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PubMed1993

Membrane fusion-inhibiting peptides do not inhibit influenza virus fusion or the Ca(2+)-induced fusion of negatively charged vesicles.

Short hydrophobic N-carbobenzoxy oligopeptides are known to inhibit the infectivity of several enveloped viruses. Recently, it was shown that they inhibited the fusion of Sendai virus with N-methyl-dioleoylphosphatidylethanolamine (N-methyl-DOPE) liposomes as well as the low pH-induced fusion of these liposomes with each other (Kelsey, D.R., Flanagan, T. D., Young, J. E., and Yeagle, P. L. (1990) J. Biol. Chem. 265, 12178-12183). Therefore it was concluded that the peptides inhibit membrane fusion, an important step in viral infectivity. Here, it is shown that this peptide and a series of similar peptides did not inhibit influenza virus fusion with N-methyl-DOPE or other liposomes. In fact, some peptides enhanced the overall rate of fusion of influenza virus with N-methyl-DOPE liposomes. In our hands, the peptides did not inhibit influenza infectivity in Madin-Darby canine kidney cells or influenza-induced hemolysis either. They also did not inhibit the Ca(2+)-induced fusion between cardiolipin or phosphatidylserine liposomes. However, the inhibitory effect of one of the peptides on the fusion of Sendai virus with N-methyl-DOPE liposomes and on N-methyl-DOPE liposome-liposome fusion could be reproduced. These data indicate that the peptides do not, as had been suggested (Yeagle, P.L., Young, J.E., Hui, S.W., and Epand, R. M. (1992) Biochemistry 31, 3177-3183), act by preventing the formation of lipid structures with small radii of curvature, such as the inverted phase intermediates that are thought to be involved in N-methyl-DOPE fusion. The results also suggest that the mechanism of inhibition of Sendai virus infection and N-methyl-DOPE fusion by the peptides may be different after all.

Amino Acid Sequence↗

PubMed1993

The role of the data manager in clinical cancer research. An opportunity for nurses.

A clinical trial is a research study conducted in humans and designed to answer specific questions using scientifically controlled methods. These trials require considerable effort to assure that the data obtained are reliable, reproducible, and readily available. Data managers play a key role in this research effort. A nurse with a clinical background, computer knowledge, and some experience in the research environment is well suited for the role of data manager. The data manager performs a variety of tasks in this position that will enhance the quality of the data gathered in a research study. These responsibilities include designing forms, monitoring protocol accrual, abstracting data, entering data onto protocol-specific forms and/or specifically designed computerized data-entry screens, assuring the quality and the integrity of the data, and providing investigators with interim and summary reports. In addition, the data manager can be responsible for the management of a computerized clinical data base system, including the training of users and the designing of basic reports for the investigators. A nurse, functioning as a data manager, who understands research methodology, is detail oriented, and is well organized, could be a valuable asset to the clinical trials team in the successful management of any clinical study.

Clinical Trials as Topic↗

PubMedDate not supplied

Morphometric analysis of the corpus callosum using MR: correlation of measurements with aging in healthy individuals.

PURPOSE: To analyze changes of the human corpus callosum and MR midsagittal brain structures during normal aging. METHODS: A morphometric evaluation strategy for quantification of these brain structures on MR scans was developed. This computerized measuring program did allow the acquisition of more than 100 one- and two-dimensional parameters. RESULTS: During normal aging, the anterior parts of the corpus callosum (genu and anterior parts of the trunk) were significantly decreased, suggesting alterations of frontal and temporal interhemispheric fiber systems. Further changes were seen in callosal thickness and callosal width of the anterior parts of the corpus callosum. The profile area of the telencephalon was significantly reduced during normal aging. The size of the mesencephalon showed age-specific changes. CONCLUSIONS: The proposed computer program proved to be a powerful and reliable tool to get objective and reproducible quantitative data of corpus callosum and midsagittal brain structures. Specific age changes were found in the corpus callosum, indicating alteration of the frontotemporal interhemispheric fiber systems.

Adult↗

PubMed1995

Standard operating procedures (SOPs): reason for, types of, adequacy, approval, and deviations from and revisions to.

Standard Operating Procedures (SOPs) are required in order to comply with the Good Laboratory Practice Standards (GLPS) as promulgated in the Federal Insecticide, Fungicide and Rodenticide Act (FIFRA) 40 CFR Part 160. Paragraph 160.81 (a) states: "A testing facility shall have standard operating procedures in writing setting forth study methods that management is satisfied are adequate to insure the quality and integrity of the data generated in the course of a study." Types of SOPs include administrative and personnel, analyses, substances, quality assurance and records, test system, equipment, and field related. All SOPs must be adequate in scope to describe the function in sufficient detail such that the study data are reproducible. All SOPs must be approved by a management level as described in a corporate organization chart. Signatures for SOP responsibility, authorship, and Quality Assurance review adds strength and accountability to the SOP. In the event a procedure or method is performed differently from what is stated in the SOP, an SOP deviation is necessary. As methods and procedures are improved, SOP revisions are necessary to maintain SOP adequacy and applicability. The replaced SOP is put into a historical SOP file and all copies of the replaced SOPs are destroyed.

Facility Regulation and Control↗

PubMed1997

[The tilt-table test: is it essential for adequate treatment of vasovagal syncope? Arguments against].

The knowledge about vasovagal syncope has hugely grown since its initial description by Lewis in 1932. Nevertheless some critical gaps remain, affecting specially to the patient management. There are not enough data about the natural history of the process and, because of that, no useful markers are known to identify patients who need or would benefit from a specific treatment. A diagnostic test with a sensibility/specificity relationship good enough to be a diagnostic gold standard is lacking. Although tilt-table test can be helpful in diagnosis, its sensitivity is, nowadays, unknown. Available data about reproducibility of tilt test are scarce and sometimes contradictory, specially with positive tilt test results. Should the lack of reproducibility of positive results found by some authors be confirmed, the usefulness of serial tilt tests in selecting treatment would be seriously affected. No evidence about the existence of an effective treatment for vasovagal syncope has been published yet, not either about the advantage of an specific strategy in selecting it. Therefore, tilt test has not been proved to be a more useful tool in selecting therapy for patients with vasovagal syncope.

Humans↗

PubMed1976

A computer program for parallel line bioassays.

PARLIN is a program for the statistical analysis of biological assays that are either completely randomized, or in randomized blocks, in which the regression on log dose is linear with a constant variance per response. An earlier program (McArthur et al., J. Pharmacol. Exp. Ther. 153: 573-580, 1966) has been completely rewritten, improved and extended in its facilities. PARLIN, written in FORTRAN IV, will handle up to 99 test preparations, up to 100 doses in all, and up to 50 responses per dose. It is designed with special attention to simplicity for routine use, versatility of facilities and output immediately available for all forms of reporting results. A wide choice of transformations of response is available. The output reproduces the data for verification and tabulates potency estimates with limits at probabilities .95, .99; optional output includes an analysis of variance, information on validity, values of residuals and a rough plot of the dose-response relation.

Analysis of Variance↗

PubMedDate not supplied

Pollen, mite and mould samplings by a personal collector at high altitude in Nepal.

The new personal portable sampler for detection of environmental biologic particles (Partrap FA52, Coppa, Biella, Italy) was used to evaluate both atmospheric and indoor biologic particles in bedding at high altitudes during two Italian scientific expeditions in Nepal, in 1994 and 1996 respectively. The sampling was performed outdoors and indoors at the following altitudes: Katmandu 1,330 meters (m), LuKla 2,800 m, Namche 3,500 m, Pericle 4,200 m and Piramide 5,050 m. In both expeditions each sample of outdoor and indoor air was obtained by sucking air into the sampler either against the wind during a 6-h period, from 9 am to 3 pm, or from bedding of inhabitants resident at the different altitudes for 5 min. The number of pollens, moulds and mites trapped in each sample were assessed. The statistical analysis of the results by Spearman correlation test revealed a significant inverse correlation (p < 0.02) between altitude and the number of the considered biologic particles for sampling carried out during both the 1994 and 1996 expeditions. Moreover, Wilcoxon paired test showed no significant difference between the biologic sampling obtained in the two expeditions. These results confirm the decrease of the environmental biologic charge in relation to the increase of altitude and prove the efficacy of Partrap FA52 in obtaining reproducible quantitative data.

Air Pollution↗

PubMed1998

Discovering simple DNA sequences by compression.

An information-theoretic DNA compression scheme devised by Milosavljevic and Jurka (1993) has been used in many places in the literature for both the discovery of new genes and the compression of DNA. Their compression method applies an encoding of previously occurring runs. They use 5 different code-words: four being the DNA bases, A, C, G and T, and the other being a pointer to a previously occurring run. They advocate a code-word of length log2 5 for each of these and then encoding a run by a code-word of length 2 x log2 n, where n is the length of the sequence. This scheme encodes the start of the sequence with a code-word of length log2 n and likewise encodes the end of the sequence with a code-word of length log2 n. In this paper, we show the above coding scheme to be inefficient in various ways and improve upon it so that it can compress DNA. We discuss our implementation of various schemes some of which run in linear time.

Algorithms↗

PubMed1988

[Effect of intravenous diltiazem on stress-induced myocardial ischemia (study of hemodynamics and reproducibility of repeated studies].

UNLABELLED: To obtain data about (a) the reproducibility of repeated standardized exercise tests, under blank and placebo conditions and (b) the improvement of ischaemic symptoms and of haemodynamics after intravenous application of diltiazem (0.3 mg/kg body weight), 20 patients with angina pectoris and angiographically proven coronary heart disease were analysed in a randomized double-blind study. RESULTS: a) A control exercise test 1 h after the first blank test showed no significant changes of the following parameters neither at rest nor during exercise: heart rate, systolic and diastolic blood pressure, double product, pulmonary capillary wedge pressure, cardiac output, peripheral vascular resistance, stroke volume, ST-segment depression, symptoms of angina pectoris, and maximal work tolerance (steady state, supine position). b) After intravenous application of diltiazem, at rest, both systolic blood pressure (-13 mm Hg, p less than 0.03); diastolic blood pressure (-10 mm Hg, p less than 0.01) and peripheral vascular resistance (-189 dyn x s x cm-5, p less than 0.02) decreased. During exercise testing, diastolic blood pressure (-9 mm Hg, p less than 0.02), pulmonary capillary wedge pressure (-13 mm Hg, p less than 0.01) and peripheral vascular resistance (-152 dyn x s x cm-5, p less than 0.02) were reduced, and angina pectoris was less severe (p less than 0.01): in comparison to placebo the onset of anginal symptoms occurred later (24 vs 49 W, p less than 0.01). Maximal exercise tolerance and maximal cardiac output were improved, and ST-segment depression was less pronounced. The study shows that haemodynamic data and ischaemic parameters are well reproducible in repeated exercise tests.(ABSTRACT TRUNCATED AT 250 WORDS)

Adult↗

PubMed2002

Cross-species hybridisation of pig RNA to human nylon microarrays.

BACKGROUND: The objective of this research was to investigate the reproducibility of cross-species microarray hybridisation. Comparisons between same- and cross-species hybridisations were also made. Nine hybridisations between a single pig skeletal muscle RNA sample and three human cDNA nylon microarrays were completed. Three replicate hybridisations of two different amounts of pig RNA, and of human skeletal muscle RNA were completed on three additional microarrays. RESULTS: Reproducibility of microarray hybridisations of pig cDNA to human microarrays was high, as determined by Spearman and Pearson correlation coefficients and a Kappa statistic. Variability among replicate hybridisations was similar for human and pig data, indicating the reproducibility of results were not compromised in cross-species hybridisations. The concordance between data generated from hybridisations using pig and human skeletal muscle RNA was high, further supporting the use of human microarrays for the analysis of gene expression in the pig. No systematic effect of stripping and re-using nylon microarrays was found, and variability across microarrays was minimal. CONCLUSION: The majority of genes generated highly reproducible data in cross-species microarray hybridisations, although approximately 6% were identified as highly variable. Experimental designs that include at least three replicate hybridisations for each experimental treatment will enable the variability of individual genes to be considered appropriately. The use of cross-species microarray analysis looks promising. However, additional validation is needed to determine the specificity of cross-species hybridisations, and the validity of results.

Journal Article↗

PubMedDate not supplied

Doppler echocardiography in the dog: measurement variability and reproducibility.

Serial Doppler echocardiographic examinations were carried out in random order on six boxer dogs, on 3 separate days, by two experienced Doppler echocardiographers, to assess measurement variability and reproducibility of 65 parameters. Large numbers of parameters exhibited significant differences for each of the categories of intraobserver, interobserver, interday and interoperator. The coefficients of variation for all parameters measured ranged from 5.03 to 46.43%, but most were less than 20%. In general, least variation was found for the intraobserver category, and the best reproducibility for M-mode and left ventricular volumetric data. The worst reproducibility was found for tricuspid inflow and pulmonary venous flow measurements. The results of this study suggest differences greater than 20% for serial scans must be achieved to document genuine change, although the specific data should be consulted. Furthermore, variability and reproducibility are improved if a single experienced operator/observer acquires and measures serial scans.

Animals↗

PubMed2004

Optimizing the fMRI data-processing pipeline using prediction and reproducibility performance metrics: I. A preliminary group analysis.

We argue that published results demonstrate that new insights into human brain function may be obscured by poor and/or limited choices in the data-processing pipeline, and review the work on performance metrics for optimizing pipelines: prediction, reproducibility, and related empirical Receiver Operating Characteristic (ROC) curve metrics. Using the NPAIRS split-half resampling framework for estimating prediction/reproducibility metrics (Strother et al., 2002), we illustrate its use by testing the relative importance of selected pipeline components (interpolation, in-plane spatial smoothing, temporal detrending, and between-subject alignment) in a group analysis of BOLD-fMRI scans from 16 subjects performing a block-design, parametric-static-force task. Large-scale brain networks were detected using a multivariate linear discriminant analysis (canonical variates analysis, CVA) that was tuned to fit the data. We found that tuning the CVA model and spatial smoothing were the most important processing parameters. Temporal detrending was essential to remove low-frequency, reproducing time trends; the number of cosine basis functions for detrending was optimized by assuming that separate epochs of baseline scans have constant, equal means, and this assumption was assessed with prediction metrics. Higher-order polynomial warps compared to affine alignment had only a minor impact on the performance metrics. We found that both prediction and reproducibility metrics were required for optimizing the pipeline and give somewhat different results. Moreover, the parameter settings of components in the pipeline interact so that the current practice of reporting the optimization of components tested in relative isolation is unlikely to lead to fully optimized processing pipelines.

Adult↗

PubMed2001

Conformational analysis of the HIV-1 virus reverse transcriptase nonnucleoside inhibitors: TIBO and nevirapine.

TIBO (Tetrahydro-imidazo[4,5,1-jk][1,4]-benzodiazepin-2-one) and nevirapine (11-cyclopropyl-5,11-dihydro-4-methyl-6H-dipyrido[3,2-b:2',3'-e][1,4]diazepin-6-one) are models for two classes of nonnucleoside inhibitors of the HIV-1 virus reverse transcriptase (NNRTI). This work presents the parameterization of compounds belonging to these two classes in the Cornell et al. force field through ab initio and semiempirical methods. The new parameters were used in the conformational analysis for TIBO R82913, TIBO R79882, and nevirapine. Various conformational search protocols were tested and the pseudosystematic method SUMM led to the best results. A better understanding of the distribution of conformers was obtained through clustering techniques in the data reduction stages. It was possible to reproduce various experimental data such as the crystallographic structures of the isolated or reverse transcriptase-complexed (RT) molecules. The proton-proton coupling constants (\documentclass{article}\pagestyle{empty}\begin{document}$\,J^{3}_{\mathrm{HH}}$\end{document}) obtained for TIBO through NMR were also reproduced. Cremer and Pople puckering parameters enabled a precise description of both the conformation of the seven-membered rings and the relative position of the substituents on them. These parameters also demonstrated the efficiency and precision of the two-stage clustering method. Copyright 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1817-1829, 2001

Journal Article↗

PubMed1990

Reproducibility or variability of casual and ambulatory blood pressure data: implications for clinical trials.

Lack of reproducibility in a blood pressure measurement leads to a systematic underestimate of risk when only a few highly variable blood pressure estimates are taken. This has been called the 'regression dilution bias'. To determine the real risk produced by a lifelong blood pressure elevation requires many readings in order to estimate 'usual' blood pressure. Multiple readings improve the precision of the estimate of usual blood pressure. The 1-month variability in clinic and in 1, 2, 3, 4, 8 and greater than 20 ambulatory diastolic blood pressure values, measured in 100 untreated hypertensives, showed that whether the variability is measured as the standard deviation of the difference or as intermonth autocorrelations, the precision is improved by increasing numbers of blood pressure readings. The risks calculated from an elevation in blood pressure would have been up to 69% greater had ambulatory diastolic blood pressure been used to classify subjects in epidemiological studies. Repeat epidemiological investigations of the risks posed by certain levels of ambulatory blood pressure are needed.

Bias↗

PubMed2002

Assessing sources of variability in microarray gene expression data.

Experiments using microarrays abound in genomic research, yet one factor remains in question. Without replication, how much stock can we put into the findings of microarray experiments? In addition, there is a growing desire to integrate microarray data with other molecular databases. To accomplish this in a scientifically acceptable manner, we must be able to measure the validity and quality of microarray data. Otherwise, it would be the weakest link in any integration process. Validating and evaluating the quality of data requires the ability to determine the reproducibility of results. Data obtained from a microarray experiment designed as a feasibility test provided a unique opportunity to partition and quantify several sources of variation that are likely to be present in most microarray experiments. We use this opportunity to discuss the origins of variability observed in microarray experiments and provide some suggestions for how to minimize or avoid them when designing an experiment.

Adolescent↗

PubMed2006

Aspirin in peripheral arterial disease: breakthrough or pitfall?

BACKGROUND: This paper introduces a proof-of-concept trial in progress, supposedly providing new important information on anti-platelet drugs used in patients with peripheral arterial disease (PAD). The Arteriogenesis Competence Network (Art.Net.) of the Universities of Basel, Berlin, and Freiburg could show in animal models that Aspirin (ASA), in contrast to Clopidogrel, inhibits the formation of an appropriate collateral network (arteriogenesis). This trial is supposed to reproduce the animal data in man. MATERIALS AND METHODS: In a prospective, double-blind, parallel-group, bi-national (D, CH), multicentre trial, 250 patients will be randomised to either 100 mg ASA or 75 mg Clopidogrel once daily. Patients will then enter a three months structured rehabilitation programme with daily physical training supposed to induce arteriogenesis. The claudication distances will be tested as the primary endpoint at baseline, 6 weeks, and at 3 months. Also, the 24h physical activity profile of all patients will be electronically documented. CONCLUSIONS: This trial will provide information on potential disadvantages when using ASA in PAD patients. If data emerging from animal pharmacology can be reproduced in man, the present standard scheme of anti-aggregant treatment in PAD patients has to be reconsidered.

Arterial Occlusive Diseases↗

PubMed1992

Data management and accountability in behavioral and biomedical research.

Regulations recently enacted by the Public Health Service and the National Science Foundation to address misconduct in scientific research were designed primarily to curtail deliberate forms of misconduct, such as fabrication or falsification of findings; however, researchers may also be held accountable for inadvertent deficiencies in data management. This article examines some of the problems in data quality control, documentation, and data retention that can occur when computers are used in scientific research. It focuses on deficiencies that could make it difficult to verify the integrity of research data or to reproduce statistical analyses. Strategies for prevention of data management problems are recommended.

Database Management Systems↗

PubMed2001

Reproducibility of ambulatory blood pressure measurements in essential hypertension.

BACKGROUND: Data on the reproducibility of serial measurements of ambulatory blood pressure in hypertensive patients are lacking. The purpose of this study was to examine (1) the reproducibility of four consecutive ambulatory blood pressure measurements, and (2) the reproducibility of nocturnal falls in blood pressure in hypertensive patients. METHODS: Twenty patients with mild to moderate essential hypertension underwent four separate ambulatory blood pressure monitorings, on the same day of the week, at 30-day intervals. Antihypertensive therapy was discontinued for 2 weeks before each recording. Comparing the mean values of blood pressure over 24h, as well as diurnal, nocturnal and hourly periods, among the four recordings determined the reproducibility of blood pressure measurements. A day/night difference in mean systolic and in mean diastolic blood pressure defined the nocturnal fall in blood pressure. RESULTS: No significant differences were observed in either hourly, 24-h, diurnal or nocturnal systolic blood pressure, diastolic blood pressure and heart rate, or in the nocturnal fall in systolic and diastolic blood pressure among the four recordings. CONCLUSIONS: Hourly systolic blood pressure, diastolic blood pressure, heart rate, and nocturnal fall in blood pressure were reproducible in four ambulatory blood pressure monitorings recorded over 4 months. These findings suggest that ambulatory blood pressure monitoring is a reliable tool to monitor blood pressure changes.

Aged↗