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The British Journal of Surgery May 2024Clinical auditing is a powerful tool to evaluate and improve healthcare. Deviations from the expected quality of care are identified by benchmarking the results of...
BACKGROUND
Clinical auditing is a powerful tool to evaluate and improve healthcare. Deviations from the expected quality of care are identified by benchmarking the results of individual hospitals using national averages. This study aimed to evaluate the use of quality indicators for benchmarking hepato-pancreato-biliary (HPB) surgery and when outlier hospitals could be identified.
METHODS
A population-based study used data from two nationwide Dutch HPB audits (DHBA and DPCA) from 2014 to 2021. Sample size calculations determined the threshold (in percentage points) to identify centres as statistical outliers, based on current volume requirements (annual minimum of 20 resections) on a two-year period (2020-2021), covering mortality rate, failure to rescue (FTR), major morbidity rate and textbook/ideal outcome (TO) for minor liver resection (LR), major LR, pancreaticoduodenectomy (PD) and distal pancreatectomy (DP).
RESULTS
In total, 10 963 and 7365 patients who underwent liver and pancreatic resection respectively were included. Benchmark and corresponding range of mortality rates were 0.6% (0 -3.2%) and 3.3% (0-16.7%) for minor and major LR, and 2.7% (0-7.0%) and 0.6% (0-4.2%) for PD and DP respectively. FTR rates were 5.4% (0-33.3%), 14.2% (0-100%), 7.5% (1.6%-28.5%) and 3.1% (0-14.9%). For major morbidity rate, corresponding rates were 9.8% (0-20.5%), 28.1% (0-47.1%), 36% (15.8%-58.3%) and 22.3% (5.2%-46.1%). For TO, corresponding rates were 73.6% (61.3%-94.4%), 54.1% (35.3-100), 46.8% (25.3%-59.4%) and 63.3% (30.7%-84.6%). Mortality rate thresholds indicating a significant outlier were 8.6% and 15.4% for minor and major LR and 14.2% and 8.6% for PD and DP. For FTR, these thresholds were 17.9%, 31.6%, 22.9% and 15.0%. For major morbidity rate, these thresholds were 26.1%, 49.7%, 57.9% and 52.9% respectively. For TO, lower thresholds were 52.5%, 32.5%, 25.8% and 41.4% respectively. Higher hospital volumes decrease thresholds to detect outliers.
CONCLUSION
Current event rates and minimum volume requirements per hospital are too low to detect any meaningful between hospital differences in mortality rate and FTR. Major morbidity rate and TO are better candidates to use for benchmarking.
Topics: Humans; Benchmarking; Quality Indicators, Health Care; Netherlands; Pancreatectomy; Male; Pancreaticoduodenectomy; Hepatectomy; Female; Middle Aged; Aged; Hospital Mortality
PubMed: 38747683
DOI: 10.1093/bjs/znae119 -
Frontiers in Immunology 2023Previous studies have shown a coexistence phenomenon between systemic lupus erythematosus (SLE) and inflammatory bowel disease (IBD), but the causal relationship between...
BACKGROUND
Previous studies have shown a coexistence phenomenon between systemic lupus erythematosus (SLE) and inflammatory bowel disease (IBD), but the causal relationship between them is still unclear. Therefore, we conducted a two-sample Mendelian randomization (MR) analysis using publicly available summary statistics data to evaluate whether there was a causal relationship between the two diseases.
METHODS
Summary statistics for SLE and IBD were downloaded from the Open Genome-Wide Association Study and the International Inflammatory Bowel Disease Genetics Consortium. European and East Asian populations were included in this MR work. We adopted a series of methods to select instrumental variables that are closely related to SLE and IBD. To make the conclusion more reliable, we applied a variety of different analysis methods, among which the inverse variance-weighted (IVW) method was the main method. In addition, heterogeneity, pleiotropy, and sensitivity were assessed to make the conclusions more convincing.
RESULTS
In the European population, a negative causal relationship was observed between SLE and overall IBD (OR = 0.94; 95% CI = 0.90, 0.98; P < 0.004) and ulcerative colitis (UC) (OR = 0.93; 95% CI = 0.88, 0.98; P = 0.006). After removing outliers with Mendelian Randomization Pleiotropy RESidual Sum and Outlier (MR-PRESSO), the results remained consistent with IVW. However, there was no causal relationship between SLE and Crohn's disease. In the East Asian population, no causal relationship was found between SLE and IBD.
CONCLUSION
Our results found that genetic susceptibility to SLE was associated with lower overall IBD risk and UC risk in European populations. In contrast, no association between SLE and IBD was found in East Asian populations. This work might enrich the previous research results, and it may provide some references for research in the future.
Topics: Humans; Colitis, Ulcerative; East Asian People; Genome-Wide Association Study; Inflammatory Bowel Diseases; Lupus Erythematosus, Systemic; Mendelian Randomization Analysis; European People
PubMed: 38022503
DOI: 10.3389/fimmu.2023.1199896 -
Scientific Reports Oct 20233D reconstruction is the process of obtaining the three-dimensional shape or surface structure of an object, which is widely used in advanced manufacturing fields such...
3D reconstruction is the process of obtaining the three-dimensional shape or surface structure of an object, which is widely used in advanced manufacturing fields such as automotive, aerospace, industrial inspection, and reverse engineering. However, due to the structural characteristics of the component itself, the reflective properties of the coating material, and other factors, there may be specular reflection during image acquisition, making it difficult to achieve complete 3D reconstruction of the component. This paper proposes a method to address the problem of incomplete 3D reconstruction of strongly reflective objects by recognizing outlier points and filling point cloud holes. The proposed View-Transform-PointNet outlier point recognition network improves the alignment of the initial point cloud plane and implements secondary alignment of the point cloud based on the perpendicularity between the outlier plane in mixed reflection and the point cloud plane. The point cloud hole-filling method is based on the principle of outlier formation and approximates a local Gaussian distribution to linear variation. The distance between the end of each outlier plane and the real surface is calculated to repair the depth information of outlier points. The proposed method achieves a 39.4% increase in the number of point cloud filling, a 45.2% increase in the number of triangular mesh faces, a 46.9% increase in surface area, and a chamfer distance (CD) of 0.4471009, which is better than existing geometric repair methods in terms of standard deviation and smoothness. The method improves the alignment of initial point cloud planes and enhances the accuracy of outlier point recognition, which are the main innovative points of this study. The 3D reconstruction of the repaired point cloud model is achieved through Poisson equation and parameter adjustment. The proposed method reduces the error caused by large curvature in the boundary region and improves the smoothness and accuracy of the reconstructed model.
PubMed: 37898706
DOI: 10.1038/s41598-023-45648-5 -
Frontiers in Neuroscience 2023Numerous studies have suggested a connection between circadian rhythm and neurological disorders with cognitive and consciousness impairments in humans, yet little...
INTRODUCTION
Numerous studies have suggested a connection between circadian rhythm and neurological disorders with cognitive and consciousness impairments in humans, yet little evidence stands for a causal relationship between circadian rhythm and the brain cortex.
METHODS
The top 10,000 morningness-related single-nucleotide polymorphisms of the Genome-wide association study (GWAS) summary statistics were used to filter the instrumental variables. GWAS summary statistics from the ENIGMA Consortium were used to assess the causal relationship between morningness and variates like cortical thickness (TH) or surficial area (SA) on the brain cortex. The inverse-variance weighted (IVW) and weighted median (WM) were used as the major estimates whereas MR-Egger, MR Pleiotropy RESidual Sum and Outlier, leave-one-out analysis, and funnel-plot were used for heterogeneity and pleiotropy detecting.
RESULTS
Regionally, morningness decreased SA of the rostral middle frontal gyrus with genomic control (IVW: β = -24.916 mm, 95% CI: -47.342 mm to -2.490 mm, = 0.029. WM: β = -33.208 mm, 95% CI: -61.933 mm to -4.483 mm, = 0.023. MR Egger: β < 0) and without genomic control (IVW: β = -24.581 mm, 95% CI: -47.552 mm to -1.609 mm, = 0.036. WM: β = -32.310 mm, 95% CI: -60.717 mm to -3.902 mm, = 0.026. MR Egger: β < 0) on a nominal significance, with no heterogeneity or no outliers.
CONCLUSIONS AND IMPLICATIONS
Circadian rhythm causally affects the rostral middle frontal gyrus; this sheds new light on the potential use of MRI in disease diagnosis, revealing the significance of circadian rhythm on the progression of disease, and might also suggest a fresh therapeutic approach for disorders related to the rostral middle frontal gyrus-related.
PubMed: 37547136
DOI: 10.3389/fnins.2023.1222551 -
Heliyon Nov 2023Researchers have investigated the causal effect between serum uric acid (SUA) concentrations and kidney function for decades, but studies produced inconsistent results....
INTRODUCTION
Researchers have investigated the causal effect between serum uric acid (SUA) concentrations and kidney function for decades, but studies produced inconsistent results. This study aimed to clarify the bidirectional causal effects between SUA concentrations and kidney function and to explore the potential ethnic disparities by conducting a -ethnic Mendelian randomization study in European, African, and Asian ancestries.
MATERIALS AND METHODS
The summary-level data for this study were obtained from the Global Urate Genetics Consortium, CKDGen Consortium, UK Biobank, and Japan Biobank for different outcomes and exposures, respectively. The traits of kidney function were estimated glomerular filtration rate from serum creatinine (eGFRcr), estimated glomerular filtration rate from cystatin C (eGFRcys), and blood urea nitrogen (BUN). Using the multiplicative random-effects inverse variance weighting mode, our primary analysis produced robust results despite heterogeneity. Additionally, we performed the Mendelian randomization pleiotropy residual sum and outlier test to eliminate the horizontal pleiotropy and obtain accurate results.
RESULTS
Our findings revealed that elevated SUA concentrations had causal effects on declined eGFRcys, BUN, and a diagnosis of chronic kidney disease in European ancestries and eGFRcr in Asian ancestries. Additionally, the causal effects of declined eGFRcr and elevated BUN concentrations on elevated SUA concentrations were observed in both European and Asian ancestries. However, no bidirectional causal effect was found between SUA concentrations and eGFRcr among African ancestries.
CONCLUSIONS
This -ethnic Mendelian randomization study confirmed the bidirectional causal effects between SUA concentrations and kidney function and highlighted the importance of considering ethnic disparities in clinical treatments.
PubMed: 37908715
DOI: 10.1016/j.heliyon.2023.e21108 -
Clinical and Experimental Hypertension... Dec 2024Preeclampsia/eclampsia is a severe pregnancy-related disorder associated with hypertension and organ damage. While observational studies have suggested a link between...
BACKGROUND
Preeclampsia/eclampsia is a severe pregnancy-related disorder associated with hypertension and organ damage. While observational studies have suggested a link between maternal iron status and preeclampsia/eclampsia, the causal relationship remains unclear. The aim of this study was to investigate the genetic causality between iron status and preeclampsia/eclampsia using large-scale genome-wide association study (GWAS) summary data and Mendelian randomization (MR) analysis.
METHODS
Summary data for the GWAS on preeclampsia/eclampsia and genetic markers related to iron status were obtained from the FinnGen Consortium and the IEU genetic databases. The "TwoSampleMR" software package in R was employed to test the genetic causality between these markers and preeclampsia/eclampsia. The inverse variance weighted (IVW) method was primarily used for MR analysis. Heterogeneity, horizontal pleiotropy, and potential outliers were evaluated for the MR analysis results.
RESULTS
The random-effects IVW results showed that ferritin (OR = 1.11, 95% CI: .89-1.38, = .341), serum iron (OR = .90, 95% CI: .75-1.09, = .275), TIBC (OR = .98, 95% CI: .89-1.07, = .613), and TSAT (OR = .94, 95% CI: .83-1.07, = .354) have no genetic causal relationship with preeclampsia/eclampsia. There was no evidence of heterogeneity, horizontal pleiotropy, or possible outliers in our MR analysis ( > .05).
CONCLUSIONS
Our study did not detect a genetic causal relationship between iron status and preeclampsia/eclampsia. Nonetheless, this does not rule out a relationship between the two at other mechanistic levels.
Topics: Female; Humans; Pregnancy; Eclampsia; Genome-Wide Association Study; Iron; Mendelian Randomization Analysis; Pre-Eclampsia
PubMed: 38471132
DOI: 10.1080/10641963.2024.2321148 -
Journal of Medical Internet Research Jul 2023Reference intervals (RIs) play an important role in clinical decision-making. However, due to the time, labor, and financial costs involved in establishing RIs using... (Observational Study)
Observational Study
BACKGROUND
Reference intervals (RIs) play an important role in clinical decision-making. However, due to the time, labor, and financial costs involved in establishing RIs using direct means, the use of indirect methods, based on big data previously obtained from clinical laboratories, is getting increasing attention. Different indirect techniques combined with different data transformation methods and outlier removal might cause differences in the calculation of RIs. However, there are few systematic evaluations of this.
OBJECTIVE
This study used data derived from direct methods as reference standards and evaluated the accuracy of combinations of different data transformation, outlier removal, and indirect techniques in establishing complete blood count (CBC) RIs for large-scale data.
METHODS
The CBC data of populations aged ≥18 years undergoing physical examination from January 2010 to December 2011 were retrieved from the First Affiliated Hospital of China Medical University in northern China. After exclusion of repeated individuals, we performed parametric, nonparametric, Hoffmann, Bhattacharya, and truncation points and Kolmogorov-Smirnov distance (kosmic) indirect methods, combined with log or BoxCox transformation, and Reed-Dixon, Tukey, and iterative mean (3SD) outlier removal methods in order to derive the RIs of 8 CBC parameters and compared the results with those directly and previously established. Furthermore, bias ratios (BRs) were calculated to assess which combination of indirect technique, data transformation pattern, and outlier removal method is preferrable.
RESULTS
Raw data showed that the degrees of skewness of the white blood cell (WBC) count, platelet (PLT) count, mean corpuscular hemoglobin (MCH), mean corpuscular hemoglobin concentration (MCHC), and mean corpuscular volume (MCV) were much more obvious than those of other CBC parameters. After log or BoxCox transformation combined with Tukey or iterative mean (3SD) processing, the distribution types of these data were close to Gaussian distribution. Tukey-based outlier removal yielded the maximum number of outliers. The lower-limit bias of WBC (male), PLT (male), hemoglobin (HGB; male), MCH (male/female), and MCV (female) was greater than that of the corresponding upper limit for more than half of 30 indirect methods. Computational indirect choices of CBC parameters for males and females were inconsistent. The RIs of MCHC established by the direct method for females were narrow. For this, the kosmic method was markedly superior, which contrasted with the RI calculation of CBC parameters with high |BR| qualification rates for males. Among the top 10 methodologies for the WBC count, PLT count, HGB, MCV, and MCHC with a high-BR qualification rate among males, the Bhattacharya, Hoffmann, and parametric methods were superior to the other 2 indirect methods.
CONCLUSIONS
Compared to results derived by the direct method, outlier removal methods and indirect techniques markedly influence the final RIs, whereas data transformation has negligible effects, except for obviously skewed data. Specifically, the outlier removal efficiency of Tukey and iterative mean (3SD) methods is almost equivalent. Furthermore, the choice of indirect techniques depends more on the characteristics of the studied analyte itself. This study provides scientific evidence for clinical laboratories to use their previous data sets to establish RIs.
Topics: Adolescent; Adult; Female; Humans; Male; Big Data; Blood Cell Count; China; Leukocyte Count; Reference Values; Clinical Decision-Making
PubMed: 37459170
DOI: 10.2196/45651 -
Entropy (Basel, Switzerland) Nov 2023Persistent homology is a natural tool for probing the topological characteristics of weighted graphs, essentially focusing on their 0-dimensional homology. While this...
Persistent homology is a natural tool for probing the topological characteristics of weighted graphs, essentially focusing on their 0-dimensional homology. While this area has been thoroughly studied, we present a new approach to constructing a filtration for cluster analysis via persistent homology. The key advantages of the new filtration is that (a) it provides richer signatures for connected components by introducing non-trivial birth times, and (b) it is robust to outliers. The key idea is that nodes are ignored until they belong to sufficiently large clusters. We demonstrate the computational efficiency of our filtration, its practical effectiveness, and explore into its properties when applied to random graphs.
PubMed: 38136467
DOI: 10.3390/e25121587 -
Genes & Diseases May 2024Metabolomics as a research field and a set of techniques is to study the entire small molecules in biological samples. Metabolomics is emerging as a powerful tool... (Review)
Review
Metabolomics as a research field and a set of techniques is to study the entire small molecules in biological samples. Metabolomics is emerging as a powerful tool generally for precision medicine. Particularly, integration of microbiome and metabolome has revealed the mechanism and functionality of microbiome in human health and disease. However, metabolomics data are very complicated. Preprocessing/pretreating and normalizing procedures on metabolomics data are usually required before statistical analysis. In this review article, we comprehensively review various methods that are used to preprocess and pretreat metabolomics data, including MS-based data and NMR -based data preprocessing, dealing with zero and/or missing values and detecting outliers, data normalization, data centering and scaling, data transformation. We discuss the advantages and limitations of each method. The choice for a suitable preprocessing method is determined by the biological hypothesis, the characteristics of the data set, and the selected statistical data analysis method. We then provide the perspective of their applications in the microbiome and metabolome research.
PubMed: 38299197
DOI: 10.1016/j.gendis.2023.04.018 -
Frontiers in Microbiology 2024Increasing evidence indicates that gut microbiota dysbiosis is related to synovitis and tenosynovitis. Nonetheless, whether these associations are causal is currently...
BACKGROUND
Increasing evidence indicates that gut microbiota dysbiosis is related to synovitis and tenosynovitis. Nonetheless, whether these associations are causal is currently unknown.
OBJECTIVES
A two-sample Mendelian randomization (MR) study was performed to reveal the causality of gut microbiota with synovitis and tenosynovitis.
METHODS
The summary statistical data from a large-scale genome-wide association study (GWAS) were applied as the basis for a two-sample MR analysis. The causal effect was estimated using inverse variance weighted (IVW), weighted median, simple mode, MR-Egger, and weighted mode methods, of which IVW was the important method. Meanwhile, the pleiotropy and heterogeneity were detected and measured using MR-Egger regression, Cochran's Q statistics, funnel plots, and MR pleiotropy residual sum and outlier (MR-PRESSO) methods.
RESULTS
The IVW technique demonstrated that genetically predicted five genera, namely [odds ratio (OR) = 0.999, 95% confidence interval (CI): (0.9977, 0.9998), = 0.019], [OR = 0.999, 95% CI: (0.9971, 0.9999), = 0.036], [OR = 0.998, 95% CI: (0.9954, 0.9999), = 0.041], [OR = 0.997, 95% CI: (0.9955, 0.9994), = 0.011], and [OR = 0.997, 95% CI: (0.9954, 0.9992), = 0.006] were negatively correlated with the risk of synovitis and tenosynovitis, while two other genera, namely [OR = 1.003, 95% CI: (1.0004, 1.0049), = 0.019] and [OR = 1.003, 95% CI: (1.0002, 1.0052), = 0.035] were positively associated with synovitis and tenosynovitis risk. In addition, the data of sensitivity analyses demonstrated that there were no outliers, horizontal pleiotropy, or heterogeneity in the causal relationship of the above-mentioned gut microbiota on synovitis and tenosynovitis ( > 0.05).
CONCLUSION
The results of the study suggested that the gut microbiota was causally involved in synovitis and tenosynovitis and identified specific bacterial taxa that affect synovitis and tenosynovitis, which provide new insights into the pathogenesis underlying the development of synovitis and tenosynovitis mediated by gut microbiota.
PubMed: 38746746
DOI: 10.3389/fmicb.2024.1355725