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PubMed1983

A comparison of automated data collection and manual data collection for toxicology studies.

Automated data collection was compared with manual data collection in terms of accuracy and man-hours devoted to data manipulation and checking. The comparison was based on experience with an automated data collection system (DOLPHIN)TM1 developed at Toxigenics for use in conducting toxicological studies. It was found that on-line data collection increases the quality of the data gathered because: 1) it facilitates scientific observation by displaying historical data and statistics on changes since the last observation period; 2) it virtually eliminates errors due to oversight and transcription; 3) it allows more careful monitoring of the course of the study by providing immediate access to interim summary statistics; 4) it provides complete documentation of all changes made to the data after initial collection. In addition, automated data collection enables more rapid completion of the final report of results because: 1) fewer departmental transfers are required; 2) auditing by Quality Assurance (Q.A.) personnel is facilitated.

Data Collection↗

PubMed2025

Glutaryl-CoA dehydrogenase (GCDH) enhances renal malignancy risk via modulating glutarylcarnitine levels.

BACKGROUND: Crotonylation, a recently identified lysine acylation, plays a critical role in post-translational modifications [1]. It has been implicated in tumorigenesis by modulating metabolic reprogramming [2], DNA repair, immune evasion [3], and oncogenic signaling pathways, including PKA-FAK-AKT and androgen receptor signaling [4]. The specific role of crotonylation in renal malignancy (RM) remains poorly understood, especially in interaction with gene expression and metabolic pathway interactions. METHODS: This study integrates genome-wide association study (GWAS) summary statistics for RM from the FinnGen database, data on crotonylation-associated gene expression obtained from the eQTLGen consortium, and metabolite GWAS data obtained from the GWAS Catalog. A combined two-sample Mendelian randomization (MR), summary data-based Mendelian randomization (SMR), and mediation analyses were performed to investigate the causal link between Glutaryl-CoA dehydrogenase (GCDH) and RM, with a specific focus on glutarylcarnitine metabolism. RESULTS: MR analysis demonstrated a significant association; increased expression of GCDH is likely to increase the risk of RM (OR = 1.25, P = 0.0045). Mediation analysis revealed that elevated GCDH expression significantly reduced glutarylcarnitine (C5-DC) levels, which in turn was inversely associated with RM risk. A three-step MR-based mediation confirmed a significant mediating effect of glutarylcarnitine (β₁₂ = 0.0680, P = 0.002), with 30.25% of the total effect attributable to it. The robustness of these findings was further demonstrated by sensitivity analyses and SMR results. CONCLUSION: This study represents the first evidence that GCDH might exert an indirect pro-RM effect via the downregulation of glutarylcarnitine, thus providing new insights into tumor metabolic pathways and positioning glutarylcarnitine as a potentially diagnostic biomarker and therapeutic target for RM.

GCDH↗

PubMed2006

Smoking increases the treatment failure for Helicobacter pylori eradication.

PURPOSE: Treatment failure for Helicobacter pylori (H. pylori) eradication is encountered in approximately 10-20% of patients, and many studies have pointed to a link with smoking. To investigate the effects of smoking on eradication outcome, we performed a meta-analysis. METHODS: A PubMed search was performed to retrieve articles published up to August 2005. Pooled odds ratio (OR) and differences rate for H. pylori eradication failure in smokers compared with nonsmokers were used as summary statistics. Meta-regression was used for examining the source of heterogeneity. RESULTS: Twenty-two published studies (5538 patients), which provided information on eradication failure according to smoking status, were included in the analysis. The summary OR for eradication failure among smokers relative to nonsmokers was 1.95 (95% confidence interval [CI]: 1.55-2.45; P <.01). It corresponds with the differences in eradication rates between smokers and nonsmokers (8.4% [95% CI: 3.3-13.5%, P <.01]). Meta-regression analysis demonstrated that a high proportion of nonulcer dyspepsia patients in studies revealed a higher failure rate among smokers, compared with a low proportion of nonulcer dyspepsia. CONCLUSIONS: Our meta-analysis demonstrated that smoking increases the treatment failure rate for H. pylori eradication.

Anti-Bacterial Agents↗

PubMed2000

An improved technique for the extraction of stochastic parameters from stabilograms.

An improved characterization of the dynamics of postural sway can provide a better understanding about the functional organization of the postural control system as well as a more robust tool for postural pattern recognition. To this aim, a novel parameterization was applied to the stabilogram diffusion analysis formerly proposed by Collins and De Luca [Collins JJ, De Luca CJ. Open-loop and closed-loop control of posture: a random-walk analysis of center-of-pressure trajectories. Exp Brain Res 1993;95:308-18] that considered the act of maintaining posture as a stochastic process. The main purpose of the present technique was to overcome some drawbacks of the model presented by Collins and De Luca that may restrain its potential application in clinical practice. The approach uses a unique non-linear model to describe the center of pressure (COP) dynamics that reduces the number of parameters and decreases their intra-subject variability; consequently, fewer trials are required to perform reliable estimates of stochastic parameters and this is of particular importance for subjects that cannot afford many repeated measurements because of age or pathology. Four new statistical mechanics parameters (NSMP) were computed on the log-log stabilogram diffusion plots and their estimates were compared in terms of reliability and sensitivity to the visual conditions with: (1) a minimal set of four summary statistic scores (SSS); and (2) the six statistical mechanics parameters (SMP) proposed by Collins and De Luca. All four NSMP showed at least a fair-to-good reliability (intraclass correlation coefficient, ICC>0.49) while SMP (ICC>0.20) showed some poor reliability. A better overall reliability was also observed with respect to SSS. Moreover, only NSMP had a similar score for eyes open and eyes closed conditions. Three out of four NSMP were also significantly sensitive to eyes open or closed conditions (P<0.001) while only three out of six SMP were sensitive to operating conditions (P<0.01).

Humans↗

PubMed1989

Nursing the statistics: a demonstration study of nurse turnover and retention.

This paper demonstrates how a health authority can use personnel records of nurses' working histories as an effective tool in manpower planning. Suggestions are given as to how these histories might be analysed and interpreted. Methods described range from the use of simple summary statistics and graphical methods to advanced statistical modelling techniques. Data from a study by researchers at the Centre for Applied Statistics and Department of Sociology at Lancaster University are used to give examples of these approaches. A description is also given of the practical difficulties experienced when attempting to extract the appropriate data from the health authority's personnel records.

Data Collection↗

PubMed2000

[Allergen-specific immune therapy in the treatment of asthma].

OBJECTIVES: 1. To identify all published randomised controlled trials of allergen specific immunotherapy in asthma. 2. To estimate the overall efficacy of allergen specific immunotherapy upon asthmatic symptoms, medication requirements, lung function, nonspecific bronchial hyperreactivity (BHR) and allergen specific BHR. SEARCH STRATEGY: A search of the asthma database by the Cochrane Airways Group at St. Georges Hospital Medical School, London identified 660 nonunique citations with the keywords Immunotherapy* or Hyposensitive or Desensiti*. This database included all studies published up to 1997 with the keywords Asthma or Wheez* from the Medline, Embase and Cinahl databases, together with other studies identified by handsearching. SELECTION CRITERIA: The review was restricted to randomised controlled trials (RCT). Only studies which focussed upon asthma were included. Allergen specific immunotherapy was defined as the subcutaneous administration of extracts of house dust mites, pollens, animal danders or moulds, chemically modified allergoids or antigen-antibody complexes. Although placebo controlled trials were methodologically stronger, studies which administered house dust or other relatively antigenically inactive preparations to the control group were also considered. Double blinded trials were preferred, but single blind and open studies were also reviewed for possible inclusion. At least one of the following clinical outcomes had to be reported: asthmatic symptoms, asthma medication requirements, lung function, nonspecific BHR or allergen specific BHR. Inclusion of studies in the review was decided by a simple majority of all three reviewers, who independently read the methods sections of papers identified by the search strategy and applied the stated criteria. Quality assessment was performed by 2 reviewers, who independently assessed the concealment of allocation. DATA COLLECTION AND ANALYSIS: The comparisons were: Allergen immunotherapy v placebo, Allergen immunotherapy v antigenically inactive control, House dust v placebo and Allergen immunotherapy v untreated control. These comparisons were performed separately for each outcome, whenever these results were reported. Outcome data were extracted and entered into RevMan 3.0.1 for statistical analysis. Categorical outcomes were analysed as odds ratios (OR) and 95% confidence intervals (95% CI) calculated by Peto's method. Continuous outcomes were analysed as standardised mean differences (SMD). Fixed effects models were used to obtain summary statistics for the overall efficacy of allergen immunotherapy and x2 tests were performed to assess heterogeneity between studies. MAIN RESULTS: Fifty four randomised controlled trials published between 1954 and 1997 satisfied the inclusion criteria. There were 25 studies reporting immunotherapy for mite allergy, 13 studies of pollen allergy, eight studies of animal dander allergy, two studies of allergy to the mould Cladosporium and six studies which attempted simultaneous immunotherapy for multiple aeroallergens. Concealment of allocation was assessed as clearly adequate in only 11 studies. The adequacy or otherwise of 40 studies could not be determined from the details published in the papers. Only three studies used a clearly inadequate method for concealment of allocation. There was a significant overall improvement in asthma symptom scores following immunotherapy (combined SMD -0.52; 95% -0.70 to -0.35). Patients randomised to immunotherapy were also significantly less likely to report a deterioration in asthma symptoms than those randomised to placebo (OR 0.27; 95% CI 0.21 to 0.35). Asthma medication requirements were significantly reduced (SMD -0.51; 95% CI -0.74 to -0.28). Patients randomized to immunotherapy were also significantly less likely to require medication than those randomised to placebo (OR 0.28; 95% CI 0.19 to 0.42). There was no overall improvement in lung function following immunotherapy and marked hete

Asthma↗

PubMed2006

A kinetic-pharmacodynamic model for clinical trial simulation of antidepressant action: application to clomipramine-lithium interaction.

A generic kinetic-pharmacodynamic (K-PD) model to describe the response to treatment assessed by a clinical score for depressed patients treated by antidepressants alone or combined with a drug that shortens the lag-time before effect was developed. The aims of this study were: (1) to verify model's ability to characterize clinical data, (2) to evaluate several statistics to summarize the clinical effect, (3) to compare the analysis based on these statistics to the conventional intent-to-treat analysis and (4) to determine the optimal dates of clinical assessment. The population K-PD model was fitted to the individual data from a randomized clinical trial assessing the efficacies of clomipramine and placebo or clomipramine and lithium to treat major depression in 141 patients. The K-PD model was able to fit the individual data even in the case of oscillating score profiles. The interindividual coefficient of variation of the model parameters ranged from 33 to 161%. The statistical analysis based on the secondary parameters yielded conclusions comparable to those of the conventional intent-to-treat analysis. The population model was then used for a clinical trial simulation. According to the simulation, the most sensitive summary statistics for detecting a difference between lithium and placebo were the fractional reduction of depression and the proportion of responders. The optimal dates to assess these parameters were day 9 and 11 respectively. The K-PD model might serve as a tool for clinical trial planning in the field of research on antidepressants and their facilitators.

Antidepressive Agents↗

PubMed2003

Common statistical methods in orthopaedic clinical studies.

We discuss the statistical representation and management of random error in orthopaedic clinical studies. Descriptive studies (such as case series) collect information about a sample that may be generalized to describe a population. Typically this description is in the form of summary statistics, such as means, proportions, or rates. Error in these variables may be represented by confidence intervals. Correlation and regression are techniques for investigation of the relationship between two or more variables. Descriptive statistics, comparisons of groups, especially hypothesis tests, and assessment of association including correlation and regression are important statistical concepts for clinicians involved in the conduct or appraisal of orthopaedic clinical research.

Chi-Square Distribution↗

PubMed2004

Redefining the confidence interval.

The confidence interval, its close cousin the p-value, and other statistical summaries of data are widely used in science, including the occupational and environmental health sciences, but they are almost as widely misused. My purpose here is to review some basic matters that should be covered in every introductory statistics course, but are generally omitted. More specifically, some of the many assumptions that are needed in the usual forms of analysis are reviewed.

Confidence Intervals↗

PubMed2003

Percutaneous transluminal rotational atherectomy for coronary artery disease.

BACKGROUND: Percutaneous transluminal coronary rotational atherectomy (PTCRA) debulks atherosclerotic plaque from coronary arteries using an abrasive burr. On rotation, the burr selectively removes hard tissue. OBJECTIVES: To assess the effects of PTCRA for coronary artery disease in patients with non-complex and complex lesions (e.g., ostial, long, or diffuse lesions or those arising from in-stent restenosis) of the coronary arteries. SEARCH STRATEGY: We searched the Heart Group specialised register, the Cochrane Library to Issue 2, 2001, and MEDLINE, CINAHL, EMBASE and Current Contents to December 2002 and reviewed reference lists for relevant articles. SELECTION CRITERIA: We included randomised and quasi-randomised controlled trials of PTCRA compared with placebo, no treatment or another intervention and excluded cross-over trials. DATA COLLECTION AND ANALYSIS: Data were extracted independently by two authors. We asked authors of trials to provide information when missing data was encountered. Statistical summaries used risk ratios (RR) and weighted mean differences. MAIN RESULTS: We included 9 trials enrolling 3,066 patients. There was no evidence of the effectiveness of PTCRA in non-complex lesions. In complex lesions, there were no statistically significant differences in restenosis rates at 6 months (relative risk 1.00; 95% confidence interval 0.83 to 1.20) and 1 year (relative risk 1.21; 95% confidence interval =0.95 to 1.55) in those receiving PTCRA with adjunctive PTCA (PTCRA/PTCA) compared to those receiving PTCA alone. Morphological characteristics distinguishing complex lesions have not been examined in parallel-arm randomised controlled trials. There is equivocal evidence of the effectiveness of PTCRA in in-stent restenosis. Compared to angioplasty alone, PTCRA/PTCA did not result in a statistically significant increase in the risk of major adverse cardiac events (myocardial infarction, emergency cardiac surgery or death) during the in-hospital period (relative risk 1.19; 95% confidence interval =0.78 to 1.83). Compared to angioplasty, PTCRA was associated with 9 times the risk of an angiographically-detectable vascular spasm (relative risk 9.23; 95% confidence interval 4.61 to 18.47), 4 times the risk of perforation (relative risk 3.87; 95% confidence interval 0.82 to 18.21) and about 2 times the risk of transient vessel occlusions (relative risk 2.28; 95% confidence interval 1.00, 5.19) while angiographic dissections (relative risk 0.49; 95% confidence interval 0.33 to 0.75) and stents used as a bailout procedure (relative risk 0.38; 95% confidence interval 0.22 to 0.65) were less common. REVIEWER'S CONCLUSIONS: When conventional PTCA is feasible, PTCRA appears to confer no additional benefits. There is limited published evidence and no long-term data to support the routine use of PTCRA in in-stent restenosis. In certain circumstances (e.g., patients ineligible for cardiac surgery, those with architecturally complex lesions, or those with lesions that fail PTCA), PTCRA may achieve satisfactory revascularisation in subsequent procedures.

Angioplasty, Balloon, Coronary↗

PubMed1982

Sensitivity of trends in geometric mean blood levels to random measurement errors.

A statistical model is investigated that expresses observations, such as blood lead levels, as an additive function of true levels and random measurement errors. Both empirical results (obtained from a series of computer simulation experiments) and theoretical results indicate how certain summary statistics for the observations vary in response to random measurement errors. Such results are applied to a very large data base of pediatric blood lead levels collected in New York City during 1970-1976, and they indicate that the observed trends in geometric mean blood lead levels are not significantly altered by the possible presence of measurement errors.

Child, Preschool↗

PubMed2001

All half-lives are wrong, but some half-lives are useful.

The half-life of a drug, which expresses a change in concentration in units of time, is perhaps the most easily understood pharmacokinetic parameter and provides a succinct description of many concentration-time profiles. The calculation of a half-life implies a linear, first-order, time-invariant process. No drug perfectly obeys such assumptions, although in practise this is often a valid approximation and provides invaluable quantitative information. Nevertheless, the physiological processes underlying half-life should not be forgotten. The concept of clearance facilitates the interpretation of factors affecting drug elimination, such as enzyme inhibition or renal impairment. Relating clearance to the observed concentration-time profile is not as naturally intuitive as is the case with half-life. As such, these 2 approaches to parameterising a linear pharmacokinetic model should be viewed as complementary rather than alternatives. The interpretation of pharmacokinetic parameters when there are multiple disposition phases is more challenging. Indeed, in any pharmacokinetic model, the half-lives are only one component of the parameters required to specify the concentration-time profile. Furthermore, pharmacokinetic parameters are of little use without a dose history. Other factors influencing the relevance of each disposition phase to clinical end-points must also be considered. In summarising the pharmacokinetics of a drug, statistical aspects of the estimation of a half-life are often overlooked. Half-lives are rarely reported with confidence intervals or measures of variability in the population, and some approaches to this problem are suggested. Half-life is an important summary statistic in pharmacokinetics, but care must be taken to employ it appropriately in the context of dose history and clinically relevant pharmacodynamic end-points.

Algorithms↗

PubMed2001

A review and meta-analysis of the genetic epidemiology of anxiety disorders.

OBJECTIVE: The authors conducted meta-analyses of data from family and twin studies of panic disorder, generalized anxiety disorder, phobias, and obsessive-compulsive disorder (OCD) to explore the roles of genetic and environmental factors in their etiology. METHOD: MEDLINE searches were performed to identify potential primary studies of these disorders. Data from studies that met inclusion criteria were incorporated into meta-analyses that estimated summary statistics of aggregate familial risk and heritability for each disorder. RESULTS: For family studies, odds ratios predicting association of illness in first-degree relatives with affection status of the proband (disorder present or absent) were homogeneous across studies for all disorders. The calculated summary odds ratios ranged from 4 to 6, depending on the disorder. Only for panic disorder and generalized anxiety disorder could the authors identify more than one large-scale twin study for meta-analysis. These yielded heritabilities of 0.43 for panic disorder and 0.32 for generalized anxiety disorder. For panic disorder, the remaining variance in liability could be attributed primarily to nonshared environment. For generalized anxiety disorder, this was true for men, but for women, a potentially significant role for common familial environment was also seen. CONCLUSIONS: Panic disorder, generalized anxiety disorder, phobias, and OCD all have significant familial aggregation. For panic disorder, generalized anxiety disorder, and probably phobias, genes largely explain this familial aggregation; the role of family environment in generalized anxiety disorder is uncertain. The role of nonshared environmental experience is significant, underscoring the importance of identifying putative environmental risk factors that predispose individuals to anxiety.

Anxiety Disorders↗

PubMed2000

Towards better research: a discussion of some common mistakes in statistical analyses.

Statistical errors are common in clinical research. This paper presents a set of hypothetical but realistic scenarios in complementary medicine research. Each scenario contains at least one mistake typical of those made in analyses. These are discussed. The general principles are that charts and summary statistics can be misleading or even meaningless if not chosen carefully; objectives of the research need to be clearly defined and related to statistical hypotheses; assumptions of tests need to be checked; discussing the practical implications of observed effects is better than merely quoting P-values and data trawling should be avoided.

Complementary Therapies↗

PubMed1985

Detection, enumeration, and sizing of planktonic bacteria by image-analyzed epifluorescence microscopy.

Epifluorescence microscopy is now being widely used to characterize planktonic procaryote populations. The tedium and subjectivity of visual enumeration and sizing have been largely alleviated by our use of an image analysis system consisting of a modified Artek 810 image analyzer and an Olympus BHT-F epifluorescence microscope. This system digitizes the video image of autofluorescing or fluorochrome-stained cells in a microscope field. The digitized image can then be stored, edited, and analyzed for total count or individual cell size and shape parameters. Results can be printed as raw data, statistical summaries, or histograms. By using a stain concentration of 5 micrograms of 4'6-diamidino-2-phenylindole per ml of sample and the optimal sensitivity level and mode, counts by image analysis of natural bacterial populations from a variety of habitats were found to be statistically equal to standard visual counts. Although the time required to prepare slides, focus, and change fields is the same for visual and image analysis methods, the time and effort required for counting is eliminated since image analysis is instantaneous. The system has been satisfactorily tested at sea. Histograms of cell silhouette areas indicate that rapid and accurate estimates of bacterial biovolume and biomass will be possible with this system.

Bacteriological Techniques↗

PubMed2005

Phase I/II enzyme gene polymorphisms and esophageal cancer risk: a meta-analysis of the literature.

AIM: Phase I/II enzymes metabolize environmental carcin-ogens and several functional polymorphisms have been reported in their encoding genes. Although their significance with regard to esophageal carcinogenicity has been examined epidemiologically, it remains controversial. The present systematic review of the literature was performed to clarify associations. METHODS: Eligible studies were case-control or cohort studies published until September 2004 that were written in any language. From PubMed and a manual review of reference lists in relevant review articles, we obtained 16 studies related to the CYP1A1 Ile-Val substitution in exon 7, CYP1A1 MspI polymorphisms, CYP2E1 RsaI polymorphisms, GSTM1 null type, GSTT1 null type and GSTP1 Ile104Val. All were of case-control design. Summary statistics were odds ratios (ORs) comparing heterozygous-, homozygous-non-wild type or these two in combination with the homozygous wild type, or the null type with the non-null type for GSTM1 and GSTT1. A random effect model was used to estimate the summary ORs. A meta-regression analysis was applied to explore sources of heterogeneity. RESULTS: Individuals with the Ile-Val substitution in CYP1A1 exon 7 had increased esophageal cancer risk, with ORs (95%CI) compared with Ile/Ile of 1.37 (1.09-1.71), 2.52 (1.62-3.91) and 1.44 (1.17-1.78) for Ile-Val, Val/Val genotype and the combined group. No significant association was found between esophageal cancer risk and the other genetic parameters. CONCLUSION: A significant association exists between the CYP1A1 Ile-Val polymorphism and risk of esophageal cancer. Polymorphisms that increase the internal exposure to activated carcinogens may increase the risk of esophageal cancer.

Cytochrome P-450 CYP1A1↗

PubMed2024

Biobank-wide association scan identifies risk factors for late-onset Alzheimer's disease and endophenotypes.

Rich data from large biobanks, coupled with increasingly accessible association statistics from genome-wide association studies (GWAS), provide great opportunities to dissect the complex relationships among human traits and diseases. We introduce BADGERS, a powerful method to perform polygenic score-based biobank-wide association scans. Compared to traditional approaches, BADGERS uses GWAS summary statistics as input and does not require multiple traits to be measured in the same cohort. We applied BADGERS to two independent datasets for late-onset Alzheimer's disease (AD; n=61,212). Among 1738 traits in the UK biobank, we identified 48 significant associations for AD. Family history, high cholesterol, and numerous traits related to intelligence and education showed strong and independent associations with AD. Furthermore, we identified 41 significant associations for a variety of AD endophenotypes. While family history and high cholesterol were strongly associated with AD subgroups and pathologies, only intelligence and education-related traits predicted pre-clinical cognitive phenotypes. These results provide novel insights into the distinct biological processes underlying various risk factors for AD.

Alzheimer Disease↗

PubMed2005

Summarizing data through a piecewise linear growth curve model.

Most of the research in clinical trials is based on longitudinal designs, which involve repeated measurements of a variable of interest. Such designs are very powerful, both statistically and scientifically. Recent advances in statistical theory and software development incorporate the covariance structures such as unstructured, compound symmetry, auto-regressive and random effects, etc., for analysing longitudinal data. Hathaway et al. propose a technique for summarizing longitudinal data using linear growth curve model and establish that the number of summary statistics is fixed as four irrespective of the length of study. In this paper, we develop a procedure for analysing the longitudinal data through a piecewise linear growth curve model on the lines of Hathaway et al. Under different covariance structures, the linear model is fitted for Leprosy data and the residual sum of squares computed. Goodness of fit has also been considered for various models. In order to prove that the proposed method is robust and better than the others in terms of goodness of fit, simulation studies are carried out and the results presented.

Biometry↗