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At least 163 records · Page 9

spammR: an R package designed for analysis and integration of spatial multi-omic measurements

Spatial omics is a young and evolving field and as such shows rapid development of novel technologies and analysis methods to measure transcripts, proteins, metabolites, and post-translational modifications at high spatial resolution. These advances in technology have enabled the simultaneous generation of abundance profiles for multiple different omics types and associated microscopy imaging data, as well as their analysis in a spatial context. However, most analytical tools are designed for spatial transcriptomics platforms and are challenging to use in other contexts such as mass spectrometry-based measurements or metagenomics. To this end we present spammR (spatial analysis of multi-omics measurements in R), an R package that enables end-to-end analysis with a specific focus on mass-spectrometry derived spatial omics datasets with (1) smaller sample sizes and spatial sparsity of samples, (2) considerable missingness, and (3) no a-priori knowledge about proteins or genes of interest, relying on a fully data-driven approach.

spammR↗

Spatially resolved nanostructural analysis of disordered phases in carbonated alkali-activated slag

Alkali-activated slag (AAS) is a promising low-CO 2 alternative cement consisting of several disordered phases of similar composition. Although their local atomic arrangements are known to influence macroscopic behavior, determination of structural changes in response to external stimuli remains a challenge. Here, X-ray diffraction-computed tomography (XRD-CT), pair distribution function-CT (PDF-CT), and nanoprobe X-ray fluorescence (nano-XRF) have been used to uncover how an increase of magnesium in AAS affects the atomic structure and spatial arrangement of phases after aggressive carbonation (100% dry CO 2 ), conditions experienced in applications such as oil and gas wells and geological storage of CO 2 . From PDF-CT it is found that a higher magnesium content decreases the average nanoscale crystallite size of disordered calcium carbonate. At the same time, higher magnesium content is correlated with a less decalcified C-(N)-A-S-H gel, as determined via analysis of Ca-Si atom-atom correlations from PDF-CT and Ca/Si ratios from nano-XRF. Finally, nano-XRF reveals that the disordered (i.e., amorphous) calcium carbonate is stabilized by the presence of silicates.

McCaslin, Eric R. [Princeton Univ., NJ (United Sta↗

A spatial, kinematical, and dynamical analysis of Abell 400

The paper presents a detailed spatial, kinematical, and dynamical analysis for the cluster A400, based on a nearly complete redshift survey of bright galaxies within 1 Mpc of the cluster center. A dispersed component with a high fraction of spiral galaxies at a velocity of 8200 km/s, and a background group with a mean velocity of 13,400 km/s are identified. It is proposed that the main body of A400 is composed of at least two individual subclusters. If subclustering is ignored, the derived dispersion of the 88 galaxies with measured velocities within 4000 km/s of the bright dumbbell galaxy near the cluster center is 702 km/s. When kinematic information is used to split A400 into likely subclusters, the velocity dispersions of the individual units which make up this cluster are on the order of 200-300 km/s. If A400 is considered a single entity, the inferred blue mass-to-light ratio is 1210 solar masses/solar luminosities. It is argued that A400 is an example of a presently occurring merger, and that the individual components of the dumbbell galaxy were once individual D galaxies within the premerger subclusters.

Beers, Timothy C.↗

An Analysis of the Spatial Variations in the Relationship Between Built Environment and Severe Crashes

Traffic crashes significantly contribute to global fatalities, particularly in urban areas, highlighting the need to evaluate the relationship between urban environments and traffic safety. This study extends former spatial modeling frameworks by drawing paths between global models, including spatial lag (SLM), and spatial error (SEM), and local models, including geographically weighted regression (GWR), multi-scale geographically weighted regression (MGWR), and multi-scale geographically weighted regression with spatially lagged dependent variable (MGWRL). Utilizing the proposed framework, this study analyzes severe traffic crashes in relation to urban built environments using various spatial regression models within Leon County, Florida. According to the results, SLM outperforms OLS, SEM, and GWR models. Local models with lagged dependent variables outperform both the global and generic versions of the local models in all performance measures, whereas MGWR and MGWRL outperform GWR and GWRL. Local models performed better than global models, showing spatial non-stationarity; so, the relationship between the dependent and independent variables varies over space. The better performance of models with lagged dependent variables signifies that the spatial distribution of severe crashes is correlated. Finally, the better performance of multi-scale local models than classical local models indicates varying influences of independent variables with different bandwidths. According to the MGWRL model, census block groups close to the urban area with higher population, higher education level, and lower car ownership rates have lower crash rates. On the contrary, motor vehicle percentage for commuting is found to have a negative association with severe crash rate, which suggests the locality of the mentioned associations.

Alisan, Onur (ORCID:0000000193113984)↗

Southern Arizona riparian habitat: Spatial distribution and analysis

The objectives of this study were centered around the demonstration of remote sensing as an inventory tool and researching the multiple uses of riparian vegetation. Specific study objectives were to: (1) map riparian vegetation along the Gila River, San Simon Creek, San Pedro River, Pantano Wash, (2) determine the feasibility of automated mapping using LANDSAT-1 computer compatible tapes, (3) locate and summarize existing mpas delineating riparian vegetation, (4) summarize data relevant to Southern Arizona's riparian products and uses, (5) document recent riparian vegetation changes along a selected portion of the San Pedro River, (6) summarize historical changes in composition and distribution of riparian vegetation, and (7) summarize sources of available photography pertinent to Southern Arizona.

Lacey, J. R.↗

The analysis of high spatial resolution UV and X-ray images by computational modeling

Very high resolution stereoscopic images of high temperature loop structures observed at UV and X-ray wavelengths in the solar corona can be used to understand physical processes in the corona. An existing computational model is described and sample results are given to demonstrate that computational modeling of coronal structures can indeed take advantage of very high resolution images. The sample results include the run of temperature and number density along a typical loop and the variation of the differential emission measure with temperature. The integration of the differential emission measure with temperature along a column commensurate with an instrument's spatial resolution is the relevant parameter obtained from UV and X-ray observations. The effects of loop geometry and energy input are examined.

Vesecky, J. F.↗

Discrete analysis of spatial-sensitivity models

Procedures for reducing the computational burden of current models of spatial vision are described, the simplifications being consistent with the prediction of the complete model. A method for using pattern-sensitivity measurements to estimate the initial linear transformation is also proposed which is based on the assumption that detection performance is monotonic with the vector length of the sensor responses. It is shown how contrast-threshold data can be used to estimate the linear transformation needed to characterize threshold performance.

Nielsen, Kenneth R. K.↗

Application of finite-element methods to dynamic analysis of flexible spatial and co-planar linkage systems, part 2

An approach is described to modeling the flexibility effects in spatial mechanisms and manipulator systems. The method is based on finite element representations of the individual links in the system. However, it should be noted that conventional finite element methods and software packages will not handle the highly nonlinear dynamic behavior of these systems which results form their changing geometry. In order to design high-performance lightweight systems and their control systems, good models of their dynamic behavior which include the effects of flexibility are required.

Dubowsky, Steven↗

Characteristics of Impact Craters and Interior Deposits: Analysis of the Spatial and Temporal Distribution of Volatiles in the Highlands of Mars

The martian southern highlands contain impact craters that display pristine to degraded morphologies, and preserve a record of degradation that can be attributed to fluvial, eolian, mass wasting, volcanic and impact-related processes. However, the relative degree of modification by these processes and the amounts of material contributed to crater interiors are not well constrained. Impact craters (D>10 km) within Terra Cimmeria (0deg-60degS, 190deg-240degW), Terra Tyrrhena (0deg-30degS, 260deg-310degW) and Noachis Terra (20deg-50degS, 310deg-340degW) are being examined to better understand the degradational history and evolution of highland terrains. The following scientific objectives will be accomplished. 1) Determine the geologic processes that modified impact craters (and surrounding highland terrains). 2) Determine the sources (e.g. fluvial, lacustrine, eolian, mass wasting, volcanic, impact melt) and relative amounts of material composing crater interior deposits. 3) Document the relationships between impact crater degradation and highland fluvial systems. 4) Determine the spatial and temporal relationships between degradational processes on local and regional scales. And 5) develop models of impact crater (and highland) degradation that can be applied to these and other areas of the martian highlands. The results of this study will be used to constrain the geologic, hydrologic and climatic evolution of Mars and identify environments in which subsurface water might be present or evidence for biologic activity might be preserved.

Mest, S. C.↗

Analysis of Rawinsonde Spatial Separation for Space Launch Vehicle Applications at the Eastern Range

Space launch vehicles use day-of-launch steering commands based upon the upper-level (UL) atmospheric environments in order to alleviate wind induced structural loading and optimize ascent trajectory. Historically, UL wind measurements to support launch operations at the National Aeronautics and Space Administration's (NASA) Kennedy Space Center (KSC), co-located on the United States Air Force's Eastern Range (ER) at the Cape Canaveral Air Force Station use high-resolution (HR) rawinsondes. One inherent limitation with rawinsondes is the approximately one-hour sampling time necessary to measure tropospheric winds. Additionally, rawinsonde drift during ascent due to the ambient wind environment can result in the balloon being hundreds of kilometers down range, which results in questioning whether the measured winds represent the wind environment the vehicle will experience during ascent. This paper will describe the use of balloon profile databases to statistically assess the drift distance away from the ER launch complexes during HR rawinsonde ascent as a function of season. Will also discuss an alternative method to measure UL wind environments in closer proximity to the vehicle trajectory when launching from the ER.

Decker, Ryan K.↗

Analysis of Rawinsonde Spatial Separation for Space Launch Vehicle Applications at the Eastern Range

Spatial separation of HR rawinsonde data is directly correlated with climatological tropospheric wind environment over ER. Stronger winds in the winter result in further downrange drift. Lighter winds in the summer result in the less horizontal drift during ascent. Maximum downrange distance can exceed 200 km during winter months. Data could misrepresent the environment the vehicle will experience during ascent. PRESTO uses all available data sources to produce the best representative, vertically complete atmosphere for launch vehicle DOL operations. Capability planned for use by NASA Space Launch System vehicle's first flight scheduled for Fall 2018.

Decker, Ryan K.↗

Analysis of Rawinsonde Spatial Separation for Space Launch Vehicle Applications at the Eastern Range

Space launch vehicles develop day-of-launch steering commands based upon the upper-level atmospheric environments in order to alleviate wind induced structural loading and optimize ascent trajectory. Historically, upper-level wind measurements to support launch operations at the National Aeronautics and Space Administration's (NASA's) Kennedy Space Center co-located on the United States Air Force's Eastern Range (ER) at the Cape Canaveral Air Force Station use high-resolution rawinsondes. One inherent limitation with rawinsondes consists of taking approximately one hour to generate a vertically complete wind profile. Additionally, rawinsonde drift during ascent by the ambient wind environment can result in the balloon being hundreds of kilometers down range, which results in questioning whether the measured winds represent the wind environment the vehicle will experience during ascent. This paper will describe the use of balloon profile databases to statistically assess the drift distance away from the ER launch complexes during rawinsonde ascent as a function of season and discuss an alternative method to measure upper level wind environments in closer proximity to the vehicle trajectory launching from the ER.

Decker, Ryan K.↗

The Stability of Radiatively Cooling Jets I. Linear Analysis

The results of a spatial stability analysis of a two-dimensional slab jet, in which optically thin radiative cooling is dynamically important, are presented. We study both magnetized and unmagnetized jets at external Mach numbers of 5 and 20. We model the cooling rate by using two different cooling curves: one appropriate to interstellar gas, and the other to photoionized gas of reduced metallicity. Thus, our results will be applicable to both protostellar (Herbig-Haro) jets and optical jets from active galactic nuclei. We present analytical solutions to the dispersion relations in useful limits and solve the dispersion relations numerically over a broad range of perturbation frequencies. We find that the growth rates and wavelengths of the unstable Kelvin-Helmholtz (K-H) modes are significantly different from the adiabatic limit, and that the form of the cooling function strongly affects the results. In particular, if the cooling curve is a steep function of temperature in the neighborhood of the equilibrium state, then the growth of K-H modes is reduced relative to the adiabatic jet. On the other hand, if the cooling curve is a shallow function of temperature, then the growth of K-H modes can be enhanced relative to the adiabatic jet by the increase in cooling relative to heating in overdense regions. Inclusion of a dynamically important magnetic field does not strongly modify the important differences between an adiabatic jet and a cooling jet, provided the jet is highly supermagnetosonic and not magnetic pressure-dominated. In the latter case, the unstable modes behave more like the transmagnetosonic magnetic pressure-dominated adiabatic limit. We also plot fluid displacement surfaces associated with the various waves in a cooling jet in order to predict the structures that might arise in the nonlinear regime. This analysis predicts that low-frequency surface waves and the lowest order body modes will be the most effective at producing observable features in the jet.

Hardee, Philip E.↗

Geodata Modeling and Query in Geographic Information Systems

Geographic information systems (GIS) deal with collecting, modeling, man- aging, analyzing, and integrating spatial (locational) and non-spatial (attribute) data required for geographic applications. Examples of spatial data are digital maps, administrative boundaries, road networks, and those of non-spatial data are census counts, land elevations and soil characteristics. GIS shares common areas with a number of other disciplines such as computer- aided design, computer cartography, database management, and remote sensing. None of these disciplines however, can by themselves fully meet the requirements of a GIS application. Examples of such requirements include: the ability to use locational data to produce high quality plots, perform complex operations such as network analysis, enable spatial searching and overlay operations, support spatial analysis and modeling, and provide data management functions such as efficient storage, retrieval, and modification of large datasets; independence, integrity, and security of data; and concurrent access to multiple users. It is on the data management issues that we devote our discussions in this monograph. Traditionally, database management technology have been developed for business applications. Such applications require, among other things, capturing the data requirements of high-level business functions and developing machine- level implementations; supporting multiple views of data and yet providing integration that would minimize redundancy and maintain data integrity and security; providing a high-level language for data definition and manipulation; allowing concurrent access to multiple users; and processing user transactions in an efficient manner. The demands on database management systems have been for speed, reliability, efficiency, cost effectiveness, and user-friendliness. Significant progress have been made in all of these areas over the last two decades to the point that many generalized database platforms are now available for developing data intensive applications that run in real-time. While continuous improvement is still being made at a very fast-paced and competitive rate, new application areas such as computer aided design, image processing, VLSI design, and GIS have been identified by many as the next generation of database applications. These new application areas pose serious challenges to the currently available database technology. At the core of these challenges is the nature of data that is manipulated. In traditional database applications, the database objects do not have any spatial dimension, and as such, can be thought of as point data in a multi-dimensional space. For example, each instance of an entity EMPLOYEE will have a unique value corresponding to every attribute such as employee id, employee name, employee address and so on. Thus, every Employee instance can be thought of as a point in a multi-dimensional space where each dimension is represented by an attribute. Furthermore, all operations on such data are one-dimensional. Thus, users may retrieve all entities satisfying one or more constraints. Examples of such constraints include employees with addresses in a certain area code, or salaries within a certain range. Even though constraints can be specified on multiple attributes (dimensions), the search for such data is essentially orthogonal across these dimensions.

Adam, Nabil↗

Efficient computation of spatial eigenvalues for hydrodynamic stability analysis

The simple procedure presented for spatial stability computations can substantially reduce the computational requirements of such analyses, as illustrated for the cases of both internal and external cases of compressible and incompressible flows, and both viscous and inviscid instability modes. Excellent estimates of spatial eigenvalues are obtained.

Khorrami, Mehdi R.↗