bluuebunny/crossref_metadata_2025 huggingface dataset:
Automated mapping of large-scale chromatin structure in ENCODE
Authors: Lian Heng , Thompson William A. , Thurman Robert , Stamatoyannopoulos John A. , Noble William Stafford , Lawrence Charles E.
Published: July 2008

Motivation: A recently developed DNaseI assay has given us our first genome-wide view of chromatin structure. In addition to cataloging DNaseI hypersensitive sites, these data allows us to more completely characterize overall features of chromatin accessibility. We employed a Bayesian hierarchical change-point model (CPM), a generalization of a hidden Markov Model (HMM), to characterize tiled microarray DNaseI sensitivity data available from the ENCODE project.

Results: Our analysis shows that the accessibility of chromatin to cleavage by DNaseI is well described by a four state model of local segments with each state described by a continuous mixture of Gaussian variables. The CPM produces a better fit to the observed data than the HMM. The large posterior probability for the four-state CPM suggests that the data falls naturally into four classes of regions, which we call major and minor DNaseI hypersensitive sites (DHSs), regions of intermediate sensitivity, and insensitive regions. These classes agree well with a model of chromatin in which local disruptions (DHSs) are concentrated within larger domains of intermediate sensitivity, the accessibility islands. The CPM assigns 92% of the bases within the ENCODE regions to the insensitive regions. The 5.8% of the bases that are in regions of intermediate sensitivity are clearly enriched in functional elements, including genes and activating histone modifications, while the remaining 2.2% of the bases in hypersensitive regions are very strongly enriched in these elements.

Availability: The CPM software is available upon request from the authors.

Contact:  jstam@stamlab.org; noble@gs.washington.edu; Charles_Lawrence@brown.edu

Supplementary information:  Supplementary data are available at Bioinformatics online. Source code is available at http://noble.gs.washington.edu/proj/segment.
Stiffness gradients in vascular bundles of the palmWashingtonia robusta
Authors: Rüggeberg Markus , Speck Thomas , Paris Oskar , Lapierre Catherine , Pollet Brigitte , Koch Gerald , Burgert Ingo
Published: July 2008

Palms can grow at sites exposed to high winds experiencing large dynamic wind and gust loads. Their stems represent a system of stiff fibrous elements embedded in the soft parenchymatous tissue. The proper design of the interface of the stiffening elements and the parenchyma is crucial for the functioning of the stem. The strategy of the palm to compromise between stiff fibre caps and the soft parenchymatous tissue may serve as a model system for avoiding stress discontinuities in inhomogeneous and anisotropic fibre-reinforced composite materials. We investigated the mechanical, structural and biochemical properties of the fibre caps of the palmWashingtonia robustaat different levels of hierarchy with high spatial resolution. A gradual decrease in stiffness across the fibre cap towards the surrounding parenchymatous tissue was observed. Structural adaptations at the tissue level were found in terms of changes in cell cross sections and cell wall thickness. At the cell wall level, gradients across the fibre cap were found in the degree of orientation of the microfibrils and in the lignin level and composition. The impact of these structural variations in the local material stiffness distribution is discussed.
The bacterial cell division protein FtsZ assembles into cytoplasmic rings in fission yeast
Authors: Srinivasan Ramanujam , Mishra Mithilesh , Wu Lifang , Yin Zhongchao , Balasubramanian Mohan K.
Published: July 2008

During cytokinesis, most bacteria assemble a ring-like structure that is composed of the tubulin homolog FtsZ. The mechanisms regulating assembly and organization of FtsZ molecules into rings are not fully understood. Here, we express bacterial FtsZ in the fission yeast Schizosaccharomyces pombe and find that FtsZ filaments assemble into cytoplasmic rings. Investigation of the Escherichia coli FtsZ revealed that ring assembly occurred by a process of closure and/or spooling of linear bundles. We conclude that FtsZ rings can assemble in the absence of all other bacterial cytokinetic proteins and that the process might involve hydrolysis of FtsZ-bound GTP and lateral associations between FtsZ filaments.
DLC1: a significant GAP in the cancer genome
Authors: Lahoz Aurelia , Hall Alan
Published: July 2008

Rho GTPases are believed to make important contributions to the development and progression of human cancer, but direct evidence in the form of somatic mutations analogous to those affecting Ras has been lacking. A recent study inGenes & Developmentby Xue and colleagues (1439–1444)now provides in vivo evidence thatDLC1, a negative regulator of Rho, is a tumor suppressor gene deleted almost as frequently as p53 in common cancers such as breast, colon, and lung.
Signaling silence—breaking ground and spreading out: Figure 1.
Authors: Woo Hye Ryun , Richards Eric J.
Published: July 2008

Among the persistent mysteries in epigenetics are the criteria by which specific regions of the genome are chosen for deposition of distinguishing chromatin marks. Once a particular region is modified, will the newly acquired epigenetic state spill onto neighboring regions of the genome or be confined to tidy patches? The report by Henderson and Jacobsen in the the previous issue of Genes & Development (1597–1606) addresses these questions while providing insight into the utility of DNA methylation for a eukaryotic genome.
POT of gold: modeling dyskeratosis congenita in the mouse: Figure 1.
Authors: Autexier Chantal
Published: July 2008

Dyskeratosis congenita (DC) is a rare syndrome, characterized by cutaneous abnormalities and premature death caused by bone marrow failure. In this issue of Genes & Development, Hockemeyer and colleagues (pp. 1773–1785) report a new mouse model that reconstitutes key features of DC. Disease phenotypes are generated by a POT1b deletion in a telomerase-deficient background that accelerates the shortening of telomeres by degradation.
PERspective on PER phosphorylation
Authors: Blau Justin
Published: July 2008

Period (PER) proteins are essential parts of the molecular clocks that control circadian rhythms in flies and mammals. Phosphorylation regulates PER’s stability and subcellular localization; however, the physiologically relevant sites have been difficult to identify in spite of knowing the relevant kinase. In this issue of Genes & Development, Chiu and colleagues (1758–1772) identify a key phosphorylation site on PER that recruits the F-box protein Slimb to trigger PER degradation and set clock speed.
Translational regulation of glutathione peroxidase 4 expression through guanine-rich sequence-binding factor 1 is essential for embryonic brain development
Authors: Ufer Christoph , Wang Chi Chiu , Fähling Michael , Schiebel Heike , Thiele Bernd J. , Billett E. Ellen , Kuhn Hartmut , Borchert Astrid
Published: July 2008

Phospholipid hydroperoxide glutathione peroxidase (GPx4) is a moonlighting selenoprotein, which has been implicated in basic cell functions such as anti-oxidative defense, apoptosis, and gene expression regulation. GPx4-null mice die in utero at midgestation, and developmental retardation of the brain appears to play a major role. We investigated post-transcriptional mechanisms of GPx4 expression regulation and found that the guanine-rich sequence-binding factor 1 (Grsf1) up-regulates GPx4 expression. Grsf1 binds to a defined target sequence in the 5′-untranslated region (UTR) of the mitochondrial GPx4 (m-GPx4) mRNA, up-regulates UTR-dependent reporter gene expression, recruits m-GPx4 mRNA to translationally active polysome fractions, and coimmunoprecipitates with GPx4 mRNA. During embryonic brain development, Grsf1 and m-GPx4 are coexpressed, and functional knockdown (siRNA) of Grsf1 prevents embryonic GPx4 expression. When compared with mock controls, Grsf1 knockdown embryos showed significant signs of developmental retardations that are paralleled by apoptotic alterations (TUNEL staining) and massive lipid peroxidation (isoprostane formation). Overexpression of m-GPx4 prevented the apoptotic alterations in Grsf1-deficient embryos and rescued them from developmental retardation. These data indicate that Grsf1 up-regulates translation of GPx4 mRNA and implicate the two proteins in embryonic brain development.
Separate roles for the DNA damage checkpoint protein kinases in stabilizing DNA replication forks
Authors: Segurado Monica , Diffley John F.X.
Published: July 2008

The DNA damage checkpoint plays a crucial role in maintaining functional DNA replication forks when cells are exposed to genotoxic agents. In budding yeast, the protein kinases Mec1 (ATR) and Rad53 (Chk2) are especially important in this process. How these kinases act to stabilize DNA replication forks is currently unknown but is likely to have important implications for understanding how genomic instability is generated during oncogenesis and how chemotherapies that interfere with DNA replication could be improved. Here we show that the sensitivity of rad53 mutants to DNA-damaging agents can be almost completely suppressed by deletion of the EXO1 gene, which encodes an enigmatic flap endonuclease. Deletion of EXO1 also suppresses DNA replication fork instability in rad53 mutants. Surprisingly, deletion of EXO1 is completely ineffective in suppressing both the sensitivity and replication fork breakdown in mec1 mutants, indicating that Mec1 has a genetically separable role in replication fork stabilization from Rad53. Finally, our analysis indicates that a second downstream effector kinase, Chk1, can stabilize replication forks in the absence of Rad53. These results reveal previously unappreciated complexity in the downstream targets of the checkpoint kinases and provide a framework for elucidating the mechanisms of DNA replication fork stabilization by these kinases.
Pax3 regulation of FGF signaling affects the progression of embryonic progenitor cells into the myogenic program
Authors: Lagha Mounia , Kormish Jay D. , Rocancourt Didier , Manceau Marie , Epstein Jonathan A. , Zaret Kenneth S. , Relaix Frédéric , Buckingham Margaret E.
Published: July 2008

Pax3/7-dependent stem cells play an essential role in skeletal muscle development. We now show that Fgfr4 lies genetically downstream from Pax3 and is a direct target. In chromatin immunoprecipitation (ChIP)-on-chip experiments, Pax3 binds to a sequence 3′ of the Fgfr4 gene that directs Pax3-dependent expression at sites of myogenesis in transgenic mouse embryos. The activity of this regulatory element is also partially dependent on E-boxes, targets of the myogenic regulatory factors, which are expressed as progenitor cells enter the myogenic program. Other FGF signaling components, notably Sprouty1, are also regulated by Pax3. In vivo manipulation of Sprouty expression reveals that FGF signaling affects the balance between Pax-positive progenitor cells and committed myoblasts. These results provide new insight into the Pax-initiated regulatory network that modulates stem cell maintenance versus tissue differentiation.
The biological effects of simple tandem repeats: Lessons from the repeat expansion diseases: Table 1.
Authors: Usdin Karen
Published: July 2008

Tandem repeats are common features of both prokaryote and eukaryote genomes, where they can be found not only in intergenic regions but also in both the noncoding and coding regions of a variety of different genes. The repeat expansion diseases are a group of human genetic disorders caused by long and highly polymorphic tandem repeats. These disorders provide many examples of the effects that such repeats can have on many biological processes. While repeats in the coding sequence can result in the generation of toxic or malfunctioning proteins, noncoding repeats can also have significant effects including the generation of chromosome fragility, the silencing of the genes in which they are located, the modulation of transcription and translation, and the sequestering of proteins involved in processes such as splicing and cell architecture.
Identification of Differential Genes by Suppression Subtractive Hybridization: I. Preparation of Subtracted cDNA or Genomic DNA Library
Authors: Rebrikov Denis V.
Published: July 2008

INTRODUCTION

Suppression subtractive hybridization (SSH) is one of the most powerful and popular methods for generating subtracted cDNA or genomic DNA libraries. This technique can be used to compare two mRNA populations and obtain cDNAs representing genes that are either overexpressed or exclusively expressed in one population as compared to another. It can also be used for comparison of genomic DNA populations. This protocol describes the preparation of a subtracted cDNA or genomic DNA library, and includes methods for cDNA synthesis, tester and driver DNA digestion, and adapter ligation.
Identification of Differential Genes by Suppression Subtractive Hybridization: III. PCR Amplification of Differentially Presented DNAs
Authors: Rebrikov Denis V.
Published: July 2008

INTRODUCTION

Suppression subtractive hybridization (SSH) is one of the most powerful and popular methods for generating subtracted cDNA or genomic DNA libraries. This technique can be used to compare two mRNA populations and obtain cDNAs representing genes that are either overexpressed or exclusively expressed in one population as compared to another. It can also be used for comparison of genomic DNA populations. In this protocol, differentially presented DNAs are selectively amplified using PCR. It is strongly recommended that subtractions be performed in both directions for each tester/driver DNA pair. Forward subtraction is designed to enrich for differentially presented molecules present in the tester but not in the driver; reverse subtraction is designed to enrich for differentially presented sequences present in the driver but not in the tester. Therefore, each experiment should have at least four reactions: (1) subtracted tester DNAs, (2) unsubtracted tester control, (3) reverse-subtracted tester DNAs, and (4) unsubtracted control for the reverse subtraction.
Identification of Differential Genes by Suppression Subtractive Hybridization: IV. Mirror Orientation Selection (MOS)
Authors: Rebrikov Denis V.
Published: July 2008

INTRODUCTION

Suppression subtractive hybridization (SSH) is one of the most powerful and popular methods for generating subtracted cDNA or genomic DNA libraries. This technique can be used to compare two mRNA populations and obtain cDNAs representing genes that are either overexpressed or exclusively expressed in one population as compared to another. It can also be used for comparison of genomic DNA populations. The major drawback of SSH is the presence of background clones that represent nondifferentially expressed DNA species in the subtracted libraries. In some cases, the number of background clones may considerably exceed the number of target clones. This protocol describes mirror orientation selection (MOS)--a simple procedure that substantially decreases the number of background clones in libraries generated by SSH. The MOS technique is based on the rationale that after PCR amplification, during SSH, background molecules will be present in one orientation only, relative to the adapter sequences. Genuine SSH clones will be present in both sequence orientations.
Identification of Differential Genes by Suppression Subtractive Hybridization: V. PCR-Based DNA Dot Blot
Authors: Rebrikov Denis V.
Published: July 2008

INTRODUCTION

Suppression subtractive hybridization (SSH) is one of the most powerful and popular methods for generating subtracted cDNA or genomic DNA libraries. This technique can be used to compare two mRNA populations and obtain cDNAs representing genes that are either overexpressed or exclusively expressed in one population as compared to another. It can also be used for comparison of genomic DNA populations. This protocol describes a method for the use of PCR-based DNA dot blots in the differential screening of arrayed subtracted DNA clones. For high-throughput screening, a 96-well or 384-well format PCR from one of several thermal cycler manufacturers is recommended. Alternatively, single tubes can be used.
Phenotypic Analysis of Arabidopsis Mutants: Flowering Time
Authors: Blázquez Miguel
Published: July 2008

INTRODUCTION

Flowering in Arabidopsis thaliana is modulated by a number of environmental factors. It is therefore important to perform flowering-time measurements under controlled environmental conditions, including light quality and intensity, day length, temperature, watering, and spacing between plants. Ideally, pots of plants are rotated, and individual plants of different genotypes are placed randomly within the experimental setup. Because of the large influence of environmental effects, it is imperative that only plants grown at the same time and in the same place be compared. Flowering is also modulated by endogenous factors and can thus be affected by mutations in genes that are not primarily involved in the control of flowering time. The variation of flowering time between ecotypes is generally large. Therefore, only those mutants that are induced in the same background can be compared. This protocol describes a method for determining the flowering time of Arabidopsis plants.
Browsing HapMap Data Using the Genome Browser
Authors: Smith Albert Vernon
Published: July 2008

INTRODUCTION

The primary goal of the International Haplotype Map Project has been to develop a haplotype map of the human genome that describes the common patterns of genetic variation, in order to accelerate the search for the genetic causes of human disease. Within the project, ~3.9 million distinct single-nucleotide polymorphisms (SNPs) have been genotyped in 270 individuals from four worldwide populations. The project data are available for unrestricted public use at the HapMap website. This site, which is the primary portal to genotype data produced by the project, offers bulk downloads of the data set, as well as interactive data browsing and analysis tools that are not available elsewhere. Research into the genetic contributions to a human disease commonly focuses on candidate genes identified from linkage and/or association studies, as well as from pathways suspected to be involved in a particular disease process. In studying candidate genes, a researcher will want to know whether there are any common SNPs in the immediate vicinity, what those SNPs’ alleles are, and the relative frequencies of the alleles in the population. The researcher will also be particularly interested in coding SNPs, whose alleles change the amino acid sequence of the gene product and therefore might represent functional variations. This protocol provides details on how to use the genome browser to navigate to and explore HapMap data for a gene or region of interest.
Retrieving HapMap Data via Bulk Download
Authors: Smith Albert Vernon
Published: July 2008

INTRODUCTION

The primary goal of the International Haplotype Map Project has been to develop a haplotype map of the human genome that describes the common patterns of genetic variation, in order to accelerate the search for the genetic causes of human disease. Within the project, ~3.9 million distinct single-nucleotide polymorphisms (SNPs) have been genotyped in 270 individuals from four worldwide populations. The project data are available for unrestricted public use at the HapMap Web site. This site, which is the primary portal to genotype data produced by the project, offers bulk downloads of the data set, as well as interactive data browsing and analysis tools that are not available elsewhere. Bulk downloads of chromosome- or genome-wide data provide text dumps of the entire HapMap data set. Although complete, such downloads do not provide any filtering or selection services. This protocol describes the retrieval of HapMap data via bulk download.
An Efficient Feasibility Robust Optimization Method Using a Sensitivity Region Concept
Authors: Gunawan S. , Azarm S.
Published: July 2008

We present a new robust optimization method that ensures feasibility of an optimized design when there are uncontrollable variations in design parameters. This method is developed based on the notion of a sensitivity region, which is a measure of how far a feasible design is from the boundary of a feasible domain in the parameter variation space. As the design moves further inside the feasible domain, and thus becoming more feasibly robust, the sensitivity region becomes larger. Our method is not sampling-based so it does not require a presumed probability distribution as input and is efficient in terms of function evaluations. In addition, our method does not use gradient approximation and thus is applicable to problems having non-differentiable constraint functions and large parameter variations. As a demonstration, we applied our method to an engineering example, the design of a control valve actuator linkage. In this example, we show that the method is efficient and the optimum design obtained is robust.
Freeform Feature Retrieval by Signal Processing
Authors: Wang Chensheng , Vergeest Joris S. M. , Stappers Pieter J. , Bronsvoort Willem F.
Published: July 2008

Feature retrieval is of great importance in shape modelling, in terms of supporting design reuse by obtaining reusable geometric entities. However, conventional techniques for feature retrieval are generally limited to the extraction of feature lines, curve segments, or surfaces, and the feature distortion imposed by feature interaction remains unconsidered. This paper investigates approaches for freeform feature retrieval by means of signal processing techniques. By treating features or regions of interest as surface signals, we employ digital filters to separate the feature signal from that of the domain surface, retrieving the “pure” feature from an existing shape model. Strategies for different model types are elaborated, for instance, the exact feature retrieval method designed for shape models with explicit data structure, such as B-Rep, or other accessible representations; and the signal filtering method for models with structured or unstructured data sets, such as that in mesh or point cloud models. Specifically, in the signal filtering method feature retrieval is implemented by the convolving operator in the frequency domain. By transforming the problem of shape decomposition from geometric extraction in the spatial domain to computation in the frequency domain, the proposed methods not only brings in significant computational efficiency, but also reduces the complexity of problem solving for feature retrieval. Provided examples show that the proposed approaches can achieve satisfactory results for simple geometries, whereas for sophisticated shapes guidelines for the design of dedicated filters are elaborated.
Covariance Modeling Method for Use in Compliant Assembly Tolerance Analysis
Authors: Tonks Michael R. , Chase Ken W.
Published: July 2008

In assemblies involving compliant parts, springback and residual stress are caused when geometric variation in the assembly requires the parts be deformed to allow for assembly. A method is needed to predict the deformation due to the geometric variations. Researchers in the areas of Statistical Tolerance Analysis and Stochastic Finite Element Analysis have developed methods to account for statistical variation of parameters in a finite element model. A new statistical method uses an orthogonal polynomial-based covariance model to account for surface variation of the compliant parts over a wide range of wavelengths. The method has been demonstrated to match the accuracy of Monte Carlo simulation with a single calculation, and accurately model covariance data taken from real parts.
A Comparison of Commonality Indices for Product Family Design
Authors: Thevenot Henri J. , Simpson Timothy W.
Published: July 2008

Today’s highly competitive and global marketplace is redefining the way companies do business: many companies are being faced with the challenge of providing as much variety as possible for the market with as little variety as possible between products. In order to achieve this, product families have been developed, allowing the realization of a sufficient variety of products to meet the customers’ demands while keeping costs relatively low. The challenge when designing a family of products is in resolving the tradeoff between product commonality and distinctiveness: if commonality is too high, products lack distinctiveness, and their individual performance is not optimized; on the other hand, if commonality is too low, manufacturing costs will increase dramatically. Toward this end, several commonality indices have been proposed to assess the amount of commonality within a product family. In this paper, we compare and contrast six of the commonality indices from the literature based on their ease of data collection, repeatability and consistency. Eight families of products are dissected and analyzed, and the commonality of each product family is computed using each commonality index. The results are then analyzed and compared, and recommendations are given on their usefulness for product family design. This study lays a foundation for understanding the relationship between different platform leveraging strategies and the resulting degree of commonality within a product family.
Front Structure Design Procedure for Optimal Pedestrian Leg Impact Performance
Authors: Neal Mark O.
Published: July 2008

This paper describes a procedure to optimize the front structure of a vehicle for improved performance in the leg impact portion of pedestrian safety regulations proposed by the European Enhanced Vehicle-Safety Committee (EEVC). The first step in this procedure was to perform a simulation of the EEVC leg impact test with detailed finite element models of the EEVC leg impactor and the baseline design of a vehicle front structure. Next, a simplified, parametric finite element model of the vehicle front structure was used with the leg impactor model to simulate the leg impact test, and the results were correlated to the detailed finite element model and the test results. The leg impact simulation with the parametric vehicle model was then incorporated into an optimization procedure developed within the optimization code ISIGHT. In this procedure the parameters that controlled the vehicle geometry and structural stiffness in the simplified model were altered by ISIGHT to improve performance in the leg impact test.
Parameter and Tolerance Constraints Modeling for Assembly
Authors: Hu Jie , Peng Yonghong
Published: July 2008

Geometric parameter and tolerance design are two important phase in product design, and will affect the assembly functionality of the product. The aim of the article is to present a new method of parameter and tolerance constraints modeling for assembly. In the nominal domain, a graphical representation of the linkage of geometric constraints is termed the nominal loop circuit (NLC), which helps to formulate the stack path of parameters into parameter equations. In the variational domain, assembly stackup functions are established. In the tolerance domain, tolerance inequations are formulated. The parameter equations, tolerance inequations and assembly stackup functions constitute parameter and tolerance constraints model, which can be used to optimize of parameter and tolerance. The method is demonstrated by a gear pump design problem.
A Single-Loop Method for Reliability-Based Design Optimization
Authors: Liang Jinghong , Mourelatos Zissimos P. , Tu Jian
Published: July 2008

Reliability-Based Design Optimization (RBDO) can provide optimum designs in the presence of uncertainty. It can therefore, be a powerful tool for design under uncertainty. The traditional, double-loop RBDO algorithm requires nested optimization loops, where the design optimization (outer) loop, repeatedly calls a series of reliability (inner) loops. Due to the nested optimization loops, the computational effort can be prohibitive for practical problems. A single-loop RBDO algorithm is proposed in this paper for both normal and non-normal random variables. Its accuracy is the same with the double-loop approach and its efficiency is almost equivalent to deterministic optimization. It collapses the nested optimization loops into an equivalent single-loop optimization process by imposing the Karush-Kuhn-Tucker optimality conditions of the reliability loops as equivalent deterministic equality constraints of the design optimization loop. It therefore, converts the probabilistic optimization problem into an equivalent deterministic optimization problem, eliminating the need for calculating the Most Probable Point (MPP) in repeated reliability assessments. Several numerical applications including an automotive vehicle side impact example, demonstrate the accuracy and superior efficiency of the proposed single-loop RBDO algorithm.
A Saddlepoint Approximation Method for Uncertainty Analysis
Authors: Du Xiaoping , Sudjianto Agus
Published: July 2008

The availability of computationally efficient and accurate methods for probabilistic computation is crucial to the success of applications of probabilistic design using complex engineering simulation models. To address this need, a Saddlepoint Approximation method for probabilistic engineering analysis is introduced. A general performance function is approximated at the Most Likelihood Point with either linear or quadratic forms and the Saddlepoint Approximation is then applied to evaluate the probability associated with the performance. The proposed approach provides highly accurate probabilistic results while maintaining minimum computational requirement. Two examples are presented to demonstrate the effectiveness of the proposed method.
Design for Project Change Management: Part 1 — Configuration Design
Authors: Xue D. , Cheing S. Y. , Gu P.
Published: July 2008

A new systematic approach to identify the optimal design configuration and attributes to minimize potential construction project changes is introduced in this research. The first part of this paper focuses on the configuration design aspect. In this research, the relations between design configurations and construction tasks are modeled by axiomatic design matrices. The design configuration that is most independent to the construction tasks is identified based upon the axiomatic design approach. In addition, estimation of potential project change cost due to the potential design configuration changes is also discussed. Case studies in pipeline engineering design and construction have been conducted to show the effectiveness of the introduced approach.
Design Optimization of Hierarchically Decomposed Multilevel Systems Under Uncertainty
Authors: Kokkolaras Michael , Mourelatos Zissimos P. , Papalambros Panos Y.
Published: July 2008

This paper presents a methodology for design optimization of decomposed systems in the presence of uncertainties. We extend the analytical target cascading (ATC) formulation to probabilistic design by treating stochastic quantities as random variables and parameters and posing reliability-based design constraints. We model the propagation of uncertainty throughout the multilevel hierarchy of elements that comprise the decomposed system by using the advanced mean value (AMV) method to generate the required probability distributions of nonlinear responses. We utilize appropriate metamodeling techniques for simulation-based design problems. A simple yet illustrative hierarchical bi-level engine design problem is used to demonstrate the proposed methodology.
A Method for Determining the Optimal Direction of the Principal Moment of Inertia in Frame Element Cross-Sections
Authors: Takezawa Akihiro , Nishiwaki Shinji , Izui Kazuhiro , Yoshimura Masataka
Published: July 2008

This paper discusses a method to determine the optimal direction of the principal moment of inertia in frames element cross-sections for the design of mechanical structures at the conceptual design phase. The direction in each frame element is determined by maximizing the structural stiffness. Construction of the optimization procedure is based on the KKT-conditions and the balance of bending moments applied to each frame element. This method is implemented as an application in a structural topology optimization procedure that uses frame elements. Finally, several examples are presented to confirm that the proposed method is useful for the topology optimization method discussed here.
A Collaborative Rapid Analysis Method for Decision-Making in Assembly Line Design
Authors: Yoshimura Masataka , Yoshida Satoshi , Konishi Yoshinori , Izui Kazuhiro , Nishiwaki Shinji , Inamori Yutaka , Nomura Ayako , Mitsuyuki Keiji , Kawaguchi Yuji , Inagaki Toru
Published: July 2008

Many highly accurate computer simulation tools have been developed for assembly line design, such as for simulation of assembly processes, but these tools require much input information and are generally utilized only in detailed design stages. This paper proposes a rapid analysis method for manual assembly line design, which can be utilized in the conceptual design stage. This method is based on a layout tool where design engineers can construct assembly line models using 2- and 3-D views. This method provides design evaluation techniques for multiple important criteria such as volume flexibility, visibility, and so on, using the layout data. Spatial evaluation and quantitative efficiency analyses can be simultaneously performed, which enhance collaborative decision-making in the conceptual design stage.
Design of a Bimorph Driven Meander-Line Structure for Parts Feeder Application
Authors: Ting Yung , Jar Ho-Chin , Lin Chung-Yi , Huang Jeng-Shen
Published: July 2008

A novel meander-line structure implemented with bimorph piezoelectric actuators driven by alternating current power is developed in this article. Via the generated traveling wave, this mechanism is able to transport parts. Dynamic model of the structure as well as motion trajectory and optimal transport feed rate is studied, and also verified by the practical experiment.
A Reliability-Based Design Method Using Simulation Techniques and Efficient Optimization Approach
Authors: Zou Tong , Mahadevan Sankaran , Sopory Akhil
Published: July 2008

A novel reliability-based design optimization (RBDO) method using simulation-based techniques for reliability assessments and efficient optimization approach is presented in this paper. In RBDO, model-based reliability analysis needs to be performed to calculate the probability of not satisfying a reliability constraint and the gradient of this probability with respect to each design variable. Among model-based methods, the most widely used in RBDO is the first-order reliability method (FORM). However, FORM could be inaccurate for nonlinear problems and is not applicable for system reliability problems. This paper develops an efficient optimization methodology to perform RBDO using simulation-based techniques. By combining analytical and simulation-based reliability methods, accurate probability of failure and sensitivity information is obtained. The use of simulation also enables both component and system-level reliabilities to be included in RBDO formulation. Instead of using a traditional RBDO formulation in which optimization and reliability computations are nested, a sequential approach is developed to greatly reduce the computational cost. The efficiency of the proposed RBDO approach is enhanced by using a multi-modal adaptive importance sampling technique for simulation-based reliability assessment; and by treating the inactive reliability constraints properly in optimization. A vehicle side impact problem is used to demonstrate the capabilities of the proposed method.
Unified Distance Queries in a Heterogeneous Model Environment
Authors: Johnson David E. , Cohen Elaine
Published: July 2008

Computing the minimum distance between two models in a virtual scene is a fundamental operation useful in simulation, path planning, haptics, and modeling. In an environment with heterogeneous model representations, distance functions can be difficult to formulate and may require multiple specialized methods. In this paper, we demonstrate a generalized method for finding the distance between models with different representations and demonstrate it on a variety of models.
Analytical Variance-Based Global Sensitivity Analysis in Simulation-Based Design Under Uncertainty
Authors: Chen Wei , Jin Ruichen , Sudjianto Agus
Published: July 2008

The importance of sensitivity analysis in engineering design cannot be over-emphasized. In design under uncertainty, sensitivity analysis is performed with respect to the probabilistic characteristics. Global sensitivity analysis (GSA), in particular, is used to study the impact of variations in input variables on the variation of a model output. One of the most challenging issues for GSA is the intensive computational demand for assessing the impact of probabilistic variations. Existing variance-based GSA methods are developed for general functional relationships but require a large number of samples. In this work, we develop an efficient and accurate approach to GSA that employs analytic formulations derived from metamodels of engineering simulation models. We examine the types of GSA needed for design under uncertainty and derive generalized analytical formulations of GSA based on a variety of metamodels commonly used in engineering applications. The benefits of our proposed techniques are demonstrated and verified through both illustrative mathematical examples and the robust design for improving vehicle handling performance.
Building Surrogate Models Based on Detailed and Approximate Simulations
Authors: Qian Zhiguang , Seepersad Carolyn Conner , Joseph V. Roshan , Wu C. F. Jeff , Allen Janet K.
Published: July 2008

Preliminary design of a complex system often involves exploring a large design space. This may require repeated use of computationally expensive simulations. To ease the computational burden, surrogate models are built to provide rapid approximations of more expensive models. However, the surrogate models themselves are often expensive to build because they are based on repeated experiments with computationally expensive simulations. An alternative approach is to replace the detailed simulations with simplified approximate simulations, thereby sacrificing accuracy for reduced computational time. Naturally, surrogate models built from these approximate simulations will also be imprecise. A strategy is needed for improving the precision of surrogate models based on approximate simulations without significantly increasing computational time. In this paper, a new approach is taken to integrate data from approximate and detailed simulations to build a surrogate model to describe the relationship between output and input parameters. Experimental results from approximate simulations form the bulk of the data, and they are used to build a model based on a Gaussian process. The fitted model is then ‘adjusted’ by incorporating small amounts of data from detailed simulations to obtain a more accurate prediction model. The effectiveness of this approach is demonstrated with a design application for a cellular material that is used to cool a microprocessor. The emphasis is on the method and not on the results per se.
Design Configuration of Vehicle With Domain Knowledge Enhancement
Authors: Miao Yi , Blouin Vincent Y. , Fadel Georges M.
Published: July 2008

Configuration design and packaging optimization correspond to finding the optimal placement of a series of objects in a system while satisfying functional requirements and minimizing criteria. The research presented in this paper is applied to the configuration design of vehicles and more specifically the US Army FMTV (Family of Medium Tactical Vehicles). This paper presents the latest developments of the design methodology based on a multiple objective genetic algorithm. A swap operator specifically constructed for packaging problems is presented. For this multi-criteria problem, the goal of the methodology is to explore the objective space in order to find multiple Pareto designs. This research is motivated by the need to add non-conventional components, namely, a fuel cells auxiliary power unit and its associated modules, on the FMTV. Three objectives are considered: vehicle dynamic behavior, maintainability, and survivability. The methodology uses several in-house and commercial analysis packages to evaluate the fitness of the evolving designs. The new approach is systematically evaluated comparing the results to those of the original method with respect to its ability in generating the Pareto front of the multi-criteria design problem.
Global Feature Based Interactive Reduct Evolutional Computation for Aesthetic Design
Authors: Yanagisawa Hideyoshi , Fukuda Shuichi
Published: July 2008

In this paper, we verify the enhancement of IREC, which is a computer algorithm for interactive design support system, to support global design features as design attributes. IREC (Interactive Reduct Evolutional Computation) is a method to evolve designs based on users’ personal preferences. The method works through an interaction between the user and a computer system. The computer system with IREC generates design samples consisting of random attributes and the user evaluates and scores each samples depending on his/her psychological preferences. The system estimates the design attributes that the user pays more attention to (favored features) with reduct in Rough set theory and reflects it to generate new design samples. This interaction continues until the samples converge to a satisfactory design. So far design parameters such as coordinate of nodes for spline curve have been regarded as design attributes. However, design attributes consist of not only detailed local parameters but also global features such as convexity, softness etc. In earlier design process, designers first drew a rough sketch to determine the outline of a design, and designed the details later. Therefore it is important to introduce global features to accelerate the convergence and to increase user friendliness. We develop G-IREC (Global feature based IREC) which allows to introduce global features in IREC. This method is applied to design an automobile side-view shape model. The effectiveness of the method is demonstrated by comparing the results of the experiments carried out.
Automation of Process Planning for Rough Boring of Turned Components With Arbitrary Internal Geometry From a Semi-Finished Stock
Authors: Motipalli V. V. Satish K. , Krishnaswami Prakash
Published: July 2008

This paper describes a novel method for automated process planning for rough boring of turned components with arbitrary internal geometry from a semi-finished stock. Earlier work has been reported on process planning for boring of components with monotonic internal geometry made from bar stock. This paper addresses the more general problem of process planning of parts with non-monotonic internal feature list from arbitrary given initial geometry, i.e., from a casting or from a semi-finished stock. With the algorithms developed, we are able to achieve full automation of all aspects of the process plan, including operations sequencing, parameter selection, NC code generation, etc. Thus, it becomes possible to go from design to NC code in a fully automated fashion. In the present work we focus on a tightly defined part family, which results in very simple but robust automation algorithms. This is in contrast to much of the reported work on automated process planning, which generally targets broad part families, leading to complex algorithms that fall short of complete design-to-NC automation.
A Framework for Integrated Computer-Aided Design, Process Planning and Manufacturing Systems Engineering for Powertrain Machining
Authors: Yip-Hoi Derek , Li Jianming , Zhou Liang , Wang Wencai , Ramesh Madhumati , Subramanian Samba , Swisher Steve
Published: July 2008

Machined powertrain components are a subset of machined parts that introduce unique and difficult problems to product design, process planning and manufacturing system design for the automotive industry. They are complex, high value-added components that must be produced at large volumes to stringent quality standards. Accordingly product development cycles are typically long. Integrated computer-aided approaches are thus desirable for reducing this time and helping manufacturing engineers design the best process and specify the optimal manufacturing system configuration. This paper presents a framework for integrating Computer-Aided Design (CAD), Computer-Aided Process Planning (CAPP) and Computer-Aided Manufacturing Systems Engineering (CAE-MS) for producing machined powertrain components. It describes the key components of this framework and in some cases details of the methods and technologies adopted for their realization. This solution is based upon a feature-centric philosophy. This stands in contrast to the product-variant approach that has been common practice in this industry.
Multiresolution Finite Element Mesh Generation
Authors: Date Hiroaki , Kanai Satoshi , Kishinami Takeshi , Nishigaki Ichiro , Dohi Takayuki
Published: July 2008

Effective and robust automatic generation methods of finite element mesh of product model are required for CAE. Although many researches for them have been done, robust mesh generation for complex solid shapes with small features and flexible mesh property control are still difficult in current finite element meshers. In this paper, we propose a new method for automatic finite element mesh generation of a product model based on multiresolution representation of high-density mesh which are stably generated by existing finite element meshers. In our approach, geometrical and topological mesh properties required for FEA can be controlled using user-specified parameters, and mesh elements corresponding to the solid model elements used for setting the analysis conditions are preserved on the simplified meshes. Using our method, robust finite element mesh generation where the mesh property is controllable could be realized.
An Open Code for the Dynamic Simulation of Multibody Systems
Authors: Fanghella Pietro , Galletti Carlo , Torre Giorgio
Published: July 2008

The paper presents several features of a dynamic simulator for multibody systems. Its main characteristics are the following: it can deal with mechanisms with open and closed kinematic chains, allows definitions of rigid and flexible bodies, permits definitions of complex non-standard dynamic actions by a powerful and well-known general-purpose simulation package, and provides links to user-friendly interfaces for result displaying and interfacing with external control systems. In order to perform all these actions, a common environment based on Matlab has been established. The software is implemented using the Matlab object-oriented language. The first part of the paper provides a basic discussion of the mathematical approach followed to model multibody systems, then the actual software implementation is described. The designed software architecture is open and allows great model generality; moreover, the software can be optimized and tailored to specific multibody models in order to obtain good computational efficiency. Integration aspects in Simulink and VRML environments are analyzed.