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Results for “Spatial heterogeneity”

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PubMed2026

Spatial Total RNA Sequencing of Formalin-Fixed Paraffin-Embedded Tissue by spRandom-seq.

The molecular pathogenesis of infectious diseases and cancer is orchestrated by nanoscale of host and microbial RNA transcripts within the tissue microenvironment. Nevertheless, spatially resolving the comprehensive transcriptional landscape within complex clinical tissues, like formalin-fixed paraffin-embedded (FFPE) specimens, still poses a formidable challenge. Here, we present spRandom-seq, a random primer-based spatial total RNA sequencing technology designed to spatially resolve complete transcriptomes from host, bacteria, and even nanoscale viruses in FFPE tissues. Capitalizing on the random primer design, our technology not only facilitated the discovery of specific lncRNAs and alternative splicing events in mouse brain and olfactory bulb, but also delineated pronounced spatial heterogeneity in clinical FFPE sections-across distinct tumor regions in breast cancer and microbial infection sites in Klebsiella pneumoniae-infected tissues. Importantly, integrated analysis of host and viral RNAs in FFPE samples from hepatitis B virus (HBV)‑positive hepatocellular carcinoma (HCC) demonstrated that complement and coagulation pathways were specifically activated across expansive HBV‑infected tumor areas, which also exhibited an increased burden of copy number variations (CNVs). Owing to its compatibility with existing spatial transcriptomics platforms and minimal operational complexity, spRandom-seq represents a practical and scalable approach for clinical pathology applications and infection diagnostics.

Paraffin Embedding↗

PubMed2006

Process-based reactive transport modeling of a permeable reactive barrier for the treatment of mine drainage.

Reactive transport modeling of a permeable reactive barrier for the treatment of mine drainage was used to integrate a comprehensive data set including pore water chemistry and solid phase data from several sampling events over a >3-year time period. The simulations consider the reduction of sulfate by the organic carbon-based treatment material and the removal of sulfate and iron by precipitation of reduced mineral phases including iron monosulfides and siderite. Additional parameters constraining the model include dissolved H2S, alkalinity and pH, as well as a suite of solid phase S-fractions identified by extractions. Influences of spatial heterogeneity necessitated the use of a 2-dimensional modeling approach. Simulating observed seasonal fluctuations and long-term changes in barrier reactivity required the use of temperature dependent rate coefficients and a multimodal Monod-type rate expression accounting for the variable reactivity of different organic carbon fractions. Simulated dissolved concentrations of SO4, Fe, H2S, alkalinity and pH, as well as solid phase accumulations of reduced sulfur phases generally compare well to observed trends over 23 months. Spatial variations, seasonal fluctuations and the time-dependent decline in reactivity were also captured. The modeling results generally confirm, and further strengthen, the existing conceptual model for the site. Overall sulfate reduction and S-accumulation rates are constrained with confidence within a factor of 1.5.

Hydrogen-Ion Concentration↗

PubMed2004

Spontaneous and evoked intracellular calcium transients in donor-derived myocytes following intracardiac myoblast transplantation.

Skeletal myoblast transplantation is a potential treatment for congestive heart failure. To study the functional activity of both donor and host myocytes following transplantation, skeletal myoblasts expressing an enhanced green fluorescent protein (EGFP) transgene were transplanted into hearts of nontransgenic recipients, and changes in intracellular calcium concentration ([Ca2+]i) were monitored in donor and host cells. While the vast majority of donor-derived myocytes were observed to be functionally isolated from the host myocardium, a small population of donor myocytes exhibited action potential-induced calcium transients in synchrony with adjacent host cardiomyocytes. In many cases, the durations of these [Ca2+]i transients were heterogeneous compared with those in neighboring host cardiomyocytes. In other studies, EGFP-expressing donor myoblasts were transplanted into the hearts of adult transgenic recipient mice expressing a cardiomyocyte-restricted beta-gal reporter gene. A small population of myocytes was observed to express both reporter transgenes, indicating that the transplanted myoblasts fused with host cardiomyocytes at a very low frequency. These cells also expressed connexin43, a component of gap junctions. Thus engraftment of skeletal myoblasts generated spatial heterogeneity of [Ca2+]i signaling at the myocardial/skeletal muscle interface, most likely as a consequence of fusion events between donor myoblasts and host cardiomyocytes.

Action Potentials↗

PubMed2006

Local population size in a flightless insect: importance of patch structure-dependent mortality.

In spatially heterogeneous systems, utilizing population models to integrate the effects of multiple population rates can yield powerful insights into the relative importance of the component rates. The relative importance of demographic rates and dispersal in shaping the distribution of the western tussock moth (Orgyia vetusta) among patches of its host plant was explored using stage-structured population models. Tussock moth dispersal occurs passively in first-instar larvae and is poor or absent in all other life stages. Spatial surveys suggested, however, that moth distribution is not well explained by passive dispersal; moth populations were greater on small patches and on isolated ones. Further analysis showed that several local demographic rates varied significantly with patch characteristics. Two mortality factors in particular may explain the observed patterns. First, crawler mortality both increased with patch size and was density-dependent. A single-patch difference equation model showed mortality related to patch size is strong enough to overcome the homogenizing effect of density dependence; greater equilibrium densities were predicted for smaller patches. Second, although three rates were found to vary with local patch density, only pupal parasitism by a chalcid wasp could potentially account for higher moth abundances on isolated patches. A spatially explicit simulation model of the multiple-patch system showed that spatial variation in pupal parasitism is indeed strong enough to generate such a pattern. These results demonstrate that habitat spatial structure can affect multiple population processes simultaneously, and even relatively low attack rates imposed on a reproductively valuable life stage of the host can have a dominant effect on population distribution among habitat patches.

Animals↗

PubMed2006

Changes of soil organic carbon in an intensively cultivated agricultural region: a denitrification-decomposition (DNDC) modelling approach.

Regional modelling of soil organic carbon (SOC) dynamics is important for predicting large-scale patterns in carbon cycling and for assessing potential responses of soil carbon pools to land-use change. However, data uncertainties related to both spatial heterogeneity and small-scale differences in farming practice related to cropping systems affect the accuracy of regional models. A case study is presented from Quzhou County in the North China Plain, an area characterized by highly intensive farming. For this county, the DNDC model was validated using sampling data from 68 sites around the county under generalized farm practices. Unique modelling units based on soil type, soil texture and crop type were created and then used to model the spatial change of SOC under different farming practices. Considering the main factors affecting SOC sequestration, the results indicate that the DNDC model delivers acceptable modelling results at county level. The results show that there is a great potential for SOC sequestration in Quzhou County in its central, southern and eastern parts. Changes in farming practices show a strong effect on carbon sequestration. A very efficient and environmental friendly sequestration of SOC pools could be achieved even by decreasing nitrogen fertilizer inputs, when the amount of straw returned to the field is greatly increased.

Agriculture↗

PubMed1999

Early perfusion after controlled cortical impact in rats: quantification by arterial spin-labeled MRI and the influence of spin-lattice relaxation time heterogeneity.

Early posttraumatic cerebral hypoperfusion is implicated in the evolution of secondary damage after experimental and clinical traumatic brain injury (TBI). This is the first report of cerebral blood flow (CBF) measurement by continuous arterial spin-labeled magnetic resonance imaging (MRI) early after TBI in rats using the controlled cortical impact (CCI) model. CCI reduced CBF globally at approximately 3 hr (versus normal), with 85% and 49% reductions in a contused cortical region and contralateral cortex, respectively. In contrast, a prior MRI study from this laboratory showed at 24 hr post trauma a focal CBF reduction restricted to the injury site. In vivo spin-lattice relaxation time (T(1obs)), which is used in CBF quantification, was spatially heterogeneous early after CCI, a time when edema is developing in injured brain tissue. At 4.7 T, T(1obs) values are increased 29% in the contusion (versus normal), consequently reducing CBF quantification to a similar degree. MRI should facilitate coupling posttraumatic CBF with long-term functional outcome. Magn Reson Med 42:673-681, 1999.

Animals↗

PubMed1999

Spatial distribution of leaf dry weight per area and leaf nitrogen concentration in relation to local radiation regime within an isolated tree crown.

To assess the spatial distribution of photosynthetic capacity within an isolated 20-year-old walnut tree (Juglans regia L.) crown, the distribution of relevant leaf characteristics was measured. Variations in leaf dry weight per area (W(a)), and nitrogen content on a weight (N(w)) and area basis (N(a)) were studied along two horizontal and one vertical gradients of leaf irradiance, at two dates (July 30 and September 3). In addition, the content of total nonstructural carbon on a weight (TNC(w)) and area basis (TNC(a)) was measured on July 30. Concurrently, the spatial distribution of daily integrated leaf irradiance within the crown was simulated by a three-dimensional radiation transfer model over a one week period before sampling at each date. High spatial heterogeneity was observed for W(a) (from 50 to 140 g m(-2)), TNC(a) (from 4 to 17 g m(-2)) and N(a) (from 1.2 to 3.6 g m(-2)) among the foliage. Although TNC(w) and N(w) were not correlated and only weakly correlated to daily leaf irradiance, respectively, W(a), TNC(a) and N(a) were strongly correlated to daily leaf irradiance. The relationship between observed N(a) and simulated daily leaf irradiance was used to assess the spatial distribution of N(a) within the crown at each date. Total leaf nitrogen in the foliage was estimated to be 339 g in late July and 317g in early September. For the whole crown (i.e., 1729 current-year shoots), N(a) increased strongly with basal shoot diameter (an index of "shoot vigor"), highlighting the fact that large shoots were mainly located in sunlit locations and exhibited high photosynthetic capacity.

Journal Article↗

PubMed1992

A statistical approach to the regional use of critical loads.

The premise of this paper is that: (1) effects of spatial heterogeneity of watershed response to acid deposition must be considered when models are used to set abatement policies, and (2) the evaluation of critical chemical values is a better measure off the effects of abatement policies than the comparison of deposition values to critical loads. The authors used Monte Carlo methods to apply a site-specific version of the RAINS-Lake-Model to a regional data set from The Netherlands. Statistical methods were then used to identify the important parameters affecting the spatial and temporal response, i.e. a change in pH, of watersheds to acid deposition and a subset of sensitive and insensitive watersheds were derived. The results show that the failure to subset a region into sensitive and insensitive zones may result in an erroneous estimation of the effect of abatement policies based on critical loads alone.

Journal Article↗

PubMed2004

A priori prediction of disease invasion dynamics in a novel environment.

Directly transmitted infectious diseases spread through wildlife populations as travelling waves away from the sites of original introduction. These waves often become distorted through their interaction with environmental and population heterogeneities and by long-distance translocation of infected individuals. Accurate a priori predictions of travelling waves of infection depend upon understanding and quantifying these distorting factors. We assess the effects of anisotropies arising from the orientation of rivers in relation to the direction of disease-front propagation and the damming effect of mountains on disease movement in natural populations. The model successfully predicts the local and large-scale prevaccination spread of raccoon rabies through New York State, based on a previous spatially heterogeneous model of raccoon-rabies invasion across the state of Connecticut. Use of this model provides a rare example of a priori prediction of an epidemic invasion over a naturally heterogeneous landscape. Model predictions matched to data can also be used to evaluate the most likely points of disease introduction. These results have general implications for predicting future pathogen invasions and evaluating potential containment strategies.

Animals↗

PubMed1997

The identification of thresholds of acceptability and danger: the chemical presence route.

European Union chemical legislation requires the calculation of local and regional Predicted Environmental Concentrations (PEC) for the assessment of the exposure of new and existing chemicals to aquatic and terrestrial ecosystems. Current methods use local models for air, water and soil to estimate chemical concentrations close to the source and a generic multimedia 'unit world' approach to estimate regional PECs. These models assume generic environmental scenarios representing typical situations in European countries and do not account for the spatial heterogeneity and temporal variability in ecosystem characteristics, soil properties, river flow rates, chemical emissions, etc. The environmental and ecological complexity can best be represented in a Geographic Information System (GIS). By coupling a GIS with a fate simulation model the concentrations of substances in a specific environment are predicted more realistically. The GREAT-ER project (Geography-referenced Regional Exposure Assessment Tool for European Rivers) was launched to refine regional and local exposure assessments for down-the-drain chemicals by applying real, spatial-referenced datasets instead of generic or average values. A modular approach was developed consisting of a hydrological model and a waste-flow, river quality and fate model which are linked to a regional GIS-database. For the calibration and validation in two European study areas representative detergent chemicals (LAS, boron) are used. In a parallel study, high-volume intermediates discharged into the river Rhine are simulated.

Alkanesulfonates↗

PubMed2000

Hypoxia and necrosis in rat 9L glioma and Morris 7777 hepatoma tumors: comparative measurements using EF5 binding and the Eppendorf needle electrode.

PURPOSE: The purpose of this study was to assess the presence of tumor hypoxia using two independent techniques: binding of the 2-nitroimidazole EF5 and Eppendorf needle electrode measurements. The distribution of tumor hypoxia was assessed with respect to tumor necrosis in corresponding histological studies. METHODS AND MATERIALS: Each of several rats bearing a subcutaneous 9L glioma or Morris 7777 hepatoma tumor was given EF5 i.v. to a final, whole-body concentration of 100 microM. About 2.5 h later, each rat was anesthetized, and needle electrode measurements were made in the tumor along 1-5 tracks (30-200 individual measurements). At 3 h post-EF5 injection, the tumor was excised and frozen. Frozen sections were analyzed for the presence and distribution of binding of EF5 and necrosis using immunohistochemical techniques followed by staining with hematoxylin and eosin (H&E). The histochemical analysis and electrode readings in similar regions of the tumor were compared. RESULTS: Electrode measurements were taken at 0.4-mm intervals along one-dimensional tracks, whereas EF5 binding measurements from tissue sections contained two-dimensional information at high spatial resolution ( approximately 2.5 micro). The EF5 measurements showed greater spatial heterogeneity than did the electrode measurements. In tumor regions with minimal necrosis, needle tracks with relatively high pO(2) readings were usually found to contain relatively low EF5 binding, and vice versa. Because EF5 binding is inversely related to tissue pO(2), this result was expected. The expected inverse correlation of the two techniques was most disparate in necrotic tumor regions (confirmed by H&E staining), where needle electrode measurements showed low to zero pO(2) values, but little or no EF5 binding was found. CONCLUSION: The two methods compared in this study operate in fundamentally different ways and provide substantially different information. EF5 binding provided detailed spatial information on the distribution of hypoxia in viable tumor tissue. There was no EF5 binding in necrotic tumor tissue because cells in such tissue were unable to metabolize the drug. In contrast, output from the needle electrode method appeared to represent a "track-average" tissue pO(2) and did not distinguish between extreme hypoxia and either macroscopic or microscopic necrosis. At the present time, the importance of tumor necrosis in determining treatment response is unknown. However, our data suggest that the Eppendorf needle electrode technique will overestimate the presence of hypoxia. Both techniques are potentially limited by sampling errors in tumors with heterogeneous distributions of hypoxia.

Animals↗

PubMed2005

Sex allocation and dispersal in a heterogeneous two-patch environment.

We investigate the evolution of sex allocation and dispersal in a two-habitat environment using a game theoretic analysis. One habitat is of better quality than the other and increased habitat quality influences the competitive ability of offspring in a sex-specific manner. Unlike previous work, we allow incomplete mixing of the population during mating. We discuss three special cases involving the evolution of sex allocation under fixed levels of dispersal between habitats. In these special cases, stable sex-allocation behaviors can be both biased and unbiased. When sex-allocation behavior and dispersal rates co-evolve we identify two basic outcomes. First-when sex-specific differences in the consequences of spatial heterogeneity are large-we predict the evolution of biased sex-allocation behavior in both habitats, with dispersal by males in one direction and dispersal by females in the other direction. Second-when sex-specific differences are small-unbiased sex-allocation is predicted with no dispersal between habitats.

Animals↗

PubMed1999

Heterogeneity in the distribution of Strongyloides ratti infective stages among the faecal pellets of rats.

The distribution of helminth parasites within their host population is usually overdispersed and can be described by the negative binomial distribution. The causes of this overdispersion are poorly understood, but heterogeneity in the distribution of infective stages within the environment has been implicated as a possible factor. Here we describe the distribution of infective stages of the rat intestinal nematode parasite Strongyloides ratti among the faecal pellets of its host. The distribution of infective stages between faecal pellets is overdispersed and well described by the negative binomial distribution. This overdispersion increases during the course of infection and occurs over a range of infection intensities. Overdispersion of nematode infective stages among faecal pellets may result in increased spatial heterogeneity of the infective stages in the environment and thus may contribute to the generation of overdispersion of adult parasitic stages. In addition, these findings raise important issues regarding the accurate quantification of helminth egg counts from faecal samples.

Animals↗

PubMed2026

Spatial Proteomics of the Normal Breast Collagen Stroma: Links to Density and Body Mass Index.

Collagen breast stroma can become a breast cancer risk factor, yet proteomic regulation of normal breast stroma remains poorly defined. This study evaluates the spatial regulation of the collagen proteome from normal breast tissue. Normal breast tissue sections from the Susan G. Komen tissue bank were used (n = 40), with data including genetic ancestry (n = 20 African ancestry; n = 20 European ancestry), body-mass-index (BMI), age, and mammogram density by the Breast Imaging Reporting and Data System (BI-RADS). 10-plex cell marker staining showed CD44 and COL1A1 markers modulated with BMI. Collagen fiber widths by second harmonic generation microscopy contrasted in BMI categories by genetic ancestry. Targeted extracellular matrix proteomics mass spectrometry imaging showed the collagen alpha-1(I) chain proteome was spatially heterogeneous across the normal breast microenvironment with site-specific post-translational modification of proline hydroxylation. Signatures computationally extracted from stroma-rich regions reported that 47 collagen peptides distinguished BI-RADS categories (area under the receiver operating curve >0.7; p-value >0.05). Multivariate modeling of collagen peptides, fiber metrics, and clinical features supported a strong positive association with BMI as a determinant of collagen alterations in the normal breast. This study provides a foundation for larger studies investigating the clinical value of spatial collagen proteome alterations in human breast.

Humans↗

PubMed2006

Spatial flow-volume dissociation of the cerebral microcirculatory response to mild hypercapnia.

The spatial and temporal response of the cerebral microcirculation to mild hypercapnia was investigated via two-photon laser-scanning microscopy. Cortical vessels, traversing the top 200 microm of somatosensory cortex, were visualized in alpha-chloralose-anesthetized Sprague-Dawley rats equipped with a cranial window. Intraluminal vessel diameters, transit times of fluorescent dextrans and red blood cells (RBC) velocities in individual capillaries were measured under normocapnic (PaCO2= 32.6 +/- 2.6 mm Hg) and slightly hypercapnic (PaCO2= 45 +/- 7 mm Hg) conditions. This gentle increase in PaCO2 was sufficient to produce robust and significant increases in both arterial and venous vessel diameters, concomitant to decreases in transit times of a bolus of dye from artery to venule (14%, P < 0.05) and from artery to vein (27%, P < 0.05). On the whole, capillaries exhibited a significant increase in diameter (16 +/- 33%, P < 0.001, n = 393) and a substantial increase in RBC velocities (75 +/- 114%, P < 0.001, n = 46) with hypercapnia. However, the response of the cerebral microvasculature to modest increases in PaCO2 was spatially heterogeneous. The maximal relative dilatation (range: 5-77%; mean +/- SD: 25 +/- 34%, P < 0.001, n = 271) occurred in the smallest capillaries (1.6 microm-4.0 microm resting diameter), while medium and larger capillaries (4.4 microm-6.8 microm resting diameter) showed no significant changes in diameter (P > 0.08, n = 122). In contrast, on average, RBC velocities increased less in the smaller capillaries (39 +/- 5%, P < 0.002, n = 22) than in the medium and larger capillaries (107 +/- 142%, P < 0.003, n = 24). Thus, the changes in capillary RBC velocities were spatially distinct from the observed volumetric changes and occurred to homogenize cerebral blood flow along capillaries of all diameters.

Animals↗

PubMed2005

Seed dispersal in heterogeneous environments: bridging the gap between mechanistic dispersal and forest dynamics models.

Seed dispersal is an important determinant of vegetation composition. We present a mechanistic model of seed dispersal by wind that incorporates heterogeneous vegetation structure. Vegetation affects wind speeds, a primary determinant of dispersal distance. Existing models combine wind speed and fall velocity of seeds. We expand on them by allowing vegetation, and thus wind profiles, to vary along seed trajectories, making the model applicable to any wind-dispersed plant in any community. Using seed trap data on seeds dispersing from forests into adjacent sites of two distinct vegetation structures, we show that our model was unbiased and accurate, even though dispersal patterns differed greatly between the two structures. Our spatially heterogeneous model performed better than models that assumed homogeneous vegetation for the same system. Its sensitivity to vegetation structure and ability to predict seed arrival when vegetation structure was incorporated demonstrates the model's utility for providing realistic estimates of seed arrival in realistic landscapes. Thus, we begin to bridge mechanistic seed dispersal and forest dynamics models. We discuss the merits of our model for incorporation into forest simulators, applications where such incorporation has been or is likely to be especially fruitful, and future model refinements to increase understanding of seed dispersal by wind.

Acer↗

PubMed1999

Depolarization-induced mitochondrial Ca accumulation in sympathetic neurons: spatial and temporal characteristics.

Several lines of evidence suggest that neuronal mitochondria accumulate calcium when the cytosolic free Ca(2+) concentration ([Ca(2+)](i)) is elevated to levels approaching approximately 500 nM, but the spatial, temporal, and quantitative characteristics of net mitochondrial Ca uptake during stimulus-evoked [Ca(2+)](i) elevations are not well understood. Here, we report direct measurements of depolarization-induced changes in intramitochondrial total Ca concentration ([Ca](mito)) obtained by x-ray microanalysis of rapidly frozen neurons from frog sympathetic ganglia. Unstimulated control cells exhibited undetectably low [Ca](mito), but high K(+) depolarization (50 mM, 45 sec), which elevates [Ca(2+)](i) to approximately 600 nM, increased [Ca](mito) to 13.0 +/- 1.5 mmol/kg dry weight; this increase was abolished by carbonyl cyanide p-(trifluoromethoxy) phenylhydrazone (FCCP). The elevation of [Ca](mito) was a function of both depolarization strength and duration. After repolarization, [Ca](mito) recovered to prestimulation levels with a time course that paralleled the decline in [Ca(2+)](i). Depolarization-induced increases in [Ca](mito) were spatially heterogeneous. At the level of single mitochondria, [Ca](mito) elevations depended on proximity to the plasma membrane, consistent with predictions of a diffusion model that considers radial [Ca(2+)](i) gradients that exist early during depolarization. Within individual mitochondria, Ca was concentrated in small, discrete sites, possibly reflecting a high-capacity intramitochondrial Ca storage mechanism. These findings demonstrate that in situ Ca accumulation by mitochondria, now directly identified as the structural correlate of the "FCCP-sensitive store, " is robust, reversible, graded with stimulus strength and duration, and dependent on spatial location.

Animals↗

PubMed1995

Ethanol induces heterogeneous reduction of cytochrome aa3 within perfused rat liver lobule assessed using microspectroscopy.

The redox state of cytochrome aa3 was measured at microspots (20 microns diameter) within the lobule of perfused rat livers, using reflectance microspectroscopy, and the effect of ethanol infusion on sublobular distribution of the redox states was evaluated. A sigmoidal relationship was observed between oxygen delivery and the reduction of cytochrome aa3 in both the periportal and pericentral regions of the liver lobule when the influent O2 concentration was decreased in a graduated manner. This sigmoidal curve was shifted to the more reduced state by ethanol infusion, with ethanol (25-100 mM) increasing the degree of cytochrome aa3 reduction in a dose-dependent manner according to the distance from the periportal region along a sinusoid. This increase was spatially heterogeneous within a liver lobule. These data indicate that ethanol accelerates cytochrome aa3 reduction, with a distinct gradient of reduction along sinusoids but a heterogeneous distribution within the liver lobule.

Animals↗