bluuebunny/crossref_metadata_2025 huggingface dataset:
Ortholog-based protein-protein interaction prediction and its application to inter-species interactions
Authors: Lee Sheng-An , Chan Cheng-hsiung , Tsai Chi-Hung , Lai Jin-Mei , Wang Feng-Sheng , Kao Cheng-Yan , Huang Chi-Ying F
Published: December 2008

Background

The rapid growth of protein-protein interaction (PPI) data has led to the emergence of PPI network analysis. Despite advances in high-throughput techniques, the interactomes of several model organisms are still far from complete. Therefore, it is desirable to expand these interactomes with ortholog-based and other methods.

Results

Orthologous pairs of 18 eukaryotic species were expanded and merged with experimental PPI datasets. The contributions of interologs from each species were evaluated. The expanded orthologous pairs enable the inference of interologs for various species. For example, more than 32,000 human interactions can be predicted. The same dataset has also been applied to the prediction of host-pathogen interactions. PPIs between P. falciparum calmodulin and several H. sapiens proteins are predicted, and these interactions may contribute to the maintenance of host cell Ca2+ concentration. Using comparisons with Bayesian and structure-based approaches, interactions between putative HSP40 homologs of P. falciparum and the H. sapiens TNF receptor associated factor family are revealed, suggesting a role for these interactions in the interference of the human immune response to P. falciparum.

Conclusion

The PPI datasets are available from POINT http://point.bioinformatics.tw/ and POINeT http://poinet.bioinformatics.tw/. Further development of methods to predict host-pathogen interactions should incorporate multiple approaches in order to improve sensitivity, and should facilitate the identification of targets for drug discovery and design.
Dynamic sensitivity analysis of biological systems
Authors: Wu Wu Hsiung , Wang Feng Sheng , Chang Maw Shang
Published: December 2008

Background

A mathematical model to understand, predict, control, or even design a real biological system is a central theme in systems biology. A dynamic biological system is always modeled as a nonlinear ordinary differential equation (ODE) system. How to simulate the dynamic behavior and dynamic parameter sensitivities of systems described by ODEs efficiently and accurately is a critical job. In many practical applications, e.g., the fed-batch fermentation systems, the system admissible input (corresponding to independent variables of the system) can be time-dependent. The main difficulty for investigating the dynamic log gains of these systems is the infinite dimension due to the time-dependent input. The classical dynamic sensitivity analysis does not take into account this case for the dynamic log gains.

Results

We present an algorithm with an adaptive step size control that can be used for computing the solution and dynamic sensitivities of an autonomous ODE system simultaneously. Although our algorithm is one of the decouple direct methods in computing dynamic sensitivities of an ODE system, the step size determined by model equations can be used on the computations of the time profile and dynamic sensitivities with moderate accuracy even when sensitivity equations are more stiff than model equations. To show this algorithm can perform the dynamic sensitivity analysis on very stiff ODE systems with moderate accuracy, it is implemented and applied to two sets of chemical reactions: pyrolysis of ethane and oxidation of formaldehyde. The accuracy of this algorithm is demonstrated by comparing the dynamic parameter sensitivities obtained from this new algorithm and from the direct method with Rosenbrock stiff integrator based on the indirect method. The same dynamic sensitivity analysis was performed on an ethanol fed-batch fermentation system with a time-varying feed rate to evaluate the applicability of the algorithm to realistic models with time-dependent admissible input.

Conclusion

By combining the accuracy we show with the efficiency of being a decouple direct method, our algorithm is an excellent method for computing dynamic parameter sensitivities in stiff problems. We extend the scope of classical dynamic sensitivity analysis to the investigation of dynamic log gains of models with time-dependent admissible input.
An integrated database-pipeline system for studying single nucleotide polymorphisms and diseases
Authors: Yang Jin Ok , Hwang Sohyun , Oh Jeongsu , Bhak Jong , Sohn Tae-Kwon
Published: December 2008

Background

Studies on the relationship between disease and genetic variations such as single nucleotide polymorphisms (SNPs) are important. Genetic variations can cause disease by influencing important biological regulation processes. Despite the needs for analyzing SNP and disease correlation, most existing databases provide information only on functional variants at specific locations on the genome, or deal with only a few genes associated with disease. There is no combined resource to widely support gene-, SNP-, and disease-related information, and to capture relationships among such data. Therefore, we developed an integrated database-pipeline system for studying SNPs and diseases.

Results

To implement the pipeline system for the integrated database, we first unified complicated and redundant disease terms and gene names using the Unified Medical Language System (UMLS) for classification and noun modification, and the HUGO Gene Nomenclature Committee (HGNC) and NCBI gene databases. Next, we collected and integrated representative databases for three categories of information. For genes and proteins, we examined the NCBI mRNA, UniProt, UCSC Table Track and MitoDat databases. For genetic variants we used the dbSNP, JSNP, ALFRED, and HGVbase databases. For disease, we employed OMIM, GAD, and HGMD databases. The database-pipeline system provides a disease thesaurus, including genes and SNPs associated with disease. The search results for these categories are available on the web page http://diseasome.kobic.re.kr/, and a genome browser is also available to highlight findings, as well as to permit the convenient review of potentially deleterious SNPs among genes strongly associated with specific diseases and clinical phenotypes.

Conclusion

Our system is designed to capture the relationships between SNPs associated with disease and disease-causing genes. The integrated database-pipeline provides a list of candidate genes and SNP markers for evaluation in both epidemiological and molecular biological approaches to diseases-gene association studies. Furthermore, researchers then can decide semi-automatically the data set for association studies while considering the relationships between genetic variation and diseases. The database can also be economical for disease-association studies, as well as to facilitate an understanding of the processes which cause disease. Currently, the database contains 14,674 SNP records and 109,715 gene records associated with human diseases and it is updated at regular intervals.
CMKb: a web-based prototype for integrating Australian Aboriginal customary medicinal plant knowledge
Authors: Gaikwad Jitendra , Khanna Varun , Vemulpad Subramanyam , Jamie Joanne , Kohen Jim , Ranganathan Shoba
Published: December 2008

Background

The customary medicinal plant knowledge possessed by the Australian Aboriginal people is a significant resource. Published information on it is scattered throughout the literature, in heterogeneous data formats, and is scattered among various Aboriginal communities across Australia, due to a multiplicity of languages. This ancient knowledge is at risk due to loss of biodiversity, cultural impact and the demise of many of its custodians. We have developed the Customary Medicinal Knowledgebase (CMKb), an integrated multidisciplinary resource, to document, conserve and disseminate this knowledge.

Description

CMKb is an online relational database for collating, disseminating, visualising and analysing initially public domain data on customary medicinal plants. The database stores information related to taxonomy, phytochemistry, biogeography, biological activities of customary medicinal plant species as well as images of individual species. The database can be accessed at http://biolinfo.org/cmkb. Known bioactive molecules are characterized within the chemoinformatics module of CMKb, with functions available for molecular editing and visualization.

Conclusion

CMKb has been developed as a prototype data resource for documenting, integrating, disseminating, analysing multidisciplinary customary medicinal plant data from Australia and to facilitate user-defined complex querying. Each species in CMKb is linked to online resources such as the Integrated Taxonomic Information System (ITIS), NCBI Taxonomy, Australia's SpeciesLinks-Integrated Botanical Information System (IBIS) and Google images. The bioactive compounds are linked to the PubChem database. Overall, CMKb serves as a single knowledgebase for holistic plant-derived therapeutics and can be used as an information resource for biodiversity conservation, to lead discovery and conservation of customary medicinal knowledge.
Predicting RNA-binding sites of proteins using support vector machines and evolutionary information
Authors: Cheng Cheng-Wei , Su Emily Chia-Yu , Hwang Jenn-Kang , Sung Ting-Yi , Hsu Wen-Lian
Published: December 2008

Background

RNA-protein interaction plays an essential role in several biological processes, such as protein synthesis, gene expression, posttranscriptional regulation and viral infectivity. Identification of RNA-binding sites in proteins provides valuable insights for biologists. However, experimental determination of RNA-protein interaction remains time-consuming and labor-intensive. Thus, computational approaches for prediction of RNA-binding sites in proteins have become highly desirable. Extensive studies of RNA-binding site prediction have led to the development of several methods. However, they could yield low sensitivities in trade-off for high specificities.

Results

We propose a method, RNAProB, which incorporates a new smoothed position-specific scoring matrix (PSSM) encoding scheme with a support vector machine model to predict RNA-binding sites in proteins. Besides the incorporation of evolutionary information from standard PSSM profiles, the proposed smoothed PSSM encoding scheme also considers the correlation and dependency from the neighboring residues for each amino acid in a protein. Experimental results show that smoothed PSSM encoding significantly enhances the prediction performance, especially for sensitivity. Using five-fold cross-validation, our method performs better than the state-of-the-art systems by 4.90%~6.83%, 0.88%~5.33%, and 0.10~0.23 in terms of overall accuracy, specificity, and Matthew's correlation coefficient, respectively. Most notably, compared to other approaches, RNAProB significantly improves sensitivity by 7.0%~26.9% over the benchmark data sets. To prevent data over fitting, a three-way data split procedure is incorporated to estimate the prediction performance. Moreover, physicochemical properties and amino acid preferences of RNA-binding proteins are examined and analyzed.

Conclusion

Our results demonstrate that smoothed PSSM encoding scheme significantly enhances the performance of RNA-binding site prediction in proteins. This also supports our assumption that smoothed PSSM encoding can better resolve the ambiguity of discriminating between interacting and non-interacting residues by modelling the dependency from surrounding residues. The proposed method can be used in other research areas, such as DNA-binding site prediction, protein-protein interaction, and prediction of posttranslational modification sites.
Extracting transcription factor binding sites from unaligned gene sequences with statistical models
Authors: Lu Chung-Chin , Yuan Wei-Hao , Chen Te-Ming
Published: December 2008

Background

Transcription factor binding sites (TFBSs) are crucial in the regulation of gene transcription. Recently, chromatin immunoprecipitation followed by cDNA microarray hybridization (ChIP-chip array) has been used to identify potential regulatory sequences, but the procedure can only map the probable protein-DNA interaction loci within 1–2 kb resolution. To find out the exact binding motifs, it is necessary to build a computational method to examine the ChIP-chip array binding sequences and search for possible motifs representing the transcription factor binding sites.

Results

We developed a program to find out accurate motif sites from a set of unaligned DNA sequences in the yeast genome. Compared with MDscan, the prediction results suggest that, overall, our algorithm outperforms MDscan since the predicted motifs are more consistent with previously known specificities reported in the literature and have better prediction ranks. Our program also outperforms the constraint-less Cosmo program, especially in the elimination of false positives.

Conclusion

In this study, an improved sampling algorithm is proposed to incorporate the binomial probability model to build significant initial candidate motif sets. By investigating the statistical dependence between base positions in TFBSs, the method of dependency graphs and their expanded Bayesian networks is combined. The results show that our program satisfactorily extract transcription factor binding sites from unaligned gene sequences.
VarDetect: a nucleotide sequence variation exploratory tool
Authors: Ngamphiw Chumpol , Kulawonganunchai Supasak , Assawamakin Anunchai , Jenwitheesuk Ekachai , Tongsima Sissades
Published: December 2008

Background

Single nucleotide polymorphisms (SNPs) are the most commonly studied units of genetic variation. The discovery of such variation may help to identify causative gene mutations in monogenic diseases and SNPs associated with predisposing genes in complex diseases. Accurate detection of SNPs requires software that can correctly interpret chromatogram signals to nucleotides.

Results

We present VarDetect, a stand-alone nucleotide variation exploratory tool that automatically detects nucleotide variation from fluorescence based chromatogram traces. Accurate SNP base-calling is achieved using pre-calculated peak content ratios, and is enhanced by rules which account for common sequence reading artifacts. The proposed software tool is benchmarked against four other well-known SNP discovery software tools (PolyPhred, novoSNP, Genalys and Mutation Surveyor) using fluorescence based chromatograms from 15 human genes. These chromatograms were obtained from sequencing 16 two-pooled DNA samples; a total of 32 individual DNA samples. In this comparison of automatic SNP detection tools, VarDetect achieved the highest detection efficiency.

Availability

VarDetect is compatible with most major operating systems such as Microsoft Windows, Linux, and Mac OSX. The current version of VarDetect is freely available at http://www.biotec.or.th/GI/tools/vardetect.
Imputation of missing genotypes: an empirical evaluation of IMPUTE
Authors: Zhao Zhenming , Timofeev Nadia , Hartley Stephen W , Chui David HK , Fucharoen Supan , Perls Thomas T , Steinberg Martin H , Baldwin Clinton T , Sebastiani Paola
Published: December 2008

Background

Imputation of missing genotypes is becoming a very popular solution for synchronizing genotype data collected with different microarray platforms but the effect of ethnic background, subject ascertainment, and amount of missing data on the accuracy of imputation are not well understood.

Results

We evaluated the accuracy of the program IMPUTE to generate the genotype data of partially or fully untyped single nucleotide polymorphisms (SNPs). The program uses a model-based approach to imputation that reconstructs the genotype distribution given a set of referent haplotypes and the observed data, and uses this distribution to compute the marginal probability of each missing genotype for each individual subject that is used to impute the missing data. We assembled genome-wide data from five different studies and three different ethnic groups comprising Caucasians, African Americans and Asians. We randomly removed genotype data and then compared the observed genotypes with those generated by IMPUTE. Our analysis shows 97% median accuracy in Caucasian subjects when less than 10% of the SNPs are untyped and missing genotypes are accepted regardless of their posterior probability. The median accuracy increases to 99% when we require 0.95 minimum posterior probability for an imputed genotype to be acceptable. The accuracy decreases to 86% or 94% when subjects are African Americans or Asians. We propose a strategy to improve the accuracy by leveraging the level of admixture in African Americans.

Conclusion

Our analysis suggests that IMPUTE is very accurate in samples of Caucasians origin, it is slightly less accurate in samples of Asians background, but substantially less accurate in samples of admixed background such as African Americans. Sample size and ascertainment do not seem to affect the accuracy of imputation.
Genetic variation in South Indian castes: evidence from Y-chromosome, mitochondrial, and autosomal polymorphisms
Authors: Watkins WS , Thara R , Mowry BJ , Zhang Y , Witherspoon DJ , Tolpinrud W , Bamshad MJ , Tirupati S , Padmavati R , Smith H , Nancarrow D , Filippich C , Jorde LB
Published: December 2008

Background

Major population movements, social structure, and caste endogamy have influenced the genetic structure of Indian populations. An understanding of these influences is increasingly important as gene mapping and case-control studies are initiated in South Indian populations.

Results

We report new data on 155 individuals from four Tamil caste populations of South India and perform comparative analyses with caste populations from the neighboring state of Andhra Pradesh. Genetic differentiation among Tamil castes is low (RST= 0.96% for 45 autosomal short tandem repeat (STR) markers), reflecting a largely common origin. Nonetheless, caste- and continent-specific patterns are evident. For 32 lineage-defining Y-chromosome SNPs, Tamil castes show higher affinity to Europeans than to eastern Asians, and genetic distance estimates to the Europeans are ordered by caste rank. For 32 lineage-defining mitochondrial SNPs and hypervariable sequence (HVS) 1, Tamil castes have higher affinity to eastern Asians than to Europeans. For 45 autosomal STRs, upper and middle rank castes show higher affinity to Europeans than do lower rank castes from either Tamil Nadu or Andhra Pradesh. Local between-caste variation (Tamil Nadu RST= 0.96%, Andhra Pradesh RST= 0.77%) exceeds the estimate of variation between these geographically separated groups (RST= 0.12%). Low, but statistically significant, correlations between caste rank distance and genetic distance are demonstrated for Tamil castes using Y-chromosome, mtDNA, and autosomal data.

Conclusion

Genetic data from Y-chromosome, mtDNA, and autosomal STRs are in accord with historical accounts of northwest to southeast population movements in India. The influence of ancient and historical population movements and caste social structure can be detected and replicated in South Indian caste populations from two different geographic regions.
Biosynthesis of storage compounds by Rhodococcus jostii RHA1 and global identification of genes involved in their metabolism
Authors: Hernández Martín A , Mohn William W , Martínez Eliana , Rost Enrique , Alvarez Adrián F , Alvarez Héctor M
Published: December 2008

Background

Members of the genus Rhodococcus are frequently found in soil and other natural environments and are highly resistant to stresses common in those environments. The accumulation of storage compounds permits cells to survive and metabolically adapt during fluctuating environmental conditions. The purpose of this study was to perform a genome-wide bioinformatic analysis of key genes encoding metabolism of diverse storage compounds by Rhodococcus jostii RHA1 and to examine its ability to synthesize and accumulate triacylglycerols (TAG), wax esters, polyhydroxyalkanoates (PHA), glycogen and polyphosphate (PolyP).

Results

We identified in the RHA1 genome: 14 genes encoding putative wax ester synthase/acyl-CoA:diacylglycerol acyltransferase enzymes (WS/DGATs) likely involved in TAG and wax esters biosynthesis; a total of 54 genes coding for putative lipase/esterase enzymes possibly involved in TAG and wax ester degradation; 3 sets of genes encoding PHA synthases and PHA depolymerases; 6 genes encoding key enzymes for glycogen metabolism, one gene coding for a putative polyphosphate kinase and 3 putative exopolyphosphatase genes. Where possible, key amino acid residues in the above proteins (generally in active sites, effectors binding sites or substrate binding sites) were identified in order to support gene identification. RHA1 cells grown under N-limiting conditions, accumulated TAG as the main storage compounds plus wax esters, PHA (with 3-hydroxybutyrate and 3-hydroxyvalerate monomers), glycogen and PolyP. Rhodococcus members were previously known to accumulate TAG, wax esters, PHAs and polyP, but this is the first report of glycogen accumulation in this genus.

Conclusion

RHA1 possess key genes to accumulate diverse storage compounds. Under nitrogen-limiting conditions lipids are the principal storage compounds. An extensive capacity to synthesize and metabolize storage compounds appears to contribute versatility to RHA1 in its responses to environmental stresses.
The PPARGC1AGly482Ser polymorphism is associated with left ventricular diastolic dysfunction in men
Authors: Ingelsson Erik , Bennet Louise , Ridderstråle Martin , Söderström Marianne , Råstam Lennart , Lindblad Ulf
Published: December 2008

Background

The Gly482Ser polymorphism in peroxisome proliferator-activated receptor gamma coactivator-1 alpha (PPARGC1A) has been demonstrated to be associated with diabetes, obesity and hypertension, all of which are important risk factors for left ventricular diastolic dysfunction.

Methods

The PPARGC1A Gly482Ser polymorphism was genotyped in a community-based cohort of 499 men and 533 women, who also underwent an echocardiographic examination to determine their left ventricular diastolic function. The association between the polymorphism and the presence of diastolic dysfunction was evaluated using logistic regression models.

Results

The Ser allele of the PPARGC1A Gly482Ser polymorphism was significantly associated with a lower risk of diastolic dysfunction in men, but not in women. In a model adjusting for potential confounders (age, body mass index, leisure time physical activity, hypertension and diabetes) the results were still significant and substantial (odds ratio 0.13, 95% confidence interval 0.03–0.54, p for trend = 0.004). The results were consistent in a series of models, and they imply a multiplicative, protective effect of the Ser allele, with lower risk of diastolic dysfunction for each copy of the allele.

Conclusion

The Ser allele of the PPARGC1A Gly482Ser polymorphism was associated with decreased risk of diastolic left ventricular dysfunction in men, but not in women, in our large community-based sample. It was associated with a substantially decreased risk, even after adjustment for potential confounders. The clinical importance of the findings has to be established in further studies.
Knottin cyclization: impact on structure and dynamics
Authors: Heitz Annie , Avrutina Olga , Le-Nguyen Dung , Diederichsen Ulf , Hernandez Jean-François , Gracy Jérôme , Kolmar Harald , Chiche Laurent
Published: December 2008

Background

Present in various species, the knottins (also referred to as inhibitor cystine knots) constitute a group of extremely stable miniproteins with a plethora of biological activities. Owing to their small size and their high stability, knottins are considered as excellent leads or scaffolds in drug design. Two knottin families contain macrocyclic compounds, namely the cyclotides and the squash inhibitors. The cyclotide family nearly exclusively contains head-to-tail cyclized members. On the other hand, the squash family predominantly contains linear members. Head-to-tail cyclization is intuitively expected to improve bioactivities by increasing stability and lowering flexibility as well as sensitivity to proteolytic attack.

Results

In this paper, we report data on solution structure, thermal stability, and flexibility as inferred from NMR experiments and molecular dynamics simulations of a linear squash inhibitor EETI-II, a circular squash inhibitor MCoTI-II, and a linear analog lin-MCoTI. Strikingly, the head-to-tail linker in cyclic MCoTI-II is by far the most flexible region of all three compounds. Moreover, we show that cyclic and linear squash inhibitors do not display large differences in structure or flexibility in standard conditions, raising the question as to why few squash inhibitors have evolved into cyclic compounds. The simulations revealed however that the cyclization increases resistance to high temperatures by limiting structure unfolding.

Conclusion

In this work, we show that, in contrast to what could have been intuitively expected, cyclization of squash inhibitors does not provide clear stability or flexibility modification. Overall, our results suggest that, for squash inhibitors in standard conditions, the circularization impact might come from incorporation of an additional loop sequence, that can contribute to the miniprotein specificity and affinity, rather than from an increase in conformational rigidity or protein stability. Unfolding simulations showed however that cyclization is a stabilizing factor in strongly denaturing conditions. This information should be useful if one wants to use the squash inhibitor scaffold in drug design.
Lipocalin 2 promotes lung metastasis of murine breast cancer cells
Authors: Shi Han , Gu Yuchao , Yang Jing , Xu Liang , Mi Wenyi , Yu Wengong
Published: December 2008

Background

Lipocalin 2, an iron binding protein, is abnormally expressed in some malignant human cancers and may play an important role in tumor metastasis. However, the roles of lipocalin 2 in breast cancer formation and metastasis have not been clearly shown. This study aimed to investigate the roles of lipocalin 2 in breast tumor metastasis.

Methods

Lipocalin 2 was overexpressed in the metastatic 4T1 murine mammary cancer cells. The effects of lipocalin 2 overexpression on the malignancy of breast cancer cells were examined using cell proliferation assay, migration assay, invasion assay, and soft agar assayin vitro. Tumor formation and metastasis abilities were examined using a well established mouse mammary tumor modelin vivo.

Results

Lipocalin 2 overexpression significantly enhanced the migration and invasion abilities of 4T1 cellsin vitro, and lung metastasisin vivo. But overexpression of lipocalin 2 in 4T1 cells didn't affect cell proliferation and anchorage-independent growthin vitro, and primary tumor weightin vivo. Further studies demonstrated that the inhibition of the PI3K/Akt pathway could be a causative mechanism for the promotion of breast cancer migration/invasion induced by lipocalin 2 overexpression.

Conclusion

These results clarified that lipocalin 2 could promote lung metastasis of 4T1 cells through the inhibition of the PI3K/Akt pathway, suggesting that lipocalin 2 was a potential target for therapy of breast cancer.
Simulation of DC dual-laterolog measurements in complex formations: A Fourier-series approach with nonorthogonal coordinates and self-adapting finite elements
Authors: Nam Myung Jin , Pardo David , Torres-Verdín Carlos
Published: December 2008

Dual laterolog (DLL) makes use of a galvanic conduction principle to focus electrical currents into rock formations, thereby minimizing shoulder and borehole effects in the measurement of formation resistivity. The tool includes two separate focusing systems: deep-sensing (LLd) and shallow-sensing modes (LLs). Laterolog current-focusing systems were designed for operation primarily in vertical boreholes penetrating horizontal layers; only recently their design has been revised for operation in deviated wells in the presence of electrical anisotropy. We simulated three-dimensional (3D) DLL measurements in dipping, invaded, and electrically anisotropic formations and appraised the corresponding effects on apparent resistivity logs. Simulations were performed by combining the use of a Fourier-series expansion in a nonorthogonal system of coordinates with an existing 2D goal-oriented, higher-order, and self-adaptive finite-element method. This numerical algorithm yields accurate solutions in limited CPU time because only a few Fourier modes are needed to simulate practical applications. For the calculation of focused currents, we introduced an embedded postprocessing method that incorporates a synthetic focusing principle to compute current intensities at each iterative step of optimal mesh refinements. Our numerical method accurately simulates 3D DLL measurements in rock formations that exhibit extreme contrasts of electrical resistivity. Simulations indicate that LLs resistivity logs are more sensitive to both invaded and anisotropic layers than LLd resistivity logs. In deviated wells, shoulder-bed effects on apparent resistivity logs increase with an increase of dip angle, and are emphasized across thin conductive layers. Electrical anisotropy effects on apparent resistivity logs increase substantially with dip angle.
The Paleoproterozoic Kristineberg mining area, northern Sweden: Results from integrated 3D geophysical and geologic modeling, and implications for targeting ore deposits
Authors: Malehmir Alireza , Thunehed Hans , Tryggvason Ari
Published: December 2008

The Kristineberg mining area in the western part of the Paleoproterozoic Skellefte Ore District, northern Sweden, is well known for its base-metal and recent gold discoveries. A pilot 3D geologic model has been constructed on a crustal scale, covering an area of [Formula: see text] to depths of [Formula: see text]. Constrained 3D inverse and forward gravity modeling have been performed to confirm and refine previous modeling along seismic profiles using mainly 2.5D techniques. The 3D inverse gravity modeling was geared to generating isodensity surfaces that enclose regions within the model of anomalous density contrast. The 3D forward gravity modeling was conducted to include faulting and folding systems that are difficult to include in the inversion. The 3D geologic model supports many previous interpretations but also reveals new features of the regional geology that are important for future targeting of base-metal and gold deposits. The margins of a thick granite in the south dip steeply inward, suggesting the possibility of room to accommodate another large base-metal deposit if the granitic rocks are juxtaposed with volcanic rocks at depth. Gravity modeling also suggests the observed Bouguer gravity high within the western metasediments can be explained by a large mafic intrusion that has dioritic to tonalitic composition and no significant magnetic signature. Because mafic-ultramafic intrusions within metasediments can indicate gold, this interpretation suggests the western metasediments have a high gold potential.
f-x adaptive seismic-trace interpolation
Authors: Naghizadeh Mostafa , Sacchi Mauricio D.
Published: December 2008

We use exponentially weighted recursive least squares to estimate adaptive prediction filters for frequency-space [Formula: see text] seismic interpolation. Adaptive prediction filters can model signals where the dominant wavenumbers vary in space. This concept leads to an [Formula: see text] interpolation method that does not require windowing strategies for optimal results. In other words, adaptive prediction filters can be used to interpolate waveforms that have spatially variant dips. The interpolation method’s performance depends on two parameters: filter length and forgetting factor. We pay particular attention to selection of the forgetting factor because it controls the algorithm’s adaptability to changes in local dip. Finally, we use synthetic- and real-data examples to illustrate the performance of the proposed adaptive [Formula: see text] interpolation method.
Theory and modeling of constant-Q P- and S-waves using fractional time derivatives
Authors: Carcione José M.
Published: December 2008

I have developed and solved the constant-[Formula: see text] model for the attenuation of P- and S-waves in the time domain using a new modeling algorithm based on fractional derivatives. The model requires time derivatives of order [Formula: see text] applied to the strain components, where [Formula: see text] and [Formula: see text], with [Formula: see text] the P-wave or S-wave quality factor. The derivatives are computed with the Grünwald-Letnikov and central-difference fractional approximations, which are extensions of the standard finite-difference operators for derivatives of integer order. The modeling uses the Fourier method to compute the spatial derivatives, and therefore can handle complex geometries and general material-property variability. I verified the results by comparison with the 2D analytical solution obtained for wave propagation in homogeneous Pierre Shale. Moreover, the modeling algorithm was used to compute synthetic seismograms in heterogeneous media corresponding to a crosswell seismic experiment.
Plastic limit loads for thick-walled branch junctions
Authors: Lee K-H , Kim Y-J , Budden P J , Nikbin K
Published: December 2008

This technical note extends the validity of limit load solutions for thin-walled branch junctions, previously proposed by the current author, to thick-walled cases. It is achieved simply by re-normalizing the thin-wall expressions by the limit loads of thick-walled tubes instead of those of thin-walled tubes. Comparison with finite element results shows overall good agreement.
Computation of load factors in bolted connections
Authors: Cornwell R E
Published: December 2008

An accurate computation of the joint load factors is critical for the safe design of bolted connections. This study provides a four-step procedure for the direct computation of the joint load factors for a variety of bolt diameters, joint thicknesses, individual plate thicknesses, and plate material combinations. The finite element method was used to calculate the bolt and plate deformations necessary to directly compute the load factor for 4424 unique combinations of the four joint design parameters. The procedure developed in this study provides accurate estimates of the joint load factor over the entire range of the four joint design parameters. All 4424 joint designs originally analysed with the finite element method were recomputed using the proposed procedure. The root mean square error was found to be 0.58 per cent with a correlation coefficient between the load factors computed by using the original finite element analyses and the proposed procedure to be 0.9998.
Stability and bifurcation of a non-linear bearing-flexible rotor coupling dynamic system
Authors: Lu Y J , Dai R , Hei D , Zhang Y F , Liu H , Yu L
Published: December 2008

The non-linear coupling dynamic behaviour of a hydrodynamic bearing-flexible rotor system is analysed. A local iteration method consisting of the improved Wilson-θ method, the predictor—corrector mechanism, and the Newton—Raphson method is proposed to calculate the non-linear dynamic response. Using the proposed method, the iterations are executed only on non-linear degrees of freedom. The iteration process shows improved convergence by taking the prediction value as the initial value. The stability and bifurcation type of periodic responses are determined by the Floquet theory. According to the physical characteristics of the oil film, a variational constraint approach is proposed to revise continuously the variational form of the Reynolds equation at each step of the iterative process. Non-linear oil film forces and their Jacobians are calculated simultaneously without an increase in computational costs, and compatible accuracy is obtained. Numerical results reveal periodic, quasi-periodic, coexisting, and jump solutions of rich and complex non-linear behaviours of the system and show that the proposed methods not only save computational costs but also have high precision.
Spectral entropy: A complementary index for rolling element bearing performance degradation assessment
Authors: Pan Y N , Chen J , Li X L
Published: December 2008

Performance degradation assessment has been proposed to realize equipment's near-zero downtime and maximum productivity. Exploring effective indices is crucial for it. In this study, rolling element bearing has been taken as a research object, spectral entropy is proposed to be as a complementary index for its performance degradation assessment, and its accelerated life test has been performed to collect vibration data over a whole lifetime (normal-fault-failure). Results of both simulation and experiment show that spectral entropy is an effective complementary index.
Chaos control and anticontrol of a tachometer system by Ge—Yao—Chen partial region stability theory
Authors: Ge Z-M , Chiang C-Y
Published: December 2008

In this paper, chaos control and anticontrol of a tachometer system by Ge—Yao—Chen (GYC) partial region stability are proposed. The Lyapunov function becomes a simple linear homogeneous function and the controllers become simpler by using the GYC partial region stability theory. The simulation results are more precise because the controllers are in lower degree than that of traditional controllers. Finally, chaos control and anticontrol of the tachometer system by GYC partial region stability are obtained and verified by numerical simulations.
Analysis of a pilot valve and taper groove-based compound damping device
Authors: Bhatnagar R M , Bhattacharya B , Biswas G
Published: December 2008

This paper describes the lumped mass parameter model of a pilot valve and taper rod-type compounded damping device used for high-speed and high-loading applications such as heavy artillery guns. The modelling of pilot valve and fluid interaction has been described by Euler equations and Laplace equations of potential flow in cylindrical polar coordinates for the axisymmetric situation. The viscosity effects in the model have been accounted through the inclusion of the damping term in the equation of motion of the pilot valve. The model presented has been experimentally validated using a test rig which is capable of simulating the firing impulse in the case of an artillery gun. The pilot valve results in a logarithmic variation in the orifice area of the damper leading to mechanical implementation of fault tolerance in the damper.
Optimal design of mechanical components using the Bees Algorithm
Authors: Pham D T , Ghanbarzadeh A , Otri S , Koç E
Published: December 2008

This paper describes the first application of the Bees Algorithm to mechanical design optimization. The Bees Algorithm is a search procedure inspired by the way honey bees forage for food. Two standard mechanical design problems, the design of a welded beam structure and the design of coil springs, were used to benchmark the Bees Algorithm against other optimization techniques. The paper presents the results obtained showing the robust performance of the Bees Algorithm.
Lay-up sequence design of laminate composite plates and a cylindrical skirt using ant colony optimization
Authors: Rama Mohan Rao A
Published: December 2008

For laminated composite materials, the stacking sequence design is indispensable to make efficient use of the material properties. Laminated composites are usually fabricated from unidirectional plies of given thickness with fibre orientations limited to a small set of angles (e.g. 0°, +45°, −45°, and 90°). This leads to a combinatorial optimization problem, which is rather complex to solve. In this article, an adaptation of a popular swarm intelligence-based combinatorial optimization technique called ant colony optimization (ACO) for lay-up sequence optimization of laminate composite structures is explored. The basic ACO algorithm is hybridized with a neighbourhood search algorithm built with tabu search features to improve the overall performance of the algorithm. Numerical experiments have been carried out by first considering the popularly used bench mark problem of buckling and failure load optimization of a laminate composite plate. Later, the ACO is employed to solve a multi-objective problem of simultaneous optimization of cost and weight of a hybrid laminate composite cylindrical skirt. Numerical studies carried out in this article clearly indicate that the ACO combined with an appropriate neighbourhood search can be an effective combinatorial optimization tool for stacking sequence optimization of laminate composite structures and the computational performance is found to be superior when compared to other popular meta-heuristic algorithms.
Forward dynamics simulation of human walking employing an iterative feedback tuning approach
Authors: Ghafari Selk A , Meghdari A , Vossoughi G R
Published: December 2008

Inverse dynamics analysis as well as the generation of an optimal goal oriented human motion both lead to the problem of finding suitable activations of the redundant muscles involved. This paper employs an iterative feedback tuning approach to perform the forward dynamics simulation of the human musculoskeletal system during level walking. A modified form of the proportional-integral-derivative (PID) controller is proposed to stabilize the movement and provide tracking of problems of the desired lower extremity joint profiles. Controller parameters were determined iteratively using an optimization algorithm to minimize tracking errors during forward dynamics simulation. Static optimization was employed simultaneously to compute a set of desired musculotendon forces in the closed-loop simulation to resolve muscle redundancy. Quantitative comparisons of the simulation results with the gait experimental measurements and the reference muscle activity show the accuracy and efficiency of the proposed method to provide a stable gait.
A proportional intensity segmented model for maintained systems
Authors: Syamsundar A , Naikan V N A
Published: December 2008

The failure times of a maintained system are generally modelled using point processes, the most common being the homogeneous and the non-homogeneous point processes representing maximal and minimal repairs. Additional information obtained with regard to the maintained system which may have influenced the failure characteristics of the maintained system can be used in the form of covariates to ascertain their effect on the system's failure intensity. These covariates are deemed to act multiplicatively on the system's failure intensity using a suitable link function; the usual link function being the exponential. These processes are generally able to model maintained systems with a fair degree of accuracy. However, whenever there is a change in the environment of the maintained system these models are not able to exactly identify and take into account the corresponding change in the intensity unless the covariates chosen are able to totally account for the changes. Also, the covariates themselves may be subject to change, and then such systems need to be modelled by segmented models with the system domain divided into segments at the points of changes in the environment. The individual segments can then be modelled by a point process and/or proportional intensity model, and these can be combined to form a composite model. This paper develops a statistical model of the failure process of a maintained system in such an environment and applies it to the field data from an industrial setting to demonstrate that appropriate parameter estimates for such phenomena can be obtained, and such models are shown to more accurately describe the maintained system in a changing environment than the single point process/proportional intensity models usually used.
Using Bayesian networks to predict software defects and reliability
Authors: Fenton N , Neil M , Marquez D
Published: December 2008

This paper reviews the use of Bayesian networks (BNs) in predicting software defects and software reliability. The approach allows analysts to incorporate causal process factors as well as combine qualitative and quantitative measures, hence overcoming some of the well-known limitations of traditional software metrics methods. The approach has been used and reported on by organizations such as Motorola, Siemens, and Philips. However, one of the impediments to more widespread use of BNs for this type of application was that, traditionally, BN tools and algorithms suffered from an obvious ‘Achilles’ heel’ – they were not able to handle continuous nodes properly, if at all. This forced modellers to have to predefine discretization intervals in advance and resulted in inaccurate predictions where the range, for example, of defect counts was large. Fortunately, recent advances in BN algorithms now make it possible to perform inference in BNs with continuous nodes, without the need to prespecify discretization levels. Using such ‘dynamic discretization’ algorithms results in significantly improved accuracy for defects and reliability prediction type models.
Preparation and Characterization of Spherical and Balloon-Like Calcium Phosphate Particles
Authors: Kandori Kazuhiko , Tada Kiri , Fukusumi Masao , Morisada Yoshiaki
Published: December 2008

Calcium phosphate particles were prepared by aging a solution of CaCl2 and sodium triphosphate (sodium tripolyphosphate, Natpp: Na5P3O10) at 100–150 °C for 16 h in a Teflon-lined screw-capped Pyrex test tube. The rod-like and spherical particles were precipitated at an extremely fast rate of reaction under 100 °C. The spherical particles were only produced in a very narrow region at 100 °C by aggregation of primary small particles. The rod-like particles were CaNa2P2O7·4H2O but the uniform spherical ones were amorphous and the latter ones were crystallized to β-Ca2P2O7 after being calcined above 600 °C. The aging temperature drastically varied the particle shape under conditions for producing uniform spherical particles; solid spherical particles were produced up to the aging temperature of 115 °C but balloon-like hollow spheres were precipitated at 120 °C. However, large and irregular agglomerates made up of extremely small rod-like particles were precipitated after aging the solution above 125 °C. TEM observation and ICP-AES measurements revealed that the balloon-like hollow spheres were produced by dissolving the interior of solid spherical particles after reinforced their shell by the adsorption of unhydrolyzed tpp. The spherical and balloon-like calcium phosphate particles with amorphous crystal form showed high selective adsorption of H2O by rehydration of Ca2+ ions by penetrated H2O molecules into the particles. In particular, the balloon-like hollow spheres of calcium phosphate may hold potential as drug delivery vehicles and have biocompatibility advantages.
Matrix Isolation Infrared Spectroscopic and Density Functional Theory Studies on the Reactions of Dysprosium Hydride with Carbon Monoxide
Authors: Teng Yun-Lei , Xu Qiang
Published: December 2008

Laser-ablated dysprosium hydride has been co-deposited at 4 K with carbon monoxide in excess argon. Product HDyCO has been formed in the present experiments and characterized using infrared spectroscopy on the basis of the results of the isotopic shifts, mixed isotopic splitting patterns, stepwise annealing, and the comparison with theoretical predictions. Density functional theory calculations have been performed. The agreement between the experimental and calculated vibrational frequencies, and isotopic shifts supports the identification of the molecule from the matrix infrared spectra. A plausible reaction mechanism has been proposed to account for the formation of this molecule.