-location patterns. Specifically, an alternate prevalence measure of regional co-location patterns was defined based on the likelihood ratio statistic. A network-constrained k-nearest neighbor method was used to construct instances of candidate co-location patterns, and a heuristic two-phase expansion method was proposed to identify candidate localities of regional co-location patterns. The statistical significance of regional co-location patterns was evaluated using a Monte Carlo simulation. Experiments using extensive simulated datasets showed that our method was superior to three state-of-the-art methods. The proposed method was also applied to a Beijing points of interest (POI) dataset. The identified regional POI co-location patterns could support a better understanding of the spatial organization of urban functions and may be useful for facilitating urban planning.

Discovering co-location patterns in multivariate spatial flow data

ABSTRACT Spatial flow co-location patterns (FCLPs) are important for understanding the spatial dynamics and associations of movements. However, conventional point-based co-location pattern discovery methods ignore spatial movements between locations and thus may generate erroneous findings when applied to spatial flows. Despite recent advances, there is still a lack of methods for analyzing multivariate flows. To bridge the gap, this paper formulates a novel problem of FCLP discovery and presents an effective detection method based on frequent-pattern mining and spatial statistics. We first define a flow co-location index to quantify the co-location frequency of different features in flow neighborhoods, and then employ a bottom-up method to discover all frequent FCLPs. To further establish the statistical significance of the results, we develop a flow pattern reconstruction method to model the benchmark null hypothesis of independence conditioning on univariate flow characteristics (e.g. flow autocorrelation). Synthetic experiments with predefined FCLPs verify the advantages of our method in terms of correctness over available alternatives. A case study using individual home-work commuting flow data in the Chicago Metropolitan Area demonstrates that residence- or workplace-based co-location patterns tend to overestimate the co-location frequency of people with different occupations and could lead to inconsistent results.

A single-cell tumor immune atlas for precision oncology.

The tumor immune microenvironment is a main contributor to cancer progression and a promising therapeutic target for oncology. However, immune microenvironments vary profoundly between patients, and biomarkers for prognosis and treatment response lack precision. A comprehensive compendium of tumor immune cells is required to pinpoint predictive cellular states and their spatial localization. We generated a single-cell tumor immune atlas, jointly analyzing published data sets of >500,000 cells from 217 patients and 13 cancer types, providing the basis for a patient stratification based on immune cell compositions. Projecting immune cells from external tumors onto the atlas facilitated an automated cell annotation system. To enable in situ mapping of immune populations for digital pathology, we applied SPOTlight, combining single-cell and spatial transcriptomics data and identifying colocalization patterns of immune, stromal, and cancer cells in tumor sections. We expect the tumor immune cell atlas, together with our versatile toolbox for precision oncology, to advance currently applied stratification approaches for prognosis and immunotherapy.

Multilayer network structure and city size: A cross-sectional analysis of global cities to detect the correlation between street and terrain

The high share of impermeable surfaces in cities modifies the terrain characteristics that facilitate natural water flow and balance. The street network, an impervious surface on its own, is also the impetus for developing other impervious surfaces by facilitating access. The purpose of this work is to assess the interconnectedness between the underlying structural lines of the terrain and the street network for making informed decisions on locating green infrastructure to maintain water balance. For this purpose, the work measures the spatio-structural similarity between the co-located networks, assesses the variation of the measure with city size and relation to an indicator of water balance. Cross-sectional analysis is performed across a large sample of cities of varying sizes to extract generalized patterns of spatial structure and variations to size. The larger cities have low index values of spatio-structural similarity ranging between –0.2 and 0.2. The low index values for larger cities relate to the emergence of small-world properties in large street networks for functional efficiency and large street networks' web-like shape. Next, the paper identifies two zones based on the interconnectedness of the roads and the terrain. The spatial extent of a zone based on points where the arterial road intersects higher orders of drainage channels and ridgelines is associated with the number of above-normal wet conditions (SPEI ≥ 2.0) with the r-value of –0.30 at a p-value of 0.05. In summary, spatial statistics on spatial network data are helpful to extract trends inherent in the multi-layered network structure of cities to provide informed solutions. The policymakers and planners can use the spatial co-location patterns between street and terrain to make data-driven decisions to locate interventions for a nature-based resilient city.

Defining Nutrient Colocation Typologies for Human-Derived Supply and Crop Demand To Advance Resource Recovery.

Resource recovery from human excreta can advance circular economies while improving access to sanitation and renewable agricultural inputs. While national projections of nutrient recovery potential provide motivation for resource recovery sanitation, elucidating generalizable strategies for sustainable implementation requires a deeper understanding of country-specific overlap between supply and demand. For 107 countries, we analyze the colocation of human-derived nutrients (in urine) and crop demands for nitrogen, phosphorus, and potassium. To characterize colocation patterns, we fit data for each country to a generalized logistic function. Using fitted logistic curve parameters, three typologies were identified: (i) dislocated nutrient supply and demand resulting from high density agriculture (with low population density) and nutrient islands (e.g., dense cities) motivating nutrient concentration and transport; (ii) colocated nutrient supply and demand enabling local reuse; and (iii) diverse nutrient supply-demand proximities, with countries spanning the continuum between (i) and (ii). Finally, we explored connections between these typologies and country-specific contextual characteristics via principal component analysis and found that the Human Development Index was clustered by typology. By providing a generalizable, quantitative framework for characterizing the colocation of human-derived nutrient supply and agricultural nutrient demand, these typologies can advance resource recovery by informing resource management strategies, policy, and investment.

Celiac disease associated liver dysfunction: Study of the histological features and co-localisation patterns of IgA and IgG anti-tissue transglutaminase antibody (TTG-2) in liver biopsies

Celiac disease (CeD) associated liver dysfunctions (CALD) have wide range of manifestation ranging from milder symptoms alleviating on gluten free diet (GFD), to pathological conditions such as autoimmune hepatitis, cirrhosis etc. However, characteristic histopathological signatures diagnostic of this entity have not been described yet. Diagnosis relies solely on clinical suspicion due to co-occurrence of two pathologies. The aim of this study is to elucidate histological features of CALD and demonstrate IgA/IgG anti-tTG colocalization patterns as a hypothetic evidence towards etiology. 28 formalin fixed paraffin embedded (FFPE) core liver biopsies from patients with treatment naïve CeD with associated liver dysfunction and another 5 FFPE liver core biopsies from patients with other proven pathologies and normal serum anti-tTG titres, were retrieved and IgA/IgG anti-tTG colocalization was carried out both by dual immunohistochemistry (IHC) and dual confocal immunofluorescence (IF) techniques. After a period of GFD, clinically indicated liver biopsies from 5 of these 28 patients were obtained and subjected to repeat testing via the same techniques. Histopathological examination in CALD revealed the following spectrum: steatohepatitis 4 (14.2%), autoimmune hepatitis 4 (14.2%), non-cirrhotic portal venopathy 1 (3.5%), secondary hemochromatosis 1 (3.5%), steatohepatitis with necrotising granuloma 1 (3.5%), cirrhosis 3 (10.7%), irregular sinusoidal dilatation 14 (50%). In CALD, IgA/IgG anti-tTG colocalization was noted in 85.6% cases by dual IHC technique and in 92.8% cases by dual IF technique. Follow up biopsies in 5 CeD cases showed no co-localisation. Deposition of the circulating IgA/IgG anti-tTG antibodies in suspected patients of CALD seems to be a sensitive and specific technique for diagnosing their celiac association, thereby opening up newer insights into management protocols.

Integration of spatial and single-cell transcriptomics localizes epithelial cell-immune cross-talk in kidney injury.

Single-cell sequencing studies have characterized the transcriptomic signature of cell types within the kidney. However, the spatial distribution of acute kidney injury (AKI) is regional and affects cells heterogeneously. We first optimized coordination of spatial transcriptomics and single-nuclear sequencing data sets, mapping 30 dominant cell types to a human nephrectomy. The predicted cell-type spots corresponded with the underlying histopathology. To study the implications of AKI on transcript expression, we then characterized the spatial transcriptomic signature of 2 murine AKI models: ischemia/reperfusion injury (IRI) and cecal ligation puncture (CLP). Localized regions of reduced overall expression were associated with injury pathways. Using single-cell sequencing, we deconvoluted the signature of each spatial transcriptomic spot, identifying patterns of colocalization between immune and epithelial cells. Neutrophils infiltrated the renal medulla in the ischemia model. Atf3 was identified as a chemotactic factor in S3 proximal tubules. In the CLP model, infiltrating macrophages dominated the outer cortical signature, and Mdk was identified as a corresponding chemotactic factor. The regional distribution of these immune cells was validated with multiplexed CO-Detection by indEXing (CODEX) immunofluorescence. Spatial transcriptomic sequencing complemented single-cell sequencing by uncovering mechanisms driving immune cell infiltration and detection of relevant cell subpopulations.