Computer Program For Analysis Research Articles

DIPANALYST: A computer program for quantitative kinematic analysis of rock slope failures

Kinematic analysis is used to analyze the potential for the various modes of structurally controlled rock slope failures (plane, wedge, and toppling failures) due to the presence of unfavorably oriented discontinuities. Traditionally kinematic analysis is performed after plotting discontinuity orientations, slope angle, slope azimuth and representative friction angle value on a stereonet. Due to large number of discontinuities, only representative orientation values (dip/dip direction) for identified cluster sets are considered. This stereonet-based analysis is qualitative in nature and requires the presence of tight data clusters for which a reasonable representative orientation value can be assigned. However, there are cases when a tight circular clustering of discontinuity orientations does not exist, making stereonet-based analysis unreliable. Also, variability of discontinuity data in cluster sets is not easy to consider using the stereonet-based method.To overcome these problems, an application software, DIPANALYST, has been developed by the first author to perform quantitative kinematic analysis based on not just representative discontinuity values, but all discontinuities and their possible intersections. The software calculates ratios of discontinuities or their possible intersections that can potentially cause failures (plane, wedge or toppling) to the total number of discontinuities or their possible intersections. The calculated ratios are known as failure indices, and the method is termed as the quantitative approach for kinematic analysis. DIPANALYST is also capable of performing the traditional stereonet-based method.

Deficiency of Growth Factor Midkine Exacerbates Necrotizing Glomerular Injuries in Progressive Glomerulonephritis

Inflammatory cell infiltration and fibrin deposition play important roles in the development of crescentic glomerulonephritis (GN). In particular, activation of coagulation is an indispensable factor in crescent formation. However, the mechanisms underlying the pathogenesis of crescent formation have not been completely elucidated. We identified the growth factor midkine (MK) as a novel key molecule in the progression of crescentic GN induced by anti-glomerular basement membrane antibody. Despite the lack of significant differences in autologous and heterologous reactions, MK-deficient (Mdk(-/-)) mice unexpectedly showed a greater number of necrotizing glomerular injuries than wild-type (Mdk(+/+)) mice. Likewise, more tubulointerstitial damage was observed in Mdk(-/-) mice, and this damage positively correlated with glomerular injury. Plasminogen activator inhibitor (PAI)-1 was strongly induced in the injured glomerulus of Mdk(-/-) mice, particularly in crescents and endothelial cells. This enhanced PAI-1 production was associated with an increase in inflammatory cell infiltration and matrix deposition in the glomerulus and the interstitium of Mdk(-/-) mice. In line with these invivo data, primary cultured endothelial cells derived from Mdk(-/-) mice exhibited higher PAI-1 mRNA expression on fibrin challenge and less fibrinolysis than Mdk(+/+) mice. In contrast, the expression of plasminogen activators was not affected. Our combined data suggest that MK leads to a blockade of PAI-1, which is closely associated with the suppression of crescentic GN.

An alternative solution method for the damped response of laminated Mindlin plates

The present study aims to investigate the damped response of laminated Mindlin plates subjected to dynamic loads. The solutions of damped response of anti-symmetric, cross-ply and angle-ply laminates have been obtained by FEM in conjunction with the Laplace transform method using the first order shear deformation theory. The governing equations of motion of the problem are first obtained in the time domain. Subsequently, Laplace transform is applied and the linear algebraic equations are solved numerically. Materials of the laminates are assumed to be linear elastic or viscoelastic. In the viscoelastic material case the Kelvin model is employed. According to the correspondence principle the material constants are replaced with their complex counterparts in the Laplace domain. Therefore, the presented model incorporates damping very easily in the transformed domain. The solutions obtained are transformed to the time domain using the modified Durbin’s numerical inverse Laplace transform method. For the suggested model, a general-purpose finite element analysis computer program is coded. Verification of the numerical procedure is performed by comparing the results of present method with semi-analytical results available in the literature. Obtaining the equation first discretely in the time domain using FEM and then applying the Laplace transform has proved to be a procedure highly accurate and efficient compared to other numerical methods available in the literature.

Maximum sustainable yield estimates of spiny lobster fishery in Pakistan using non-equilibrium CEDA package

Maximum sustainable yield estimates of spiny lobster fishery were analyzed using catch effort data analysis (CEDA) computer programme. The major parameters of this package are: Maximum sustainable yield (MSY), catchability coefficient (q) carrying capacity (K), intrinsic growth rate (r), Replacement yield and Final population. CEDA has ability to assess the parameters of Fox, Schaefer and PellaTomlinson mod� els. In addition it has an ability to estimate three error assumptions i.e. normal, log normal and gamma. In this study, the Maximum sustainable yield outputs of three models of Fox, Schaefer and PellaTomlinson are: 828 t, 970 t and 970 t respectively. The outputs of error assumption of normal and log normal are 983 t (R 2 = 0.57) and 950 t (R 2 = 0.53) in Schaefer and PellaTomlinson models respectively. MSY outputs of normal error assumption of Fox are 817 t (R 2 = 0.56). All the gamma error assumptions are (790 t) similar. The coef� ficient of variation (cv) of the estimated MSY was about 0.7 and the larger value (1.0) whereas lowest (0.5) were recorded. The Fox model output are more conservative hence the best fits and is close to the annual aver� age landings of the spiny lobster fishery in Pakistan.

Leaf Area Assessment By Image Analysis

A measurement of leaf area is apparently simple and fundamental. Various methods are available to measure leaf area. Available methods are time consuming, humdrum and laborious. Less expensive methods involving image processing based on video camera images and computer programs for analysis of these images have been alternative for all other techniques for leaf area assessment. In this paper we introduce a computer program that can calculate leaf area meter based on the pixel count in very short time and highly accurate by image processing. This program provides very fast, inexpensive and highly accurate measurement.

MRI profile and response to endovascular reperfusion after stroke (DEFUSE 2): a prospective cohort study

Whether endovascular stroke treatment improves clinical outcomes is unclear because of the paucity of data from randomised placebo-controlled trials. We aimed to establish whether MRI can be used to identify patients who are most likely to benefit from endovascular reperfusion. In this prospective cohort study we consecutively enrolled patients scheduled to have endovascular treatment within 12 h of onset of stroke at eight centres in the USA and one in Austria. Aided by an automated image analysis computer program, investigators interpreted a baseline MRI scan taken before treatment to establish whether the patient had an MRI profile (target mismatch) that suggested salvageable tissue was present. Reperfusion was assessed on an early follow-up MRI scan (within 12 h of the revascularisation procedure) and defined as a more than 50% reduction in the volume of the lesion from baseline on perfusion-weighted MRI. The primary outcome was favourable clinical response, defined as an improvement of 8 or more on the National Institutes of Health Stroke Scale between baseline and day 30 or a score of 0-1 at day 30. The secondary clinical endpoint was good functional outcome, defined as a modified Rankin scale score of 2 or less at day 90. Analyses were adjusted for imbalances in baseline predictors of outcome. Investigators assessing outcomes were masked to baseline data. 138 patients were enrolled. 110 patients had catheter angiography and of these 104 had an MRI profile and 99 could be assessed for reperfusion. 46 of 78 (59%) patients with target mismatch and 12 of 21 (57%) patients without target mismatch had reperfusion after endovascular treatment. The adjusted odds ratio (OR) for favourable clinical response associated with reperfusion was 8·8 (95% CI 2·7-29·0) in the target mismatch group and 0·2 (0·0-1·6) in the no target mismatch group (p=0·003 for difference between ORs). Reperfusion was associated with increased good functional outcome at 90 days (OR 4·0, 95% CI 1·3-12·2) in the target mismatch group, but not in the no target mismatch group (1·9, 0·2-18·7). Target mismatch patients who had early reperfusion after endovascular stroke treatment had more favourable clinical outcomes. No association between reperfusion and favourable outcomes was present in patients without target mismatch. Our data suggest that a randomised controlled trial of endovascular treatment for patients with the target mismatch profile is warranted. National Institute for Neurological Disorders and Stroke.

Thinking music with precision, depth, and passion

This text contains Mazzola's answers to the four questions proposed by Anja Volk and Aline Honingh about benefits of mathematical approaches to the field of music research, pitfalls that occurred within computational and/or mathematical approaches to music research, challenges we are facing now within computational and/or mathematical approaches to music, and how can we strengthen the connections between the three fields of mathematical, computational, and musicological approaches to music. My answers are given from the point of view of mathematical music theory and corresponding computer programs for analysis, composition, and performance.

압출추진코와 ILM 교량 상부구조 상호작용 해석식의 단순화

압출공법(incremental launching method)은 교대 배후에 거더 제작장소를 설치하고, 콘크리트를 이어쳐서 교량거더를 제작하고, 이것을 잭(jack)으로 밀어내는 가설방법이다. 이 공법에 의해 시공되는 교량의 상부단면은 시공 중에 지간의 중앙부와 지점부에 일시적이나마 모두 위치하게 된다. 따라서 단면들은 자중에 의해 발생되는 최대 정모멘트와 최대 부모멘트, 그리고 최대 전단력을 모두 경험하게 되는 구조적 특성을 가지고 있다. 한편 거더의 캔틸레버 작용을 감소시키기 위하여 거더의 선단에 압출추진코(launching nose)를 부착시킨다. 이때 상부단면에 발생하는 일시적인 응력의 크기는 압출추진코의 단면특성에 따라 달라진다. 이 연구에서는 압출추진코와 상부단면의 상호작용에 관한 해석식의 정확성을 유지하고, 활용도를 높이기 위해서 압출추진코를 유사등단면(강성;등단면, 중량;변단면)으로 가정하여 단순화된 해석식을 제안하였고, 압출추진코의 단면이 등단면으로 가정한 기존 해석식의 정확성을 향상시키기 위해서 다이아프램의 중량을 집중하중으로 치환시켜 변형된 등단면 해석식을 제안하였다. 그리고 제안된 2개의 해석식의 정확성과 활용성을 판단하기 위해 실제 ILM 교량 설계자료들을 통해 전산구조해석 프로그램과, 기존 해석식들과 비교 분석하였다. ILM(incremental launching method) is a way of construction, installing a girder producing spot behind the abutment, making the bridge girder infilled with concrete continuously and launching with using by jack. The superstructure of the bridge constructed by this method is temporarily located on the center of the span and the supporting points under construction. Therefore, the sections are structurally undergone maximum positive moment, maximum negative moment, and maximum shear force arising from self weight. On the other hand, launching nose is attached to the front of the girder to decrease the cantilever effect. The magnitude of this temporary stress creating on the upper section is dependent upon the launching nose's characteristics. This study has proposed an analysis formula simplified on the assumption that the launching nose section is a quasi-equivalent section(rigid; equivalent section, weight; tapered section) in order to ensure the accuracy of the analysis formula and improve its usage with reference to the interaction between the launching nose and the upper section; and a prismatic analysis formula modified by displacing a diaphragm's weight by a concentrated load in order to improve the accuracy of the existing analysis formula that assumes the launching nose section as the equivalent section. To judge the accuracy and usage of two analysis formulas proposed, we have compared and analyzed computational structural analysis programs and existing analysis formulas based on actual ILM bridge data. As a result, all of two reveal the superior accuracy and also their usage has been improved by the simplification of analysis formulas.

Spectral and cross-spectral analysis of uneven time series with the smoothed Lomb–Scargle periodogram and Monte Carlo evaluation of statistical significance

Many spectral analysis techniques have been designed assuming sequences taken with a constant sampling interval. However, there are empirical time series in the geosciences (sediment cores, fossil abundance data, isotope analysis, …) that do not follow regular sampling because of missing data, gapped data, random sampling or incomplete sequences, among other reasons. In general, interpolating an uneven series in order to obtain a succession with a constant sampling interval alters the spectral content of the series. In such cases it is preferable to follow an approach that works with the uneven data directly, avoiding the need for an explicit interpolation step. The Lomb–Scargle periodogram is a popular choice in such circumstances, as there are programs available in the public domain for its computation. One new computer program for spectral analysis improves the standard Lomb–Scargle periodogram approach in two ways: (1) It explicitly adjusts the statistical significance to any bias introduced by variance reduction smoothing, and (2) it uses a permutation test to evaluate confidence levels, which is better suited than parametric methods when neighbouring frequencies are highly correlated.Another novel program for cross-spectral analysis offers the advantage of estimating the Lomb–Scargle cross-periodogram of two uneven time series defined on the same interval, and it evaluates the confidence levels of the estimated cross-spectra by a non-parametric computer intensive permutation test. Thus, the cross-spectrum, the squared coherence spectrum, the phase spectrum, and the Monte Carlo statistical significance of the cross-spectrum and the squared-coherence spectrum can be obtained.Both of the programs are written in ANSI Fortran 77, in view of its simplicity and compatibility. The program code is of public domain, provided on the website of the journal (http://www.iamg.org/index.php/publisher/articleview/frmArticleID/112/).Different examples (with simulated and real data) are described in this paper to corroborate the methodology and the implementation of these two new programs.

EDMA: a computer program for topological analysis of discrete electron densities

EDMAis a computer program for topological analysis of discrete electron densities according to Bader's theory of atoms in molecules. It locates critical points of the electron density and calculates their principal curvatures. Furthermore, it partitions the electron density into atomic basins and integrates the volume and charge of these atomic basins.EDMAcan also assign the type of the chemical element to atomic basins based on their integrated charges. The latter feature can be used for interpretation ofab initioelectron densities obtained in the process of structure solution. A particular feature ofEDMAis that it can handle superspace electron densities of aperiodic crystals in arbitrary dimensions.EDMAfirst generates real-space sections at a selected set of phases of the modulation wave, and subsequently analyzes each section as an ordinary three-dimensional electron density. Applications ofEDMAto model electron densities have shown that the relative accuracy of the positions of the critical points, the electron densities at the critical points and the Laplacian is of the order of 10−4or better.

Atomic stress tensor analysis of proteins

We performed stress tensor analysis of polypeptides at the atomic level by molecular dynamics simulations. Most of the approaches to stress tensor analysis of molecules in the literature assume that the interatomic forces are pairwise; however commonly used force-field functions contain multi-body interactions. To address this issue, we derived new mathematical formulae for atomic forces based on force-field functions, in which the total force acting on each atom is expressed as a summation of pairwise interatomic forces. Then, a computer program for stress tensor analysis was developed, and it successfully characterized the mechanical features of molecules at the atomic level.

The reliability of assessing rotation of teeth on photographed study casts

To examine the intra- and interexaminer reliability of assessing rotation of teeth on photographed study casts. In addition, the reliability parameters of two examiners scoring in mutual consultation were compared with the reliability parameters by one observer. Standardized photographs of sets of maxillary and mandibular plaster casts of 10 patients before treatment (T1), after treatment (T2), and a long time after retention (T3) were digitized. Tooth rotation was assessed relative to a correct position in the ideal dental arch form. A computer analysis program was used to process the measurements. Two examiners assessed each study cast twice with a washout period of 3 weeks. A third examiner assessed each cast, together with one of the other examiners. The intra- and interexaminer agreements were calculated using intraclass correlation coefficients (ICCs). Wilcoxon signed-rank tests were used to determine significant differences between the intra- and interexaminer reliability coefficients of the three examiners. The ICCs ranged from 0.430 to 0.991. Incisors showed the highest ICCs and molars showed the lowest ICCs. Intraexaminer ICCs of the experienced examiners were significantly higher than those of the examiner with less experience. No significant differences in the reliability between a single examiner and the combination of two examiners were found. The method of assessing tooth rotation in the present study has proved to be reproducible, except for the molars. This method can be helpful for clinicians assessing tooth rotation from photographed study casts.

Analytical and experimental studies on seismic behavior of double-layer barrel vault systems with different open angles

This paper presents the seismic behavior of double-layer barrel vault systems with different open angles through analytical and experimental studies with modeling of thin-walled steel tubes. For the analytical study, different six open angles and four fundamental frequencies were incorporated into the barrel vault analysis models and analyzed. A total of 24 double-layer structures were developed using the MIDAS computer analysis program and these structures were subjected to three different ground motions with a 5% damping ratio. The characteristics of the dynamic responses for the X, Y, and Z directions of the analytical model, subjected to both horizontal and vertical earthquakes, were investigated. In addition to the analytical study, an experimental study using scaled down thin-walled steel tube models was undertaken using a shaking table test. Comparing the analytical and experimental studies, the dynamic behaviors were very similar in terms of the distributions of the acceleration responses. Both the analytical and experimental models had maximum values at the 1/4 and 3/4 nodes, while having relatively smaller responses at the center node from horizontal earthquakes. It is believed that the barrel vault model with an open angle of 90 degrees has the most advantageous shape of the analytical barrel vault models used in this study.

Computer Program for Multimodel Reliability and Optimization Analysis

A computer program is developed to carry out reliability and optimization analysis with many interconnected probabilistic models. The program is freely available online and it contains a library of versatile models. The user can also implement new models—without any recompilation of the program—by several means, including a powerful scripting option. Other novel features include a comprehensive parameterization that facilitates flexible and effective model communication and the computation of direct-differentiation response sensitivities in multimodel analysis. The new program has already been successfully employed for regional risk analysis with thousands of model objects and hundreds of random variables. This paper presents the software architecture and a multimodel example of a structure that is modeled in an external finite-element program and subjected to multiple hazards, damage, and long-term deterioration.

TCF/Lef1-Mediated Control of Lipid Metabolism Regulates Skin Barrier Function

Defects in the function of the skin barrier are associated with a wide variety of skin diseases, many of which are not well characterized at the molecular level. Using Lef1 (lymphoid enhancer-binding factor 1) dominant-negative mutant mice, we demonstrate here that altered epidermal TCF (T cell factor)/Lef1 signaling results in severe impairment of the stratum corneum skin barrier and early postnatal death. Barrier defects were accompanied by major changes in lipid composition and ultrastructural abnormalities in assembly and extrusion of lipid lamellae of the interfollicular epidermis, as well as abnormal processing of profilaggrin. In contrast, tight-junction formation and stratified organization of the interfollicular epidermis was not obviously disturbed in Lef1 mutant mice. Molecular analysis revealed that TCF/Lef1 signaling regulates expression of lipid-modifying enzymes, such as Elovl3 and stearoyl coenzyme A desaturase 1 (SCD1), which are key regulators of barrier function. Promoter analysis and chromatin immunoprecipitation experiments indeed showed that SCD1 is a direct target of Lef1. Together, our data demonstrate that functional TCF/Lef1 signaling governs important aspects of epidermal differentiation and lipid metabolism, thereby regulating skin barrier function.

Analysis of Temperature Distribution in Rotating Arc Welding

Mathematical model of heat source in rotating arc welding (RAW) process was developed for investigating the heat and temperature distribution. The effect of rotating parameters on the temperature field in complex welding motion trajectory was studied. In this work, a transient three-dimensional (3D) model was established and computed by a finite element analysis computer program MARC as well as its subroutine. Comparing with non-rotating arc (NRAW) process, the width of temperature distribution enlarges, and the peak temperature of weld pool decreases. The effect of the rotating arc process becomes more and more significant with the increasing of rotating radius. In the weld center, the peak temperature increases with the rotating frequency. But in peripheral region of the weld, when rotating frequency is lower than 10 Hz, the peak temperature increases firstly and then decreases with the increasing of the rotating frequency. It is contradictory with the traditional view. Good agreement is shown between the computed results and experimental results of thermal circle in rotating arc welding process.

Three dimensional flow in anisotropic zoned porous media using boundary element method

Coupling the adjacent zones for seepage analysis in porous media needs compatibility and equilibrium equations (equality of potential on coinciding nodes and conservation of flowing mass between zones, respectively). When stretched coordinate transformation is applied to the anisotropic zones, the Dirichlet boundary conditions remain unchanged, but the Neumann boundary condition should also be transformed. Similarly in a zoned problem, for the interface between zones, compatibility equations remain unchanged during the transformation while the equilibrium equations should be transformed. In this paper, transformed Neumann boundary conditions and equilibrium equations for the interface of neighbor anisotropic zones for seepage problems have been developed in three dimensions. A computer program for seepage analysis of zoned anisotropic media based on the Boundary Element Method is developed. The code is used to solve several examples with isotropic and anisotropic zones. Some examples are also solved by finite element method for verification. Illustrated results show the ability and accuracy of the mathematical and the numerical model for solving different types of applied three-dimensional seepage problems that arise in engineering practice.

Growth Defects and Impaired Cognitive–Behavioral Abilities in Mice with Knockout for Eif4h, a Gene Located in the Mouse Homolog of the Williams-Beuren Syndrome Critical Region

Protein synthesis is a tightly regulated, energy-consuming process. The control of mRNA translation into protein is fundamentally important for the fine-tuning of gene expression; additionally, precise translational control plays a critical role in many cellular processes, including development, cellular growth, proliferation, differentiation, synaptic plasticity, memory, and learning. Eukaryotic translation initiation factor 4h (Eif4h) encodes a protein involved in the process of protein synthesis, at the level of initiation phase. Its human homolog, WBSCR1, maps on 7q11.23, inside the 1.6 Mb region that is commonly deleted in patients affected by the Williams-Beuren syndrome, which is a complex neurodevelopmental disorder characterized by cardiovascular defects, cerebral dysplasias and a peculiar cognitive-behavioral profile. In this study, we generated knockout mice deficient in Eif4h. These mice displayed growth retardation with a significant reduction of body weight that began from the first week of postnatal development. Neuroanatomical profiling results generated by magnetic resonance imaging analysis revealed a smaller brain volume in null mice compared with controls as well as altered brain morphology, where anterior and posterior brain regions were differentially affected. The inactivation of Eif4h also led to a reduction in both the number and complexity of neurons. Behavioral studies revealed severe impairments of fear-related associative learning and memory formation. These alterations suggest that Eif4h might contribute to certain deficits associated with Williams-Beuren syndrome.

SASqPCR: Robust and Rapid Analysis of RT-qPCR Data in SAS

Reverse transcription quantitative real-time PCR (RT-qPCR) is a key method for measurement of relative gene expression. Analysis of RT-qPCR data requires many iterative computations for data normalization and analytical optimization. Currently no computer program for RT-qPCR data analysis is suitable for analytical optimization and user-controllable customization based on data quality, experimental design as well as specific research aims. Here I introduce an all-in-one computer program, SASqPCR, for robust and rapid analysis of RT-qPCR data in SAS. This program has multiple macros for assessment of PCR efficiencies, validation of reference genes, optimization of data normalizers, normalization of confounding variations across samples, and statistical comparison of target gene expression in parallel samples. Users can simply change the macro variables to test various analytical strategies, optimize results and customize the analytical processes. In addition, it is highly automatic and functionally extendable. Thus users are the actual decision-makers controlling RT-qPCR data analyses. SASqPCR and its tutorial are freely available at http://code.google.com/p/sasqpcr/downloads/list.

Models of hydro power plant in dynamic security analyses of electric power interconnections

This paper presents hydropower plant models used in dynamic security analyses of electric power interconnections. The general structure and functional block diagram of a hydropower plant are given, as well as a review of the current state of hydropower plants within the electrical power system of Serbia. A hydropower plant model used for analyses of short-term dynamics, where transient stability analyses are dominant, is presented. Additionally, a hydropower plant model used for the analyses of long-term dynamics is presented, providing insight into the role and effects of a hydropower plant, which would be included in the secondary and tertiary load-frequency control. Following verification based on experimental measurements, all these models have been incorporated into appropriate computer programs for dynamic security analyses of electric power interconnections. The computer programs mentioned have been developed at the Institute 'Nikola Tesla' and some typical examples of their application have been provided.