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At least 667 records · Page 37Linked to original sources
PubMed2026

PYRAMA: an open-source tool for advanced meta-analysis of genome wide association studies.

MOTIVATION: Genome-wide association study (GWAS) meta-analysis tools are essential for integrating summary statistics across multiple cohorts, thereby increasing statistical power and validating genetic associations. Widely cited tools, such as METAL, PLINK, and GWAMA, have facilitated numerous significant discoveries in the field of GWAS. Nevertheless, these tools offer a limited set of meta-analysis methods and typically require users to have prior experience with command-line tools to be executed. RESULTS: We present here PYRAMA, an open-source tool which is designed for meta-analysis of genome wide association studies. This work introduces an easy-to-use software package that includes several meta-analysis methods that are absent in similar software packages. PYRAMA is faster compared to other tools, supports robust methods for analysis and meta-analysis, fixed-effects, random-effects and Bayesian meta-analysis and it is currently the only tool that supports meta-analysis with imputation of summary statistics. It is available both as a standalone tool and as a freely available web server. AVAILABILITY AND IMPLEMENTATION: https://github.com/pbagos/PYRAMA, https://doi.org/10.5281/zenodo.17830449.

Genome-Wide Association Study↗
PubMedDate not supplied

[Taxonomic value of the characterization of Pseudomonas by the analysis of volatile fatty acids produced in culture].

Gas liquid-chromatography was used in order to characterize the volatile fatty acids produced in culture supernatants by 632 Pseudomonas strains. Statistical analysis of these results allowed testing of the discriminatory power of this analytical methodology (factor analysis) to point out the presence of subgroups (clustering according to the variance) and to show the relationship between species and subspecies (three-dimensional plot). Fourteen Pseudomonas species could be accurately characterized by this methodology; the classification of Pseudomonas build up, on the basis of qualitative and quantitative aspects of their volatile fatty acids production, agrees with the current classification based on rRNA/DNA homology complexes.

Chromatography, Gas↗
PubMed2004

Repeated use of transscleral cyclophotocoagulation laser G-probes.

PURPOSE: To evaluate the energy transmission of transscleral cyclophotocoagulation laser G-probes after repeated use. METHODS: In this prospective study, eight new laser probes were each used for 30 transscleral cyclophotocoagulation (TSCPC) sessions in cadaver human eyes with the laser settings of 2000 mW power, 2000 milliseconds duration, and 18 shots. The laser power output was measured using a laser energy output meter before and after each TSCPC session, after swabbing the laser probe tip with alcohol, and finally after thorough cleaning by flushing 70% alcohol inside the plastic footplate tip and swabbing with alcohol the fiberoptic tip. Laser probes were inspected for deterioration. Statistical analysis was done using Analysis of Covariance (ANCOVA). RESULTS: The laser power output increased on average by 1.99 +/- 0.18 mW after each cycle (P < 0.01, 95% confidence interval: 1.63-2.35 mW, ANCOVA). No deterioration of the probes was found after 30 TSCPC and sterilization cycles. Laser energy output increased on average 6% (P < 0.01) from the baseline to the first TSCPC cycle. Probe number one broke during the tenth cycle and accordingly data was recorded for this probe until that cycle. CONCLUSION: G-probes not only remain fully functional after repeated use and sterilization with 70% alcohol but also slightly increase in energy output.

Cadaver↗
PubMed2006

Effectiveness of darbepoetin alfa versus epoetin alfa for the treatment of chemotherapy induced anemia in patients with gynecologic malignancies.

OBJECTIVE: Chemotherapy induced anemia (CIA) commonly occurs in gynecologic oncology patients. This often leads to treatment with erythropoietic stimulating agents in order to prevent chemotherapy delays, dose modifications and transfusion of red blood cells. Our objective was to determine the subsequent transfusion rates following administration of either darbepoetin alfa or epoetin alfa. METHODS: A single institution retrospective chart review was performed utilizing patients from January 2003 to September 2004 who received either darbepoetin alfa or epoetin alfa for CIA (Hgb < or = 10.0). Data collection variables included patient demographics, cancer diagnosis, chemotherapy treatment(s), laboratory data, erythropoeisis stimulation data, and transfusions. Sample size calculations were set to detect a 20% transfusion rate difference between the two groups. Chi-square, Fisher exact test and student t tests were used for statistical analysis. RESULTS: 123 patients were eligible for analysis (60 darbepoetin alfa; 62 epoetin alfa). 93% of darbepoetin alfa patients received 200 mg every other week, while 86% of epoetin alfa patients received 40,000 U weekly. The darbepoetin alfa and epoetin alfa groups were similar in respect to age, race, tumor type, histology, previous chemotherapy, number of chemotherapy agents, weeks of erythropoietic stimulation, and baseline serum levels of creatinine and hemoglobin. The mean baseline Hgb and change in Hgb was similar for each group (darbepoetin alfa = 11.2, 2.5 and epoetin alfa = 11.3, 2.3). Twenty one (35%) of the darbepoetin alfa patients received a transfusion of packed red blood cells compared to 12 (19%) of epoetin alfa patients (p = 0.05). CONCLUSIONS: This retrospective analysis powered to detect differences in transfusion rates revealed a statistically significant difference in transfusion rates between darbepoetin alfa and epoetin alfa for the treatment of CIA. These data warrant a randomized prospective trial in gynecologic oncology patients with careful attention to the timing of initiation of treatment, dosing regimens, and titration of growth factor.

Anemia↗
PubMed2004

Power analysis.

Explore the source record for details and available documents.

Algorithms↗
PubMed2005

Subtree power analysis and species selection for comparative genomics.

Sequence comparison across multiple organisms aids in the detection of regions under selection. However, resource limitations require a prioritization of genomes to be sequenced. This prioritization should be grounded in two considerations: the lineal scope encompassing the biological phenomena of interest, and the optimal species within that scope for detecting functional elements. We introduce a statistical framework for optimal species subset selection, based on maximizing power to detect conserved sites. Analysis of a phylogenetic star topology shows theoretically that the optimal species subset is not in general the most evolutionarily diverged subset. We then demonstrate this finding empirically in a study of vertebrate species. Our results suggest that marsupials are prime sequencing candidates.

Animals↗
PubMed1982

HLA and ophthalmic disease associations: a critical review and improved method for statistical analysis.

A critical review of published ophthalmic histocompatibility antigen association studies found numerous conflicting or ambiguous reports. Methodologic errors that could account for these discrepancies were categorized into 3 groups (1) arbitrary application of statistical methods to determine significance, (2) poor sampling design, and (3) variable disease definition. Multivariate analysis, not previously applied in this area provides a more powerful tool for assessing statistical significance. A computer program using this methodology for large studies is now available.

Computers↗
PubMed1999

Differences in spirometry reference values: a statistical comparison of a Mongolian and a Caucasian study.

New reference value studies for spirometry are commonly compared to existing reference value studies using average data derived from existing reference equations. Such comparisons are inherently flawed because they do not account for differences in distributions of the independent and dependent variables and they do not have identical methodologies. This study was undertaken 1) to derive reference equations for forced vital capacity (FVC) and forced expiratory volume in one second (FEV1) for natives of Mongolia and 2) to compare the Mongolian data with data from a 1981 reference study of Caucasians in Salt Lake City, UT, USA. Spirometry was performed on 344 (176 male, 168 female) healthy, nonsmoking urban natives of Mongolia to generate reference equations for FVC, FEV1, and FEV1/FVC. These data were compared with data from a 1981 reference study of Caucasians in Salt Lake City, using both an analysis of covariance of the raw data and parametric and nonparametric comparisons of a matched pair subset. Average measured forced vital capacity and forced expiratory volume in one second in native Mongolians were within 1-2% of the Caucasian predicted values. These small differences are not statistically significant in any of the multiple methods of comparisons. Power analysis suggests that, if real differences exist, the differences in forced vital capacity are <155 mL for males, <105 mL for females, and the differences in forced expiratory volume in one second are <107 mL for males and <76 mL for females.

Adolescent↗
PubMed2001

Treatment of intrabony defects with enamel matrix proteins or bioabsorbable membranes. A 4-year follow-up split-mouth study.

BACKGROUND: Treatment with enamel matrix proteins (EMD) and guided tissue regeneration (GTR) with bioabsorbable membranes has been shown to promote periodontal regeneration; however, until now, there were only limited data on the long-term clinical results following these regenerative techniques. Therefore, the aim of the present study was to present the 4-year results following treatment of intrabony defects with EMD or guided tissue regeneration (GTR). METHODS: Twelve patients, each displaying one pair of intrabony defects located contralaterally in the same jaw, were randomly treated with EMD or with GTR by means of bioabsorbable membranes. The following clinical parameters were evaluated at baseline, at 1 year, and at 4 years after treatment: plaque index (P1), gingival index (G1), bleeding on probing (BOP), probing depth (PD), gingival recession (GR), and clinical attachment level (CAL). The primary outcome variable was CAL. No statistically significant differences between the groups were found at baseline. Power analysis to determine superiority of EMD treatment showed that the available sample size would yield 70% power to detect a 1 mm difference. RESULTS: The sites treated with EMD demonstrated mean CAL change from 9.8 +/- 2.0 mm to 6.4 +/- 1.6 mm (P<0.001) and to 6.8 +/- 1.8 mm (P<0.001) at 1 and 4 years, respectively. No statistically significant differences were found between the CAL mean at 1 and 4 years postoperatively. The sites treated with GTR showed a mean CAL change from 9.8 +/- 2.3 mm to 6.6 +/- 1.7 mm (P<0.001) at 1 year and to 6.9 +/- 1.8 mm (P<0.001) at 4 years. The CAL change between I and 4 years did not present statistically significant differences. No statistically significant differences in any of the investigated parameters were observed at 1 and 4 years between the treatment groups. CONCLUSIONS: It was concluded that the CAL gain obtained following treatment with EMD or GTR can be maintained over a 4-year period.

Absorbable Implants↗
PubMed2005

Better success rate for root canal therapy when treatment includes obturation short of the apex.

DATA SOURCES: Medline and reference lists of identified articles in English only. STUDY SELECTION: Initial screening identified studies on humans with radiographic information on the terminal point of obturation. Subsequently studies with (a) a minimum follow-up of at least 2 years; (b) data on termination of obturation/instrumentation; (c) failures of treatment defined adequately (with a minimum radiographic evaluation for failure outlined and defined); (d) data available on success/failure of root canal therapy in relationship to the obturation/instrumentation length; and (e) presence or absence of rarefaction included. DATA EXTRACTION AND SYNTHESIS: This meta-analysis considered three categories of obturation length from the radiographic apex: (a) 0-1 mm (group A), (b) >1 mm but <3 mm (group B), (c) obturated past the radiographic apex, including sealer (group C). The studies were independently assessed for quality with readers blinded to the names of the authors and their institutions, names of the journals, sources of funding, and acknowledgements. Statistical analyses were done using the DerSimonian and Laird estimates. RESULTS: Four studies met the inclusion criteria. In terms of percentage rates of success, the meta-analysis showed that obturation 0-1 mm short of the apex (group A) was better than obturation 1-3 mm short of the apex (group B); both were superior to obturation beyond the apex (group C). The success rate in group A was 28.9% better than group C and 5.9% better than group B (95% CI=-3.8%, 61.5%), P=0.08 and (95% CI=-1.3%, 13.1%), P=0.11, respectively. After adjustment for quality, the results remained unchanged. CONCLUSIONS: The results demonstrate that obturating materials extruding beyond the radiographic apex correlated with a poorer prognosis. In addition, we realised that standardised protocols are necessary in endodontic procedures and in dental research. If studies are to be compared and the information used clinically, the design of the studies must be similar and repeatable. The results of prospective studies will then be comparable and the data can be combined statistically, thereby creating a more powerful, clinically useful meta-analysis.

Comment↗
PubMed2002

Role of ancillary variables in the design, analysis, and interpretation of animal experiments.

During the course of an experiment using animals, many variables (e.g., age, body weight at several times, food and water consumption, hematology, and clinical biochemistry) and other characteristics are often recorded in addition to the primary response variable(s) specified by the experimenter. These additional variables have an important role in the design and interpretation of the experiment. They may be formally incorporated into the design and/or analysis and thus increase precision and power. However, even if these variables are not incorporated into the primary statistical design or into the formal analysis of the experiment, they may nevertheless be used in an ancillary or exploratory way to provide valuable information about the experiment, as shown by various examples. Used in this way, ancillary variables may improve analysis and interpretation by providing an assessment of the randomization process and an approach to the identification of outliers, lead to the generation of new hypotheses, and increase generality of results or account for differences in results when compared across different experiments. Thus, appropriate use of additional variables may lead to reduction in the number of animals required to achieve the aims of the experiment and may provide additional scientific information as an extra benefit. Unfortunately, this type of information is sometimes effectively discarded because its potential value is not recognized. Guidelines for use of animals include, in addition to the obligation to follow humane procedures, the obligation to use no more animals than necessary. Ethical experimental practice thus requires that all information be properly used and reported.

Animals↗
PubMed2004

The conditional relative odds ratio provided less biased results for comparing diagnostic test accuracy in meta-analyses.

OBJECTIVE: Meta-analytic techniques are used to combine the results of different studies that have evaluated the accuracy of a given diagnostic test. The techniques commonly generate values that either describe the performance of a particular test or compare the discriminative ability of two tests. The later has received very little attention in the literature, and is the focus of this article. STUDY DESIGN AND SETTING: We summarize existing methods based on an odds ratio (OR) and propose a novel technique for conducting such analysis, the conditional relative odds ratio (CROR). We demonstrate how to extract the required data and calculate several different comparative indexes using a hypothetic example. RESULTS: A paired analysis is preferred to decrease selection bias and increase statistical power. There is no standard method of obtaining the standard error (SE) of each relative OR; thus, the SE of the summary index might be underestimated under the assumption of no within-study variability. CONCLUSION: The CROR method estimates less biased indexes with SEs, and conditioned on discordant results, it is much less problematic ethically and economically. However, small cell counts may lead to larger SEs, and it might be impossible to construct McNemar's 2 x 2 tables for some studies.

Data Interpretation, Statistical↗
PubMed1996

Random regression with imputed values for dropouts.

The random regression model (RRM) has been advocated as a potential solution to problems of statistical analysis posed by dropouts in clinical trials. However, the power of the RRM tests for differences in rates of change can be seriously attenuated by presence of dropouts. The use of imputed scores and other modifications are examined in an attempt to render a simple growth-curve form of the RRM analysis more robust against dropouts. Methods that extrapolate from an individual's own performance were found effective, although inclusion of time-in-treatment as a covariate was documented to be important under identifiable conditions. Of the methods evaluated, those that used group data to impute missing values for dropouts produced nonconservative bias. The results suggest the importance of careful evaluation of potential bias when integrating any group-based imputation procedure into the RRM analyses.

Clinical Trials as Topic↗
PubMed1988

Primary cytomegalovirus infection in pediatric nurses: a meta-analysis.

A meta-analysis of six controlled studies was performed to evaluate the risk of cytomegalovirus (CMV) infection among pediatric nurses. The pooled risk ratio for CMV infection in pediatric nurses using cumulative incidence data was statistically significant (risk ratio [RR] 2.7; 95% confidence interval [CI] 1.33 - 5.52), but person-year analysis taking account of follow-up periods demonstrated a trend toward increased risk that failed to reach statistical significance (RR 1.8; 95% CI 0.88 - 3.55). Despite pooling, there was low statistical power for comparing person-year rates. The studies included in this analysis failed to provide data on several potential confounding variables. We conclude that studies published prior to the widespread adoption of universal precautions suggest that pediatric nurses may have been at increased risk for CMV infection due to occupational exposure, but inadequate design and sample size of the studies prevent a definitive conclusion. Well-designed, controlled studies are still needed to define the occupational risk of CMV infection.

Cytomegalovirus Infections↗
PubMed2000

Establishing the relation between detrended fluctuation analysis and power spectral density analysis for stochastic processes

Stochastic fractal signals can be characterized by the Hurst coefficient H, which is related to the exponents of various power-law statistics characteristic of these processes. Two techniques widely used to estimate H are spectral analysis and detrended fluctuation analysis (DFA). This paper examines the analytical link between these two measures and shows that they are related through an integral transform. Numerical simulations confirm this relationship for ideal synthesized fractal signals. Their performance as estimators of H is compared based on a mean square error criterion and found to be similar. DFA measures are derived for physiological signals of heartbeat R-R intervals through the integral transform of a spectral density estimate. These agree with directly calculated DFA estimates, indicating that the relationship holds for signals with nonideal fractal properties. It is concluded that DFA and spectral measures provide equivalent characterizations of stochastic signals with long-term correlation.

Journal Article↗
PubMed1989

[Meta-analysis on randomized trials comparing the results of low-molecular weight heparins to those of fractioned heparins in the prevention of deep venous thrombosis].

The main reason for using low molecular weight heparin (LMWH) is its capacity to keep the antithrombotic effect of standard non-fractioned heparin (NFH) while reducing its hemorrhagic power. Various studies comparing LMWH to NFH gave contradictory results, so we carried out a meta-analysis of randomized trials comparing these two treatments in prevention of deep-vein thrombosis (DVT) (and in prevention of deep-vein thrombosis or pulmonary embolism). From a selection of ten trials we could not show any significant difference in the DVT rates, as well as for the whole of surgical indications as for the subgroups of abdominal and orthopedic surgery. The weighted global difference between the DVT rates is so low that, in spite of the use of meta-analysis, the power is clearly insufficient. The hemorrhagic risk is not statistically reduced as well for the whole of surgical indications as for the subgroups.

Heparin↗