bluuebunny/crossref_metadata_2025_split huggingface dataset:
Computations of flow over a flexible plate using the hybrid Cartesian/immersed boundary method
Authors: Shin Sangmook , Bae Sung Yong , Kim In Chul , Kim Yong Jig , Goo Ja Sam 
Published: February 2007

AbstractA hybrid Cartesian/immersed boundary code is developed and applied to interactions between a flexible plate and a surrounding fluid. The velocities at the immersed boundary (IB) nodes are reconstructed by interpolations along local normal lines to an interface. A new criterion is suggested to distribute the IB nodes near an interface. The suggested criterion guarantees a closed fluid domain by a set of the IB nodes and it is applicable to a zero‐thickness body. To eliminate the pressure interpolation at the IB nodes, the hybrid staggered/non‐staggered grid method is adapted. The developed code is validated by comparisons with other experimental and computational results of flow around an in‐line oscillating cylinder. Good agreements are achieved for velocity profiles and vorticity and pressure contours. As applications to the fluid–structure interaction, oscillations of flexible plate in a resting fluid and flow over a flexible plate are simulated. The elastic deformations of the flexible plate are modelled based on the equations of motion for plates considering the fluid pressure as the external load on the plate. Two non‐dimensional parameters are identified and their effects on the damping of the plate motion are examined. Grid convergence tests are carried out for both cases. Copyright © 2007 John Wiley & Sons, Ltd.
Array comparative genomic hybridization analysis of chromosomal imbalances and their target genes in gastrointestinal stromal tumors
Authors: Ässämäki Reetta , Sarlomo‐Rikala Maarit , Lopez‐Guerrero José Antonio , Lasota Jerzy , Andersson Leif C. , Llombart‐Bosch Antonio , Miettinen Markku , Knuutila Sakari 
Published: February 2007

AbstractGastrointestinal stromal tumor (GIST) is the most common mesenchymal tumor of the gastrointestinal tract. The tumors characteristically harbor KIT or PDGFRA mutations, and mutant tumors respond to imatinib mesylate (Glivec™). Chromosomal imbalances resulting in altered gene dosage are known to have a role in the molecular pathogenesis of these tumors, but the target genes remain to be identified. The present study aimed to identify some of these genes. In total, 35 GIST samples were screened for chromosomal imbalances by array‐based comparative genomic hybridization. A cDNA array was used to define the minimal common overlapping areas of DNA copy number change. Eight confirmative, replicate hybridizations were performed using an oligonucleotide array. The most recurrent copy number losses were localized to 14q, 22q, and 1p. Gains were less common with 8q being the most recurrent. Two recurrent deleted regions of 14q were 14q11.2 harboring the PARP2, APEX1, and NDRG2 genes and 14q32.33 harboring SIVA. Additional target candidates were NF2 at chromosome 22, CDKN2A/2B at 9p, and ENO1 at 1p for copy number losses, and MYC at 8q for copy number gains. Array CGH proved to be an effective tool for the identification of chromosome regions involved in the development and progression of GISTs. © 2007 Wiley‐Liss, Inc.
Tag SNPs chosen from HapMap perform well in several population isolates
Authors: Service Susan , Sabatti Chiara , Freimer Nelson 
Published: February 2007

AbstractPopulation isolates may be particularly useful for association studies of complex traits. This utility, however, largely depends on the transferability of tag SNPs chosen from reference samples, such as HapMap, to samples from such populations. Factors that characterize population isolates, such as widespread genetic drift, could impede such transferability. In this report, we show that tag SNPs chosen from HapMap perform well in several population isolates; this is true even for populations that differ substantially from the HapMap sample either in levels of linkage disequilibrium or in SNP allele frequency distributions. Genet. Epidemiol. 2007. © 2007 Wiley‐Liss, Inc.
A balanced accuracy function for epistasis modeling in imbalanced datasets using multifactor dimensionality reduction
Authors: Velez Digna R. , White Bill C. , Motsinger Alison A. , Bush William S. , Ritchie Marylyn D. , Williams Scott M. , Moore Jason H. 
Published: February 2007

AbstractMultifactor dimensionality reduction (MDR) was developed as a method for detecting statistical patterns of epistasis. The overall goal of MDR is to change the representation space of the data to make interactions easier to detect. It is well known that machine learning methods may not provide robust models when the class variable (e.g. case‐control status) is imbalanced and accuracy is used as the fitness measure. This is because most methods learn patterns that are relevant for the larger of the two classes. The goal of this study was to evaluate three different strategies for improving the power of MDR to detect epistasis in imbalanced datasets. The methods evaluated were: (1) over‐sampling that resamples with replacement the smaller class until the data are balanced, (2) under‐sampling that randomly removes subjects from the larger class until the data are balanced, and (3) balanced accuracy [(sensitivity+specificity)/2] as the fitness function with and without an adjusted threshold. These three methods were compared using simulated data with two‐locus epistatic interactions of varying heritability (0.01, 0.025, 0.05, 0.1, 0.2, 0.3, 0.4) and minor allele frequency (0.2, 0.4) that were embedded in 100 replicate datasets of varying sample sizes (400, 800, 1600). Each dataset was generated with different ratios of cases to controls (1 : 1, 1 : 2, 1 : 4). We found that the balanced accuracy function with an adjusted threshold significantly outperformed both over‐sampling and under‐sampling and fully recovered the power. These results suggest that balanced accuracy should be used instead of accuracy for the MDR analysis of epistasis in imbalanced datasets. Genet. Epidemiol.. 2007. © 2007 Wiley‐Liss, Inc.
Weighted variance FBAT: a powerful method for including covariates in FBAT analyses
Authors: Lu Ake Tzu‐Hui , Cantor Rita M. 
Published: February 2007

AbstractThe family‐based association test (FBAT), an extension of transmission/disequilibrium test, capitalizes on linkage disequilibrium to assess the association of genetic markers and traits in nuclear families. It does not permit a formal inclusion of covariates, although an offset under the FBAT ‐o option allows for an overall trait‐intercept adjustment. The PBAT software provides additional features and permits the inclusion of covariates in the FBAT test statistic, but does not account for the parental genotype information when the traits are adjusted for the covariates. We propose the weighted variance FBAT (WVF) method to generate trait values adjusted for both parental genotypes and covariate values. WVF is expected to be more powerful, because the variance is minimized considering both of these factors simultaneously using a weighted Gauss‐Newton algorithm. Two simulated parent/child trio data sets, both with a covariate and the second with a gene by covariate interaction, were simulated to compare WVF power with FBAT and PBAT for a quantitative trait. WVF is most powerful when levels of significance are greater and covariates have a larger influence, indicating WVF may be especially effective when multiple comparisons are an important consideration, such as with whole genome association studies. WVF will also improve the cost of an association study when environmental covariates are considered. A SAS program (www.SAS.com) for generating WVF residuals that can be input to the current versions of the FBAT (www.biostat.harvard.edu/fbat/fbat.html) and PBAT (www.biostat.harvard.edu/clange/default.htm) software is provided. Genet. Epidemiol. 2007. © 2007 Wiley‐Liss, Inc.
Heritability estimation of sex‐specific effects on human quantitative traits
Authors: Pan Lin , Ober Carole , Abney Mark 
Published: February 2007

AbstractRecent studies have suggested that sex‐specific genetic architecture could be because of the effects of autosomal genes that are differentially expressed in males and females. Yet, few studies have explored the effects of X‐linked genes on sex‐specific genetic architecture. In this study, we extended the variance component, maximum likelihood method to evaluate the relative contributions of sex‐specific effects on both autosomes and the X chromosome to estimates of heritability of 20 quantitative human phenotypes in the Hutterites. Seventeen of these traits were previously analyzed in this population under a model that did not include X chromosomal effects; three traits are analyzed for the first time (age at menarche, percent fat and fat‐free mass [FFM]). Seven traits (systolic blood pressure (SBP), adult height, fasting insulin, triglycerides, lipoprotein (a) [Lp(a)], serotonin, and age at menarche) showed significant X‐linked effects; three of these (SBP, adult height, and triglycerides) showed X‐linked effects only in males. Four traits (Lp(a), low‐density lipoprotein cholesterol, ratio of percent predicted forced expiratory volume at 1 s/forced vital capacity, and FFM) showed significant sex‐environment interactions, and two traits (high‐density lipoprotein cholesterol and FFM) showed significant sex‐specific autosomal effects. Our analyses demonstrate that sex‐specific genetic effects may not only be common in human quantitative traits, but also that the X chromosome both plays a large role in these effects and has a variable influence between the sexes. Genet. Epidemiol. 2007. © 2007 Wiley‐Liss, Inc.
Haplotype uncertainty in association studies
Authors: Mensah F.K. , Gilthorpe M.S. , Davies C.F. , Keen L.J. , Adamson P.J. , Roman E. , Morgan G.J. , Bidwell J.L. , Law G.R. 
Published: February 2007

AbstractInferring haplotypes from genotype data is commonly undertaken in population genetic association studies. Within such studies the importance of accounting for uncertainty in the inference of haplotypes is well recognised. We investigate the effectiveness of correcting for uncertainty using simple methods based on the output provided by the PHASE haplotype inference methodology. In case‐control analyses investigating non‐Hodgkin lymphoma and haplotypes associated with immune regulation we find little effect of making adjustment for uncertainty in inferred haplotypes. Using simulation we introduce a higher degree of haplotype uncertainty than was present in our study data. The simulation represents two genetic loci, physically close on a chromosome, forming haplotypes. Considering a range of allele frequencies, degrees of linkage between the loci, and frequency of missing genotype data, we detail the characteristics of genetic regions which may be susceptible to the influence of haplotype uncertainty. Within our evaluation we find that bias is avoided by considering haplotype probabilities or using multiple imputation, provided that for each of these methods haplotypes are inferred separately for case and control populations; furthermore using multiple imputation provides the facility to incorporate haplotype uncertainty in the estimation of confidence intervals. We discuss the implications of our findings within the context of the complexity of haplotype inference for larger marker rich regions as would typically be encountered in genetic analyses. Genet. Epidemiol. 2007. © 2007 Wiley‐Liss, Inc.
Understanding the conceptual development phase of applied theory‐building research: A grounded approach
Authors: Storberg‐Walker Julia 
Published: February 2007

AbstractThis article presents a provisional grounded theory of conceptual development for applied theory‐building research. The theory described here extends the understanding of the components of conceptual development and provides generalized relations among the components. The conceptual development phase of theory‐building research has been widely debated and discussed in a variety of disciplines, most notably in sociology and management theory. The breadth and number of these contributions makes it difficult for many human resource development (HRD) theorists to select the most appropriate process or framework to follow, and guidelines or a framework are needed to further the development of HRD theory. This grounded study contributes toward that gap. The study found that a five‐component framework of conceptual development emerged from creating an HRD theory on human capital transformation.
Diversity training: Analysis of the impact of self‐efficacy
Authors: Combs Gwendolyn M. , Luthans Fred 
Published: February 2007

AbstractAlthough the importance of diversity in organizations is widely recognized, diversity training is under attack. Drawing from self‐efficacy theory and research, we developed a questionnaire to measure one's efficacy of successfully coping with widely recognized diversity initiatives. Then we conducted a study examining the effect of self‐efficacy‐based diversity training on the level of participant's measured diversity self‐efficacy (DSE) and the possible mediation of this DSE on intentions to pursue positive diversity‐related initiatives. The field experimental design showed that training incorporating efficacy components significantly increased trainees' (N = 276) measured DSE. Diversity training was also shown to be positively related to the trainees' stated levels of difficulty and magnitude in coping with diversity initiatives. Finally, the DSE was found to mediate training and intentions. Importantly, one‐year follow‐up data supported the impact of the intentions. The practical implications of these findings for HRD in general and diversity training in particular conclude this article.
Activator protein‐2 in carcinogenesis with a special reference to breast cancer—A mini review
Authors: Pellikainen Johanna M. , Kosma Veli‐Matti 
Published: February 2007

AbstractActivator protein‐2 (AP‐2) transcription factors are involved in the regulation of cell proliferation, differentiation, apoptosis and carcinogenesis. AP‐2α has been suggested to function as a tumor suppressor in many cancers and AP‐2γ to be a marker of testicular and germ cell malignancies. At least 3 of the 5 AP‐2 family members identified to date, AP‐2α, AP‐2β and AP‐2γ, are known to be expressed in breast tissue and thought to coordinate the growth and development of the breast via regulation of several breast‐related genes such as human epidermal growth factor receptor‐2 (HER2) and estrogen receptor (ER). The function of AP‐2α seems to be tumor suppressive in breast tissue, whereas the role of the other AP‐2 family members is less well known. In this review, we summarize the current knowledge of AP‐2 in carcinogenesis, especially in breast cancer. © 2007 Wiley‐Liss, Inc.
Ultrasonographic demonstration of a placental maternal lake
Authors: Cooperberg P. L. , Wright V. J. , Carpenter C. W. 
Published: February 2007

AbstractA 30 year old woman was seen at 32 weeks of gestation because of severe abdominal pain. A sonogram revealed an irregular, 5 cm‐diameter cystic structure in the placenta. Examination of the placenta after cesarean section showed an extremely large maternal lake.
Correlation between sectional area of the spleen by ultrasonic tomography and actual volume of the removed spleen
Authors: Koga Takashi 
Published: February 2007

AbstractThe sectional area of the splenotomogram scanned parallel to the ribs provides useful information for differential diagnosis and determination of prognosis in liver diseases. To establish a relationship between sectional area and actual spleen volume, 10 spleens obtained at splenectomy or autopsy were studied. A good linear correlation (r = 0.956) was present between the sectional area (S) and the actual spleen volume (V). The spleen volume could be calculated as V = 7.5S – 77.5. Therefore the value of the sectional area obtained from one ultrasonic splenotomogram has practical application as a parameter reflecting the spleen volume in vivo.
Sonically guided renal biopsy
Authors: Mets T. , Lameire N. , Matthys E. , Afschrift M. 
Published: February 2007

AbstractThe results of 91 sonically guided renal biopsies are reported. In the 53 cases where renal size and function allowed other localization techniques, renal tissue was obtained in 100 percent and glomeruli in 88.6 percent. In 38 cases no other techniques could have been used because of poor renal function (serum creatinine ≥ 4.0 mg/dl) and/or decreased renal size (≤ 10 cm); in these biopsies renal tissue was obtained in 86.8 percent and glomeruli in 73.7 percent.
The sonographic findings of splenic metastases
Authors: Murphy James F. , Bernardino Michael E. 
Published: February 2007

AbstractThe sonographic findings in five patients with metastases to the spleen are demonstrated. Hypoechoic lesions were seen in patients with histiocytic lymphoma, and both echogenic and hypoechoic lesions were seen in patients with melanoma. The clinical significance of these findings is discussed.
In vitro investigation of gallstone shadowing with ultrasound tomography
Authors: Filly Roy A. , Moss Albert A. , Way Lawrence W. 
Published: February 2007

AbstractA phantom was constructed to simulate the in vivo situation of gallstone detection. Gallstone specimens from 37 patients were scanned. All gallstones cast acoustic shadows, regardless of the specific properties of the stones. Experimental evidence concerning factors that affect the detection of acoustic shadows from gallstones is discussed.
Ultrasound evaluation of american burkitt's lymphoma
Authors: Shawker Thomas H. , Dunnick N. Reed , Head Gordon L. , Magrath Ian T. 
Published: February 2007

AbstractBurkitt's lymphoma is a childhood disease that characteristically produces large, bulky abdominal tumors. Although these are potentially curable, chemotherapy can produce rapid tumor lysis, with subsequent life‐threatening metabolic abnormalities, especially in those patients with large tumors or those who have compromised renal function. Twenty‐two patients with proven Burkitt's lymphoma were evaluated by ultrasound. Thirteen patients had abdominal masses. These masses tended to be large, solitary, and acoustically homogeneous. Although most of these tumors were found in the pelvis, upper abdominal and retroperitoneal tumors were also encountered. None of the patients had the typical paravertebral mantle of enlarged nodes seen in other types of lymphoma. In 11 patients with abnormal intravenous pyelograms, ultrasound successfully distinguished between renal lymphoma, hydronephrosis, and, by exclusion, metabolic renal disease. The absence of lymph node disease and the presence of bulky homogeneous extranodal tumor are characteristic ultrasound findings in Burkitt's lymphoma. By locating and quantifying tumor mass and distinguishing between renal lymphoma and hydronephrosis, ultrasound proved to be clinically useful in the management of this disease.
Evaluation of echoencephalography
Authors: de Vlieger Marinus 
Published: February 2007

AbstractClinical use of A‐ and B‐mode echoencephalography in neurology, neurosurgery, and pediatrics is discussed, and some results are presented. Descriptions are given of several techniques to obtain two‐dimensional echoencephalographic pictures. Two‐dimensional echoencephalography can be particularly helpful with hydrocephalic babies. Recording techniques for pulsatile echoencephalography and the factors influencing the shape of cerebral echo pulsations are considered. Also, the diagnostic value of pulsatile echoencephalography in several brain diseases is discussed.
Real‐time cross‐sectional echocardiographic diagnosis of infiltrative cardiomyopathy due to amyloid
Authors: Chiaramida Salvatore A. , Goldman Mitchell A. , Zema Michael J. , Pizzarello Roy A. , Goldberg Herbert M. 
Published: February 2007

AbstractWe report the real‐time cross‐sectional echocardiographic findings in a case of cardiac amyloidosis. Alterations in cardiac structure and function previously demonstrated by M‐mode echocardiography were also demonstrable on cross‐sectional examination. A new finding of an altered pattern of myocardial echoes detected by cross‐sectional echocardiography alone is described.
The source of ultrasound contrast effect
Authors: Meltzer Richard S. , Tickner E. Glenn , Sahines Thomas P. , Popp Richard L. 
Published: February 2007

AbstractEvidence that microbubbles are the main sources of ultrasound contrast in injected solutions has been largely indirect. To investigate this directly, we examined freshly agitated indocyanine green, freshly agitated water, commercially prepared precision microbubbles (diameter 75 ± 25 μ) in gelatin, carbonated water, “degassed” indocyanine green solution, and “degassed” water in one or more of four different assay systems. Only fluids with microbubbles produced ultrasound contrast. Injected contrast material rose in a water bath at a rate that identified it as being caused by microbubbles. Indocyanine green and gelatin surface tensions were measured and found to be low (43 dynes/cm2), thus explaining their tendency to stabilize the microbubbles that cause ultrasound contrast effect when injected and to hold foam after agitation. The force of hand injections (force similar to that used clinically through catheters and 19‐gauge or 23‐gauge needles) was below the force needed to cause cavitation or ultrasound contrast effect. Microbubble content could be quantified by the decrease in amplitude of the echo from a structure distant to the microbubbles. We conclude that the ultrasound contrast effect seen in peripherally injected fluids is caused by microbubbles present in the injectant. The contrast is not due to cavitation at needle tips, and it can be quantified over a limited range. Improved design for a peripheral contrast agent is suggested.
Sonography in the diagnosis and management of anterior sacral meningocele
Authors: McCreath Georgina T. , Macpherson Peter 
Published: February 2007

AbstractFour cases of anterior sacral meningocele (ASM) are described, with comparisons between radiological and sonographic findings. On plain films, 2 cases showed the classic scimitar sign, and 1 case showed a defect in the anterior sacrum. The other lesion appeared radiologically to be a purely intrasacral meningocele. Myelography outlined part of the ASM in two cases. Sonography demonstrated the anterior sacral cysts in all cases. Sonography is a noninvasive method of monitoring progress or contraction of a lesion, and it can be used to demonstrate any associated pathology. The combination of plain‐film appearances and sonographic findings should be sufficient for diagnostic purposes. If an operative procedure is contemplated, then myelography may be performed in an attempt to outline the stalk.
The ultrasound cardioscope: A hand‐held scanner for real‐time cardiac imaging
Authors: Roelandt Jos , Bom Klaas , Hugenholtz Paul G. 
Published: February 2007

AbstractA miniaturized hand‐held ultrasound scanner that permits two‐dimensional echocardiography is described. The device has been routinely used in our emergency department, coronary care unit, wards, and outpatient department. The device has advantages in situations where rapid decisions are demanded of the expert echocardiographer. It permits improved bedside analysis of patients with puzzling cardiac conditions. An important feature is that the instrument can be used as a substitute for cardiac fluoroscopy in office practice. Tests performed in 100 consecutive patients have demonstrated that reasonable semiquantitative estimation of the sizes of left‐side heart structures is possible. This new‐generation instrument can make diagnostic ultrasound more readily available in emergency situations and should have considerable influence on the use of cardiac ultrasound for bedside diagnosis. It will undoubtedly affect future developments in automatic, portable, and special dedicated ultrasound equipment.