Tag: statistics

JAMA Netw Open. 2023 Jan 3;6(1):e2253301. doi: 10.1001/jamanetworkopen.2022.53301.

ABSTRACT

IMPORTANCE: Randomized clinical trials (RCTs) on COVID-19 are increasingly being posted as preprints before publication in a scientific, peer-reviewed journal.

OBJECTIVE: To assess time to journal publication for COVID-19 RCT preprints and to compare differences between pairs of preprints and corresponding journal articles.

EVIDENCE REVIEW: This systematic review used a meta-epidemiologic approach to conduct a literature search using the World Health Organization COVID-19 database and Embase to identify preprints published between January 1 and December 31, 2021. This review included RCTs with human participants and research questions regarding the treatment or prevention of COVID-19. For each preprint, a literature search was done to locate the corresponding journal article. Two independent reviewers read the full text, extracted data, and assessed risk of bias using the Cochrane Risk of Bias 2 tool. Time to publication was analyzed using a Cox proportional hazards regression model. Differences between preprint and journal article pairs in terms of outcomes, analyses, results, or conclusions were described. Statistical analysis was performed on October 17, 2022.

FINDINGS: This study included 152 preprints. As of October 1, 2022, 119 of 152 preprints (78.3%) had been published in journals. The median time to publication was 186 days (range, 17-407 days). In a multivariable model, larger sample size and low risk of bias were associated with journal publication. With a sample size of less than 200 as the reference, sample sizes of 201 to 1000 and greater than 1000 had hazard ratios (HRs) of 1.23 (95% CI, 0.80-1.91) and 2.19 (95% CI, 1.36-3.53) for publication, respectively. With high risk of bias as the reference, medium-risk articles with some concerns for bias had an HR of 1.77 (95% CI, 1.02-3.09); those with a low risk of bias had an HR of 3.01 (95% CI, 1.71-5.30). Of the 119 published preprints, there were differences in terms of outcomes, analyses, results, or conclusions in 65 studies (54.6%). The main conclusion in the preprint contradicted the conclusion in the journal article for 2 studies (1.7%).

CONCLUSIONS AND RELEVANCE: These findings suggest that there is a substantial time lag from preprint posting to journal publication. Preprints with smaller sample sizes and high risk of bias were less likely to be published. Finally, although differences in terms of outcomes, analyses, results, or conclusions were observed for preprint and journal article pairs in most studies, the main conclusion remained consistent for the majority of studies.

PMID:36705921 | DOI:10.1001/jamanetworkopen.2022.53301

Methods Mol Biol. 2023;2586:233-249. doi: 10.1007/978-1-0716-2768-6_14.

ABSTRACT

Understanding the three-dimensional structure of an RNA molecule is often essential to understanding its function. Sampling algorithms and energy functions for RNA structure prediction are improving, due to the increasing diversity of structural data available for training statistical potentials and testing structural data, along with a steady supply of blind challenges through the RNA-Puzzles initiative. The recent FARFAR2 algorithm enables near-native structure predictions on fairly complex RNA structures, including automated selection of final candidate models and estimation of model accuracy. Here, we describe the use of a publicly available webserver for RNA modeling for realistic scenarios using FARFAR2, available at https://rosie.rosettacommons.org/farfar2 . We walk through two cases in some detail: a simple model pseudoknot from the frameshifting element of beet western yellows virus modeled using the “basic interface” to the webserver and a replication of RNA-Puzzle 20, a metagenomic twister sister ribozyme, using the “advanced interface.” We also describe example runs of FARFAR2 modeling including two kinds of experimental data: a c-di-GMP riboswitch modeled with low-resolution restraints from MOHCA-seq experiments and a tandem GA motif modeled with ¹H NMR chemical shifts.

PMID:36705908 | DOI:10.1007/978-1-0716-2768-6_14

Methods Mol Biol. 2023;2586:107-120. doi: 10.1007/978-1-0716-2768-6_7.

ABSTRACT

A point mutation in coding RNA can cause not only an amino acid substitution but also a dynamic change of RNA secondary structure, leading to a dysfunctional RNA. Although in silico structure prediction has been used to detect structure-disrupting point mutations known as riboSNitches, exhaustive simulation of long RNAs is needed to detect a significant enrichment or depletion of riboSNitches in functional RNAs. Here, we have developed a novel algorithm Radiam (RNA secondary structure Analysis with Deletion, Insertion, And substitution Mutations) for a comprehensive riboSNitch analysis of long RNAs. Radiam is based on the ParasoR framework, which efficiently computes local RNA secondary structures for long RNAs. ParasoR can compute a variety of structure scores over globally consistent structures with maximal span constraints for the base pair distance. Using the reusable structure database made by ParasoR, Radiam performs an efficient recomputation of the secondary structures for mutated sequences. An exhaustive simulation of Radiam is expected to find reliable riboSNitch candidates on long RNAs by evaluating their statistical significance in terms of the change of local structure stability.

PMID:36705901 | DOI:10.1007/978-1-0716-2768-6_7

Methods Mol Biol. 2023;2586:35-48. doi: 10.1007/978-1-0716-2768-6_3.

ABSTRACT

The information of RNA secondary structure has been widely applied to the inference of RNA function. However, a classical prediction method is not feasible to long RNAs such as mRNA due to the problems of computational time and numerical errors. To overcome those problems, sliding window methods have been applied while their results are not directly comparable to global RNA structure prediction. In this chapter, we introduce ParasoR, a method designed for parallel computation of genome-wide RNA secondary structures. To enable genome-wide prediction, ParasoR distributes dynamic programming (DP) matrices required for structure prediction to multiple computational nodes. Using the database of not the original DP variable but the ratio of variables, ParasoR can locally compute the structure scores such as stem probability or accessibility on demand. A comprehensive analysis of local secondary structures by ParasoR is expected to be a promising way to detect the statistical constraints on long RNAs.

PMID:36705897 | DOI:10.1007/978-1-0716-2768-6_3

Arch Osteoporos. 2023 Jan 27;18(1):27. doi: 10.1007/s11657-023-01213-1.

ABSTRACT

The current study shows that patients aged 50 or more who have sustained an osteoporotic fracture have a significant risk of suffering a new fracture. Refracture risk is also increased when anatomic site of both index and subsequent fracture are the same.

PURPOSE: The purpose of this study is to describe the profile of a patient sustaining a fragility fracture, the influence of the initial or index fracture on subsequent fracture risk and the role that anatomic site of index and subsequent fracture play on fracture risk.

METHODS: In this retrospective observational cohort study, individuals aged ≥ 50 years who sustained at least one clinical fragility fracture were identified from the public health service register between January 1, 2014, and December 31, 2015. Two separate analysis cohorts were identified. Group 1 (index FF) included patients that sustained at least one clinical fragility fracture during the study period. Group 2 (subsequent FF) included those patients from group 1 who sustained at least one clinical subsequent fracture during the following 2 years after index fracture.

RESULTS: A total of 11,986 fractures constituted group 1 (index FF), and 792 constituted group 2 (subsequent FF). The incidence of subsequent fractures was 6.61%, with a major percentage of them (36.99%) identified within the first 6 months following index FF. Hip was the most frequent site for index (30.09%) and subsequent fracture (34.85%). We found an increased risk mainly when anatomic site of index and subsequent FF are the same.

CONCLUSIONS: Sustaining a subsequent fracture after an index fracture is a common event in the population over age 50, more commonly occurring within 6 months of index fracture. Analysis of fracture site correlation shows that refracture risk is increased mainly when index and subsequent fracture site are the same.

PMID:36705860 | DOI:10.1007/s11657-023-01213-1

J Med Syst. 2023 Jan 27;47(1):14. doi: 10.1007/s10916-023-01910-x.

ABSTRACT

The study aims to (1) investigate current levels of patient acceptance of mHealth in Germany; (2) determine the influencing factors of patients’ intention to use, and (3) test the influence of prescription and reimbursement status on patient acceptance. Online survey with 1349 participants, of which 1051 were complete and included for statistical analysis, from a broad cross-section of the German population, addressing both users of mobile health (mHealth) applications and people without prior experience. SEM modeling based on a combination of two theoretical frameworks: the extended Unified Theory of Acceptance and Use of Technology and Health Protective Behavior Theories were used to assess acceptance. Users of mHealth in Germany are mostly patients between the ages of 30 – 50 with mental health or endocrine conditions. General willingness to use mHealth apps / DiGAs (mHealth apps fully reimbursed by social health insurance) is high at 76%, especially if they are governmentally certified, however only 27% of respondents were willing to pay out of pocket. With the exception of a spike in performance expectancy and data security, DiGAs lack a clear differentiation from mHealth apps. Perceived self-efficacy and performance expectancy are significant predictors of willingness to use digital health interventions; with age, attitude, and e-literacy being key demographic predictors. A key takeaway for regulators, providers of mHealth apps/ DiGAs, and other stakeholders involved in mHealth adoption is the importance of addressing negative beliefs early on, targeted communication around effortless usage of mHealth services across age groups and demographics, and focus on highlighting expected benefits of mHealth app/ DiGA usage.

PMID:36705853 | DOI:10.1007/s10916-023-01910-x

J Endocrinol Invest. 2023 Jan 27. doi: 10.1007/s40618-023-02013-7. Online ahead of print.

ABSTRACT

PURPOSE: Minimally invasive surgery is the gold standard treatment for adrenal masses, but it may be a challenging procedure in the case of pheochromocytoma (PHEO). The aim of the present study is to report the results of transperitoneal laparoscopic adrenalectomy (TLA) in cases of PHEO in comparison to other types of adrenal lesions.

METHODS: From 1994 to 2021, 629 patients underwent adrenalectomy. Twenty-two and thirty-five patients, respectively, were excluded because they underwent bilateral and open adrenalectomy, leaving 572 patients for inclusion. Of these, 114 patients had PHEO (Group A), and 458 had other types of lesions (Group B). To adjust for potential baseline confounders, a propensity score matching (PSM) analysis was conducted.

RESULTS: After PSM, 114 matched pairs of patients were identified from each group. Statistically significant differences were not observed when comparing the median operative time (85 and 90 min in Groups A and B, respectively, p = 0.627), conversion rate [6 (5.3%) in each group, p = 1.000], transfusion rate [4 (3.5%) and 3 (2.6%) in Groups A and B, respectively, p = 1.000], complication rate [7 (6.1%) and 9 (7.9%) in Groups A and B, respectively, p = 0.796), median postoperative hospital stay (3.9 and 3.6 days in Groups A and B, respectively, p = 0.110), and mortality rate [1 (0.9%) in each group, p = 1.000].

CONCLUSIONS: Based on this analysis, the results of TLA for PHEO are equivalent to those of TLA for other types of adrenal lesions, but the fundamental requirements are multidisciplinary patient management and adequate surgeon experience. Further prospective studies are required to draw definitive conclusions.

PMID:36705839 | DOI:10.1007/s40618-023-02013-7

Environ Sci Pollut Res Int. 2023 Jan 27. doi: 10.1007/s11356-023-25463-1. Online ahead of print.

ABSTRACT

This study aimed to explore the spatial distribution and influencing factors of thyroid cancer hospitalization rates in Fujian Province from 2012 to 2016. Hospitalization reimbursement records for thyroid cancer were obtained from 2025 hospitals in Fujian Province from 2012 to 2016. The Moran’s I method was used for spatial autocorrelation analysis and to further draw a spatial cluster map in Fujian. Geographic detectors were used to explore the effect of risk factors on spatial heterogeneity of inpatient service utilization for thyroid cancer. The study showed that there was obvious temporal and spatial heterogeneity in the utilization rate of inpatient services for thyroid cancer in Fujian Province, which were mainly concentrated in Fuzhou, with Lianjiang County as the center, and the gathering area involves 26 counties and cities. Among a variety of environmental factors, air quality index (AQI) (q = 0.481), carbon sequestration (q = 0.161), and carbon emissions (q = 0.155) were the main factors affecting the hospitalization rates. AQI and carbon emissions were generally positively correlated with hospitalization rates, and carbon sequestration was negatively correlated. After the interaction of the two factors, the interpretation of the hospitalization rate was enhanced. The obvious spatial heterogeneity will help the relevant departments to adjust measures to local conditions and allocate medical resources rationally to ease the pressure of seeking medical attention in high-demand areas.

PMID:36705824 | DOI:10.1007/s11356-023-25463-1

J Exp Orthop. 2023 Jan 27;10(1):9. doi: 10.1186/s40634-023-00575-2.

ABSTRACT

PURPOSE: The Area Measurement And Depth Underlying Structures (AMADEUS) classification system has been proposed as a valuable tool for magnetic resonance (MR)-based grading of preoperatively encountered chondral defects of the knee joint. However, the potential relationship of this novel score with clinical data was yet to determine. It was the primary intention of this study to assess the correlative relationship of the AMADEUS with patient reported outcome scores in patients undergoing medial open-wedge high tibial valgus osteotomy (HTO). Furthermore, the arthroscopic ICRS (International Cartilage Repair Society) grade evaluation was tested for correlation with the AMADEUS classification system.

METHODS: This retrospective, monocentric study found a total of 70 individuals that were indicated for HTO due to degenerative chondral defects of the medial compartment between 2008 and 2019. A preoperative MR image as well as a pre-osteotomy diagnostic arthroscopy for ICRS grade evaluation was mandatory for all patients. The Knee Osteoarthritis Outcome Score (KOOS) including its five subscale scores (KOOS-ADL, KOOS-QOL, KOOS-Sports, KOOS-Pain, KOOS-Symptoms) was obtained preoperatively and at a mean follow-up of 41.2 ± 26.3 months. Preoperative chondral defects were evaluated using the AMADEUS classification system and the final AMADEUS scores were correlated with the pre- and postoperative KOOS subscale sores. Furthermore, arthroscopic ICRS defect severity was correlated with the AMADEUS classification system.

RESULTS: There was a statistically significant correlation between the AMADEUS BME (bone marrow edema) subscore and the KOOS Symptoms subscore at the preoperative visit (r = 0.25, p = 0.04). No statistically significant monotonic association between the AMADEUS total score and the AMADEUS grade with pre- and postoperative KOOS subscale scores were found. Intraoperatively obtained ICRS grade did reveal a moderate correlative relation with the AMADEUS total score and the AMADEUS grade (r = 0.28, p = 0.02).

CONCLUSIONS: The novel AMADEUS classification system largely lacks correlative capacity with patient reported outcome measures in patients undergoing HTO. The MR tomographic appearance of bone marrow edema is the only parameter predictive of the clinical outcome at the preoperative visit.

PMID:36705820 | DOI:10.1186/s40634-023-00575-2

Ann Surg Oncol. 2023 Jan 27. doi: 10.1245/s10434-022-13084-w. Online ahead of print.

NO ABSTRACT

PMID:36705817 | DOI:10.1245/s10434-022-13084-w