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PubMed2005

Increased power of microarray analysis by use of an algorithm based on a multivariate procedure.

MOTIVATION: The power of microarray analyses to detect differential gene expression strongly depends on the statistical and bioinformatical approaches used for data analysis. Moreover, the simultaneous testing of tens of thousands of genes for differential expression raises the 'multiple testing problem', increasing the probability of obtaining false positive test results. To achieve more reliable results, it is, therefore, necessary to apply adjustment procedures to restrict the family-wise type I error rate (FWE) or the false discovery rate. However, for the biologist the statistical power of such procedures often remains abstract, unless validated by an alternative experimental approach. RESULTS: In the present study, we discuss a multiplicity adjustment procedure applied to classical univariate as well as to recently proposed multivariate gene-expression scores. All procedures strictly control the FWE. We demonstrate that the use of multivariate scores leads to a more efficient identification of differentially expressed genes than the widely used MAS5 approach provided by the Affymetrix software tools (Affymetrix Microarray Suite 5 or GeneChip Operating Software). The practical importance of this finding is successfully validated using real time quantitative PCR and data from spike-in experiments. AVAILABILITY: The R-code of the statistical routines can be obtained from the corresponding author. CONTACT: Schuster@imise.uni-leipzig.de

Algorithms↗

PubMed2003

Virtual microscopy as a tool for proficiency testing in cytopathology: a model using multiple digital images of Papanicolaou tests.

BACKGROUND: Modern digital cameras can acquire images from cytologic slides at sufficient resolution to allow for digital enlargement and scrolling on a video monitor, allowing for the simulation of microscopy using a computer. OBJECTIVE: The purpose of this study was to develop a tool for proficiency testing in cytopathology using multiple digital images of Papanicolaou tests. METHODS: Nine images were photographed from each of 10 Papanicolaou tests at x100 optical magnification, 3400 x 2300-pixel resolution, using a light microscope and a digital camera. All images from each case were tiled in a single canvas with Photoshop 4.0 software. Two cytopathologists and 3 cytotechnologists interpreted these "virtual slides" using a computer and graded diagnostic codes (PAP program, College of American Pathologists). Subjects were retested a year later using the glass slides from the same cases and routine microscopy. Both test results, by diagnostic code, were compared with the McNemar test of symmetry. RESULTS: The 5 test subjects provided 42 and 50 correct diagnostic codes by "virtual microscopy" and light microscopy, respectively. No significant asymmetry in results obtained by virtual microscopy and light microscopy was encountered with the McNemar test of symmetry. All test answers were correctly classified by selection series, using both virtual microscopy and light microscopy, and the responses would have been graded as 100% by current PAP program scoring guidelines. This suggests that virtual microscopy could be used for proficiency testing purposes. CONCLUSIONS: A simple virtual microscopy method designed to challenge participants to locate and diagnose cells of interest was effective for the administration of standardized proficiency tests. Virtual microscopy methods that rely on single-plane images to locate and diagnose cells of interest could provide effective proficiency testing tools prior to the development of more computationally intensive systems that represent an entire Papanicolaou test at multiple focal planes.

Computer Simulation↗

PubMed2002

Estimates of genetic parameters for single- and multiple-country test-day models.

Single- and multiple-country random regression models were applied to estimate genetic parameters for first-lactation test-day milk yield of cows from four countries: Australia, Canada, Italy, and New Zealand. Selected countries represented a wide range of production systems and environments. Milk production in Canada and Italy is based mainly on intensive management systems, while Australia and New Zealand are largely based on rotational grazing. Legendre polynomials with five coefficients were used to model genetic and environmental lactation curves. Covariance components of lactation curve coefficients within and across countries, and selected functions of those, were estimated by Bayesian methods with Gibbs sampling, on selected subsets of data. Countries differed in both phenotypic and genetic parameters of lactation curves between d 5 and 305 of lactation. Principal component analysis of single-trait genetic and environmental covariance matrices showed, however, that the pattern of variability in test-day milk yield was very similar between countries. General level of milk production in lactation and persistency components accounted for more than 90% of the total variance. Estimated genetic correlations between countries for total yield in lactation ranged from 0.65 (Italy and New Zealand) to 0.83 (Australia and New Zealand), indicating a possibility of genotype by environment interaction for some pairs of countries.

Animal Husbandry↗

PubMed2000

[Analyses of factors prolonging the length of hospital stay in elderly patients beginning hemodialysis].

The aim of the present study is to clarify the factors causing prolongation of the length of hospital stay in elderly patients beginning hemodialysis. Patients aged over 60 years who had newly started hemodialysis (98 cases) were studied. These were 59 men and 39 women. The age was 73 +/- 7 years (mean +/- standard deviation). In each patient, the cause of renal failure (non-diabetes/diabetes), body mass index, comorbid conditions (cerebrovascular disease, ischemic heart disease, etc.), ambulation, cognitive function, urgency of the initiation of dialysis, occurrence of access failure, marital status, younger cohabitants, and the length of stay after initiation of dialysis were surveyed. The median and the mean of the length of stay were 37 and 49 days. Because of this disparity, a normal distribution of the length of stay could not be obtained. However, the distribution was transformed to close to normal by logarithmic conversion of the number of days. We used the log-converted value as the length of stay for statistical analyses. We investigated the influence of the differences of each factor on the length of stay. The subjects were divided into two groups for each factor. The mean and standard deviation of the length of stay was calculated respectively. Comparisons were carried out by unpaired t-test. Multiple regression analysis was also performed using background factors as explanatory variables, and the length of stay as a dependent variable. The factors presented by the nominal scale were converted to dummy variables. Eight variables in the unpaired t-test and seven variables in multiple regression analysis were statistically significant. All but one variable were common to both analyses. The gender was statistically significant only in the unpaired t-test. It could be explained by close correlation of gender with marital status. Access failure and urgent initiation of dialysis were dominant factors for the prolongation of the length of stay. Ischemic heart disease, diabetes, inability to walk, impaired cognitive function, and absence of a partner also prolonged the length of stay.

Aged↗

PubMed1979

A micro macrophage migration inhibition test for the detection of cellular immunity in vitro.

A simple, economical, macrophage migration inhibition assay enabling multiple tests to be performed using microculture plates has been developed. The system confers many advantages over the standard in vitro assay of macrophage migration inhibition factor. It requires only 5 X 10(5) macrophages for each assay, small volumes (100 microliter) of test factors are consumed, 96 tests in each culture plate are easily assessed microscopically and the technique is easily and reproducibly executed. An adherent monolayer of activated fresh mouse peritoneal exudate cells (PEC) is established in each microculture well. A 'starting line' is scored across the monolayer by the application of a trimmed razor blade and the cells are dislodged and aspirated from one side of the line. Test factors from cultures of stimulated lymphocytes were added to the 'wounded' monolayer and the migration of macrophages from test and control cultures was measured after staining. The cells across the line were counted after incubation. Miration was shown to be time and temperature dependent, markedly stimulated by colchicine and appeared to associate with tuberculin antigen (PPD) skin testing and lymphocyte transformation in human subjects.

Animals↗

PubMed2006

Comparison of tests to detect oxacillin resistance in Staphylococcus intermedius, Staphylococcus schleiferi, and Staphylococcus aureus isolates from canine hosts.

Multiple tests were compared to the reference standard PBP2a latex agglutination test for detection of mecA-mediated oxacillin resistance in canine staphylococci. Cefoxitin disk diffusion, using breakpoints for human isolates of coagulase-negative Staphylococcus spp., had low sensitivity for detection of oxacillin resistance in members of the Staphylococcus intermedius group.

Animals↗

PubMed1977

Pituitary autonomy in hyperprolactinemic secondary amenorrhea: results of hypothalamic-pituitary testing.

Twenty-seven women with secondary amenorrhea of greater than six months duration were subjected to multiple testing of hypothalamo-pituitary function. They were divided into normo-prolactinemic (Group 1 mean serum prolactin (PRL) 9.8 ng/ml; range 6.8 to 13.0 ng/ml; n=9) and hyperprolactinemic (Group 2 mean 37.5 ng/ml; range 19.2 to 93.7 ng/ml; n=18) groups on the basis of 4 weekly baseline determinations. Group 2 had significantly (P less than .05) lower serum LH and urinary pregnanediol levels than did Group 1; there was no statistical difference between the groups in serum FSH, T4, T3 or urinary estrogen measurements. Two women in Group 2 were found to have a pituitary chromophobe adenoma. Group 2 women showed no significant rises in serum PRL following stimulation tests with thyrotropin releasing hormone (TRH, 200 microng iv) and metoclopramide (10 mg orally), which caused significant responses in Group 1. The TSH response to TRH was, however, preserved in Group 2, while it was subnormal in Group 1 subjects. Both groups showed similar FSH and LH responses to luteinizing hormone-releasing hormone (LHRH, 25 microng iv). No significant suppression of serum PRL was seen in Group 2 patients given L-Dopa (500 mg orally),, which produced a significant response (P less than 0.05) in Group 1 subjects, while all patient showed marked reduction in serum PRL values following 2-bromo-alpha-ergocryptine (CB-154, 2.5 mg orally). When compared with other Group 2 members, the 2 cases with proven pituitary adenomata gave similar responses to the stimulation-inhibition tests and were not clearly distinguished on this basis. We conclude: 1. The pattern of PRL responses to dynamic tests, although of pathophysiological interest an autonomous pituitary lesions in patients with hyperprolactinemic secondary amenorrhea. 2. Such dynamic tests, although a pathophysiological interest, provide no clinical information additional to that provided by the mean basal serum PRL value. 3. In clinical practice, such dynamic tests should be confined to patients with mean serum PRL levels at around the upper limit of the normal range.

Adult↗

PubMed1998

Detection of patients with multiple drug allergy syndrome by elective tolerance tests.

BACKGROUND: Multiple drug allergy syndrome (MDAS) caused by antibiotics is frequently observed in allergy departments; however, risk factors for such a condition as well as the means to detect patients prone to MDAS are poorly defined. OBJECTIVE: The identification of patients prone to MDAS and the detection of risk factors for multiple antibiotic sensitivity. METHODS: Two hundred fifty-three elective oral challenges with alternative antimicrobial drugs were performed in 120 patients with histories of recent allergic reactions to antibiotics. RESULTS: Twenty-three (19%) subjects reacted to at least one antibiotic class. All reactions were mild and easily controlled by conventional therapy. Female sex, history of multiple antibiotic reactions, and reactions to nonsteroidal antinflammatory drugs were the main risk factors for reactions to alternative antibiotics. To date, no patient has reported immediate adverse reactions to drugs negative on oral challenge tests but one had urticaria/angioedema on the fifth day of full dose treatment with ofloxacin. CONCLUSIONS: Elective oral challenges with alternative antibiotics are a sensitive, specific, and safe means to detect patients with MDAS, thus sparing them more severe adverse reactions caused by full dose therapies. The recommendation to perform oral challenge tests with antibiotics just before their therapeutic use seems unnecessary and should be reconsidered.

Administration, Oral↗

PubMed2003

The clinical predictors of sleepiness correlated with the multiple sleep latency test in an Asian Singapore population.

STUDY OBJECTIVES: To explore the clinical predictors of sleepiness as objectively determined by the Multiple Sleep Latency Test with the Epworth Sleepiness Scale, age, body mass index, and overnight polysomnographic parameters at a tertiary referral center Sleep Disorders Unit. DESIGN: Retrospective, consecutive case series review. SETTING: A multidisciplinary sleep disorders unit in Singapore General Hospital, a tertiary-care university-affiliated hospital. PATIENTS: 72 consecutive patients evaluated for sleep disorders with overnight polysomnograms and Multiple Sleep Latency Tests between March 2002 and September 2002. INTERVENTIONS: N/A. MEASUREMENTS AND RESULTS: Mean sleep latency on the Multiple Sleep Latency Test was 9.0 +/- 4.4 minutes, and mean Epworth Sleepiness Scale score was 10.8 +/- 5.8. On univariate analysis, mean sleep latency on the Multiple Sleep Latency Test showed a significant negative correlation with the Epworth Sleepiness Scale score, apnea-hypopnea index, body mass index, arousal index, and time spent below 90% oxygen saturation during overnight polysomnography. After performing multiple linear regression, only Epworth Sleepiness Scale score and apnea-hypopnea index remained significantly correlated (P = .039 and P = .008, respectively). An Epworth Sleepiness Scale score of 8 or above predicted a mean sleep latency on the Multiple Sleep Latency Test of less than 10 minutes with a sensitivity of 73.9% and specificity of 50.0%. CONCLUSIONS: The Epworth Sleepiness Scale and apnea-hypopnea index are useful predictors of sleepiness in our Asian Singapore population.

Adult↗

PubMed2000

Categorizing a prognostic variable: review of methods, code for easy implementation and applications to decision-making about cancer treatments.

Categorizing prognostic variables is essential for their use in clinical decision-making. Often a single cutpoint that stratifies patients into high-risk and low-risk categories is sought. These categories may be used for making treatment recommendations, determining study eligibility, or to control for varying patient prognoses in the design of a clinical trial. Methods used to categorize variables include: biological determination (most desirable but often unavailable); arbitrary selection of a cutpoint at the median value; graphical examination of the data for a threshold effect; and exploration of all observed values for the one which best separates the risk groups according to a chi-squared test. The last method, called the minimum p-value approach, involves multiple testing which inflates the type I error rates. Several methods for adjusting the inflated p-values have been proposed but remain infrequently used. Exploratory methods for categorization and the minimum p-value approach with its various p-value corrections are reviewed, and code for their easy implementation is provided. The combined use of these methods is recommended, and demonstrated in the context of two cancer-related examples which highlight a variety of the issues involved in the categorization of prognostic variables.

Antineoplastic Agents↗

PubMed2007

The repeatability of submaximal endurance exercise testing in cystic fibrosis.

Submaximal endurance cycle ergometer exercise tests are used to measure the efficacy of an exercise intervention, but the repeatability of these tests in patients with cystic fibrosis (CF) has not been established. The purpose of this study was to examine the repeatability of submaximal endurance testing in stable CF. Fifteen adults with CF underwent two submaximal endurance tests carried out over a 7-day period. A subset of six subjects returned 28 days later for a third submaximal endurance test. Workload was set at 80% of maximum workload and exercise was performed to exhaustion. Oxygen consumption, minute ventilation, tidal volume, carbon dioxide output, respiratory rate, heart rate, and oxygen saturation were measured at rest, at end exercise and at four matched times during the submaximal endurance tests (20, 40, 60, and 80% of exercise duration calculated from the first endurance test). Submaximal endurance test time was highly repeatable with no significant learning effect identified on multiple testing. Submaximal endurance exercise time demonstrated a variability of 5.7% which is consistent with high levels of repeatability. Metabolic, ventilatory and cardiac variables were all also highly reproducible between test days. Submaximal endurance testing is repeatable in stable CF, confirming that submaximal endurance tests are a reliable tool for assessment of therapeutic benefit in patients with CF.

Adult↗

PubMed2005

A comparison of multiplicity adjustment strategies for correlated binary endpoints.

Several Bonferroni-type adjustments have been proposed to control for family wise type I error among multiple tests. However, many of the approaches disregard the correlation among endpoints. This can result in a conservative hypothesis testing strategy. The James procedure is an alternative approach that accounts for multiplicity among correlated continuous endpoints. Here a simulation study compares four Bonferroni-type alpha-adjustments (Bonferroni, Dunn-Sidák, Holm, and Hochberg) and the James p-value adjustment when used for multiple correlated binary variables. These procedures provided adequate protection against familywise type I error for correlated binary endpoints, albeit, at times, in an overly cautious manner. That is, when correlations among endpoints exceed 0.60, the result is somewhat conservative for the approaches that do not account for those correlations. Among the adjustments examined, the James approach appears to be the uniformly preferred method. Analyses of data from a randomized controlled clinical trial of treatments for mania in bipolar disorder are used to illustrate the application of the multiplicity adjustments.

Antipsychotic Agents↗

PubMed1969

Tumour-specific antibodies in human malignant melanoma and their relationship to the extent of the disease.

Biopsy specimens and sera were obtained from 103 melanoma patients. Autoantibodies were demonstrated by (1) complement-dependent cytotoxicity of autologous melanoma cells in short-term culture; (2) complement-dependent inhibition of ribonucleic acid synthesis; (3) immunofluorescent staining of the cytoplasm of killed melanoma cells and of the surface membrane of viable melanoma cells. Over one-third of the sera studied had antibodies to autologous melanoma cells. Although for technical reasons all three tests could not be performed with the cells from every melanoma, whenever multiple testing was possible there was complete concordance. The autoantibodies were virtually confined to patients in whom the disease was not widely disseminated, and over 80% of such patients had positive sera. In a limited number of patients who have been followed autoantibodies disappeared as the disease progressed to become widely disseminated. Two patients with generalized disease developed autoantibodies following inoculation by their own irradiated tumour cells.TWO TYPES OF AUTOANTIBODIES WERE RECOGNIZED: one, active against antigen(s) in the cell surface membrane, was specific for each tumour-that is, only the autologous serum reacted-and was concerned in the cytotoxic activity; the other reacted with cytoplasmic antigens which appeared to be present in most or all melanoma cells.

Autoantibodies↗

PubMed2005

Dissociations of face and object recognition in developmental prosopagnosia.

Neuropsychological studies with patients suffering from prosopagnosia have provided the main evidence for the hypothesis that the recognition of faces and objects rely on distinct mechanisms. Yet doubts remain, and it has been argued that no case demonstrating an unequivocal dissociation between face and object recognition exists due in part to the lack of appropriate response time measurements (Gauthier et al., 1999). We tested seven developmental prosopagnosics to measure their accuracy and reaction times with multiple tests of face recognition and compared this with a larger battery of object recognition tests. For our systematic comparison, we used an old/new recognition memory paradigm involving memory tests for cars, tools, guns, horses, natural scenes, and houses in addition to two separate tests for faces. Developmental prosopagnosic subjects performed very poorly with the face memory tests as expected. Four of the seven prosopagnosics showed a very strong dissociation between the face and object tests. Systematic comparison of reaction time measurements for all tests indicates that the dissociations cannot be accounted for by differences in reaction times. Contrary to an account based on speed accuracy tradeoffs, prosopagnosics were systematically faster in nonface tests than in face tests. Thus, our findings demonstrate that face and nonface recognition can dissociate over a wide range of testing conditions. This is further support for the hypothesis that face and nonface recognition relies on separate mechanisms and that developmental prosopagnosia constitutes a disorder separate from developmental agnosia.

Adult↗

PubMed1985

The problem of multiple inference in psychiatric research.

This paper deals with the problem of multiple inference in psychiatric research, an issue which arises whenever a researcher has to make more than one statistical inference in a single research study. It frequently arises in psychiatric research because of multivariate study designs, with subjects being measured on more than one dependent variable with the intention of studying differences between groups in mean scores. The disadvantages of the commonly adopted strategy of using multiple univariate tests (e.g. multiple t-tests) are outlined. Two broad strategies--Bonferroni-adjusted univariate tests and multivariate statistical analysis--are introduced. Their advantages and disadvantages are discussed in terms of their usefulness in confirmatory and exploratory research in psychiatry.

Analysis of Variance↗

PubMed1987

A prospective longitudinal study of neuropsychological and psychosocial factors in asymptomatic individuals at risk for HTLV-III/LAV infection in a methadone program: preliminary findings.

To test the hypothesis that cognitive impairment may be present early in the course of HTLV-III/LAV infection, intravenous drug abusers (IDVAs) without overt symptoms of AIDS related illness were tested with standard neuropsychological and psychosocial measures. This study is the baseline for a prospective longitudinal study of the natural history of HTLV-III/LAV infection in this high risk population. Of 211 subjects initially evaluated, 70 (33%) were HTLV-III/LAV seropositive and 141 (67%) were seronegative. At the baseline, by univariate analysis, the seropositive IVDAs were significantly (p less than .05) more impaired than seronegatives on 4 of 8 measures: Finger Tapping--dominant, hand, Digit Span Forward, Trail making A and WAIS-Similarities. However, by multivariate analysis the seropositives were significantly more impaired only on the WAIS-Similarities and Wechsler--Associative Learning tests. Multiple factors such as drug use and psychological stress may have influenced test performance. These preliminary results, however, suggest that seropositive IVDAs may show evidence of impaired neuropsychological function even in the absence of AIDS related symptoms and are consistent with the hypothesis of the early neurotropism of HTLV-III/LAV.

Acquired Immunodeficiency Syndrome↗

PubMed2026

Gene-Temperature Interactions and Risk of Childhood Acute Lymphoblastic Leukemia.

BACKGROUND: High ambient temperature in early pregnancy has been linked to an increased risk of childhood acute lymphoblastic leukemia (ALL). To better understand biological mechanisms, the current study evaluated potential interaction between temperature and genetic characteristics. METHODS: We used data from California birth records (1982-2008) and California Cancer Registry (1988-2011) to identify ALL cases (n=3,353) diagnosed ≤14 years of age and non-cancer controls (n=3,530) matched 1:1 on sex, race, ethnicity, and birth year and month. Weekly ambient temperatures throughout pregnancy were assessed on a 1-km grid around the birth address, while genetic data were available from a genome-wide association study using neonatal blood spots. We evaluated the association between ambient temperature and ALL risk by quartiles of established genetic risk score for ALL. Next, we formally tested gene-temperature interactions in the association with ALL, correcting for multiple testing, for genes previously identified with epigenetic changes due to both temperature and ALL. All analyses were adjusted for potential confounders. RESULTS: The elevated risk of ALL per 5 °C increase of weekly mean ambient temperature, confined to early pregnancy, was more pronounced among children with the lowest genetic susceptibility to ALL, especially among Latino children (first quartile: odds ratio [OR] = 1.50, 95% confidence interval [CI]: 1.14-1.97); fourth quartile: OR=1.03, 95% CI: 0.83-1.28). There were significant interactions (p<0.002) between ambient temperature and polymorphisms in BNC1 among non-Latino White children, and suggestive interactions (p<0.05) with TBPL2 and NRXN1 in the full population. CONCLUSIONS: Our findings suggest that there may be interactions between ambient temperature in early pregnancy and offspring genotype in the risk of childhood ALL. IMPACT: If replicated, these findings could help elucidate the biological mechanisms linking high ambient temperature in early pregnancy and the risk of childhood ALL.

Journal Article↗

PubMed2000

Genetic associations with clinical characteristics in bipolar affective disorder and recurrent unipolar depressive disorder.

Genetic factors may be associated with disease subtype as well as susceptibility. We have therefore typed polymorphisms at the serotonin transporter, dopamine receptor, tryptophan hydroxylase, tyrosine hydoxylase, and monoamine oxidase A (MAOA) loci in 139 unipolar and 131 bipolar patients and investigated associations with gender, number of episodes, age of onset, history of psychotic symptoms, history of suicidal behavior, and history of substance abuse. In bipolar subjects, the promoter variable number tandem repeat (VNTR) allele 132 of MAOA was associated with history of suicide attempts, P = 0.029, particularly in females, P = 0.006. The Fnu4HI allele 1 of MAOA was also associated with history of suicide attempts in females, P = 0.0162. The serotonin transporter promoter allele 2 was associated with increasing number of manic episodes, P = 0.02, and history of psychotic symptoms, P = 0.0243. One significant association was found in the unipolar group: dopamine D2 receptor promoter allele 2 with history of psychotic symptoms, P = 0. 0165. We have tested multiple loci for a variety of different clinical variables and performed 228 tests of significance in total. It is possible that these preliminary findings are type 1 errors, because one would expect 11 of the 228 tests to reach a nominal significance level of P < 0.05 by chance alone if all the tests were independent. The associations with the MAOA and serotonin transporter loci are consistent with previous data suggesting associations with susceptibility to bipolar affective disorder. Am. J. Med. Genet. (Neuropsychiatr. Genet.) 96:36-42, 2000

Base Sequence↗