CONSORT-TM: Text classification models for assessing the completeness of randomized controlled trial publications.

Objective: To develop text classification models for determining whether the checklist items in the CONSORT reporting guidelines are reported in randomized controlled trial publications. Materials and Methods: Using a corpus annotated at the sentence level with 37 fine-grained CONSORT items, we trained several sentence classification models (PubMedBERT fine-tuning, BioGPT fine-tuning, and in-context learning with GPT-4) and compared their performance. To address the problem of small training dataset, we used several data augmentation methods (EDA, UMLS-EDA, text generation and rephrasing with GPT-4) and assessed their impact on the fine-tuned PubMedBERT model. We also fine-tuned PubMedBERT models limited to checklist items associated with specific sections (e.g., Methods) to evaluate whether such models could improve performance compared to the single full model. We performed 5-fold cross-validation and report precision, recall, F1 score, and area under curve (AUC). Results: Fine-tuned PubMedBERT model that takes as input the sentence and the surrounding sentence representations and uses section headers yielded the best overall performance (0.71 micro-F1, 0.64 macro-F1). Data augmentation had limited positive effect, UMLS-EDA yielding slightly better results than data augmentation using GPT-4. BioGPT fine-tuning and GPT-4 in-context learning exhibited suboptimal results. Methods-specific model yielded higher performance for methodology items, other section-specific models did not have significant impact. Conclusion: Most CONSORT checklist items can be recognized reasonably well with the fine-tuned PubMedBERT model but there is room for improvement. Improved models can underpin the journal editorial workflows and CONSORT adherence checks and can help authors in improving the reporting quality and completeness of their manuscripts.

Publication of Results of Registered Trials With Published Study Protocols, 2011-2022.

Importance: Publishing study protocols might reduce research waste because of unclear methods or incomplete reporting; on the other hand, there might be few additional benefits of publishing protocols for registered trials that are never completed or published. No study has investigated the proportion of published protocols associated with published results. Objective: To estimate the proportion of published trial protocols for which there are not associated published results. Design, Setting, and Participants: This cross-sectional study used stratified random sampling to identify registered clinical trials with protocols published between January 2011 and August 2022 and indexed in PubMed Central. Ongoing studies and those within 1 year of the primary completion date on ClinicalTrials.gov were excluded. Published results were sought from August 2022 to March 2023 by searching ClinicalTrials.gov, emailing authors, and using an automated tool, as well as through incidental discovery. Main Outcomes and Measures: The primary outcome was a weighted estimate of the proportion of registered trials with published protocols that also had published main results. The proportion of trials with unpublished results was estimated using a weighted mean. Results: From 1500 citations that were screened, 308 clinical trial protocols were included, and it was found that 87 trials had not published their main results. Most included trials were investigator-initiated evaluations of nonregulated products. When published, results appeared a mean (SD) of 3.4 (2.0) years after protocol publications. With the use of a weighted mean, an estimated 4754 (95% CI, 4296-5226) eligible clinical trial protocols were published and indexed in PubMed Central between 2011 and 2022. In the weighted analysis, 1708 of those protocols (36%; 95% CI, 31%-41%) were not associated with publication of main results. In a sensitivity analysis excluding protocols published after 2019, an estimated 25% (95% CI, 20%-30%) of 3670 (95% CI, 3310-4032) protocol publications were not associated with publication of main results. Conclusions and Relevance: This cross-sectional study of clinical trial protocols published on PubMed Central between 2011 and 2022 suggests that many protocols were not associated with subsequent publication of results. The overall benefits of publishing study protocols might outweigh the research waste caused by unnecessary protocol publications.

The efficacy of sleep lifestyle interventions for the management of overweight or obesity in children: a systematic review and meta-analysis.

BACKGROUND: Childhood obesity remains a significant public health concern. Sleep duration and quality among children and youth are suboptimal worldwide. Accumulating evidence suggests an association between inadequate sleep and obesity risk, yet it is unclear whether this relationship is causal. This systematic review examines the efficacy of sleep interventions alone or as a part of lifestyle interventions for the management of overweight or obesity among children and adolescents. METHODS: A keyword/reference search was performed twice, in January 2021 and May 2022 in MEDLINE/PubMed, EMBASE/Ovid, PsycINFO/EBSCO, The Cochrane Library, Web of Science Core Collection/Web of Science, SciELO/Web of Science, and CINAHL/EBSCO. Study eligibility criteria included youth with overweight or obesity between 5 and 17, were RCTs or quasi-randomized, and focused on the treatment of overweight and obesity with a sleep behavior intervention component. Risk of bias was assessed using the Cochrane Risk of Bias assessment tool (RoB2). A Meta-analysis was conducted to estimate the effect of interventions with a sleep component on BMI. The study protocol was registered in PROSPERO (CRD42021233329). RESULTS: A total of 8 studies (2 quasi-experiments, 6 RCTs) met inclusion criteria and accounted for 2,231 participants across 7 countries. Only one study design isolated the effect of sleep in the intervention and reported statistically significant decreases in weight and waist circumference compared to control, though we rated it at high risk of bias. Our meta-analysis showed no significant overall effect on children's BMI as a result of participation in an intervention with a sleep component (Cohen's d = 0.18, 95% CI= -0.04, 0.40, Z = 1.56, P = .11), though caution is warranted due to substantial heterogeneity observed across studies (Tau2 = 0.08; X2 = 23.05, df = 7; I2 = 83.73%). CONCLUSIONS: There were mixed results on the effect of sleep interventions across included studies on BMI, other weight-related outcomes, diet, physical activity, and sleep. Except for one study at low risk of bias, three were rated as 'some concerns' and four 'high risk of bias'. Findings from this study highlight the need for additional RCTs isolating sleep as a component, focusing on children and adolescents living with overweight and obesity.

The Third Annual Symposium of the Midwest Aging Consortium.

The geroscience hypothesis suggests that addressing the fundamental mechanisms driving aging biology will prevent or mitigate the onset of multiple chronic diseases, for which the largest risk factor is advanced age. Research that investigates the root causes of aging is therefore of critical importance given the rising healthcare burden attributable to age-related diseases. The third annual Midwest Aging Consortium symposium was convened as a showcase of such research performed by investigators from institutions across the Midwestern United States. This report summarizes the work presented during a virtual conference across topics in aging biology, including immune function in the lung-particularly timely given the Corona Virus Immune Disease-2019 pandemic-along with the role of metabolism and nutrient-regulated pathways in cellular function with age, the influence of senescence on stem cell function and inflammation, and our evolving understanding of the mechanisms underlying observation of sex dimorphism in aging-related outcomes. The symposium focused on early-stage and emerging investigators, while including keynote presentations from leaders in the biology of aging field, highlighting the diversity and strength of aging research in the Midwest.

Corrected analysis of "the effects of bright light treatment on affective symptoms in people with dementia: a 24-week cluster randomized controlled trial" that accounts for clustering and nesting verifies conclusions.

In this correspondence, we explain the reasoning for invalidity of the analysis choices by Kolberg et al., and provide the results produced using correct statistical procedures for their study design. Reassuringly, we could verify the original conclusions. That is, results of the corrected statistical models are similar to the results of the original analysis. Regardless of the magnitude of difference that corrected statistical methods make, results and conclusions that are derived from invalid methods are unsubstantiated. By verifying the results, we allow the readers to be assured that the published conclusions in the study by Kolberg et al. now rest on a sound evidential basis.

Completeness of Reporting in Diet- and Nutrition-Related Randomized Controlled Trials and Systematic Reviews With Meta-Analysis: Protocol for 2 Independent Meta-Research Studies.

BACKGROUND: Journal articles describing randomized controlled trials (RCTs) and systematic reviews with meta-analysis of RCTs are not optimally reported and often miss crucial details. This poor reporting makes assessing these studies' risk of bias or reproducing their results difficult. However, the reporting quality of diet- and nutrition-related RCTs and meta-analyses has not been explored. OBJECTIVE: We aimed to assess the reporting completeness and identify the main reporting limitations of diet- and nutrition-related RCTs and meta-analyses of RCTs, estimate the frequency of reproducible research practices among these RCTs, and estimate the frequency of distorted presentation or spin among these meta-analyses. METHODS: Two independent meta-research studies will be conducted using articles published in PubMed-indexed journals. The first will include a sample of diet- and nutrition-related RCTs; the second will include a sample of systematic reviews with meta-analysis of diet- and nutrition-related RCTs. A validated search strategy will be used to identify RCTs of nutritional interventions and an adapted strategy to identify meta-analyses in PubMed. We will search for RCTs and meta-analyses indexed in 1 calendar year and randomly select 100 RCTs (June 2021 to June 2022) and 100 meta-analyses (July 2021 to July 2022). Two reviewers will independently screen the titles and abstracts of records yielded by the searches, then read the full texts to confirm their eligibility. The general features of these published RCTs and meta-analyses will be extracted into a research electronic data capture database (REDCap; Vanderbilt University). The completeness of reporting of each RCT will be assessed using the items in the CONSORT (Consolidated Standards of Reporting Trials), its extensions, and the TIDieR (Template for Intervention Description and Replication) statements. Information about practices that promote research transparency and reproducibility, such as the publication of protocols and statistical analysis plans will be collected. There will be an assessment of the completeness of reporting of each meta-analysis using the items in the Preferred Reporting Items for Systematic reviews and Meta-Analysis (PRISMA) statement and collection of information about spin in the abstracts and full-texts. The results will be presented as descriptive statistics in diagrams or tables. These 2 meta-research studies are registered in the Open Science Framework. RESULTS: The literature search for the first meta-research retrieved 20,030 records and 2182 were potentially eligible. The literature search for the second meta-research retrieved 10,918 records and 850 were potentially eligible. Among them, random samples of 100 RCTs and 100 meta-analyses were selected for data extraction. Data extraction is currently in progress, and completion is expected by the beginning of 2023. CONCLUSIONS: Our meta-research studies will summarize the main limitation on reporting completeness of nutrition- or diet-related RCTs and meta-analyses and provide comprehensive information regarding the particularities in the reporting of intervention studies in the nutrition field. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): DERR1-10.2196/43537.

Only one cluster per condition is an invalid design for a cluster randomized trial and should be re-labeled a quasi-experimental study. Response to: "Effect of behavioral activation on time and frequency domain heart rate variability in older adults with subthreshold depression: a cluster randomized controlled trial in Thailand".

Ayudhaya et al. examined the effect of Behavioral Activation on daily step count and heart rate variability among older adults with depression in a study labeled a cluster randomized controlled trial (cRCT). However, only one cluster was assigned to either of the study conditions. Such a design would have zero degrees of freedom for inferential testing, because the variation due to cluster membership cannot be estimated apart from the variation due to treatment assignment. Thus, the intervention effect is completely confounded with the cluster effect. The study should be labeled a quasi-experimental study, not a cRCT. Accordingly, the numerical results should be interpreted as associations but not evidence for causal relationships.

Toward more rigorous and informative nutritional epidemiology: The rational space between dismissal and defense of the status quo.

To date, nutritional epidemiology has relied heavily on relatively weak methods including simple observational designs and substandard measurements. Despite low internal validity and other sources of bias, claims of causality are made commonly in this literature. Nutritional epidemiology investigations can be improved through greater scientific rigor and adherence to scientific reporting commensurate with research methods used. Some commentators advocate jettisoning nutritional epidemiology entirely, perhaps believing improvements are impossible. Still others support only normative refinements. But neither abolition nor minor tweaks are appropriate. Nutritional epidemiology, in its present state, offers utility, yet also needs marked, reformational renovation. Changing the status quo will require ongoing, unflinching scrutiny of research questions, practices, and reporting-and a willingness to admit that "good enough" is no longer good enough. As such, a workshop entitled "Toward more rigorous and informative nutritional epidemiology: the rational space between dismissal and defense of the status quo" was held from July 15 to August 14, 2020. This virtual symposium focused on: (1) Stronger Designs, (2) Stronger Measurement, (3) Stronger Analyses, and (4) Stronger Execution and Reporting. Participants from several leading academic institutions explored existing, evolving, and new better practices, tools, and techniques to collaboratively advance specific recommendations for strengthening nutritional epidemiology.

Acute High Dietary Phosphorus Following Low-Phosphorus Diet Acclimation Does Not Enhance Intestinal Fractional Phosphorus Absorption in Nephrectomized Male Rats.

Dietary phosphorus restriction and phosphorus binders are commonly prescribed for patients with chronic kidney disease (CKD). However, occurrences of non-adherence to these interventions are common. As low-phosphorus (LP) diets have been consistently experimentally shown in vitro to increase intestinal phosphorus absorption efficiency, a bout of non-adherence to diet or binders may cause an unintended consequence of enhanced intestinal phosphorus absorption. Thus, we aimed to determine the effect of a single bout of high-phosphorus (HP) intake after acclimation to a LP diet. Male Sprague Dawley rats with 5/6 nephrectomy (n = 36) or sham operation (n = 36) were block-randomized to 1 of 3 diets: LP (0.1% P w/w), HP (1.2%), or LP followed by acute HP (LPHP 0.1% then 1.2%). Phosphorus absorption tests were conducted using 33P radioisotope administrated by oral gavage or intravenously (iv). Although the overall two-way ANCOVA model for intestinal fractional phosphorus absorption was non-significant, exploratory comparisons showed intestinal fractional phosphorus absorption efficiency tended to be higher in rats in the LP compared with HP or LPHP groups. Rats in the HP or LPHP groups had higher plasma phosphorus compared with rats in the LP group, but the LPHP group was not different from the HP group. Gene expression of the major intestinal phosphate transporter, NaPi-2b, was lower in the jejunum of rats in the LPHP group compared with rats in the HP group but not different in the duodenum. These results demonstrate that an acute HP load after acclimation to a LP diet does not lead to enhanced intestinal fractional phosphorus absorption efficiency in 5/6 nephrectomized male rats. These data provide evidence against the notion that dietary phosphorus restriction or binder use adversely increases absorption efficiency after a single instance of dietary or binder non-adherence. However, other adverse consequences of fluctuating dietary phosphorus intake cannot be ruled out. © 2022 The Authors. JBMR Plus published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research.

Protocol for a meta-research study of protocols for diet or nutrition-related trials published in indexed journals: general aspects of study design, rationale and reporting limitations.

INTRODUCTION: The Standard Protocol Items: Recommendations for Interventional Trials (SPIRIT) reporting guideline establishes a minimum set of items to be reported in any randomised controlled trial (RCT) protocol. The Template for Intervention Description and Replication (TIDieR) reporting guideline was developed to improve the reporting of interventions in RCT protocols and results papers. Reporting completeness in protocols of diet or nutrition-related RCTs has not been systematically investigated. We aim to identify published protocols of diet or nutrition-related RCTs, assess their reporting completeness and identify the main reporting limitations remaining in this field. METHODS AND ANALYSIS: We will conduct a meta-research study of RCT protocols published in journals indexed in at least one of six selected databases between 2012 and 2022. We have run a search in PubMed, Embase, CINAHL, Web of Science, PsycINFO and Global Health using a search strategy designed to identify protocols of diet or nutrition-related RCTs. Two reviewers will independently screen the titles and abstracts of records yielded by the search in Rayyan. The full texts will then be read to confirm protocol eligibility. We will collect general study features (publication information, types of participants, interventions, comparators, outcomes and study design) of all eligible published protocols in this contemporary sample. We will assess reporting completeness in a randomly selected sample of them and identify their main reporting limitations. We will compare this subsample with the items in the SPIRIT and TIDieR statements. For all data collection, we will use data extraction forms in REDCap. This protocol is registered on the Open Science Framework (DOI: 10.17605/OSF.IO/YWEVS). ETHICS AND DISSEMINATION: This study will undertake a secondary analysis of published data and does not require ethical approval. The results will be disseminated through journals and conferences targeting stakeholders involved in nutrition research.

Mixed Random and Nonrandom Allocation, and Group Randomization Have Been Mislabeled and Misanalysed, Necessitating Reanalysis. Comment on Conner et al. KiwiC for Vitality: Results of a Randomized Placebo-Controlled Trial Testing the Effects of Kiwifruit or Vitamin C Tablets on Vitality in Adults with Low Vitamin C Levels. Nutrients 2020, 12, 2898.

We read the report by Conner and colleagues that tested whether kiwifruit or vitamin C affected measures of vitality [...].

Accounting for the clustering and nesting effects verifies most conclusions. Corrected analysis of: "Randomized nutrient bar supplementation improves exercise-associated changes in plasma metabolome in adolescents and adult family members at cardiometabolic risk".

In a published randomized controlled trial, household units were randomized to a nutrient bar supplementation group or a control condition, but the non-independence of observations within the same household (i.e., the clustering effect) was not accounted for in the statistical analyses. Therefore, we reanalyzed the data appropriately by adjusting degrees of freedom using the between-within method, and accounting for household units using linear mixed effect models with random intercepts for family units and subjects nested within family units for each reported outcome. Results from this reanalysis showed that ignoring the clustering and nesting effects in the original analyses had resulted in anticonservative (i.e., too small) time x group interaction p-values. Still, majority of the conclusions remained unchanged.