Category: Statistics

J Am Acad Orthop Surg Glob Res Rev. 2021 May 4;5(5):e21.00073. doi: 10.5435/JAAOSGlobal-D-21-00073.

ABSTRACT

INTRODUCTION: Within the geriatric hip fracture population, there exists a subset of patients whose length of inpatient hospital stay is excessive relative to the average. A better understanding of the risk factors associated with this group would be of value so that targeted prevention efforts can be properly directed. The goal of this study was to identify and characterize the risk factors associated with an extended length of hospital stay (eLOS) in the geriatric hip fracture population. In addition, a statistical model was created to predict the probability of eLOS in a geriatric hip fracture patient.

METHODS: The National Surgical Quality Improvement Program database (2005 to 2018) was searched for patients aged ≥65 years who underwent hip fracture surgery. Patients with a hospital stay greater than or equal to 14 days were considered to have an eLOS. A multivariate logistic regression model using 24 patient characteristics from two-thirds of the study population was created to determine independent risk factors predictive of having an eLOS; the remaining one-third of the population was used for internal model validation. Regression analyses were performed to determine preoperative and postoperative risk factors for having an eLOS.

RESULTS: A total of 77,144 patients were included in the study. Preoperatively, male sex, dyspnea, ventilator use, chronic obstructive pulmonary disease, American Society of Anesthesiologist class 3 and 4, and increased admission-to-operation time were among the factors associated with higher odds of having an eLOS (all P < 0.001). Postoperatively, patients with acute renal failure had the highest likelihood of eLOS (odds ratio [OR] 7.664), followed by ventilator use >48 hours (OR 4.784) and pneumonia (OR 4.332).

DISCUSSION: Among geriatric hip fracture patients, particular efforts should be directed toward optimizing those with preoperative risk factors for eLOS. Preemptive measures to target the postoperative complications with the strongest eLOS association may be beneficial for both the patient and the healthcare system as a whole.

PMID:33945514 | DOI:10.5435/JAAOSGlobal-D-21-00073

PLoS Comput Biol. 2021 May 4;17(5):e1008976. doi: 10.1371/journal.pcbi.1008976. Online ahead of print.

ABSTRACT

Analyses of gene set differential coexpression may shed light on molecular mechanisms underlying phenotypes and diseases. However, differential coexpression analyses of conceptually similar individual studies are often inconsistent and underpowered to provide definitive results. Researchers can greatly benefit from an open-source application facilitating the aggregation of evidence of differential coexpression across studies and the estimation of more robust common effects. We developed Meta Gene Set Coexpression Analysis (MetaGSCA), an analytical tool to systematically assess differential coexpression of an a priori defined gene set by aggregating evidence across studies to provide a definitive result. In the kernel, a nonparametric approach that accounts for the gene-gene correlation structure is used to test whether the gene set is differentially coexpressed between two comparative conditions, from which a permutation test p-statistic is computed for each individual study. A meta-analysis is then performed to combine individual study results with one of two options: a random-intercept logistic regression model or the inverse variance method. We demonstrated MetaGSCA in case studies investigating two human diseases and identified pathways highly relevant to each disease across studies. We further applied MetaGSCA in a pan-cancer analysis with hundreds of major cellular pathways in 11 cancer types. The results indicated that a majority of the pathways identified were dysregulated in the pan-cancer scenario, many of which have been previously reported in the cancer literature. Our analysis with randomly generated gene sets showed excellent specificity, indicating that the significant pathways/gene sets identified by MetaGSCA are unlikely false positives. MetaGSCA is a user-friendly tool implemented in both forms of a Web-based application and an R package “MetaGSCA”. It enables comprehensive meta-analyses of gene set differential coexpression data, with an optional module of post hoc pathway crosstalk network analysis to identify and visualize pathways having similar coexpression profiles.

PMID:33945541 | DOI:10.1371/journal.pcbi.1008976

IEEE Trans Biomed Eng. 2021 May 4;PP. doi: 10.1109/TBME.2021.3077582. Online ahead of print.

ABSTRACT

OBJECTIVE: While performing surgical excision for breast cancer (lumpectomy), it is important to ensure a clear margin of normal tissue around the cancer to achieve complete resection. The current standard is histopathology; however, it is time-consuming and labour-intensive requiring skilled personnel.

METHOD: We describe a Hybrid Spectral-IRDx – a combination of the previously reported Spectral-IRDx tool with multimodal ultrasound and NIR spectroscopy techniques. We show how this portable, cost-effective, minimal-contact tool could provide rapid diagnosis of cancer using formalin-fixed (FF) and deparaffinized (DP) breast biopsy tissues.

RESULTS: Using this new tool, measurements were performed on cancerous/fibroadenoma and its adjacent normal tissues from the same patients (N=14). The acoustic attenuation coefficient () and reduced scattering coefficient (s) (at 850, 940, and 1060 nm) for the cancerous/fibroadenoma tissues were reported to be higher compared to adjacent normal tissues, a basis of delineation. Comparing FF cancerous and adjacent normal tissue, the difference in s at 850 nm and 940 nm were statistically significant (p=3.17e-2 and 7.94e-3 respectively). The difference in between the cancerous and adjacent normal tissues for DP and FF tissues were also statistically significant (p=2.85e-2 and 7.94e-3 respectively). Combining multimodal parameters and s (at 940 nm) show highest statistical significance (p=6.72e-4) between FF cancerous/fibroadenoma and adjacent normal tissues.

CONCLUSION: We show that Hybrid Spectral-IRDx can accurately delineate between cancerous and adjacent normal breast biopsy tissue.

SIGNIFICANCE: The results obtained establish the proof-of-principle and large-scale testing of this multimodal breast cancer diagnostic platform for core biopsy diagnosis.

PMID:33945469 | DOI:10.1109/TBME.2021.3077582

IEEE Trans Image Process. 2021 May 4;PP. doi: 10.1109/TIP.2021.3076310. Online ahead of print.

ABSTRACT

Inpainting arbitrary missing regions is challenging because learning valid features for various masked regions is nontrivial. Though U-shaped encoder-decoder frameworks have been witnessed to be successful, most of them share a common drawback of mask unawareness in feature extraction because all convolution windows (or regions), including those with various shapes of missing pixels, are treated equally and filtered with fixed learned kernels. To this end, we propose our novel mask-aware inpainting solution. Firstly, a Mask-Aware Dynamic Filtering (MADF) module is designed to effectively learn multi-scale features for missing regions in the encoding phase. Specifically, filters for each convolution window are generated from features of the corresponding region of the mask. The second fold of mask awareness is achieved by adopting Point-wise Normalization (PN) in our decoding phase, considering that statistical natures of features at masked points differentiate from those of unmasked points. The proposed PN can tackle this issue by dynamically assigning point-wise scaling factor and bias. Lastly, our model is designed to be an end-to-end cascaded refinement one. Supervision information such as reconstruction loss, perceptual loss and total variation loss is incrementally leveraged to boost the inpainting results from coarse to fine. Effectiveness of the proposed framework is validated both quantitatively and qualitatively via extensive experiments on three public datasets including Places2, CelebA and Paris StreetView.

PMID:33945479 | DOI:10.1109/TIP.2021.3076310

Hum Vaccin Immunother. 2021 May 4:1-9. doi: 10.1080/21645515.2021.1910000. Online ahead of print.

ABSTRACT

Introduction: Rabies is an infectious zoonotic viral disease which mainly occurs in Africa and Asia. Dogs are predominantly responsible for rabies transmission contributing up to 99% of all human rabies cases. Rabies is a vaccine preventable disease in both animals and humans.Objective: This study aimed to quantify and characterize the scientific literature and identify the top most cited studies in rabies vaccine research (RVR) from 1991 to 2020.Methods: The data used in this study were downloaded from Web of Science Core Collection (WoSCC), Science Citation Index-Expanded (SCI-E) database. Network visualization analysis was performed using VOSviewer software.Results: A total of 1,042 papers (article: n = 986, 94.6%, review: n = 56, 5.4%) were included in this study. These have been cited 17,390 times with an average citation per paper was 16.69 times. The most frequent publication year was 2019 (n = 75, 7.2%). More than 55% studies were published from the United State of America (USA) (n = 380, 36.5%), France (n = 128, 12.3%), and China (n = 97, 9.3%). The most studied Web of Science (WoS) category was immunology (n = 344, 33%). The most prolific author in RVR was Rupprecht CE (n = 55, 5.3%). ‘Vaccine’ was the leading journal (n = 218, 20.9%). Rabies was the most widely used keyword.Conclusion: Abundant literature has been published on RVR in developed countries. This study might provide a reference to understand the current and future research trends in RVR. In developing countries research collaboration and co-operation among institutes and researchers needs to be strengthened with developed countries.

PMID:33945433 | DOI:10.1080/21645515.2021.1910000

Expert Rev Respir Med. 2021 May 4. doi: 10.1080/17476348.2021.1925546. Online ahead of print.

ABSTRACT

OBJECTIVES: The questions remained if mortality benefits with dexamethasone seen in patients with coronavirus disease 2019 (COVID-19) also extend to other systemic corticosteroids such as methylprednisolone. This article presents a meta-analysis of randomized controlled trials (RCTs) to ascertain if methylprednisolone can be recommended for use in patients with COVID-19 to prevent deaths.

METHODS: Systematic literature search was performed in PubMed, Scopus, Cochrane Central Register of Controlled Trials, and preprint servers until 13^th April 2021. The outcome of interest was all-cause mortality. The random-effects model for the meta-analysis was utilized to estimate the pooled odds ratio (OR) at 95% confidence intervals (CI).

RESULTS: Five RCTs were included in the meta-analysis. The pooled OR for all-cause mortality was 0.64 (95% CI: 0.29 -1.43, n=652) comparing methylprednisolone with the control, indicating no mortality benefits. A similar finding was noted with a sub-group analysis including four trials that used low-dose methylprednisolone. However, the only trial that administered high doses of methylprednisolone indicated a statistically significant mortality benefit (OR 0.08, 95% CI: 0.02-0.42).

CONCLUSIONS: A short duration (3 to 5 days) pulse therapy of high-dose methylprednisolone can be a promising alternative to the low-dose dexamethasone therapy in severely ill patients with COVID-19 to prevent deaths.

PMID:33945381 | DOI:10.1080/17476348.2021.1925546

Expert Rev Respir Med. 2021 May 4. doi: 10.1080/17476348.2021.1923482. Online ahead of print.

ABSTRACT

BACKGROUND: Different scoring systems (A2DS2, AISAPS, ISAN) have been designed to predict the risk of in-hospital stroke-associated pneumonia (SAP). Studies have assessed the accuracy of these scores for predicting SAP. We performed this meta-analysis to consolidate the evidence on the predictive accuracies for SAP of the A2DS2, AISAPS, and ISAN scores.

MATERIALS AND METHODS: We conducted a systematic search for all studies reporting the SAP predictive accuracy of A2DS2, AISAPS, or ISAN scores in the databases of PubMed Central, SCOPUS, MEDLINE, Embase, and Cochrane from inception until December 2020. We used the STATA software for the meta-analysis.

RESULTS: : We included 19 studies with 35 849 patients. The pooled score sensitivities were 78% (95% CI, 71%-83%) for A2DS2, 79% (95% CI, 77%-81%) for AISAPS, and 79% (95% CI, 77%-81%) for ISAN. The pooled score specificities were 73% (95% CI, 65%-80%) for A2DS2, 74% (95% CI, 69%-79%) for AISAPS, and 74% (95% CI, 69%-79%) for ISAN. We found significant heterogeneity for all the scoring systems based on the chi-square test results and an I² statistic > 75%. We performed meta-regression to explore the source of heterogeneity and found that patient selection (p<0.05) and reference standards (p<0.05) in the sensitivity model, index test standards (p<0.05), flow and timing of tests (p<0.01) in the specificity model, and mean age (p<0.001) in the joint model were the source of heterogeneity.

CONCLUSIONS: To summarize, we found that A2S2, AISAPS and ISAN have moderate predictive accuracy for SAP with A2S2 having a stable cut-off value.

PMID:33945394 | DOI:10.1080/17476348.2021.1923482

Hum Vaccin Immunother. 2021 May 4:1-9. doi: 10.1080/21645515.2021.1914804. Online ahead of print.

ABSTRACT

Objective: A bibliometric analysis was conducted to build an all-inclusive view of the status of research on hepatitis A virus (HAV) for facilitating researchers, health professionals, and policymakers to understand the characteristics of research output in this particular domain.Methods: A comprehensive search was conducted in the Web of Science database. The obtained data were exported into Microsoft Excel 2019, OriginPro 2018 and VOSviewer software for windows.Results: From 1985 to 2019, a total of 5,950 studies on HAV were published, with an overall h-index of 105, and 90,350 total citations. The most cited article on HAV was “Classification of chronic viral hepatitis: a need for reassessment” authored by Scheuer in the Journal of Hepatology with a total of 1,121 citations. The most cited article on HAV vaccine was “A controlled trial of a formalin-inactivated hepatitis A vaccine in healthy children” by Werzberger et al. in the New England Journal of Medicine with 401 citations. The most frequent year of publication was 2019 (n = 250). The largest number of studies were funded by the United States Department of Health Human Services (n = 199). The organization with the highest number of publications was the United States Centers for Disease Control and Prevention (n = 228). The United State of America (n = 1,500) was the country with the most publications. ‘Vaccine’ was the leading journal with 299 publications.Conclusions: The highest numbers of studies were published in developed countries. There is a clear need for interdisciplinary research approaches to evaluate and intervene in HAV endemic areas.

PMID:33945397 | DOI:10.1080/21645515.2021.1914804

J Air Waste Manag Assoc. 2021 May 4. doi: 10.1080/10962247.2021.1923586. Online ahead of print.

ABSTRACT

Light-duty gasoline vehicle (LDGV) tailpipe emission rates can be quantified based on pollutant concentrations measured using portable emission measurement systems (PEMS). Emission rates depend on exhaust flow. For simplified and micro-PEMS, exhaust flow is inferred from engine mass air flow (MAF) and air-to-fuel ratio. For many LDGVs, MAF is broadcast via the on-board diagnostic (OBD) interface. For some vehicles, only indirect indicators of MAF are broadcast. In such cases, MAF can be estimated using the speed-density method (SDM). The SDM requires an estimate of the engine volumetric efficiency (VE), which is the ratio of actual to theoretical MAF. VE is affected by intra-vehicle variability in the engine load and inter-vehicle variability in engine characteristics (e.g., the type of valvetrain). The suitability of SDM-based estimates of MAF in conjunction with simplified and micro-PEMS has not been adequately evaluated. Therefore, the objectives are to: (1) quantify VE accounting for intra- and inter-vehicle variability; and (2) evaluate the accuracy of SDM-based vehicle emission rate estimation approaches. Seventy-seven naturally-aspirated LDGVs were measured using PEMS. For each vehicle, VE was estimated using three approaches: (1) constant VE calibrated to actual fuel use; (2) average estimates of VE for Vehicle Specific Power modes imputed from OBD data; and (3) modeled VE using multilinear regression (MLR). The MLR models were developed based on engine load and engine characteristics. The best model was selected based on various statistical diagnostics. When engines were under load, variability in VE was most sensitive to variations in engine load. During idling, VE differed between engines depending on engine characteristics. The constant and modeled VE estimation approaches enable the accurate estimation of microscale and mesoscale emission rates, with errors typically within ±10% compared to values imputed from OBD data. Thus, accurate emission rates can be obtained from simplified and micro-PEMS. Implications StatementSimplified and micro portable emission measurement systems (PEMS) enable widespread measurement of vehicle exhaust emission. As a cost saving measure, they estimate exhaust flow indirectly rather than via measurement, typically based on engine mass air flow (MAF). For some vehicles, MAF is not reported by the on-board diagnostic (OBD) system but can be inferred from other reported variables and volumetric efficiency (VE). However, VE is typically proprietary. Methods demonstrated here for estimating VE enable accurate quantification of emission rates, thereby enabling use of these PEMS for policy-relevant applications such as technology assessments, trends analysis, and emissions inventories.

PMID:33945402 | DOI:10.1080/10962247.2021.1923586

Genet Test Mol Biomarkers. 2021 May 4. doi: 10.1089/gtmb.2020.0334. Online ahead of print.

ABSTRACT

Aim: The aim of this study was to explore the possible associations between single nucleotide polymorphisms (SNPs) and DNA methylation levels of seven genes in the inflammatory response pathway with susceptibility to chronic periodontitis (CP) among the Uighur population of the Xinjiang Autonomous Region of China. Methods: A total of 444 eligible subjects (279 CP patients and 165 healthy controls) were enrolled in the study. Genomic DNA was obtained from gingival tissue for genotyping eight SNPs and performing methylation measurements of seven genes. Results: SNP rs2070745 in the formyl peptide receptor 1 (FPR1) gene achieved statistical significance in the standard allelic association analysis for CP (p = 0.02). The frequency of the rs2070745 minor allele G was higher in the cases than in controls (0.367 vs. 0.291). Additionally, rs2070745 was significantly associated with CP under the dominant genetic model (p = 0.03). Using logistic regression analysis, rs2070745 was found to be consistently associated with CP under the additive dominant model, and this association remained significant after covariates were taken into account [odds ratio (OR) = 1.49 (1.09-2.05), p = 0.014; OR = 1.58 (1.04-2.40), p = 0.031, respectively]. No significant gene-gene interactions were identified. Although we did not find a polymorphism in interleukin 6 (IL6) associated with CP in our study, the methylation level of a CpG island region located within the promoter region of IL6 was significantly less in CP patients compared with controls (p < 0.05). Conclusions: The genetic polymorphism rs2070745 in FPR1 and the methylation level of the promoter region of IL6 might be associated with CP in the Uighur population of China.

PMID:33945309 | DOI:10.1089/gtmb.2020.0334