Analysis Of Language Data Research Articles

Gestures Orchestrate Brain Networks for Language Understanding

Although the linguistic structure of speech provides valuable communicative information, nonverbal behaviors can offer additional, often disambiguating cues. In particular, being able to see the face and hand movements of a speaker facilitates language comprehension [1]. But how does the brain derive meaningful information from these movements? Mouth movements provide information about phonological aspects of speech [2-3]. In contrast, cospeech gestures display semantic information relevant to the intended message [4-6]. We show that when language comprehension is accompanied by observable face movements, there is strong functional connectivity between areas of cortex involved in motor planning and production and posterior areas thought to mediate phonological aspects of speech perception. In contrast, language comprehension accompanied by cospeech gestures is associated with tuning of and strong functional connectivity between motor planning and production areas and anterior areas thought to mediate semantic aspects of language comprehension. These areas are not tuned to hand and arm movements that are not meaningful. Results suggest that when gestures accompany speech, the motor system works with language comprehension areas to determine the meaning of those gestures. Results also suggest that the cortical networks underlying language comprehension, rather than being fixed, are dynamically organized by the type of contextual information available to listeners during face-to-face communication.

High-Density Gene Expression Analysis of Tumor-Associated Macrophages from Mouse Mammary Tumors

Clinical and experimental evidence indicates that tumor-associated macrophages (TAMs) promote malignant progression. In breast cancer, TAMs enhance tumor angiogenesis, tumor cell invasion, matrix remodeling, and immune suppression against the tumor. In this study, we examined late-stage mammary tumors from a transgenic mouse model of breast cancer. We used flow cytometry under conditions that minimized gene expression changes to isolate a rigorously defined TAM population previously shown to be associated with invasive carcinoma cells. The gene expression signature of this population was compared with a similar population derived from spleens of non-tumor-bearing mice using high-density oligonucleotide arrays. Using stringent selection criteria, transcript abundance of 460 genes was shown to be differentially regulated between the two populations. Bioinformatic analyses of known functions of these genes indicated that formerly ascribed TAM functions, including suppression of immune activation and matrix remodeling, as well as multiple mediators of tumor angiogenesis, were elevated in TAMs. Further bioinformatic analyses confirmed that a pure and valid TAM gene expression signature in mouse tumors could be used to assess expression of TAMs in human breast cancer. The data derived from these more physiologically relevant autochthonous tumors compared with previous studies in tumor xenografts suggest tactics by which TAMs may regulate tumor angiogenesis and thus provide a basis for exploring other transcriptional mediators of TAM trophic functions within the tumor microenvironment.

Topological feature vectors for exploring topological relationships

Topological relationships between spatial objects such as overlap, disjoint, and inside have for a long time been a focus of research in a number of disciplines like cognitive science, robotics, linguistics, artificial intelligence, and spatial reasoning. In particular as predicates, they support the design of suitable query languages for spatial data retrieval and analysis in spatial database systems and Geographic Information Systems. While conceptual aspects of topological predicates (like their definition and reasoning with them) as well as strategies for avoiding unnecessary or repetitive predicate evaluations (like predicate migration and spatial index structures) have been emphasized, the development of correct and efficient implementation techniques for them has been rather neglected. Recently, the design of topological predicates for different combinations of complex spatial data types has led to a large increase of their numbers and accentuated the need for their efficient implementation. The goal of this article is to develop efficient implementation techniques of topological predicates for all combinations of the complex spatial data types point2D, line2D, and region2D, as they have been specified by different authors and in different commercial and public domain software packages. Our solution is a two‐phase approach. In the exploration phase, for a given scene of two spatial objects, all topological events like intersection and meeting situations are recorded in two precisely defined topological feature vectors (one for each argument object of a topological predicate) whose specifications are characteristic and unique for each combination of spatial data types. These vectors serve as input for the evaluation phase which analyzes the topological events and determines the Boolean result of a topological predicate or the kind of topological predicate. This paper puts an emphasis on the exploration phase and the definition of the topological feature vectors. In addition, it presents a straightforward evaluation method.

Rattle: A Data Mining GUI for R

Data mining delivers insights, pat- terns, and descriptive and predictive models from the large amounts of data available today in many organisations. The data miner draws heavily on methodologies, techniques and al- gorithms from statistics, machine learning, and computer science. R increasingly provides a powerful platform for data mining. However, scripting and programming is sometimes a chal- lenge for data analysts moving into data mining. The Rattle package provides a graphical user in- terface specifically for data mining using R. It also provides a stepping stone toward using R as a programming language for data analysis.

Cyclooxygenase-2 overexpression in ovarian endometriomas is associated with higher risk of recurrence

Cyclooxegenase-2 expression was evaluated by immunohistochemistry in endometrioma tissue samples taken from 109 patients, of whom 53 had recurrence by 30 months after surgery and 56 did not. Cyclooxegenase-2 overexpression, along with previous medical treatment of endometriosis and the presence of adhesion, is predictive of recurrence of ovarian endometrioma within 30 months after surgery, with a resultant sensitivity of 72.5% and a specificity of 72.4%, suggesting that there are intrinsic and identifiable biomarkers that confer recurrence risk.

Efficient Implementation Techniques for Topological Predicates on Complex Spatial Objects

Topological relationships like overlap, inside, meet, and disjoint uniquely characterize the relative position between objects in space. For a long time, they have been a focus of interdisciplinary research as in artificial intelligence, cognitive science, linguistics, robotics, and spatial reasoning. Especially as predicates, they support the design of suitable query languages for spatial data retrieval and analysis in spatial database systems and geographical information systems. While, to a large extent, conceptual aspects of topological predicates (like their definition and reasoning with them) as well as strategies for avoiding unnecessary or repetitive predicate executions (like predicate migration and spatial index structures) have been emphasized, the development of robust and efficient implementation techniques for them has been largely neglected. Especially the recent design of topological predicates for all combinations of complex spatial data types has resulted in a large increase of their numbers and stressed the importance of their efficient implementation. The goal of this article is to develop correct and efficient implementation techniques of topological predicates for all combinations of complex spatial data types including two-dimensional point, line, and region objects, as they have been specified by different authors and in different commercial and public domain software packages. Our solution consists of two phases. In the exploration phase, for a given scene of two spatial objects, all topological events like intersection and meeting situations are summarized in two precisely defined topological feature vectors (one for each argument object of a topological predicate) whose specifications are characteristic and unique for each combination of spatial data types. These vectors serve as input for the evaluation phase which analyzes the topological events and determines the Boolean result of a topological predicate (predicate verification) or the kind of topological predicate (predicate determination) by a formally defined method called nine-intersection matrix characterization. Besides this general evaluation method, the article presents an optimized method for predicate verification, called matrix thinning, and an optimized method for predicate determination, called minimum cost decision tree. The methods presented in this article are applicable to all known complete collections of mutually exclusive topological predicates that are formally based on the well known nine-intersection model.

New Insights Into the Diagnostic Accuracy of Complexed and Total Prostate Specific Antigen Using Discordance Analysis Characteristics

Comparison of diagnostic performances of total and complexed prostate specific antigen (tPSA, cPSA) using ROC curve analysis resulted in controversial interpretations. To overcome the biases due to analysis of subgroups selected by concentration ranges of only 1 marker the novel approach named discordance analysis characteristics is presented. DAC method includes only patients who are discordantly categorized by the tests under investigation using cutoffs with identical sensitivity. Within those patients parameters describing diagnostic accuracy are calculated. The systematic nature of the results is confirmed by varying the cutoffs. DAC method is demonstrated considering the example of cPSA and tPSA data from 2 prostate cancer studies with a total of 1,624 patients (study A and B, of 283 and 565 with as well as 417 and 359 men without prostate cancer, respectively). PSA concentrations were measured using the Bayer assays. The DAC method proved that cPSA outperformed tPSA regarding the criteria diagnostic specificity and positive predictive value. Among discordantly tested patients cPSA detected patients with an about 2-fold higher risk to have prostate cancer and with a 3.6 to 5.5-fold better specificity than tPSA. Using cPSA instead of tPSA more than 10% of unnecessary biopsies could be avoided in the tPSA range of 3 to 5 ng/ml. The superior diagnostic performance of cPSA in comparison with tPSA warrants the recommendation to use cPSA as initial test in prostate cancer diagnostics. The DAC method is generally recommended to replace comparative ROC analyses of subgroups to evaluate the diagnostic usefulness of markers.

Topological relationships between complex spatial objects

For a long time topological relationships between spatial objects have been a focus of research in a number of disciplines like artificial intelligence, cognitive science, linguistics, robotics, and spatial reasoning. Especially as predicates they support the design of suitable query languages for spatial data retrieval and analysis in spatial databases and geographical information systems (GIS). Unfortunately, they have so far only been defined for and applicable to simplified abstractions of spatial objects like single points, continuous lines, and simple regions. With the introduction of complex spatial data types an issue arises regarding the design, definition, and number of topological relationships operating on these complex types. This article closes this gap and first introduces definitions of general and versatile spatial data types for complex points , complex lines , and complex regions . Based on the well known 9-intersection model, it then determines the complete sets of mutually exclusive topological relationships for all type combinations. Completeness and mutual exclusion are shown by a proof technique called proof-by-constraint-and-drawing . Due to the resulting large numbers of predicates and the difficulty of handling them, the user is provided with the concepts of topological cluster predicates and topological predicate groups , which permit one to reduce the number of predicates to be dealt with in a user-defined and/or application-specific manner.

The S-Net System for Internet Packet Streams: Strategies for Stream Analysis and System Architecture

The traffic on an Internet link is a packet stream: packets of varying sizes arriving for transmission on the link. Each packet has an arrival time, and contained within the packet are headers that carry many critical variables. Packet traces, which consist of captured headers and measurements of the arrival times, convey substantial information about the Internet—security, usage, network performance, and the performance of engineering protocols. This article discusses strategies for the analysis of very large databases of packet traces, and the architecture of a software system that facilitates the use of these strategies. The system has a pipeline: (1) raw packet traces; (2) a database with objects tailored to ensuing analyses; and (3) an environment with tools for data analysis: statistical methods, model fitting, and visualization. The pipeline addresses the full set of tasks in the study of packet streams, from the initial processing of raw packet traces to the final output, often a visual display. S-Net—an extensible, open-source software implementation of this architecture—is based on the R implementation of the S language for graphics and data analysis, and has been developed on Linux.

Scatterplot3d- AnRPackage for Visualizing Multivariate Data

Scatterplot3d is an R package for the visualization of multivariate data in a three dimensional space. R is a "language for data analysis and graphics". In this paper we discuss the features of the package. It is designed by exclusively making use of already existing functions of R and its graphics system and thus shows the extensibility of the R graphics system. Additionally some examples on generated and real world data are provided.

An integration of GIS, virtual reality and the Internet for visualization, analysis and exploration of spatial data

This paper explores the way in which GIS, Virtual Reality (VR) and the Internet are closely integrated through the link of Virtual Reality Modelling Language (VRML) for spatial data visualization, analysis and exploration. Integration takes advantage of each component, and enables the dynamic 3D content to be built, visualized, interacted with and deployed all on the Web. To accomplish this, a hybrid approach that merges the conventional client-side and server-side methods is proposed, which offers the best of both worlds in terms of flexibility and capability, as well as the rational use of computing resources. Based on this approach, a Web-based prototype toolkit is designed and implemented by using an affordable desktop GIS through its macro language together with Java, Common Gateway Interface (CGI) and HTML programming. This toolkit comprises a 3D visualization tool, a 3D analysis tool, and a Java/VRML interface, which are respectively used for the creation of VRML models from 2D maps, surface analysis (e.g. profile creation and visibility analysis), and interaction (e.g. selecting and querying) with the output VRML worlds of 3D visualization and analysis. It is demonstrated that this toolkit provides an integrated environment, facilitating users to gain insights from the interaction with virtual environments that are built from existing GIS databases.

Languages for Statistics and Data Analysis

Languages for data analysis and statistics must be able to cover the entire spectrum from improvisation and fast prototyping to the implementation of streamlined, specialized systems for routine analyses. Such languages must not only be interactive but also programmable, and the distinctions between language, operating system, and user interface get blurred. The issues are discussed in the context of natural and computer languages, and of the different types of user interfaces (menu, command language, batch). It is argued that while such languages must have a completely general computing language kernel, they will contain surprisingly few items specific to data analysis—the latter items more properly belong to the “literature” (i.e., the programs) written in the language.

Languages for Statistics and Data Analysis

Languages for Statistics and Data Analysis

Using the R statistical data analysis language on GRASS 5.0 GIS database files

Many researchers wish to explore and analyse spatial data, but typical software does not readily permit such integration. This paper presents a simple interface between two open-source software systems, the GRASS geographical information system, and the R statistical data analysis language. The platform used here is GNU/Linux, because both systems compile and install cleanly; R runs cleanly in Windows environments as well. The interface allows floating point and category data to be passed both ways for raster map layers and sites files; NULL raster cells in GRASS interchange with NA (not available) values in R. Because both systems are developing rapidly and GRASS database internals change often, the interface uses ASCII transfer via temporary files generated by standard programs. The interface operates by running R from within the GRASS environment, and issues commands to GRASS programs through the R system( ) function. The accompanying code is constructed as an R package, and contains wrapper functions for R plotting, and for R analytical functions returning gridded output, such as trend surface and kriging prediction, kernel density estimation of point patterns, and bicubic spline interpolation. These typical spatial analytical techniques, also often available in some form in GIS, are amply buttressed in R by a large range of other statistical and graphical functions, giving substantial insight into the data or results being handled. The interface will be extended to vector data, and will be coordinated with other database integration packages in R and GRASS.

XGobi: Interactive Dynamic Data Visualization in the X Window System

XGobi is a data visualization system with state-of-the-art interactive and dynamic methods for the manipulation of views of data. It implements 2-D displays of projections of points and lines in high-dimensional spaces, as well as parallel coordinate displays and textual views thereof. Projection tools include dotplots of single variables, plots of pairs of variables, 3-D data rotations, various grand tours, and interactive projection pursuit. Views of the data can be reshaped. Points can be labeled and brushed with glyphs and colors. Lines can be edited and colored. Several XGobi processes can be run simultaneously and linked for labeling, brushing, and sharing of projections. Missing data are accommodated and their patterns can be examined; multiple imputations can be given to XGobi for rapid visual diagnostics. XGobi includes an extensive online help facility. XGobi can be integrated in other software systems, as has been done for the data analysis language S, the geographic information system (GIS) Arc View™, and the interactive multidimensional scaling program XGvis. XGobi is implemented in the X Window System™ for portability as well as the ability to run across a network.

Composite regions in topological queries

Spatial data are at the core of many scientific information systems. The design of suitable query languages for spatial data retrieval and analysis is still an issue on the cutting edge of research. The primary requirement of these languages is to support spatial operators. Unfortunately, current systems support only simplified abstractions of geographic objects based on simple regions which are usually not sufficient to deal with the complexity of the geographic reality. Composite regions, which are regions made up of several components, are necessary to overcome those limits. The paper introduces a two-level formal model suitable for representing topological relationships among composite regions. The contribution gives the needed formal background for adding composite regions inside a spatial query language with the purpose of answering topological queries on complex geographic objects.

Analysis and visualization tools in CFD, part I: A configurable data extraction environment

The objective is to present new ideas for the implementation of visualization and analysis environments. This is carried out with a software interface allowing the design and configuration of project-specific environments built around a core library that performs all the data extraction and manipulation. This includes processing of solutions for rendering as well as for extraction of flow features for active control on the solution procedure. While the first function is highly interactive, the second is usually a batch oriented process coupled to the numerical algorithm. To achieve this goal, it is necessary to interpret solution data in a generic sense. The grid, the primary variables of the problem, and the derived variables are all considered as a number of simple scalar (discrete) fields defined on the domain. Basic entities in the library then provide building blocks to create images for rendering purposes or new fields as required in the grid adaption control loop. A data analysis language has been created. Its entities and grammar are oriented towards the description of both the rendering and the analysis processes. This customized environment is saved in an user configuration file, with an easily understandable syntax, which is loaded at execution time, hence providing the proper configuration for each application.

The Twotran data acquisition and analysis language

A language for specifying the data acquisition and initial-event rejection requirements of experiments using the TRIUMF VAX-based CAMAC data acquisition system has been designed and implemented. Terse, low-level, assembler-like syntax was rejected in favor of a form more familiar to physicists, namely Fortran. The language, known as Twotran, is an extended subset of Fortran. A description is given of the design of the language, from its earliest inception to its present state, and of the interfacing of the language-processing support to the remainder of the data acquisition system.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>

Microcomputer System Design in the UCSD Pascal Programming Environment

ABSTRACT The potential of UCSD Pascal as a programming language for data acquisition and analysis was investigated. Cyclic voltammetry and chronoamperometry were automated by interfacing a BAS CV-27 potentiostat to an Apple II+ microcomputer. With the UCSD Pascal programming language, a modular approach was taken to solve our system design problem. Thus, smaller programs and library UNITs were written that collectively tackled a relevant electro-analytical problem. Here we focus on a modular approach to system design by discussing software techniques and applying them to the analysis of polymer modified electrode experiments. Additional conclusions relate this approach to other microcomputers, programming languages, and system designs.

Design of the S System for Data Analysis*

S is a language and system for interactive data analysis and graphics. It emphasizes interactive analysis and graphics, ease of use, flexibility, and extensibility. While sharing many characteristics with other statistical systems, S differs significantly in its design goals, its implementation, and the way it is used. This paper presents some of the design concepts and implementation techniques in S and relates these general ideas in computing to the specific design goals for S and to other statistical systems.