Genome-wide meta-analyses of smoking behaviors in African Americans.

The identification and exploration of genetic loci that influence smoking behaviors have been conducted primarily in populations of the European ancestry. Here we report results of the first genome-wide association study meta-analysis of smoking behavior in African Americans in the Study of Tobacco in Minority Populations Genetics Consortium (n = 32,389). We identified one non-coding single-nucleotide polymorphism (SNP; rs2036527[A]) on chromosome 15q25.1 associated with smoking quantity (cigarettes per day), which exceeded genome-wide significance (ß = 0.040, s.e. = 0.007, P = 1.84 × 10(-8)). This variant is present in the 5'-distal enhancer region of the CHRNA5 gene and defines the primary index signal reported in studies of the European ancestry. No other SNP reached genome-wide significance for smoking initiation (SI, ever vs never smoking), age of SI, or smoking cessation (SC, former vs current smoking). Informative associations that approached genome-wide significance included three modestly correlated variants, at 15q25.1 within PSMA4, CHRNA5 and CHRNA3 for smoking quantity, which are associated with a second signal previously reported in studies in European ancestry populations, and a signal represented by three SNPs in the SPOCK2 gene on chr10q22.1. The association at 15q25.1 confirms this region as an important susceptibility locus for smoking quantity in men and women of African ancestry. Larger studies will be needed to validate the suggestive loci that did not reach genome-wide significance and further elucidate the contribution of genetic variation to disparities in cigarette consumption, SC and smoking-attributable disease between African Americans and European Americans.

Determination of percent composition of a mixture analyzed by gas chromatography. Comparison of a helium pulsed-discharge photoionization detector with a flame ionization detector.

We present the results of a study of percent composition for a mixture which has been separated by gas chromatography and analyzed using helium pulsed-discharge photoionization detection (He-PDPID) and flame ionization detection (FID). FID has long been the means by which the percent composition of a hydrocarbon mixture has been determined since it has been previously established as a "carbon counting device". However, in this study we present results which show that He-PDPID is more accurate in determining the percent composition of a hydrocarbon mixture and, because it is a universal detection method and can detect compounds that FID cannot, it is also more effective for determining the percent composition of mixtures containing organic compounds with a variety of other functional groups.

C-myc amplification in breast cancer: a meta-analysis of its occurrence and prognostic relevance.

Data from basic research suggests that amplification of the proto-oncogene c-myc is important in breast cancer pathogenesis, but its frequency of amplification and prognostic relevance in human studies have been inconsistent. In an effort to clarify the clinical significance of c-myc amplification in breast cancer, we conducted a comprehensive literature search and a meta-analysis in which 29 studies were evaluated. The weighted average frequency of c-myc amplification in breast tumours was 15.7% (95% CI = 12.5-18.8%), although estimates in individual studies exhibited significant heterogeneity, P<0.0001. C-myc amplification exhibited significant but weak associations with tumour grade (RR = 1.61), lymph-node metastasis (RR = 1.24), negative progesterone receptor status (RR = 1.27), and postmenopausal status (RR = 0.82). Amplification was significantly associated with risk of relapse and death, with pooled estimates RR = 2.05 (95% CI = 1.51-2.78) and RR = 1.74 (95% CI = 1.27-2.39), respectively. This effect did not appear to be merely a surrogate for other prognostic factors. These results suggest that c-myc amplification is relatively common in breast cancer and may provide independent prognostic information. More rigorous studies with consistent methodology are required to validate this association, and to investigate its potential as a molecular predictor of specific therapy response.

Cell cycle basis for the onset and progression of c-Myc-induced, TGFalpha-enhanced mouse mammary gland carcinogenesis.

Using single and double transgenic mouse models, we investigated how c-Myc modulates the mammary epithelial cell cycle to induce cancer and how TGFalpha enhanced the process. In c-myc transgenic mice, c-myc expression was high in the hyperplastic mammary epithelium and in the majority of tumor areas. However, the tumors displayed focal areas of low expression of c-myc but high rates of proliferation. In contrast to E2F1 and cyclin A2, which were induced and co-localized with c-myc expression, induction of cyclins D1 and E occurred only in these tumor foci. Overexpression of cyclin D1 also occurred in the hyperplastic epithelium of tgfalpha-single and tgfalpha/c-myc-double transgenic mice. In tgfalpha/c-myc tumors, cells positive for cyclins D1 and E were randomly spread, without showing a reciprocal relationship to c-myc expression. In contrast to c-myc tumors, most tgfalpha/c-myc tumors showed undetectable levels of retinoblastoma protein (pRB), and the loss of pRB occurred in some cases at the mRNA level. These results suggest that E2F1 and cyclin A2 may be induced by c-Myc to mediate the onset of mammary cancer, whereas overexpression of cyclins D1 and E may occur later to facilitate tumor progression. TGFalpha may play its synergistic role, at least in part, by inducing cyclin D1 and facilitating the loss of pRB.

Myc/p53 interactions in transgenic mouse mammary development, tumorigenesis and chromosomal instability.

We have examined defects in mammary development and tumorigenesis in a transgenic model expressing the c-myc gene under the MMTV-LTR promoter. The stochastic tumors which arise from hyperplastic ductal and lobular lesions in this model are characterized by high rates both of apoptosis and of chromosomal instability. Since the p53 gene product is thought to be central in the maintenance of genomic integrity, in part due to its ability to induce apoptosis in cells harboring DNA damage, we examined its expression and possible mutation. Initially, we observed that unmutated p53 is strongly expressed in premalignant mammary glands and in mammary tumors derived from the MMTV-c-myc strain. We then mated the MMTV-myc strain to a p53-deficient strain as a means of examining the effect of this lesion on mammary development and tumorigenesis in the context of c-myc overexpression. A lack of both p53 alleles in the presence of c-myc overexpression resulted in a dramatic hyerplastic alteration in mammary gland development. Specifically, in female bitransgenic MMTV-c-myc/p53 null mice (MMTV-myc/p53(-/-)), lobular hyperplasias were observed at almost every ductal end bud as early as 32 days of age. In contrast, only mild ductal and lobular hyperplasias were seen in MMTV-myc mice that contained both p53 alleles (MMTV-myc/p53(+/+)); an intermediate phenotype occurred in mice with a single intact (MMTV-myc/p53(+/-)) p53 allele. Mammary carcinomas arose with a high frequency in MMTV-myc/p53(+/-) mice; the tumors were comparable in frequency, histology and apoptotic index to the tumors in MMTV-myc/p53(+/+) mice. Also, as previously observed (Elson et al., 1995), lymphomas arose with extremely short latency in MMTV-myc/p53(-/-) mice, precluding study of the fate of their hyperplastic mammary lesions in situ. The frequency of p53 mutations in MMTV-myc/p53(+/+) and MMTV-myc/p53(+/-) mammary tumors and in cell lines derived from these tumors was examined by direct sequencing. No point mutations or deletions in p53 were observed in mammary tumors or cell lines from either genotype. Finally, a detailed chromosomal analysis using multicolor spectral karyotyping (SKY) revealed that there were multiple chromosomal alterations in the c-myc-overexpressing cells that contained either one or two unmutated p53 alleles. Variable ploidy changes, a common translocation of chromosome 11, and other chromosomal aberrations were observed. Our data thus support an interaction between c-Myc and p53 in mammary development, but suggest that loss of p53 is required neither for c-myc-dependent tumorigenesis nor for c-myc-dependent chromosomal instability.

Regulation of cell migration by the integrin beta subunit ectodomain.

CS-1 melanoma cells transfected with cDNAs encoding either the beta 3 or beta 5 integrin subunit protein express alpha v beta 3 or alpha v beta 5, respectively, enabling them to adhere to vitronectin yet only alpha v beta 3 promotes cell spreading and migration on this substrate. Following exposure to insulin or insulin-like growth factor, alpha v beta 5-expressing CS-1 cells gain the ability to migrate on vitronectin. To identify structural regions in beta 3 or beta 5 that account for these distinct biological properties, CS-1 cells were transfected with one of two chimeric beta subunit proteins, in which the ecto- and cytoplasmic domains of beta 3 and beta 5 were exchanged (termed alpha v beta 3/5 or alpha v beta 5/3). Surprisingly, alpha v beta 3/5 expressing cells spread and migrate on vitronectin while cells expressing alpha v beta 5/3 do not unless they are exposed to cytokine. These findings suggest that the distinct migratory properties mediated by integrins alpha v beta 3 and alpha v beta 5 and their response to cytokine activation is determined by a sequence(s) within the ectodomain of the integrin beta subunit.

Quantitation of metal isotope ratios by laser desorption time-of-flight mass spectrometry.

Laser desorption time-of-flight mass spectrometry (LD/TOF-MS) is evaluated for the determination of stable metal isotope ratios. The isotope ratios of five metal ions (Cu, Ca, Mg, Fe, Zn) in atomic absorption standard solutions and two metal ions (Ca, Mg) in human serum samples are determined. With an existing LD/TOF-MS instrument we show that the technique can overcome the difficulties of the most commonly used methods for measuring metal isotope ratios: (1) all metals are ionizable without surface treatment, thus overcoming the major drawback of thermal ionization mass spectrometry (TIMS); (2) there is no matrix involved to interfere with the metal ion detection, thus overcoming the major disadvantage of inductively coupled plasma mass spectrometry (ICPMS); (3) there is no interference from hydride ions, a major disadvantage of fast atom bombardment secondary ionization mass spectrometry; (4) a mixture of metals can be detected simultaneously using a single laser wavelength, overcoming the major disadvantage of resonance ionization mass spectrometry; (5) accuracy and precision comparable to ICPMS can be achieved with the current instrumentation; (6) precision comparable to TIMS is feasible; and most importantly (7) high precision can be achieved on very small quantities of material because the LD/TOF-MS instrument permits all masses to be monitored simultaneously and very small differences in isotope ratio can be detected.

Requirement of the NPXY motif in the integrin beta 3 subunit cytoplasmic tail for melanoma cell migration in vitro and in vivo.

The NPXY sequence is highly conserved among integrin beta subunit cytoplasmic tails, suggesting that it plays a fundamental role in regulating integrin-mediated function. Evidence is provided that the NPXY structural motif within the beta 3 subunit, comprising residues 744-747, is essential for cell morphological and migratory responses mediated by integrin alpha v beta 3 in vitro and in vivo. Transfection of CS-1 melanoma cells with a cDNA encoding the wild-type integrin beta 3 subunit, results in de novo alpha v beta 3 expression and cell attachment, spreading, and migration on vitronectin. CS-1 cells expressing alpha v beta 3 with mutations that disrupt the NPXY sequence interact with soluble vitronectin or an RGD peptide, yet fail to attach, spread, or migrate on immobilized ligand. The biological consequences of these observations are underscored by the finding that CS-1 cells expressing wild-type alpha v beta 3 acquire the capacity to form spontaneous pulmonary metastases in the chick embryo when grown on the chorioallantoic membrane. However, migration-deficient CS-1 cells expressing alpha v beta 3 with mutations in the NPXY sequence lose this ability to metastasize. These findings demonstrate that the NPXY motif within the integrin beta 3 cytoplasmic tail is essential for alpha v beta 3-dependent post-ligand binding events involved in cell migration and the metastatic phenotype of melanoma cells.

The efficacy of using the IBM Speech Viewer Vowel Accuracy Module to treat young children with hearing impairment.

The efficacy of the IBM SpeechViewer's Vowel Accuracy Module for the treatment of vowel productions was evaluated in six preschool children with hearing-impairment over a 4-month period. A single-subject design was used, and the vowels /a/, /i/ and /u/ were treated. Untreated sounds also were probed to monitor for carryover and developmental effects. One of the children was dismissed from the study because of noncompliance. Of the remaining five children, four exhibited a treatment effect for /u/, two for /a/, and one for /i/. Four of the children demonstrated some generalization. Developmental effects, as represented by change in /s/-cluster production, were not documented. Although treatment effects were observed, difficulties with the Vowel Accuracy Module were also observed. These included inaccuracies in the feedback on low-intensity, hypernasal, and high-pitched utterances; inability to sustain the attention of preschoolers over multiple sessions; lack of instructional feedback; and nonlinearity in the criterion-adjustment control.

An evaluation of five commercial immunoassay data analysis software systems.

An evaluation of five commercial software systems used for immunoassay data analysis revealed numerous deficiencies. Often, the utility of statistical output was compromised by poor documentation. Several data sets were run through each system using a four-parameter calibration function, and the results were compared to those from an independent method. Comparable results between systems were obtained, but often several attempts at analysis were necessary. The evaluation process revealed that it is difficult to monitor the numerous options available on these types of programs, and that incorrect results could easily be obtained if comparison analyses were not used. Recommendations for improved software functionality and for using the four-parameter calibration model are presented.

An automated iterative algorithm for the quantitative analysis of in vivo spectra based on the simplex optimization method.

The success in utilizing in vivo NMR to identify and/or monitor metabolic abnormalities will be determined in large part on the reliability with which the spectral parameters of the metabolites present can be measured. For these reasons it is clear that there is a need for the development of algorithms with which to obtain quantitatively reliable estimates of the spectral parameters of the peaks present. In this report we describe an adaptation of the simplex algorithm which we have found useful in fitting in vivo spectral data in the frequency domain. This simplex algorithm was implemented on an IBM-PC AT compatible computer. We evaluated the simplex algorithm on three representative kinds of spectral data: a simulated spectrum, 31P spectrum of normal calf muscle, and the 31P spectrum of a pediatric patient with a brain tumor. In each case we generated a set of spectra by adding varying amounts of noise. On the basis of our simulations and the two examples discussed, we conclude that the simplex method generates parameters which are reliable estimates of the areas of the peaks present when the signal-to-noise is above 8:1 for phosphocreatine. We found that the speed of convergence of the algorithm was improved by overestimating the linewidths of the peaks present. We also found that the method converged more rapidly in the presence of a moderate amount of noise. We conclude that the algorithm described here can provide a robust method with which to analyze in vivo spectra in a quantitative manner. Because the method requires little user intervention, it lends itself to implementation in a semi-, or fully, automated fashion.

Chemometrics: an overview.

Chemometrics is broadly defined as the application of mathematical and statistical methods to chemistry. Because the mathematical and statistical aspects of chemistry require measured values, analytical chemists have been at the forefront of the "chemometric revolution." Using the analysis of variance as a paradigm, I present an overview of chemometrics as it is practiced today. Receiving special emphasis are: the design of experiments to acquire information from the relevant universe of possible measurements; the establishment of relationships among independent and dependent variables; the importance of minimizing purely experimental uncertainty; sequential simplex optimization; analysis of principal components; and cluster analysis.

The use of linear models and matrix least squares in clinical chemistry.

We present a unified approach to the use of linear models and matrix least squares with the intention of providing a better understanding of the techniques themselves and of the statistics that arise from these techniques as they are used in clinical chemistry. Emphasis is placed on the importance of appropriate experimental designs and adequately precise measurement processes for efficiently obtaining the desired information.

Automated development of a kinetic method for the continuous-flow determination of creatinine.

A "stopped-flow" method for the kinetic Jaffé determination of creatinine was developed, with the use of a computer-controlled continuous-flow system. Simplex optimization was used to find conditions of hydroxide and picrate giving maximum sensitivity for creatinine. We used a modified central composite experimental design to evaluate creatinine sensitivity and albumin, glucose, and acetone interferences as functions of hydroxide and picrate concentrations. More importantly, this work illustrates that the automated development of clinical chemical methods offers an efficient means of obtaining optimized, well-understood analytical procedures for subsequent routine use in the clinical chemistry laboratory.

Optimization of the extraction of iron(II) from water into cyclohexane with hexafluoroacetylacetone and tri-n-butyl phosphate.

The extraction of iron(II) from water into cyclohexane with hexafluoroacetylacetone (HHFA) and tri-n-butyl phosphate (TBP) was optimized by using a simplex algorithm; pH, [HHFA], [TBP], and mixing time were varied. A central composite design was employed to examine in detail the region of the apparent optimum. Regression analysis of the central composite data demonstrated that in the region of the optimum, the response was essentially unaffected by small variations in the levels of the factors investigated.