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PubMed2004

Critical survey of quantitative proteomics in two-dimensional electrophoretic approaches.

The present review attempts to cover a number of methods that appeared in the last few years for performing quantitative proteome analysis. However, due to the large number of methods described for both electrophoretic and chromatographic approaches, we have limited this excursus only to conventional two-dimensional (2D) map analysis, coupling orthogonally a charge-based step (isoelectric focusing) to a size-based separation (sodium dodecyl sulfate (SDS)-electrophoresis). The first and oldest method applied in 2D mapping is based on statistical analysis performed on sets of gels via powerful software packages, such as the Melanie, PDQuest, Z3 and Z4000, Phoretix and Progenesis. This method calls for separately-running a number of replicas for control and treated samples, the merging and comparing between these two sets of data being accomplished via the softwares just mentioned. Recent developments permit analyses on a single gel containing mixed samples differentially labelled and resolved by either fluorescence or isotopic means. In one approach, a set of fluorophors, called Cy3 and Cy5, are selected for differentially tagging Lys residues, via a "minimal labelling" protocol. A variant of this, adopts a newer set of fluorophors, also of the Cy3 and Cy5 type, reacting on Cys residues, via a strategy of "saturation labelling". There are at present two methods for quantitative proteomics in a 2D gel format exploiting stable isotopes: one utilizes tagging Cys residues with [2H0]/[2H3]-acrylamide; the other one, also based on a Cys reactive compound, exploits [2H0]/[2H4] 2-vinylpyridine. The latter reagent achieves 100% efficiency coupled to 100% specificity. The advantages and limitations of the various protocols are discussed.

Amino Acid Sequence↗
PubMed1997

The dopamine D4 receptor gene (DRD4) is not associated with alcoholism in three Taiwanese populations: six polymorphisms tested separately and as haplotypes.

The dopaminergic system has been implicated in alcoholism but studies at the dopamine D2 receptor gene (DRD2), one of the five dopamine receptors, have not given a consistent picture of an association with alcoholism. We have now studied the dopamine D4 receptor gene (DRD4) using six polymorphisms, both separately and as haplotypes. Three groups of alcoholics from Taiwan (Atayal, Ami, and Han) diagnosed as having severe alcohol dependence using DSM-III-R criteria, together with nonalcoholics matched for gender, ethnic group, and geographic origin, were typed by polymerase chain reaction (PCR) and/or PCR-restriction fragment length polymorphism (RFLP) for all six polymorphisms. Three out of six markers are polymorphic in all three Taiwanese populations. Although the prevalence rates of alcoholism are remarkably different, no highly significant association of this locus with alcoholism was observed in any of the three groups whether the analysis considered genotype distributions or allele frequencies at the three polymorphic markers considered individually and as haplotypes. Neither is there any obvious pattern in the data that covaries with or hints at a relationship with the very different prevalences of alcoholism in the groups studied. Especially because the powerful, multi-site haplotype analysis was not statistically significant in any of the population samples, we conclude that there is no association of the DRD4 locus with alcoholism in Taiwanese populations.

Alcoholism↗
PubMed2000

Analysis of potential causes of positive microbiological cultures in tissue donors.

The purpose of this statistical analysis is to determine what factors are the major contributors to bacterial contamination of recovered human cadaveric tissue. In this study we analyzed factors that could contribute to an increased bacterial bioburden from recovered tissues using the following independent variables: (1) the physical recovery environment; (2) recovery before or after an autopsy; (3) the length of time from death to recovery; (4) the cause of death; (5) the length of time to complete recovery; (6) the number of staff involved with the tissue recovery; and (7) the impact of organ and skin recovery on musculoskeletal contamination rates.In these analyses we used analysis of variance of main effects on data from seven tissue banks. The scale of the analysis included 1036 donors each having multiple cultures to better control for the inherent large variation in this type of data. We looked at several dependent variables. The dependent variable that was most useful was 'percent positive cultures'.The results of the combined data differed from analyzing the tissue banks individually. The differences in each tissue bank's procedures and techniques were responsible for most of the variability. Depending on how the data was organized, statistically significant increases in bioburden were seen with: (1) recoveries after autopsy; (2) location of the recovery; (3) length of time taken for a recovery; (4) size of the recovery team; and (5) the impact of organ and skin recovery on musculoskeletal contamination rates.In conclusion, statistical analysis of recovery cultures can be a powerful tool that may be used to indicate problems within any bank's recovery procedures or techniques.

Journal Article↗
PubMed1999

Surface CD14 positivity in B-cell chronic lymphocytic leukaemia is related to clinical outcome.

The aberrant expression of the myelomonocytic antigen CD14 was investigated in 128 untreated patients diagnosed with B-cell chronic lymphocytic leukaemia (B-CLL). A cut-off value of 5 x 10(9)/l CD14-positive cells was chosen for statistical analysis because it showed the best discriminating power among patients with different clinical features. 56 cases had a CD14+ cell count >5 x 10(9)/l. A significant correlation was found between Rai and Binet stages and total tumour mass (TTM) score on one hand, and the absolute CD14+ cell cut-off, on the other. This relationship was more evident in Rai 0-II and Binet A-B stages, where a CD14+ cell count >5 x 10(9)/l was preferentially distributed among patients with a higher tumoral mass. In univariate analysis the survival probability at 5 and 10 years showed a significant correlation with Rai and Binet stages, TTM score, CD14+ absolute cell count and median age. The median overall survival (OS) was 63 months for patients with a CD14+ cell count >5 x 10(9)/l and 136 months for those with a CD14+ cell count < 5 x 10(9)/l. In the multivariate Cox regression model, Rai stage, age and CD14+ cell count were independent significant factors for the prediction of OS. Finally, when the same analysis was restricted to Rai stages 0-II, CD14+ cell count was the only significant independent parameter influencing OS, with a relative death risk of 3.8. In conclusion, these data reveal that CD14+ represents an important marker for predicting OS in B-CLL patients and, therefore, we suggest that it should be included in the immunological characterization of B-CLL.

Female↗
PubMed1994

The rotarod test: an evaluation of its effectiveness in assessing motor deficits following traumatic brain injury.

The purpose of the present experiment was to examine the effectiveness of a modified rotarod test in detecting motor deficits following mild and moderate central fluid percussion brain injury. In addition, this investigation compared the performance of the rotarod task with two other commonly used measures of motor function after brain injury (beam-balance and beam-walking latencies). Rats were either injured with a mild (n = 14) or moderate (n = 8) level of fluid percussion injury or were surgically prepared but not injured (n = 8). All rats were assessed on all tasks for 5 days following their respective treatments. Results revealed that both the mild and moderate injury levels produced significant deficits in the ability of the animals to perform the rotarod task. Performance on the beam-balance and beam-walking tasks were not significantly impaired at the mild injury level. It was only at the moderate injury level that the beam-balance and beam-walking tasks detected deficits in motor performance. This result demonstrated that the rotarod task was a sensitive index of injury-induced motor dysfunction following even mild fluid percussion injury. A power analysis of the three tasks indicated that statistically significant group differences could be obtained with the rotarod task with much smaller sample sizes than with the beam-balance and beam-walking tasks. Performance on the rotarod, beam-walk, and beam-balance tasks were compared and evaluated by a multivariate stepdown analysis (multiple analysis of variance followed by univariate analyses of covariance). This analysis indicated that the rotarod task measures aspects of motor impairment that are not assessed by either the beam-balance or beam-walking latency. These findings suggest that compared to the beam-balance and beam-walking tasks, the rotarod task is a more sensitive and efficient index for assessing motor impairment produced by brain injury.

Animals↗
PubMed1979

The Chatham Blood Pressure Study. An application of Bayesian growth curve models to a longitudinal study of blood pressure in children.

Recent developments in statistics have produced powerful methods that facilitate the analysis of longitudinal studies. These methods are illustrated by an analysis of a longitudinal study of blood pressure in children. The results of the study show a clear tendency for blood pressure to increase with age, and Asian children tend to have lower blood pressures than their Caucasian counterparts of the same age. There is evidence to support the hypothesis that blood pressures track.

Age Factors↗
PubMed2006

Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Accurate inference and estimation in population genomics.

Both intra- and interspecific genomic comparisons have revealed local similarities in the level and frequency of mutational variation, as well as in patterns of gene expression. This autocorrelation between measurements leads to violations of assumptions of independence in many statistical methods, resulting in misleading and incorrect inferences. Here I show that autocorrelation can be due to many factors and is present across the genome. Using a one-dimensional spatial stochastic model, I further show how previous results can be employed to correct for autocorrelation along chromosomes in population and comparative genomics research. When multiple hypothesis tests are autocorrelated, I demonstrate that a simple correction can lead to increased power in statistical inference. I present a preliminary analysis of population genomic data from Drosophila simulans to show the ubiquity of autocorrelation and applicability of the methods proposed here.

Animals↗
PubMed1994

Personality disorders among the relatives of schizophrenia patients.

In light of current linkage studies in schizophrenia, research on the "schizophrenia spectrum" deserves increased attention for an exact determination of the affected phenotype: Those disorders that have a much higher prevalence among biological relatives of schizophrenia patients are supposed to share common etiological factors with "core" schizophrenia. However, there is controversy over which of the DSM-III-R personality disorders should be included in the spectrum. In a controlled family study of inpatients with a DSM-III-R diagnosis of schizophrenia (n = 101), schizophreniform and schizoaffective disorders (n = 69), and unipolar major depression (n = 160), familial rates of personality disorders were assessed through personal interviews and compared with prevalence rates in 109 control families from the community. As predicted, schizotypal personality disorder occurred more frequently in the nonpsychotic relatives of schizophrenia probands (2.1%) than in the families of unscreened controls (0.3%). Paranoid personality disorder was more frequent in relatives of probands with unipolar depression (2.9%) than in relatives of schizophrenia patients (1.7%), and controls revealed the lowest rate (0.9%). Schizoid personality disorder, however, was extremely rare in all sample groups (between 0.3% and 0.7%), providing no sufficient statistical power for detection of group differences. Further analysis of the DSM-III-R criterion symptoms of schizotypal personality disorder demonstrated that items describing "negative" symptomatology are the main source of familial aggregation, but "psychotic-like" personality features are also contributing factors.

Adult↗
PubMed1994

A pedigree series for mapping disease genes in bipolar affective disorder: sampling, assessment, and analytic considerations.

A series of 57 extended pedigrees with high density of bipolar affective disorder is described. Ascertainment and diagnostic procedures are documented and simulation studies to assess statistical power are carried out. The pedigrees, obtained in the US and Israel, are comprised of 1508 adult individuals with best estimate consensus diagnoses (12-71 relatives per pedigree), 490 of whom (including 401 sib pairs) meet criteria for a conservative disease definition (bipolar disorder or recurrent major depression). Cell lines have been established on 1324 of these individuals. Statistical power to detect linkage with lod score analysis, assuming autosomal dominant transmission and highly polymorphic DNA markers, is nearly 100% for alpha (proportion of linked families) = 30%, and 75% for alpha = 20%. This is the largest bipolar pedigree series reported to date; its unique features make it amenable to various gene detection techniques.

Bipolar Disorder↗
PubMed2004

Homocysteine metabolism in renal failure.

PURPOSE OF REVIEW: This review focuses on recent findings (June 2002-July 2003) on the topic of homocysteine, a sulfur amino acid associated with cardiovascular disease, and its metabolism in renal failure, a condition with a high prevalence of both hyperhomocysteinemia and cardiovascular disease. RECENT FINDINGS: A large meta-analysis of prospective studies in the general population established that hyperhomocysteinemia is a risk factor for cardiovascular disease. The results of intervention trials, once available, will also have to be tested in a meta-analysis, because of predicted problems with their statistical power. In kidney patients, intervention trials, still in the recruiting stage, target transplant patients, because of their unique characteristics related to folate responsiveness. As for the cause of hyperhomocysteinemia, new findings show that in humans, renal metabolic extraction depends on renal plasma flow in the post-absorptive state. Folate absorption or interconversion seems not to be affected. Riboflavin is a determinant of plasma homocysteine levels in uraemia. The consequences of hyperhomocysteinemia in uraemia are DNA hypomethylation and altered gene expression. SUMMARY: The causes of hyperhomocysteinemia in renal failure are still not clear. However, the possibilities include defective renal or extrarenal metabolism as a result of uraemic toxicity. Renal plasma flow is important in homocysteine renal metabolism. Among the consequences of hyperhomocysteinemia in renal failure are impaired protein and DNA methylation, with an alteration in the allelic expression of genes regulated through methylation. Intervention trials are under way to test whether hyperhomocysteinemia is causally related to cardiovascular disease in this patient population.

DNA Methylation↗
PubMed2004

Application of discordant sib-pair linkage analysis for mapping minor histocompatibility antigen loci in a novel graft-vs-host-disease model.

Graft-vs-host disease (GVHD) is an adverse effect of allogenic bone marrow transplantation. Although a major cause of GVHD following bone marrow transplantation is incompatibility of major histocompatibility antigen (human leukocyte antigen, HLA) in donor-recipient pairs, the incompatibility of minor histocompatibility antigen (mHa) is known as another cause, especially in HLA-matched donor-recipient pairs. In 1998, Lunetta and Rogus proposed the use of discordant sib-pair (DSP) linkage analysis for detecting mHa and calculated the statistical power using the GVHD model, assuming single mHa locus with multiple alleles. Recently, we proposed a different GVHD model, assuming multiple mHa loci with two alleles (biallelic), considering the single-nucleotide polymorphisms. When the effect of each mHa locus on the occurrence of GVHD is independent, the possible triangle for DSP proposed by Lunetta and Rogus is not optimum, but a new possible triangle, named here as GVHD region, is needed. We evaluated, based on Monte Carlo simulation, the test criteria [log of odds (lod) score cutoffs] and power of DSP using the GVHD region for various parameter sets. The GVHD region showed a higher power than the DSP and entire regions in plausible situations. Our results suggest that the application of GVHD region to DSP is effective for the screening of mHa loci.

Genetic Linkage↗
PubMed2000

Randomised controlled trial of non-directive counselling, cognitive-behaviour therapy, and usual general practitioner care for patients with depression. II: cost effectiveness.

OBJECTIVE: To compare the cost effectiveness of general practitioner care and two general practice based psychological therapies for depressed patients. DESIGN: Prospective, controlled trial with randomised and patient preference allocation arms. SETTING: General practices in London and greater Manchester. PARTICIPANTS: 464 of 627 patients presenting with depression or mixed anxiety and depression were suitable for inclusion. INTERVENTIONS: Usual general practitioner care or up to 12 sessions of non-directive counselling or cognitive-behaviour therapy provided by therapists. MAIN OUTCOME MEASURES: Beck depression inventory scores, EuroQol measure of health related quality of life, direct treatment and non-treatment costs, and cost of lost production. RESULTS: 197 patients were randomly assigned to treatment, 137 chose their treatment, and 130 were randomised only between the two psychological therapies. At four months, both non-directive counselling and cognitive-behaviour therapy reduced depressive symptoms to a significantly greater extent than usual general practitioner care. There was no significant difference in outcome between treatments at 12 months. There were no significant differences in direct costs, production losses, or societal costs between the three treatments at either four or 12 months. Sensitivity analyses did not suggest that the results depended on particular assumptions in the statistical analysis. CONCLUSIONS: Within the constraints of available power, the data suggest that both brief psychological therapies may be significantly more cost effective than usual care in the short term, as benefit was gained with no significant difference in cost. There are no significant differences between treatments in either outcomes or costs at 12 months.

Adult↗
PubMed2004

Loss of entrainment of high-frequency plasma insulin oscillations in type 2 diabetes is likely a glucose-specific beta-cell defect.

Spontaneous high-frequency insulin oscillations are easily entrainable to exogenous glucose in vitro and in vivo, but this property is lost in type 2 diabetes (2-DM). We hypothesized that this lack of entrainment in 2-DM would be specific to glucose. This was tested in nine control and ten 2-DM subjects. Serial blood sampling at 1-min intervals was carried out for 60 min in the basal state and for 120 min while small (1-60 mg/kg) boluses of arginine were injected intravenously at exactly 29-min intervals. Samples were analyzed for insulin concentrations, and time series analysis was carried out using spectral analysis. In control subjects, the mean period of basal plasma insulin oscillations was 10.3 +/- 1.3 min and was entrained by arginine to a mean period of 14.9 +/- 0.6 min (P < 0.00001 vs. basal). Similarly, in 2-DM subjects, spontaneous insulin oscillations were entrained by arginine; mean basal insulin period was 10.0 +/- 1.0 min and 14.5 +/- 1.8 min with arginine boluses (P < 0.00001). All of the primary peaks observed in spectral analysis were statistically significant (P < 0.05). Percent total power of primary peaks ranged from 17 to 68%. Thus arginine boluses entrain spontaneous high-frequency insulin oscillations in 2-DM subjects. This represents a distinct and striking difference from the resistance of the beta-cell to glucose entrainment in 2-DM. We conclude that loss of entrainment of spontaneous high-frequency insulin oscillations in 2-DM is likely a glucose-specific manifestation of beta-cell secretory dysfunction.

Adult↗
PubMed2006

Support vector machine learning model for the prediction of sentinel node status in patients with cutaneous melanoma.

BACKGROUND: Currently, approximately 80% of melanoma patients undergoing sentinel node biopsy (SNB) have negative sentinel lymph nodes (SLNs), and no prediction system is reliable enough to be implemented in the clinical setting to reduce the number of SNB procedures. In this study, the predictive power of support vector machine (SVM)-based statistical analysis was tested. METHODS: The clinical records of 246 patients who underwent SNB at our institution were used for this analysis. The following clinicopathologic variables were considered: the patient's age and sex and the tumor's histological subtype, Breslow thickness, Clark level, ulceration, mitotic index, lymphocyte infiltration, regression, angiolymphatic invasion, microsatellitosis, and growth phase. The results of SVM-based prediction of SLN status were compared with those achieved with logistic regression. RESULTS: The SLN positivity rate was 22% (52 of 234). When the accuracy was > or = 80%, the negative predictive value, positive predictive value, specificity, and sensitivity were 98%, 54%, 94%, and 77% and 82%, 41%, 69%, and 93% by using SVM and logistic regression, respectively. Moreover, SVM and logistic regression were associated with a diagnostic error and an SNB percentage reduction of (1) 1% and 60% and (2) 15% and 73%, respectively. CONCLUSIONS: The results from this pilot study suggest that SVM-based prediction of SLN status might be evaluated as a prognostic method to avoid the SNB procedure in 60% of patients currently eligible, with a very low error rate. If validated in larger series, this strategy would lead to obvious advantages in terms of both patient quality of life and costs for the health care system.

Artificial Intelligence↗
PubMed2004

Quantitative proteomics: a review of different methodologies.

The present review attempts to cover the vast array of methods which have appeared in the last few years for performing quantitative proteome analysis. These methods are divided into two classes: those applicable to conventional two-dimensional map analysis, coupling orthogonally a charge-based step (isoelectric focusing) to a size-based separation [sodium dodecylsulfate (SDS)-electrophoresis] and those applicable to two-dimensional chromatographic protocols. The first method, although being by and large the most popular approach, can offer differential display of paired samples with relatively few methods, the oldest one being based on statistical analysis performed on sets of gels via powerful software packages, such as the MELANIE, PDQuest, Z3 and Z4000, Phoretix and Progenesis. Recent developments comprise analysis performed on a single gel containing mixed samples differentially labeled, either with fluorophors (Cy3 and Cy5) or with d(0)/d(3) acrylamide. Conversely, chromatographic approaches, which mostly rely on analysis not of intact proteins but of their tryptic digests, offer a panoply of differential labeling protocols, most of which rely on stable isotope tagging. Essentially, all possible reactions have been described, such as those involving Lys, Asp, Glu, Cys residues, as well as a number of methods exploiting differential derivatization of amine and carboxyl groups generated during proteolysis. All such methods are described and evaluated.

Amino Acid Sequence↗
PubMed2000

Introduction to the special section on the use of computers for making judgments and decisions.

Computers have the potential to greatly increase the accuracy of judgments and decisions that are made in the area of psychological assessment. The validity of present-day computer programs are described in the first 2 articles of this Special Section. Both computer-based test interpretation programs and mechanical prediction rules (e.g., statistical prediction rules) are described. Limitations of present-day computer programs are described in the 3rd article along with methodological recommendations for building more powerful rules. In the 4th article, a statistical analysis (neural network modeling) is described that may allow us to build better rules.

Decision Making, Computer-Assisted↗
PubMedDate not supplied

[Reliability of electrophysiological measurements of motor control].

OBJECTIVES: The aim of the study was the short term test-retest-reliability of electrophyisiological correlates of simple processes of the motor control, i.e. the execution (go) and the inhibition (no go) of a prepared motor response, evoked during the Continuous Performance Test (CPT). Our interest was centered in the reliability of the topographical P300-parameters described in previous studies, i.e. the localizations of the go and no go centroids and the no go anteriorization (NGA), which is the difference between the two centroid locations. A sufficient reliability is a basic requirement for the application of these new topographical parameters for the investigation of different psychiatric illnesses with suspected dysfunctions of prefrontal motor control, e.g. schizophrenias and affective illnesses, obsessive-compulsive disorders, personality disorders with deficits in impulse control, and in children with attention deficit hyperactivity disorder. PATIENTS AND METHODS: We examined 23 healthy subjects who executed two versions of the CPT with an interval of 30 minutes. After averaging the obtained evoked potentials of each subject, we determined the latencies, amplitudes and positive centroids, at the moment of the peak of the Global Field Power in a P300 time window. RESULTS: Statistical analysis revealed sufficient test-retest-reliabilities in comparison to other electrophysiological paradigms, mainly for the localizations of the go (r = 0.93; p = 10(-10)) and no go centroid (r = 0.85; p = 10(-4)), as well as for the no go anteriorization (r = 0.63; p = 10(-3)). CONCLUSION: These results are a prerequisite for the application of these topographical parameters as measures of the prefrontal motor control in different healthy and psychiatric populations.

Adult↗
PubMed1977

Computerized EEG analysis for studying the effect of drugs on the central nervous system.

Samples of our experience in quantitative pharmaco-EEG are reviewed to discuss and define its applicability and limits. Simple processing systems, such as the computation of Hjorth's descriptors, are useful for on-line monitoring of drug-induced EEG modifications which are evident also at the visual visual analysis. Power spectral analysis is suitable to identify and quantify EEG effects not evident at the visual inspection. It demonstrated how the EEG effects of compounds in a long-acting formulation vary according to the sampling time and the explored cerebral area. EEG modifications not detected by power spectral analysis can be defined by comparing statistically (F test) the spectral values of the EEG from a single lead at the different samples (longitudinal comparison), or the spectral values from different leads at any sample (intrahemispheric comparison). The presently available procedures of quantitative pharmaco-EEG are effective when applied to the study of mutltilead EEG recordings in a statistically significant sample of population. They do not seem reliable in the monitoring of directing of neuropyschiatric therapies in single patients, due to individual variability of drug effects.

Alcoholic Intoxication↗