Framework For Quantitative Analysis Research Articles

Correlation Functions Provide a Universal Framework for Quantitative Analysis of Localization-Based Super-Resolution Microscopy Images

Super-resolution images reconstructed from single molecule coordinates reveal cellular structures close to the macromolecular scale. However, a widely applicable analysis tool that can extract a quantitative description and biophysical parameters from these images is still unavailable. Here, we propose a universal analysis concept for coordinate-based super-resolution images using correlation functions. We demonstrate how this analysis can quantify diffusion, localization precision, distance and co-localization. Moreover, we developed a framework for averaging multiple images by non-linear transformations to reveal structures with much higher resolution.First, we show that the commonly used pair-distance histogram is mathematically equivalent to pixel-based correlation analysis. Therefore, many strategies of pixel-based image correlation spectroscopy can also be applied to coordinate-based super-resolution images. In particular, the computational complexity of pair-distance calculations can be decreased by pixel-binning the coordinate image and employing the Fast Fourier Transform algorithm.Second, we demonstrate that the pair-distance histogram of molecule coordinates from consecutive frames allows measuring the diffusion coefficient of membrane lipids in live cells with high spatial resolution. Our analysis can handle extremely high fluorophore densities, in contrast to conventional single-particle tracking methods. The same frame-pair histogram can analogously be used to generate a map of molecule localization precision for super-resolution images, which is still elusive information.Third, we show how coordinate-based correlation functions can be used for image alignment involving transformations beyond translation. For example, we rotationally aligned multiple images of the nuclear pore complex from yeast, which exposes the octagonal complex with high precision.Finally, we propose a new correlation function, namely the point-set distance histogram, which allowed us to quantify both co-localization and distance of Clathrin to proteins of the Golgi apparatus, even though the super-resolution images were highly corrupted by background and two-color crosstalk.

USING ATLAS OF HEART SHAPES FOR SIMULATION OF BLOOD FLOW IN LEFT VENTRICLE

Integrative modeling of cardiac system is important for understanding the complex biophysical function of the heart]. To this end, multimodal cardiovascular imaging plays an important role in providing the computational domain, the boundary/initial conditions, and tissue function and properties. In particular, the incorporation of blood flow in the physiological models can help to simulate the hemodynamic properties and their effects on cardiac function. In this paper, we present a multimodal framework for quantitative and subject-specific analysis of blood flow in the cardiac chambers, including the left ventricle (LV). The 3D geometries of the LV at different time steps are extracted from medical images using an atlas of LV shape. The motion of the myocardium wall is used to extract the moving boundary data of the computational geometry. The data is used as a constraint for the computational fluid dynamics (CFD). An arbitrary Lagrangian–Eulerian (ALE) finite element method (FEM) formulation is used to derive a numerical solution of the transient dynamic equation of the fluid domain. With this method, simulation results describe detailed flow characteristics (such as velocity, pressure and wall shear stress) in the computational domain. The personalized hemodynamic characteristics obtained with the proposed approach can provide clinical value for diagnosis and treatment of abnormalities related to disturbed blood flow such as in myocardial remodeling and aortic sinus lesion formation.

The role of flaw size and fiber distribution on tensile ductility of PVA-ECC

Polyvinyl Alcohol-Engineered Cementitious Composites (PVA-ECC) designed based on micromechanics exhibit high tensile ductility (above 1%) and limited crack widths (below 100μm). The tensile performance of ECC is dependent on the fiber and flaw size distributions. These parameters are known to be influenced by the matrix flowability and mix processing; however, a comprehensive quantitative analysis framework linking fiber and flaw size distributions to the tensile performance of PVA-ECC is needed to supplement theoretical understanding of the relationship between micromechanical parameters and composite macro-properties. In the present work, fiber distribution (dispersion and orientation) of two different ECCs in terms of matrix flowability was investigated using fluorescence microscopy and advanced digital image analysis. The maximum flaw size distribution along the specimens was also analyzed by cross-sectional image analysis. The influences of fiber and flaw size distributions on the composite behavior of PVA-ECCs were experimentally established.

Cultural references in translation: a framework for quantitative translation analysis

Research into the translation of cultural references (CRs) often focuses on the analysis of selected CR translations or particular lexical sub-fields such as proper names or geographical terms. In most cases the procedures the translator has used are described and labeled, then critically evaluated and/or used to identify ‘foreignization’ or ‘domestication’ tendencies in the translator's approach to handling the cultural load of a text. This article argues that selective analysis of this kind may give undue weight to the selected examples or lexical sub-fields while ignoring other items. The article will therefore put forward that the validity of studies, especially those featuring a comparative element, could be enhanced by complementing selective and focused approaches with more comprehensive quantitative data. An empirical study which explored CR translation from a quantitative perspective will be described as an example to suggest a framework of quantitative analysis in CR translation and issues arising from the study will be discussed.

Quantitative set analysis for gene expression: a method to quantify gene set differential expression including gene-gene correlations

Enrichment analysis of gene sets is a popular approach that provides a functional interpretation of genome-wide expression data. Existing tests are affected by inter-gene correlations, resulting in a high Type I error. The most widely used test, Gene Set Enrichment Analysis, relies on computationally intensive permutations of sample labels to generate a null distribution that preserves gene–gene correlations. A more recent approach, CAMERA, attempts to correct for these correlations by estimating a variance inflation factor directly from the data. Although these methods generate P-values for detecting gene set activity, they are unable to produce confidence intervals or allow for post hoc comparisons. We have developed a new computational framework for Quantitative Set Analysis of Gene Expression (QuSAGE). QuSAGE accounts for inter-gene correlations, improves the estimation of the variance inflation factor and, rather than evaluating the deviation from a null hypothesis with a P-value, it quantifies gene-set activity with a complete probability density function. From this probability density function, P-values and confidence intervals can be extracted and post hoc analysis can be carried out while maintaining statistical traceability. Compared with Gene Set Enrichment Analysis and CAMERA, QuSAGE exhibits better sensitivity and specificity on real data profiling the response to interferon therapy (in chronic Hepatitis C virus patients) and Influenza A virus infection. QuSAGE is available as an R package, which includes the core functions for the method as well as functions to plot and visualize the results.

Sensitivity-based uncertainty analysis of a combined travel demand model

Travel demand forecasting is subject to great uncertainties. A systematic uncertainty analysis can provide insights into the level of confidence on the model outputs, and also identify critical sources of uncertainty for enhancing the robustness of the travel demand model. In this paper, we develop a systematic framework for quantitative uncertainty analysis of a combined travel demand model (CTDM) using the analytical sensitivity-based method. The CTDM overcomes limitations of the sequential four-step procedure since it is based on a single unifying rationale. The analytical sensitivity-based method requires less computational effort than the sampling-based method. Meanwhile, the uncertainties stemming from inputs and parameters can be treated separately so that the individual and collective effects of uncertainty on the outputs can be clearly assessed and quantified. Numerical examples are finally used to demonstrate the proposed sensitivity-based uncertainty analysis method for the CTDM.

Rational Engineering Principles in Synthetic Biology: A Framework for Quantitative Analysis and an Initial Assessment

The term “synthetic biology” is a popular label of an emerging biotechnological field with strong claims to robustness, modularity, and controlled construction, finally enabling the creation of new organisms. Although the research community is heterogeneous, it advocates a common denominator that seems to define this field: the principles of rational engineering. However, it still remains unclear to what extent rational engineering—rather than “tinkering” or the usage of random based or non-rational processes—actually constitutes the basis for the techniques of synthetic biology. In this article, we present the results of a quantitative bibliometric analysis of the realized extent of rational engineering in synthetic biology. In our analysis, we examine three issues: (1) We evaluate whether work at three levels of synthetic biology (parts, devices, and systems) is consistent with the principles of rational engineering. (2) We estimate the extent of rational engineering in synthetic biology laboratory practice by an evaluation of publications in synthetic biology. (3) We examine the methodological specialization in rational engineering of authors in synthetic biology. Our analysis demonstrates that rational engineering is prevalent in about half of the articles related to synthetic biology. Interestingly, in recent years the relative number of respective publications has decreased. Despite its prominent role among the claims of synthetic biology, rational engineering has not yet entirely replaced biotechnological methods based on “tinkering” and non-rational principles.

Sensitivity-based Uncertainty Analysis of a Combined Travel Demand Model

Travel demand forecasting is subject to great uncertainties. A systematic uncertainty analysis can provide insights into the level of confidence on the model outputs, and also identify critical sources of uncertainty for enhancing the robustness of the travel demand model. In this paper, we develop a systematic framework for quantitative uncertainty analysis of a combined travel demand model (CTDM) using the analytical sensitivity- based method. The CTDM overcomes limitations of the sequential four-step procedure since it is based on a single unifying rationale. The analytical sensitivity-based method requires less computational effort than the sampling-based method. Meanwhile, the uncertainties stemming from inputs and parameters can be treated separately so that the individual and collective effects of uncertainty on the outputs can be clearly assessed and quantified. Numerical examples are finally used to demonstrate the proposed sensitivity-based uncertainty analysis method for the CTDM.

Computer-Aided Detection and Diagnosis in Medical Imaging

Computer-Aided Detection and Diagnosis in Medical Imaging

Volume-Rendering-Based Interactive 3D Measurement for Quantitative Analysis of 3D Medical Images

3D medical images are widely used to assist diagnosis and surgical planning in clinical applications, where quantitative measurement of interesting objects in the image is of great importance. Volume rendering is widely used for qualitative visualization of 3D medical images. In this paper, we introduce a volume-rendering-based interactive 3D measurement framework for quantitative analysis of 3D medical images. In the framework, 3D widgets and volume clipping are integrated with volume rendering. Specifically, 3D plane widgets are manipulated to clip the volume to expose interesting objects. 3D plane widgets, 3D line widgets, and 3D angle widgets are then manipulated to measure the areas, distances, and angles of interesting objects. The methodology of the proposed framework is described. Experimental results indicate the performance of the interactive 3D measurement framework.

Application of GIS in Quantifying the Urban Form-A Case Study of Shanghai

This paper proposes a framework of quantitative analysis of urban form based on GIS and reports an empirical study of Shanghai city to investigate the evolutional characteristics of urban form. By using ERDAS IMAGINE and GIS, the spatial form characteristics of Shanghai has been extracted based on a series of Landsat TM and ETM imagery over the period from 1982 to 2008; by combining fractal dimension theory, compactness ratio theory, space syntax theory etc with the spatial analysis technology of GIS, the urban form characteristics of Shanghai has been analyzed quantitatively in terms of urban external shape, urban internal structure, urban population size and urban transportation. Practice has proved that the combination of GIS with the theories of fractal dimension and space syntax etc can not only help to learn the principals of urban nature but also can explore the intrinsic interactive mechanism of geographic entities by deeply mining the spatial data.

An Inquiry into the Existence and Uniqueness of Equilibrium with State-Dependent Pricing

State-dependent pricing models are now an operational framework for quantitative business cycle analysis. The analysis in Ball and Romer (1991), however, suggests that such models may be rife with multiple equilibria: in their static model price adjustment is always characterized by complementarity, a necessary condition for multiplicity. We study existence and uniqueness of equilibrium in a discrete-time state-dependent pricing model. In steady states of our model, we find only weak complementarity and no evidence of multiplicity. We likewise find no evidence of multiplicity in the presence of monetary shocks. However, nonexistence of symmetric steady-state equilibrium with pure strategies arises in a small region of the parameter space.

An Overview of Compulsory Land Acquisition in Ghana: Examining Its Applicability and Effects

In Ghana, to ensure life that is sustainable now and in the future, the government need to provide basic infrastructures that will promote economic, cultural, health and social wellbeing of its citizens. For this development to take place the government need to acquire land that will act as a platform for such interventions. Whereas in the country, land ownership is guaranteed in the lordship of customary interest, the state has no option than to employ eminent domain to acquire private rights in land without complete accepted agreement from the owners for societal benefit. The framework within which implementing organisations in the country carry out the processes is highly appalling and has resulted in detrimental outcomes. The application of compulsory acquisition in the country has led to undermine the principles of good governance. The need to strictly adhere to the rules and procedures of the legislative tool and also inadequate payment of compensation has become obvious and apparent. Considering these intricacies and complications involved in the compulsory acquisition process in the country requires some perceptible revision that will promote good practices among governments at local, regional and national level. The methodology applied for this paper was drawing on pragmatic and realistic studies pertaining to compulsory acquisition in Ghana through qualitative and quantitative analytical framework. The research design used for the research was the case study approach to put the study in context. Study difficulties as well as wide-ranging nature of research were taken into consideration in employing this approach. The research focused on how compulsory acquisition has been applied in Ghana. Issues considered include principles underpinning the legislative tool, argument in support and against compulsory acquisition. It also goes on to discuss the pattern of land ownership in Ghana and procedures for exercising compulsory acquisition. Lastly, this paper also puts much emphasis on how lands acquired by the government of Ghana have been utilised. Characteristically, compulsory acquisition in the Ghana can be described as disturbing and disruptive. This is highly manifested particularly from the ownership structure of land occupied by customary tenure. The study reveals some bottlenecks in the processes and procedures of land acquisition where involvement of land owners at the initial stage is missing. An inventory of land acquired in Central Region (Ghana) showed that about 82% of land size acquired by the state did not follow proper executive instruments. Also about 44% of lands acquired by the state have not been utilised. These implications have resulted in non-payment of fair and equitable compensation and states land been encroached. Effective determination of appropriate compensation, protection of government lands through proper safeguarding mechanisms, development of unused lands and strictly adhering to the spelt out policies governing compulsory acquisition in the country could help eliminate, if not reduce its associated impacts.

Mass-Balance Effects In Depositional Systems

Abstract Net deposition is necessarily accompanied by overall loss of sediment mass from the transport system; on long time scales the deposition compensates for subsidence and creates the stratigraphic record. Although its spatial pattern changes and it can be locally stopped or reversed, depositional mass loss is a fundamental driving influence on the morphology and behavior of depositional systems. Mass extraction to deposition leads directly to facies changes as sediment flux declines; indirectly it usually leads to down-channel sediment fining as deposition preferentially removes coarser particles. Laboratory experiments illustrate the effects of systematic mass extraction on fluvial channel stacking and deposit grain size, and show how a mass-balance framework allows consistent comparison of facies despite major shifts in depocenter location. Mass-balance analysis of experimental fluvial and turbidite systems, and a turbidite mini-basin from the Gulf of Mexico, show a change from channel-dominated to lobe-dominated deposits at about 80% total mass extraction. Experimental and field studies also show a close connection between rate of mass loss and rate of downstream grain-size fining, as predicted by a mechanistic theory based on mass balance. These are first steps towards a framework for quantitative basin analysis based on mass extraction. A mass-balance framework allows for consistent, quantitative comparison across basins of varying scale and shape. Mass-balance frameworks can account for overall and/or generic mass-balance effects, and help separate them from local effects. One way to use such generalized models effectively is to view the results as reference cases of down-transport change resulting from the basic interplay of spatial mass-extraction pattern and sediment supply. Where such reference cases do not provide detailed predictions of specific field cases, they can still provide a baseline to separate local, case-specific features from generic system behavior. The approach is analogous to the way the geoid serves as a reference case against which to measure gravity anomalies.

A System Dynamic Model for the Environmental Performance Index of Malaysia

The Third Principle which is pertaining to the right to development in Agenda 21 of the Rio Declaration or Earth Summit asserts that it must be fulfilled so that development must be sustainable which has been defined as development that meets the needs of the present without compromising the ability of future generations to meet their own need. Among the various models of environmental sustainability comparative studies was the Environmental Performance Index (EPI) model. Malaysia was ranked 54 recording a score of 65 and ranked 10 among the Asia and Pacific Countries behind two ASEAN countries: Singapore and Philippines. The environmental indicators from 2010 EPI was therefore used to develop the System Dynamics Simulation Model to provide the framework and procedure for qualitative and quantitative description, exploration and analysis of the systems in terms of their processes, information boundaries and strategies, facilitating quantitative simulation modeling for policy evaluation and predictions pertinent to sustainability. The System Dynamic Simulation Model developed for the EPI of Malaysia changed the static presentation to a dynamic scenario. Two very important components were considered: the contribution and the impact of population and the industrial activities indicated as the Industrial Productivity Index. The simulated EPI of 66.51 was shown to differ slightly from the EPI 2010 of 65 attributed to the inclusion of the population and the industrial production factors in the system dynamic model, in which the later study did not compute the EPI with respect to the two factors. Thus, the System Dynamic Simulation Model developed has shown to be reliable and be used for any country to simulate EPI for future trends.

Atlas-based analysis of resting-state functional connectivity: Evaluation for reproducibility and multi-modal anatomy–function correlation studies

Resting state functional connectivity MRI (rsfc-MRI) reveals a wealth of information about the functional organization of the brain, but poses unique challenges for quantitative image analysis, mostly related to the large number of voxels with low signal-to-noise ratios. In this study, we tested the idea of using a prior spatial parcellation of the entire brain into various structural units, to perform an analysis on a structure-by-structure, rather than voxel-by-voxel, basis. This analysis, based upon atlas parcels, potentially offers enhanced SNR and reproducibility, and can be used as a common anatomical framework for cross-modality and cross-subject quantitative analysis. We used Large Deformation Diffeomorphic Metric Mapping (LDDMM) and a deformable brain atlas to parcel each brain into 185 regions. To investigate the precision of the cross-subject analysis, we computed inter-parcel correlations in 20 participants, each of whom was scanned twice, as well as the consistency of the connectivity patterns inter- and intra-subject, and the intersession reproducibility. We report significant inter-parcel correlations consistent with previous findings, and high test-retest reliability, an important consideration when the goal is to compare clinical populations. As an example of the cross-modality analysis, correlation with anatomical connectivity is also examined.

MsCompare: A Framework for Quantitative Analysis of Label-free LC-MS Data for Comparative Candidate Biomarker Studies

Data processing forms an integral part of biomarker discovery and contributes significantly to the ultimate result. To compare and evaluate various publicly available open source label-free data processing workflows, we developed msCompare, a modular framework that allows the arbitrary combination of different feature detection/quantification and alignment/matching algorithms in conjunction with a novel scoring method to evaluate their overall performance. We used msCompare to assess the performance of workflows built from modules of publicly available data processing packages such as SuperHirn, OpenMS, and MZmine and our in-house developed modules on peptide-spiked urine and trypsin-digested cerebrospinal fluid (CSF) samples. We found that the quality of results varied greatly among workflows, and interestingly, heterogeneous combinations of algorithms often performed better than the homogenous workflows. Our scoring method showed that the union of feature matrices of different workflows outperformed the original homogenous workflows in some cases. msCompare is open source software (https://trac.nbic.nl/mscompare), and we provide a web-based data processing service for our framework by integration into the Galaxy server of the Netherlands Bioinformatics Center (http://galaxy.nbic.nl/galaxy) to allow scientists to determine which combination of modules provides the most accurate processing for their particular LC-MS data sets.

반도체 산업에서 정량적인 소프트웨어 개발 능력 측정 및 분석을 위한 프레임워크

본 논문은 반도체 사업의 하나인 SoC에서 소프트웨어의 특성을 바탕으로 정량적인 소프트웨어 개발 능력을 측정하고 분석하기 위한 프레임워크를 제시한다. 본 논문에서는 이론적 모델(능력 피라미드) 뿐만아니라 SoC 임베디드 소프트웨어의 특성에 기반을 둔 측정 모델을 제안한다. 정량적인 소프트웨어 개발 능력 측정은 단지 지표를 수집하는 것만이 아니라 수집된 지표의 품질, 비용, 납기(QCD)를 분석하는데, 외부적으로는 프로그래머가 고객의 요구를 만족하는 소프트웨어를 개발할 수 있게 해주고, 내부적으로는 가시적인 생산성의 증가로 좀 더 효율적인 소프트웨어개발이 가능하게 해준다. 제안된 프레임워크를 사용하여, 논문에서는 정량적으로 임베디드 소프트웨어 개발 능력을 측정한다. This paper presents a framework for quantitative software development performance measurement and analysis based on characteristics of software in System on Chip (SoC) industry, one of the semiconductor businesses. In this paper, we propose a measurement model based on not only theoretical model (Performance Pyramid) but also characteristics of SoC embedded software. Quantitative software development performance measurement is not just collecting indicators but analyzing quality, cost, and delivery (QCD) of collected indicators. Externally, it is possible for programmers to develop software meeting customers' needs. Internally, more efficient software development can be possible through the visible productivity increase. Using the proposed framework, the paper quantitatively measures embedded software development performance.

Influence fields: a quantitative framework for representation and analysis of active dendrites

Neuronal dendrites express numerous voltage-gated ion channels (VGICs), typically with spatial gradients in their densities and properties. Dendritic VGICs, their gradients, and their plasticity endow neurons with information processing capabilities that are higher than those of neurons with passive dendrites. Despite this, frameworks that incorporate dendritic VGICs and their plasticity into neurophysiological and learning theory models have been far and few. Here, we develop a generalized quantitative framework to analyze the extent of influence of a spatially localized VGIC conductance on different physiological properties along the entire stretch of a neuron. Employing this framework, we show that the extent of influence of a VGIC conductance is largely independent of the conductance magnitude but is heavily dependent on the specific physiological property and background conductances. Morphologically, our analyses demonstrate that the influences of different VGIC conductances located on an oblique dendrite are confined within that oblique dendrite, thus providing further credence to the postulate that dendritic branches act as independent computational units. Furthermore, distinguishing between active and passive propagation of signals within a neuron, we demonstrate that the influence of a VGIC conductance is spatially confined only when propagation is active. Finally, we reconstruct functional gradients from VGIC conductance gradients using influence fields and demonstrate that the cumulative contribution of VGIC conductances in adjacent compartments plays a critical role in determining physiological properties at a given location. We suggest that our framework provides a quantitative basis for unraveling the roles of dendritic VGICs and their plasticity in neural coding, learning, and homeostasis.

An Approach to Carbon Dioxide Particle Distribution in Accidental Releases

The main problem in calculating the consequences of a carbon dioxide dispersion following an accidental release is the formation of solid CO2 during the expansion to ambient pressure. The dispersion models more frequently used in the framework of quantitative risk analysis, cannot describe the carbon dioxide behaviour, in particular with respect to the calculation of the rainout fraction. Moreover, only scarce data is available for two phase CO2 releases. In the present study, a specific approach was developed to calculate the particle size distribution following the release of pressurized liquid (or supercritical) CO2. The approach combines several submodels accounting for the different mechanisms of jet break-up and specifically addresses the possible formation of solid particles. The model was validated using experimental data available for CO2 and for the release of other pressurised, superheated liquids. The model developed can find further applications in rain-out calculations for two-phase releases of conventional substances. Copyright © 2012, AIDIC Servizi S.r.l.