Open science practices need substantial improvement in prognostic model studies in oncology using machine learning.

OBJECTIVE: To describe the frequency of open science practices in a contemporary sample of studies developing prognostic models using machine learning methods in the field of oncology. STUDY DESIGN AND SETTING: We conducted a systematic review, searching the MEDLINE database between December 1, 2022, and December 31, 2022, for studies developing a multivariable prognostic model using machine learning methods (as defined by the authors) in oncology. Two authors independently screened records and extracted open science practices. RESULTS: We identified 46 publications describing the development of a multivariable prognostic model. The adoption of open science principles was poor. Only one study reported availability of a study protocol, and only one study was registered. Funding statements and conflicts of interest statements were common. Thirty-five studies (76%) provided data sharing statements, with 21 (46%) indicating data were available on request to the authors and seven declaring data sharing was not applicable. Two studies (4%) shared data. Only 12 studies (26%) provided code sharing statements, including 2 (4%) that indicated the code was available on request to the authors. Only 11 studies (24%) provided sufficient information to allow their model to be used in practice. The use of reporting guidelines was rare: eight studies (18%) mentioning using a reporting guideline, with 4 (10%) using the Transparent Reporting of a Multivariable Prediction Model for Individual Prognosis Or Diagnosis statement, 1 (2%) using Minimum Information About Clinical Artificial Intelligence Modeling and Consolidated Standards Of Reporting Trials-Artificial Intelligence, 1 (2%) using Strengthening The Reporting Of Observational Studies In Epidemiology, 1 (2%) using Standards for Reporting Diagnostic Accuracy Studies, and 1 (2%) using Transparent Reporting of Evaluations with Nonrandomized Designs. CONCLUSION: The adoption of open science principles in oncology studies developing prognostic models using machine learning methods is poor. Guidance and an increased awareness of benefits and best practices of open science are needed for prediction research in oncology.

Estimated fetal weight standards of the INTERGROWTH-21st project for the prediction of adverse outcomes: a systematic review with meta-analysis.

OBJECTIVE: To systematically review and assess the risk of bias in the literature evaluating the performance of INTERGROWTH-21st estimated fetal weight (EFW) standards to predict maternal, fetal and neonatal adverse outcomes. METHODS: Searches were performed in seven electronic databases (Scopus, Web of Science, Medline, Embase, Lilacs, Scielo and Google Scholar) using citation tools and keywords (intergrowth AND (standard OR reference OR formula OR model OR curve); all from 2014 to the last search on April 16th, 2021). We included full-text articles investigating the ability of INTERGROWTH-21st EFW standards to predict maternal, fetal or neonatal adverse outcomes in women with a singleton pregnancy who gave birth to infants with no congenital abnormalities. The study was registered on PROSPERO under the number CRD42020115462. Risk of bias was assessed with a customized instrument based on the CHARMS checklist and composed of 9 domains. Meta-analysis was performed using relative risk (RR [95%CI]) and summary ROC curves on outcomes reported by two or more methodologically homogeneous studies. RESULTS: Sixteen studies evaluating fifteen different outcomes were selected. The risk of bias was high (>50% of studies with high risk) for two domains: blindness of assessment (81.3%) and calibration assessment (93.8%). Considering all the outcomes investigated, for 95% of the results, the specificity was above 73.0%, but the sensitivity was below 64.1%. Pooled results demonstrated a higher RR of neonatal small for gestational age (6.71 [5.51-8.17]), Apgar <7 at 5 min (2.17 [1.48-3.18]), and neonatal intensive care unit admission (2.22 [1.76-2.79]) for fetuses classified <10th percentile when compared to those classified above this limit. The limitation of the study is the absence of heterogeneity exploration or publication bias investigation, whereas no outcomes were evaluated by more than five studies. CONCLUSIONS: The IG-21 EFW standard has low sensitivity and high specificity for adverse events of pregnancy. Classification <10th percentile identifies a high-risk group for developing maternal, fetal and neonatal adverse outcomes, especially neonatal small for gestational age, Apgar <7 at 5 min, and neonatal intensive care unit admission. Future studies should include blind assessment of outcomes, perform calibration analysis with continuous data, and evaluate alternative cutoff points.

Minimal reporting guideline for research involving eye tracking (2023 edition).

A guideline is proposed that comprises the minimum items to be reported in research studies involving an eye tracker and human or non-human primate participant(s). This guideline was developed over a 3-year period using a consensus-based process via an open invitation to the international eye tracking community. This guideline will be reviewed at maximum intervals of 4 years.

Reminding Peer Reviewers of Reporting Guideline Items to Improve Completeness in Published Articles: Primary Results of 2 Randomized Trials.

Importance: Numerous studies have shown that adherence to reporting guidelines is suboptimal. Objective: To evaluate whether asking peer reviewers to check if specific reporting guideline items were adequately reported would improve adherence to reporting guidelines in published articles. Design, Setting, and Participants: Two parallel-group, superiority randomized trials were performed using manuscripts submitted to 7 biomedical journals (5 from the BMJ Publishing Group and 2 from the Public Library of Science) as the unit of randomization, with peer reviewers allocated to the intervention or control group. Interventions: The first trial (CONSORT-PR) focused on manuscripts that presented randomized clinical trial (RCT) results and reported following the Consolidated Standards of Reporting Trials (CONSORT) guideline, and the second trial (SPIRIT-PR) focused on manuscripts that presented RCT protocols and reported following the Standard Protocol Items: Recommendations for Interventional Trials (SPIRIT) guideline. The CONSORT-PR trial included manuscripts that described RCT primary results (submitted July 2019 to July 2021). The SPIRIT-PR trial included manuscripts that contained RCT protocols (submitted June 2020 to May 2021). Manuscripts in both trials were randomized (1:1) to the intervention or control group; the control group received usual journal practice. In the intervention group of both trials, peer reviewers received an email from the journal that asked them to check whether the 10 most important and poorly reported CONSORT (for CONSORT-PR) or SPIRIT (for SPIRIT-PR) items were adequately reported in the manuscript. Peer reviewers and authors were not informed of the purpose of the study, and outcome assessors were blinded. Main Outcomes and Measures: The difference in the mean proportion of adequately reported 10 CONSORT or SPIRIT items between the intervention and control groups in published articles. Results: In the CONSORT-PR trial, 510 manuscripts were randomized. Of those, 243 were published (122 in the intervention group and 121 in the control group). A mean proportion of 69.3% (95% CI, 66.0%-72.7%) of the 10 CONSORT items were adequately reported in the intervention group and 66.6% (95% CI, 62.5%-70.7%) in the control group (mean difference, 2.7%; 95% CI, -2.6% to 8.0%). In the SPIRIT-PR trial, of the 244 randomized manuscripts, 178 were published (90 in the intervention group and 88 in the control group). A mean proportion of 46.1% (95% CI, 41.8%-50.4%) of the 10 SPIRIT items were adequately reported in the intervention group and 45.6% (95% CI, 41.7% to 49.4%) in the control group (mean difference, 0.5%; 95% CI, -5.2% to 6.3%). Conclusions and Relevance: These 2 randomized trials found that it was not useful to implement the tested intervention to increase reporting completeness in published articles. Other interventions should be assessed and considered in the future. Trial Registration: ClinicalTrials.gov Identifiers: NCT05820971 (CONSORT-PR) and NCT05820984 (SPIRIT-PR).

Reporting guidelines used varying methodology to develop recommendations.

BACKGROUND AND OBJECTIVES: We investigated the developing methods of reporting guidelines in the EQUATOR (Enhancing the QUAlity and Transparency Of health Research) Network's database. METHODS: In October 2018, we screened all records and excluded those not describing reporting guidelines from further investigation. Twelve researchers performed duplicate data extraction on bibliometrics, scope, development methods, presentation, and dissemination of all publications. Descriptive statistics were used to summarize the findings. RESULTS: Of the 405 screened records, 262 described a reporting guidelines development. The number of reporting guidelines increased over the past 3 decades, from 5 in the 1990s and 63 in the 2000s to 157 in the 2010s. Development groups included 2-151 people. Literature appraisal was performed during the development of 56% of the reporting guidelines; 33% used surveys to gather external opinion on items to report; and 42% piloted or sought external feedback on their recommendations. Examples of good reporting for all reporting items were presented in 30% of the reporting guidelines. Eighteen percent of the reviewed publications included some level of spin. CONCLUSION: Reporting guidelines have been developed with varying methodology. Reporting guideline developers should use existing guidance and take an evidence-based approach, rather than base their recommendations on expert opinion of limited groups of individuals.

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.

Musculoskeletal health state and physical function of intensive care unit survivors: protocol for a UK multicentre prospective cohort study (the MSK-ICU study).

INTRODUCTION: Survivors of critical illness frequently experience long-term physical impairment, decreased health-related quality of life and low rates of return to employment. There has been limited investigation of the underlying problems affecting physical function post-intensive care unit (ICU) admission. Musculoskeletal (MSK) conditions may be complex in presentation, with ICU survivors potentially at greater risk of their development due to the rapid muscle mass loss seen in ICU. The MSK health state of ICU survivors and its impact on physical function remain largely unknown. The aim of the MSK-ICU study is to determine and characterise the MSK health state of ICU survivors 6 months following admission to ICU, in order to inform development of targeted rehabilitation interventions. METHODS AND ANALYSIS: The MSK-ICU study is a multicentre prospective longitudinal cohort study, evaluating the MSK health state of ICU survivors 6 months after admission to ICU. The study consists of a primary study and two substudies. The primary study will be a telephone follow-up of adults admitted to ICU for more than 48 hours, collecting data on MSK health state, quality of life, employment, anxiety and depression and symptoms of post-traumatic stress disorder. The planned sample size is 334 participants. Multivariable regression will be used to identify prognostic factors for a worse MSK health state, as measured by the MSK-Health Questionnaire. In substudy 1, participants who self-report any MSK problem will undergo a detailed, in-person MSK physical assessment of pain, peripheral joint range of movement and strength. In substudy 2, participants reporting a severe MSK problem will undergo a detailed physical assessment of mobility, function and muscle architecture. ETHICS AND DISSEMINATION: Ethical approval has been obtained through the North of Scotland Research Ethics Committee 2 (21/NS/0143). We aim to disseminate the findings through international conferences, international peer-reviewed journals and social media. TRIAL REGISTRATION NUMBER: ISRCTN24998809.

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.

GoodReports: developing a website to help health researchers find and use reporting guidelines.

BACKGROUND: Th EQUATOR Network improves the quality and transparency in health research, primarily by promoting awareness and use of reporting guidelines. In 2018, the UK EQUATOR Centre launched GoodReports.org , a website that helps authors find and use reporting guidelines. This paper describes the tool's development so far. We describe user experience and behaviour of using GoodReports.org both inside and outside a journal manuscript submission process. We intend to use our findings to inform future development and testing of the tool. METHODS: We conducted a survey to collect data on user experience of the GoodReports website. We cross-checked a random sample of 100 manuscripts submitted to a partner journal to describe the level of agreement between the tool's checklist recommendation and what we would have recommended. We compared the proportion of authors submitting a completed reporting checklist alongside their manuscripts between groups exposed or not exposed to the GoodReports tool. We also conducted a study comparing completeness of reporting of manuscript text before an author received a reporting guideline recommendation from GoodReports.org with the completeness of the text subsequently submitted to a partner journal. RESULTS: Seventy percent (423/599) of survey respondents rated GoodReports 8 or more out of 10 for usefulness, and 74% (198/267) said they had made changes to their manuscript after using the website. We agreed with the GoodReports reporting guideline recommendation in 84% (72/86) of cases. Of authors who completed the guideline finder questionnaire, 14% (10/69) failed to submit a completed checklist compared to 30% (41/136) who did not use the tool. Of the 69 authors who received a GoodReports reporting guideline recommendation, 20 manuscript pairs could be reviewed before and after use of GoodReports. Five included more information in their methods section after exposure to GoodReports. On average, authors reported 57% of necessary reporting items before completing a checklist on GoodReports.org and 60% after. CONCLUSION: The data suggest that reporting guidance is needed early in the writing process, not at submission stage. We are developing GoodReports by adding more reporting guidelines and by creating editable article templates. We will test whether GoodReports users write more complete study reports in a randomised trial targeting researchers starting to write health research articles.

Home-based rehabilitation programme compared with traditional physiotherapy for patients at risk of poor outcome after knee arthroplasty: the CORKA randomised controlled trial.

OBJECTIVES: To evaluate whether a home-based rehabilitation programme for people assessed as being at risk of a poor outcome after knee arthroplasty offers superior outcomes to traditional outpatient physiotherapy. DESIGN: A prospective, single-blind, two-arm randomised controlled superiority trial. SETTING: 14 National Health Service physiotherapy departments in the UK. PARTICIPANTS: 621 participants identified at high risk of a poor outcome after knee arthroplasty using a bespoke screening tool. INTERVENTIONS: A multicomponent home-based rehabilitation programme delivered by rehabilitation assistants with supervision from qualified therapists versus usual care outpatient physiotherapy. MAIN OUTCOME MEASURES: The primary outcome was the Late-Life Function and Disability Instrument (LLFDI) at 12 months. Secondary outcomes were the Oxford Knee Score (a disease-specific measure of function), Knee injury and Osteoarthritis Outcome Score Quality of Life subscale, Physical Activity Scale for the Elderly, 5 dimension, 5 level version of Euroqol (EQ-5D-5L) and physical function assessed using the Figure of 8 Walk test, 30 s Chair Stand Test and Single Leg Stance. RESULTS: 621 participants were randomised between March 2015 and January 2018. 309 were assigned to CORKA (Community Rehabilitation after Knee Arthroplasty) home-based rehabilitation, receiving a median five treatment sessions (IQR 4-7). 312 were assigned to usual care, receiving a median 4 sessions (IQR 2-6). The primary outcome, LLFDI function total score at 12 months, was collected for 279 participants (89%) in the home-based CORKA group and 287 participants (92%) in the usual care group. No clinically or statistically significant difference was found between the groups (intention-to-treat adjusted difference=0.49 points; 95% CI -0.89 to 1.88; p=0.48). There were no statistically significant differences between the groups on any of the patient-reported or physical secondary outcome measures at 6 or 12 months.There were 18 participants in the intervention group reporting a serious adverse event (5.8%), only one directly related to the intervention, all other adverse events recorded throughout the trial related to underlying chronic medical conditions. CONCLUSIONS: The CORKA intervention was not superior to usual care. The trial detected no significant differences, clinical or statistical, between the two groups on either primary or secondary outcomes. CORKA offers an evaluation of an intervention utilising a different service delivery model for this patient group. TRIAL REGISTRATION NUMBER: ISRCTN13517704.

Exploratory Efficacy of Calcium-Vitamin D Milk Fortification and Periodontal Therapy on Maternal Oral Health and Metabolic and Inflammatory Profile.

In this 2 × 2 factorial, outcome-assessor blinded, feasibility randomised trial we explored the effect of a non-pharmaceutical multi-component intervention on periodontal health and metabolic and inflammatory profiles among pregnant women with periodontitis receiving prenatal care in a Brazilian public health centre. 69 pregnant women (gestational age ≤20 weeks, T0) were randomly allocated into four groups: (1) fortified sachet (vitamin D and calcium) and powdered milk plus periodontal therapy during pregnancy (early PT) (n = 17); (2) placebo sachet and powdered milk plus early PT (n = 15); (3) fortified sachet and powdered milk plus late PT (after delivery) (n = 19); (4) placebo sachet and powdered milk plus late PT (n = 18). Third trimester (T1) and 6-8 weeks postpartum (T2) exploratory outcomes included periodontal health (% sites with bleeding on probing (BOP)), glucose, insulin, C-Reactive Protein, serum calcium and vitamin D. The mean BOP was significantly reduced in the early PT groups, while BOP worsened in the late PT groups. No significant effect of fortification on BOP was observed. Changes in glucose levels and variation on birthweight did not differ among groups This feasibility trial provides preliminary evidence for estimating the minimum clinically important differences for selected maternal outcomes. A large-scale trial to evaluate the interventions' clinical benefits and cost-effectiveness is warranted.

Patient-Reported Outcomes as Independent Prognostic Factors for Survival in Oncology: Systematic Review and Meta-Analysis.

OBJECTIVES: Assessment of patient-reported outcomes (PROs) in oncology is of critical importance because it provides unique information that may also predict clinical outcomes. METHODS: We conducted a systematic review of prognostic factor studies to examine the prognostic value of PROs for survival in cancer. A systematic literature search was performed in PubMed for studies published between 2013 and 2018. We considered any study, regardless of the research design, that included at least 1 PRO domain in the final multivariable prognostic model. The protocol (EPIPHANY) was published and registered in the International Prospective Register of Systematic Reviews (CRD42018099160). RESULTS: Eligibility criteria selected 138 studies including 158 127 patients, of which 43 studies were randomized, controlled trials. Overall, 120 (87%) studies reported at least 1 PRO to be statistically significantly prognostic for overall survival. Lung (n = 41, 29.7%) and genitourinary (n = 27, 19.6%) cancers were most commonly investigated. The prognostic value of PROs was investigated in secondary data analyses in 101 (73.2%) studies. The EORTC QLQ-C30 questionnaire was the most frequently used measure, and its physical functioning scale (range 0-100) the most frequent independent prognostic PRO, with a pooled hazard ratio estimate of 0.88 per 10-point increase (95% CI 0.84-0.92). CONCLUSIONS: There is convincing evidence that PROs provide independent prognostic information for overall survival across cancer populations and disease stages. Further research is needed to translate current evidence-based data into prognostic tools to aid in clinical decision making.

Characteristics of L-PRP preparations for treating Achilles tendon rupture within the PATH-2 study.

Platelet-rich plasma (PRP) is an autologous preparation that has been claimed to improve healing and mechanobiological properties of tendons both in vitro and in vivo. In this sub-study from the PATH-2 (PRP in Achilles Tendon Healing-2) trial, we report the cellular and growth factor content and quality of the Leukocyte-rich PRP (L-PRP) (N = 103) prepared using a standardized commercial preparation method across 19 different UK centers. Baseline whole blood cell counts (red cells, leukocyte and platelets) demonstrated that the two groups were well-matched. L-PRP analysis gave a mean platelet count of 852.6 x 109/L (SD 438.96), a mean leukocyte cell count of 15.13 x 109/L (SD 10.28) and a mean red blood cell count of 0.91 x 1012/L (SD 1.49). The activation status of the L-PRP gave either low or high expression levels of the degranulation marker CD62p before and after ex-vivo platelet activation respectively. TGF-ß, VEGF, PDGF, IGF and FGFb mean concentrations were 131.92 ng/ml, 0.98 ng/ml, 55.34 ng/ml, 78.2 ng/ml and 111.0 pg/ml respectively with expected correlations with both platelet and leukocyte counts. While PATH-2 results demonstrated that there was no evidence L-PRP is effective for improving clinical outcomes at 24 weeks after Achilles tendon rupture, our findings support that the majority of L-PRP properties were within the method specification and performance.

Correction to: Calcium and vitamin D supplementation and/or periodontal therapy in the treatment of periodontitis among Brazilian pregnant women: protocol of a feasibility randomised controlled trial (the IMPROVE trial).

An amendment to this paper has been published and can be accessed via the original article.