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Evidence-based Mental Health Nov 2019Meta-analysis is of fundamental importance to obtain an unbiased assessment of the available evidence. In general, the use of meta-analysis has been increasing over the...
OBJECTIVE
Meta-analysis is of fundamental importance to obtain an unbiased assessment of the available evidence. In general, the use of meta-analysis has been increasing over the last three decades with mental health as a major research topic. It is then essential to well understand its methodology and interpret its results. In this publication, we describe how to perform a meta-analysis with the freely available statistical software environment R, using a working example taken from the field of mental health.
METHODS
R package meta is used to conduct standard meta-analysis. Sensitivity analyses for missing binary outcome data and potential selection bias are conducted with R package metasens. All essential R commands are provided and clearly described to conduct and report analyses.
RESULTS
The working example considers a binary outcome: we show how to conduct a fixed effect and random effects meta-analysis and subgroup analysis, produce a forest and funnel plot and to test and adjust for funnel plot asymmetry. All these steps work similar for other outcome types.
CONCLUSIONS
R represents a powerful and flexible tool to conduct meta-analyses. This publication gives a brief glimpse into the topic and provides directions to more advanced meta-analysis methods available in R.
Topics: Biomedical Research; Humans; Meta-Analysis as Topic; Software
PubMed: 31563865
DOI: 10.1136/ebmental-2019-300117 -
Journal of Periodontology Nov 2020The periodontal phenotype consists of the bone morphotype, the keratinized tissue (KT), and gingival thickness (GT). The latter two components, overlying the bone,... (Meta-Analysis)
Meta-Analysis Review
BACKGROUND
The periodontal phenotype consists of the bone morphotype, the keratinized tissue (KT), and gingival thickness (GT). The latter two components, overlying the bone, constitute the gingival phenotype. Several techniques have been proposed for enhancing or augmenting KT or GT. However, how phenotype modification therapy (PMT) affects periodontal health and whether the obtained outcomes are maintained over time have not been elucidated. The aim of the present review was to summarize the available evidence in regard to the utilized approaches for gingival PMT and assess their comparative efficacy in augmenting KT, GT and in improving periodontal health using autogenous, allogenic, and xenogeneic grafting approaches.
METHODS
A detailed systematic search was performed to identify eligible randomized clinical trials (RCTs) reporting on the changes in GT and KT (primary outcomes). The selected articles were segregated into the type of approach based on having performed a root coverage, or non-root coverage procedure. A network meta-analysis (NMA) was conducted for each approach to assess and compare the outcomes among different treatment arms for the primary outcomes.
RESULTS
A total of 105 eligible RCTs were included. 95 pertaining to root coverage (3,539 treated gingival recessions [GRs]), and 10 for non-root coverage procedures (699 total treated sites). The analysis on root coverage procedures showed that all investigated techniques (the acellular dermal matrix [ADM], collagen matrix [CM], connective tissue graft [CTG]) are able to significantly increase the GT, compared with treatment with flap alone. However, KT was only significantly increased with the use of CTG or ADM. Early post-treatment GT was found to inversely predict future GR. For non-root coverage procedures, only the changes in KT could be analyzed; all investigated treatment groups (ADM, CM, free gingival graft [FGG], living cellular construct [LCC], in combination with an apically positioned flap [APF]), resulted in significantly more KT than treatment with APF alone. Additionally, the augmented GT was shown to be sustained, and KT displayed an incremental increase over time.
CONCLUSIONS
Within its limitations, it was observed that any graft material was able to significantly enhance GT, while KT in root coverage procedures was significantly enhanced with CTG and ADM, and in non-root coverage procedures, with ADM, CM, FGG, and LCC compared with APF alone. The autogenous soft tissue graft (CTG/FGG) proved to be superior in all comparisons for both outcomes of GT and KT.
Topics: Connective Tissue; Gingiva; Gingival Recession; Humans; Network Meta-Analysis; Phenotype; Tooth Root; Treatment Outcome
PubMed: 32392401
DOI: 10.1002/JPER.19-0715 -
Medical Care Jan 2022Pilot studies test the feasibility of methods and procedures to be used in larger-scale studies. Although numerous articles describe guidelines for the conduct of pilot...
BACKGROUND
Pilot studies test the feasibility of methods and procedures to be used in larger-scale studies. Although numerous articles describe guidelines for the conduct of pilot studies, few have included specific feasibility indicators or strategies for evaluating multiple aspects of feasibility. In addition, using pilot studies to estimate effect sizes to plan sample sizes for subsequent randomized controlled trials has been challenged; however, there has been little consensus on alternative strategies.
METHODS
In Section 1, specific indicators (recruitment, retention, intervention fidelity, acceptability, adherence, and engagement) are presented for feasibility assessment of data collection methods and intervention implementation. Section 1 also highlights the importance of examining feasibility when adapting an intervention tested in mainstream populations to a new more diverse group. In Section 2, statistical and design issues are presented, including sample sizes for pilot studies, estimates of minimally important differences, design effects, confidence intervals (CI) and nonparametric statistics. An in-depth treatment of the limits of effect size estimation as well as process variables is presented. Tables showing CI around parameters are provided. With small samples, effect size, completion and adherence rate estimates will have large CI.
CONCLUSION
This commentary offers examples of indicators for evaluating feasibility, and of the limits of effect size estimation in pilot studies. As demonstrated, most pilot studies should not be used to estimate effect sizes, provide power calculations for statistical tests or perform exploratory analyses of efficacy. It is hoped that these guidelines will be useful to those planning pilot/feasibility studies before a larger-scale study.
Topics: Feasibility Studies; Guidelines as Topic; Humans; Pilot Projects; Research Design
PubMed: 34812790
DOI: 10.1097/MLR.0000000000001664 -
Heart Rhythm O2 Apr 2020Cryoballoon ablation for the treatment of atrial fibrillation has established itself as an effective and efficient modality for achieving pulmonary vein isolation. Over... (Review)
Review
Cryoballoon ablation for the treatment of atrial fibrillation has established itself as an effective and efficient modality for achieving pulmonary vein isolation. Over the past 13 years more than 100,000 Cryoballoon ablation procedures have been performed with the first to fourth generation cryoballoons. Over that time there have been significant advances in our understanding regarding the optimal procedural techniques. The purpose of this "topic in review" is to focus on the practical aspects of performing a Cryoballoon ablation procedure, within the context of the contemporary literature. Specifically there is a focus on how contemporary studies can inform clinical decision making and ensure operators are able to perform a safe and effective procedure.
PubMed: 34113858
DOI: 10.1016/j.hroo.2020.02.004 -
Journal of Thoracic Disease Aug 2021Pleural disease is common and often requires procedural intervention. Given this prevalence, pleural procedures are performed by a wide range of providers with varying... (Review)
Review
Pleural disease is common and often requires procedural intervention. Given this prevalence, pleural procedures are performed by a wide range of providers with varying skill level in both medical and surgical specialties. Even though the overall complication rate of pleural procedures is low, the proximity to vital organs and blood vessels can lead to serious complications which if left unrecognized can be life threatening. As a result, it is of the utmost importance for the provider to have a firm grasp of the local anatomy both conceptually when preparing for the procedure and physically, via physical exam and the use of a real time imaging modality such as ultrasound, when performing the procedure. With this in mind, anyone who wishes to safely perform pleural procedures should be able to appropriately anticipate, quickly identify, and efficiently manage any potential complication including not only those seen with many procedures such as pain, bleeding, and infection but also those specific to procedures performed in the thorax such as pneumothorax, re-expansional pulmonary edema, and regional organ injury. In this article, we will review the basic approach to most pleural procedures along with essential local anatomy most often encountered during these procedures. This will lay the foundation for the remainder of the article where we will discuss clinical manifestations and management of various pleural procedure complications.
PubMed: 34527363
DOI: 10.21037/jtd-2019-ipicu-04 -
Research Synthesis Methods Mar 2020Rigorous evidence identification is essential for systematic reviews and meta-analyses (evidence syntheses) because the sample selection of relevant studies determines a...
Rigorous evidence identification is essential for systematic reviews and meta-analyses (evidence syntheses) because the sample selection of relevant studies determines a review's outcome, validity, and explanatory power. Yet, the search systems allowing access to this evidence provide varying levels of precision, recall, and reproducibility and also demand different levels of effort. To date, it remains unclear which search systems are most appropriate for evidence synthesis and why. Advice on which search engines and bibliographic databases to choose for systematic searches is limited and lacking systematic, empirical performance assessments. This study investigates and compares the systematic search qualities of 28 widely used academic search systems, including Google Scholar, PubMed, and Web of Science. A novel, query-based method tests how well users are able to interact and retrieve records with each system. The study is the first to show the extent to which search systems can effectively and efficiently perform (Boolean) searches with regards to precision, recall, and reproducibility. We found substantial differences in the performance of search systems, meaning that their usability in systematic searches varies. Indeed, only half of the search systems analyzed and only a few Open Access databases can be recommended for evidence syntheses without adding substantial caveats. Particularly, our findings demonstrate why Google Scholar is inappropriate as principal search system. We call for database owners to recognize the requirements of evidence synthesis and for academic journals to reassess quality requirements for systematic reviews. Our findings aim to support researchers in conducting better searches for better evidence synthesis.
Topics: Algorithms; Biomedical Research; Databases, Bibliographic; Databases, Factual; Information Storage and Retrieval; Internet; Meta-Analysis as Topic; Periodicals as Topic; PubMed; Reproducibility of Results; Research Design; Search Engine; Software; Systematic Reviews as Topic
PubMed: 31614060
DOI: 10.1002/jrsm.1378 -
Transfusion and Apheresis Science :... Oct 2023Significant advances in procedural information displayed by current apheresis machines have been made, but analyses of cell collection efficiency (CE) still rely on...
Significant advances in procedural information displayed by current apheresis machines have been made, but analyses of cell collection efficiency (CE) still rely on calculations done by apheresis professionals. Accordingly, understanding CE equations can support the optimization of apheresis techniques and identification of incidents that could impact the procedure's effectiveness. This report summarizes classical and novel CE analyses applied to apheresis exemplified by an actual case of hematopoietic progenitor cell collection. In addition to the apheresis yield and most common CE and CE formulas, we present the instantaneous and corrected CE, fold enrichment, collection throughput, collection rate and its variants, average inlet rate, classical and adjusted captured cells, recruitment pool, recruitment factor, recruitment coefficient, blood component loss, predictive apheresis yield, and performance ratio calculations. Moreover, the mathematical relationship between these CE equations is also shown, which can be helpful in many apheresis procedures.
Topics: Humans; Leukapheresis; Blood Component Removal; Hematopoietic Stem Cells; Antigens, CD34
PubMed: 37438245
DOI: 10.1016/j.transci.2023.103758 -
Surgical Endoscopy Jul 2022The initial phases of robotic surgical skills acquisition are associated with poor technical performance, such as low knot-tensile strength (KTS). Transcranial... (Randomized Controlled Trial)
Randomized Controlled Trial
BACKGROUND
The initial phases of robotic surgical skills acquisition are associated with poor technical performance, such as low knot-tensile strength (KTS). Transcranial direct-current stimulation (tDCS) can improve force and accuracy in motor tasks but research in surgery is limited to open and laparoscopic tasks in students. More recently, robotic surgery has gained traction and is now the most common approach for certain procedures (e.g. prostatectomy). Early-phase robotic suturing performance is dependent on prefrontal cortex (PFC) activation, and this study aimed to determine whether performance can be improved with prefrontal tDCS.
METHODS
Fifteen surgical residents were randomized to either active then sham tDCS or sham then active tDCS, in two counterbalanced sessions in a double-blind crossover study. Within each session, participants performed a robotic suturing task repeated in three blocks: pre-, intra- and post-tDCS. During the intra-tDCS block, participants were randomized to either active tDCS (2 mA for 15 min) to the PFC or sham tDCS. Primary outcome measures of technical quality included KTS and error scores.
RESULTS
Significantly faster completion times were observed longitudinally, regardless of active (p < 0.001) or sham stimulation (p < 0.001). KTS was greater following active compared to sham stimulation (median: active = 44.35 N vs. sham = 27.12 N, p < 0.001). A significant reduction in error scores from "pre-" to "post-" (p = 0.029) were only observed in the active group.
CONCLUSION
tDCS could reduce error and enhance KTS during robotic suturing and warrants further exploration as an adjunct to robotic surgical training.
Topics: Cross-Over Studies; Double-Blind Method; Humans; Male; Robotic Surgical Procedures; Robotics; Surgeons; Transcranial Direct Current Stimulation
PubMed: 34724587
DOI: 10.1007/s00464-021-08823-1 -
Pediatric Surgery International Apr 2023Ladd's Procedure has been the surgical intervention of choice in the management of congenital intestinal malrotation for the past century. Historically, the procedure... (Review)
Review
BACKGROUND
Ladd's Procedure has been the surgical intervention of choice in the management of congenital intestinal malrotation for the past century. Historically, the procedure included performing an appendectomy to prevent future misdiagnosis of appendicitis, since the location of the appendix will be shifted to the left side of the abdomen. This study consists of two parts. A review of the available literature on appendectomy as part of Ladd's procedure and then a survey sent to pediatric surgeons about their approach (to remove the appendix or not) while performing a Ladd's procedure and the clinical reasoning behind their approach.
METHODS
The study consists of 2 parts: (1) a systematic review was performed to extract articles that fulfill the inclusion criteria; (2) a short online survey was designed and sent by email to 168 pediatric surgeons. The questions in the survey were centered on whether a surgeon performs an appendectomy as part of the Ladd's procedure or not, as well as their reasoning behind either choice.
RESULTS
The literature search yielded five articles, the data from the available literature are inconsistent with performing appendectomy as part of Ladd's procedure. The challenge of leaving the appendix in place has been briefly described with minimal to no focus on the clinical reasoning. The survey demonstrated that 102 responses were received (60% response rate). Ninety pediatric surgeons stated performing an appendectomy as part of the procedure (88%). Only 12% of pediatric surgeons are not performing appendectomy during Ladd's procedure.
CONCLUSION
It is difficult to implement a modification in a successful procedure like Ladd's procedure. The majority of pediatric surgeons perform an appendectomy as part of its original description. This study has identified gaps in the literature pertaining to analyze the outcomes of performing Ladd's procedure without an appendectomy which should be explored in future research.
Topics: Child; Humans; Appendectomy; Laparoscopy; Intestinal Volvulus; Digestive System Surgical Procedures
PubMed: 37010655
DOI: 10.1007/s00383-023-05437-7 -
PloS One 2022RNA-seq is a high-throughput sequencing technology widely used for gene transcript discovery and quantification under different biological or biomedical conditions. A...
RNA-seq is a high-throughput sequencing technology widely used for gene transcript discovery and quantification under different biological or biomedical conditions. A fundamental research question in most RNA-seq experiments is the identification of differentially expressed genes among experimental conditions or sample groups. Numerous statistical methods for RNA-seq differential analysis have been proposed since the emergence of the RNA-seq assay. To evaluate popular differential analysis methods used in the open source R and Bioconductor packages, we conducted multiple simulation studies to compare the performance of eight RNA-seq differential analysis methods used in RNA-seq data analysis (edgeR, DESeq, DESeq2, baySeq, EBSeq, NOISeq, SAMSeq, Voom). The comparisons were across different scenarios with either equal or unequal library sizes, different distribution assumptions and sample sizes. We measured performance using false discovery rate (FDR) control, power, and stability. No significant differences were observed for FDR control, power, or stability across methods, whether with equal or unequal library sizes. For RNA-seq count data with negative binomial distribution, when sample size is 3 in each group, EBSeq performed better than the other methods as indicated by FDR control, power, and stability. When sample sizes increase to 6 or 12 in each group, DESeq2 performed slightly better than other methods. All methods have improved performance when sample size increases to 12 in each group except DESeq. For RNA-seq count data with log-normal distribution, both DESeq and DESeq2 methods performed better than other methods in terms of FDR control, power, and stability across all sample sizes. Real RNA-seq experimental data were also used to compare the total number of discoveries and stability of discoveries for each method. For RNA-seq data analysis, the EBSeq method is recommended for studies with sample size as small as 3 in each group, and the DESeq2 method is recommended for sample size of 6 or higher in each group when the data follow the negative binomial distribution. Both DESeq and DESeq2 methods are recommended when the data follow the log-normal distribution.
Topics: Binomial Distribution; High-Throughput Nucleotide Sequencing; RNA-Seq; Sample Size; Sequence Analysis, RNA
PubMed: 36112652
DOI: 10.1371/journal.pone.0264246