Motivation
Tissue-level omics data such as transcriptomics and epigenomics are an average across diverse cell types. To extract cell-type-specific (CTS) signals, dozens of cellular deconvolution methods have been proposed to infer cell-type fractions from tissue-level data. However, these methods produce vastly different results under various real data settings. Simulation-based benchmarking studies showed no universally best deconvolution approaches. There have been attempts of ensemble methods, but they only aggregate multiple single-cell references or reference-free deconvolution methods.
Results
To achieve a robust estimation of cellular fractions, we proposed EnsDeconv (Ensemble Deconvolution), which adopts CTS robust regression to synthesize the results from eleven single deconvolution methods, ten reference datasets, five marker gene selection procedures, five data normalizations, and two transformations. Unlike most benchmarking studies based on simulations, we compiled four large real datasets of 4,937 tissue samples in total with measured cellular fractions and bulk gene expression from different tissues. Comprehensive evaluations demonstrated that EnsDeconv yields more stable, robust, and accurate fractions than existing methods. We illustrated that EnsDeconv estimated cellular fractions enable various CTS downstream analyses such as differential fractions associated with clinical variables. We further extended EnsDeconv to analyze bulk DNA methylation data.
Availability
EnsDeconv is freely available as an R-package from https://github.com/randel/EnsDeconv.
Supplementary information
Supplementary data are available at Bioinformatics online.
Non-surgical treatment is successful in controlling pain and preventing disease progress in treating thumb carpometacarpal arthritis. We used Optum’s de-identified Clinformatics® Data Mart Databases between 2015 and 2018 to conduct a study of the patient and provider characteristics associated with three types of non-surgical treatment (hand therapy, splinting and corticosteroid injection) prior to surgery. In this population-based cohort study, we found that non-surgical providers were more likely to provide three different types of non-surgical treatments, as compared with hand surgeons. In addition, women and patients with comorbid conditions, including carpal tunnel syndrome, obesity, chronic pain and depression, were less likely to exhaust the available non-surgical management options for thumb carpometacarpal arthritis. Therefore, we suggest that these specific patient populations can potentially benefit from additional non-surgical treatments that may delay or obviate surgery for this disease. These groups are target populations for future efforts to ensure that all patients receive equitable care. Level of evidence: II
Background:
Numerous surgical reconstructive techniques have been described for chronic scapholunate and lunotriquetral interosseous ligament instability.
Methods:
The authors retrospectively reviewed 16 consecutive patients who underwent bone-ligament-bone reconstruction for scapholunate or lunotriquetral intraosseous ligament predynamic and dynamic instability at a single tertiary care institution from 2013 to 2019. Clinical and radiographic outcomes, and complications, were recorded.
Results:
Eleven patients had bone-ligament-bone reconstruction for scapholunate ligament injuries and five for lunotriquetral instability. Fourteen patients (87.5 percent) underwent diagnostic arthroscopy before bone-ligament-bone reconstruction, with nine of 14 having grade 3 and four of 14 having grade 4 injury. Capitohamate bone-ligament-bone grafts were used in nine patients (56 percent) and the graft was taken from Lister tubercle in seven (44 percent). The average age at surgery was 37 years. The average follow-up was 60.6 weeks. There were no significant differences between preoperative and postoperative radiographic parameters. Median postoperative wrist flexion was 45 degrees, and mean postoperative wrist extension was 53 degrees, which were significantly less than contralateral flexion (85 degrees; p < 0.0001) and extension (78 degrees; p < 0.0001). Thirty-eight percent of patients complained of persistent pain at final follow-up, and two patients (13 percent) underwent salvage procedures, both at approximately 6.5 months after the index reconstruction.
Conclusion:
Short-term outcomes of bone-ligament-bone reconstruction for early-stage scapholunate and lunotriquetral ligament injuries reveal many patients with residual postoperative wrist pain and disability, and almost uniform limitations in flexion-extension motion.
CLINICAL QUESTION/LEVEL OF EVIDENCE:
Therapeutic, IV.
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