The value of a p-valueless paper

Mastering the scientific peer review process: tips for young authors from a young senior editor

Are you a student at a higher institution or an early-career researcher who is striving to understand and master the peer review process so to increase the odds of getting a paper published in the Journal of Forestry Research or another reputable, peer-reviewed, scientific journal? In this paper, a young, senior editor provides a handbook of the peer review process based on his decadal experience in scientific publishing. He covers major information you need to know during the entire process, from selecting journals to completing the proofing of your accepted paper. He introduces key points for consideration, such as avoidance of predatory journals, dubious research practices and ethics, interaction with peers, reviewers, and editors, and the pursuit of aretê. Finally, he points out some common statistical errors and misconceptions, such as P hacking and incorrect effect size inference. He hopes that this paper will enhance your understanding and knowledge of the peer-review process.

Quantitative Research Methods in Medical Education

There has been a dramatic growth of scholarly articles in medical education in recent years. Evaluating medical education research requires specific orientation to issues related to format and content. Our goal is to review the quantitative aspects of research in medical education so that clinicians may understand these articles with respect to framing the study, recognizing methodologic issues, and utilizing instruments for evaluating the quality of medical education research. This review can be used both as a tool when appraising medical education research articles and as a primer for clinicians interested in pursuing scholarship in medical education.

5 ways statistics can fool you--tips for practicing clinicians

Published literature suggests that many clinicians are not fully equipped to evaluate and apply research reports for the care of their patients. In this article, we introduce and illustrate five basic statistical concepts that can significantly impact the interpretation of the medical literature and its application to the care of patients, drawing examples from the vaccine literature: (i) consider clinical and statistical significance separately, (ii) evaluate absolute risks rather than relative risks, (iii) examine confidence intervals rather than p values, (iv) use caution when considering isolated significant p values in the setting of multiple testing, and (v) keep in mind that statistically nonsignificant results may not exclude clinically important benefits or harms. These tips may help busy clinicians better interpret the increasingly overwhelming amount of medical literature they are faced with in their daily practices.

Contralaterally controlled functional electrical stimulation for upper extremity hemiplegia: an early-phase randomized clinical trial in subacute stroke patients

BACKGROUND

Contralaterally controlled functional electrical stimulation (CCFES) is an experimental treatment intended to improve hand function after stroke.

OBJECTIVE

To compare the effects of 6 weeks of CCFES versus cyclic neuromuscular electrical stimulation (NMES) on upper extremity impairment and activity limitation in patients ≤6 months poststroke.

METHODS

Twenty-one participants were randomized to CCFES or cyclic NMES. Treatment for both groups consisted of daily stimulation-assisted repetitive hand-opening exercise at home plus twice-weekly lab sessions of functional task practice. Assessments were made at pretreatment and posttreatment and at 1 month and 3 months posttreatment. They included maximum voluntary finger extension angle, finger movement tracking error, upper extremity Fugl-Meyer score, Box and Blocks test, and Arm Motor Abilities test. Treatment effects were estimated using a 2-factor repeated measures analysis of variance with the value of the baseline measure as a covariate.

RESULTS

Seventeen patients completed the treatment phase (9 CCFES, 8 cyclic NMES). At all posttreatment time points, CCFES produced larger improvements than cyclic NMES on every outcome measure. Maximum voluntary finger extension showed the largest treatment effect, with a mean group difference across the posttreatment time points of 28° more finger extension for CCFES.

CONCLUSIONS

The results favor CCFES over cyclic NMES though the small sample size limits the statistical power of the study. The effect size estimates from this study will be used to power a larger trial.

Methodology for randomized trials of patients with nonvariceal upper gastrointestinal bleeding: recommendations from an international consensus conference

The aim of this document is to provide a methodological framework for the design, performance, analysis, interpretation, and communication of randomized trials that assess management of patients with nonvariceal upper gastrointestinal bleeding. Literature searches were performed and an iterative process with electronic and face-to-face meetings was used to achieve consensus among panel members as part of an International Consensus Conference on Nonvariceal Upper Gastrointestinal Bleeding. Recommendations of the panel include the following. Randomized trials must explicitly state their primary hypothesis. A nonmanipulable randomization schedule with concealed allocation should be used. Stratification (e.g., for age and stigmata of hemorrhage) may be considered, especially in smaller studies. The patient and personnel providing care or recording information should be blinded. Inclusion criteria should be overt bleeding with endoscopy performed within 24 h or less. One type of lesion (e.g., ulcer) should be studied with stigmata to be included predefined. Use of placebo/no therapy vs. active controls depends on current standard practice. Standardizing study and key non-study interventions should ensure uniform provision of interventions. Criteria for repeat endoscopy and subsequent interventions should be predefined. The primary end point should be further bleeding (persistent and recurrent bleeding) with primary assessment at 7 days; mortality, with primary assessment at 30 days, would be appropriate in very large trials. Sample size calculation based on assumptions regarding primary end point results with regard to study intervention and control must be provided, and all patients enrolled must be accounted for. In general, the primary population for analysis is all patients randomized, although a per-protocol population may be used if this is the more conservative approach (e.g., equivalence study).

A method to compute multiplicity corrected confidence intervals for odds ratios and other relative effect estimates

Epidemiological studies commonly test multiple null hypotheses. In some situations it may be appropriate to account for multiplicity using statistical methodology rather than simply interpreting results with greater caution as the number of comparisons increases. Given the one-to-one relationship that exists between confidence intervals and hypothesis tests, we derive a method based upon the Hochberg step-up procedure to obtain multiplicity corrected confidence intervals (CI) for odds ratios (OR) and by analogy for other relative effect estimates. In contrast to previously published methods that explicitly assume knowledge of P values, this method only requires that relative effect estimates and corresponding CI be known for each comparison to obtain multiplicity corrected CI.

Evaluation of patient satisfaction in gastrointestinal endoscopy

OBJECTIVE

Patient satisfaction questionnaires are a useful method for detecting opportunities for improvement on the basis of patient opinion. The aim of this study was to identify by means of a satisfaction questionnaire the main reasons for dissatisfaction in patients undergoing gastrointestinal endoscopy.

PATIENTS AND METHODS

Five hundred and thirty-seven patients (age 49+/-15 years, 53% women) who attended a gastrointestinal endoscopy unit were interviewed 3 weeks after undergoing upper endoscopy or colonoscopy, using a previously translated and validated GHAA-9 questionnaire modified for use in gastrointestinal endoscopy. In each case, the overall score median and the percentage of patients who gave negative (poor or fair) appraisals on each of the seven main questions were estimated. These data were used to perform a Pareto analysis.

RESULTS

The overall questionnaire score median was 29 (interquartiles 25 and 75 over 26 and 32, respectively). Negative appraisal percentages for each of the seven questions were: waiting time until the appointment, 9.3%; waiting time on the day of examination, 3.5%; explanations, 3.9%; personal manner of staff, 0.5%; personal manner of the physician, 0.6%; discomfort, 3.5%; overall rating, 1.9%. The vital few found by Pareto analysis were questions regarding waiting time for appointment and adequacy of explanations regarding procedure. These questions accounted for 61% of the total number of problems encountered by patients.

CONCLUSION

Questionnaires on satisfaction or quality perceived by patients allow the most frequent causes for dissatisfaction to be identified. The main problems patients encountered were waiting time until the appointment and explanations.

Safety and tolerability of transoral Bravo capsule placement after transnasal manometry using a validated conversion factor

OBJECTIVES

To prospectively calculate and validate a conversion factor in healthy volunteers that allows accurate nonsedated, transoral (TO) Bravo capsule placement after transnasal (TN) manometry, and to evaluate the ease and safety of nonendoscopic Bravo placement compared with endoscopic placement.

METHODS

Part 1. Twenty-five healthy volunteers underwent sequential TN and TO esophageal manometry to measure the distance to the lower esophageal sphincter (LES). A TN to TO conversion factor was calculated from these measurements. Part 2. Twenty volunteers underwent TN manometry followed by unsedated TO Bravo capsule placement using the conversion factor calculated in part 1. TN endoscopy then measured the location of the Bravo capsule in relationship to the squamocolumnar junction (SCJ). Part 3. During an 18-month period, 370 consecutive patients referred for a Bravo procedure underwent nonendoscopic, unsedated TO placement (308 patients) or standard endoscopically assisted placement (62 patients).

RESULTS

Part 1. All 25 volunteers completed TN and TO manometry; a conversion factor of 4 cm was calculated. Part 2. Using the calculated conversion factor of 4 cm, a Bravo capsule was deployed TO 5 cm above the proximal border of the LES. The mean +/- standard deviation (SD) TN endoscopic distance to the capsule was 6.0 cm (+/-0.3 cm) above the SCJ. Part 3. A total of 333 patients completed the entire study (90%). Analysis of 48-h pH measurements did not reveal any significant differences between the two groups.

CONCLUSIONS

A reliable and valid conversion factor of 4 cm following TN manometry permits accurate TO placement of the Bravo capsule without endoscopy. TO, unsedated Bravo placement is safe, well tolerated, and may minimize costs and potential risks associated with endoscopy.

Increasing yield also increases false positives and best serves to exclude GERD

Multiple diagnostic tests always improve diagnostic yield. However, with the addition of more true positives come more false positives. Therefore, positive predictive values likely decrease with additional testing. We show this is true even when no gold standard exists to verify the dual testing's sensitivity and specificity.

Helicobacter pylori eradication: equivalence trials and the optimal duration of therapy

Equivalence trials are gaining popularity and seek to compare the efficacy of two different types of treatment. The design of these trials requires careful consideration of clinical, statistical, and regulatory concerns. We discuss the importance and key factors relevant to equivalence trials.

Metaanalyses are observational studies: how lack of randomization impacts analysis

Although metaanalyses are often syntheses of many experiments, they are themselves observational studies. As such, when performing or reading metaanalyses, we must consider the sources of bias that we usually expect in an observational study. The main two sources of bias for metaanalysis are publication bias and systematic heterogeneity. I consider the nature of both of these sources, methods to detect this bias, and ways to correct for the bias.