Statistical methods for dealing with publication bias in meta-analysis.

Publication bias is an inevitable problem in the systematic review and meta-analysis. It is also one of the main threats to the validity of meta-analysis. Although several statistical methods have been developed to detect and adjust for the publication bias since the beginning of 1980s, some of them are not well known and are not being used properly in both the statistical and clinical literature. In this paper, we provided a critical and extensive discussion on the methods for dealing with publication bias, including statistical principles, implementation, and software, as well as the advantages and limitations of these methods. We illustrated a practical application of these methods in a meta-analysis of continuous support for women during childbirth.

Commensal bacteria-dependent select expression of CXCL2 contributes to periodontal tissue homeostasis.

The oral and intestinal host tissues both carry a heavy microbial burden. Although commensal bacteria contribute to healthy intestinal tissue structure and function, their contribution to oral health is poorly understood. A crucial component of periodontal health is the recruitment of neutrophils to periodontal tissue. To elucidate this process, gingival tissues of specific-pathogen-free and germ-free wild-type mice and CXCR2KO and MyD88KO mice were examined for quantitative analysis of neutrophils and CXCR2 chemoattractants (CXCL1, CXCL2). We show that the recruitment of neutrophils to the gingival tissue does not require commensal bacterial colonization but is entirely dependent on CXCR2 expression. Strikingly, however, commensal bacteria selectively upregulate the expression of CXCL2, but not CXCL1, in a MyD88-dependent way that correlates with increased neutrophil recruitment as compared with germ-free conditions. This is the first evidence that the selective use of chemokine receptor ligands contributes to neutrophil homing to healthy periodontal tissue.

A modified regression method to test publication bias in meta-analyses with binary outcomes.

BACKGROUND: The tendency towards publication bias is greater for observational studies than for randomized clinical trials. Several statistical methods have been developed to test the publication bias. However, almost all existing methods exhibit rather low power or have inappropriate type I error rates. METHODS: We propose a modified regression method, which used a smoothed variance to estimate the precision of a study, to test for publication bias in meta-analyses of observational studies. A comprehensive simulation study is carried out, and a real-world example is considered. RESULTS: The simulation results indicate that the performance of tests varies with the number of included studies, level of heterogeneity, event rates, and sample size ratio between two groups. Neither the existing tests nor the newly developed method is particularly powerful in all simulation scenarios. However, our proposed method has a more robust performance across different settings. In the presence of heterogeneity, the arcsine-Thompson test is a suitable alternative, and Peters' test can be considered as a complementary method when mild or no heterogeneity is present. CONCLUSIONS: Several factors should be taken into consideration when employing asymmetry tests for publication bias. Based on our simulation results, we provide a concise table to show the appropriate use of regression methods to test for publication bias based on our simulation results.

Association of biopsy core number and location with pain in patients undergoing a transperineal prostate biopsy under local anaesthesia: a secondary analysis of the APROPOS trial.

BACKGROUND: APROPOS was a multicentre, randomized, blinded trial focus on investigating the perineal nerve block versus the periprostatic block in pain control for men undergoing a transperineal prostate biopsy. In the analysis reported here, the authors aimed to evaluate the association of biopsy core count and location with pain outcomes in patients undergoing a transperineal prostate biopsy under local anesthesia. METHODS: APROPOS was performed at six medical centers in China. Patients with suspected prostate cancer were randomized to receive either a perineal nerve block or a periprostatic block (1:1), followed by a transperineal prostate biopsy. The secondary analysis outcomes were the worst pain experienced during the prostate biopsy and postbiopsy pain at 1,6, and 24 h. RESULTS: Between 12 August 2020 and 20 July 2022, a total of 192 patients were randomized in the original trial, and 188 were involved in this analysis, with 94 patients per group. Participants had a median (IQR) age of 68 (63-72) and a median (IQR) prostate volume of 42.51 (30.04-62.84). The patient population had a median (IQR) number of biopsy cores of 15 (12-17.50), and 26.06% of patients had a biopsy cores count of more than 15. After adjusting the baseline characteristics, the number of biopsy cores was associated with the worst pain during the biopsy procedure in both the perineal nerve block group ( ß 0.19, 95% CI: 0.12-0.26, P <0.001) and the periprostatic block group ( ß 0.16, 95% CI: 0.07-0.24, P <0.001). A similar association was also evident for the postbiopsy pain at 1, 6, and 24 h. A lesser degree of pain in both groups at any time (r range -0.57 to -0.01 for both groups) was associated with biopsy cores from the peripheral zone of the middle gland, while other locations were associated with a higher degree of pain. In addition, the location of the biopsy core had less of an effect on pain during the biopsy (r range -0.01-0.25 for both groups) than it did on postbiopsy pain (r range -0.57-0.60 for both groups). CONCLUSIONS: In this secondary analysis of a randomized trial, biopsy core count and location were associated with pain in patients undergoing a transperineal prostate biopsy under local anesthesia. These results may be helpful for making clinical decisions about the anesthetic approach for scheduled transperineal prostate biopsies.

Perineal nerve block versus periprostatic block for patients undergoing transperineal prostate biopsy (APROPOS): a prospective, multicentre, randomised controlled study.

Background: We aimed to investigate perineal nerve block versus periprostatic block in pain control for men undergoing a transperineal prostate biopsy. Methods: In this prospective, randomised, blinded and parallel-group trial, men in six Chinese hospitals with suspected prostate cancer were randomly assigned (1:1) at the point of local anaesthesia to receive a perineal nerve block or periprostatic block and followed by a transperineal prostate biopsy. Centres used their usual biopsy procedure. Operators who performed anaesthesia were trained in both techniques before the trial and were masked to the randomised allocation until the time of anaesthesia and were not involved in the subsequent biopsy procedure and any assessment or analysis. Other investigators and the patients were masked until trial completion. The primary outcome was the level of the worst pain experienced during the prostate biopsy procedure. Secondary outcomes included pain (post-biopsy at 1, 6 and 24 h), changes in blood pressure, heart rate and breathing rate during the biopsy procedure, external manifestations of pain during biopsy, anaesthesia satisfaction, the detection rate of PCa and clinically significant PCa. This trial is registered on ClinicalTrials.gov, NCT04501055. Findings: Between August 13, 2020, and July 20, 2022, 192 men were randomly assigned to perineal nerve block or periprostatic block, 96 per study group. Perineal nerve block was superior for the relief of pain during the biopsy procedure (mean 2.80 for perineal nerve block and 3.98 for periprostatic block; adjusted difference in means -1.17, P < 0.001). Although the perineal nerve block had a lower mean pain score at 1 h post-biopsy compared with the periprostatic block (0.23 vs 0.43, P = 0.042), they were equivalent at 6 h (0.16 vs 0.25, P = 0.389) and 24 h (0.10 vs 0.26, P = 0.184) respectively. For the change in vital signs during biopsy procedure, perineal nerve block was significantly superior to periprostatic block in terms of maximum value of systolic blood pressure, maximum value of mean arterial pressure and maximum value of heart rate. There are no statistical differences in average value of systolic blood pressure, average value of mean, average value of heart rate, diastolic blood pressure and breathing rate. Perineal nerve block was also superior to periprostatic block in external manifestations of pain (1.88 vs 3.00, P < 0.001) and anaesthesia satisfaction (8.93 vs 11.90, P < 0.001). Equivalence was shown for the detection rate of PCa (31.25% for perineal nerve block and 29.17% for periprostatic block, P = 0.753) or csPCa (23.96% for perineal nerve block and 20.83% for periprostatic block, P = 0.604). 33 (34.8%) of 96 patients in the perineal nerve block group and 40 (41.67%) of 96 patients in the periprostatic block group had at least one complication. Interpretation: Perineal nerve block was superior to periprostatic block in pain control for men undergoing a transperineal prostate biopsy. Funding: Grant 2019YFC0119100 from the National Key Research and Development Program of China.

Calcium channel blockers improve prognosis of patients with coronavirus disease 2019 and hypertension.

BACKGROUND: Hypertension is considered an important risk factor for the coronavirus disease 2019 (COVID-19). The commonly anti-hypertensive drugs are the renin-angiotensin-aldosterone system (RAAS) inhibitors, calcium channel blockers (CCBs), and beta-blockers. The association between commonly used anti-hypertensive medications and the clinical outcome of COVID-19 patients with hypertension has not been well studied. METHODS: We conducted a retrospective cohort study that included all patients admitted with COVID-19 to Huo Shen Shan Hospital and Guanggu District of the Maternal and Child Health Hospital of Hubei Province, Wuhan, China. Clinical and laboratory characteristics were extracted from electronic medical records. Hypertension and anti-hypertensive treatment were confirmed by medical history and clinical records. The primary clinical endpoint was all-cause mortality. Secondary endpoints included the rates of patients in common wards transferred to the intensive care unit and hospital stay duration. Logistic regression was used to explore the risk factors associated with mortality and prognosis. Propensity score matching was used to balance the confounders between different anti-hypertensive treatments. Kaplan-Meier curves were used to compare the cumulative recovery rate. Log-rank tests were performed to test for differences in Kaplan-Meier curves between different groups. RESULTS: Among 4569 hospitalized patients with COVID-19, 31.7% (1449/4569) had a history of hypertension. There were significant differences in mortality rates between hypertensive patients with CCBs (7/359) and those without (21/359) (1.95% vs. 5.85%, risk ratio [RR]: 0.32, 95% confidence interval [CI]: 0.13-0.76, χ2 = 7.61, P = 0.0058). After matching for confounders, the mortality rates were similar between the RAAS inhibitor (4/236) and non-RAAS inhibitor (9/236) cohorts (1.69% vs. 3.81%, RR: 0.43, 95% CI: 0.13-1.43, χ2 = 1.98, P = 0.1596). Hypertensive patients with beta-blockers (13/340) showed no statistical difference in mortality compared with those without (11/340) (3.82% vs. 3.24%, RR: 1.19, 95% CI: 0.53-2.69, χ2 = 0.17, P = 0.6777). CONCLUSIONS: In our study, we did not find any positive or negative effects of RAAS inhibitors or beta-blockers in COVID-19 patients with hypertension, while CCBs could improve prognosis.

Improving discrimination of outer membrane proteins by fusing different forms of pseudo amino acid composition.

Integral membrane proteins are central to many cellular processes and constitute approximately 50% of potential targets for novel drugs. However, the number of outer membrane proteins (OMPs) present in the public structure database is very limited due to the difficulties in determining structure with experimental methods. Therefore, discriminating OMPs from non-OMPs with computational methods is of medical importance as well as genome sequencing necessity. In this study, some sequence-derived structural and physicochemical features of proteins were incorporated with amino acid composition to discriminate OMPs from non-OMPs using support vector machines. The discrimination performance of the proposed method is evaluated on a benchmark dataset of 208 OMPs, 673 globular proteins, and 206 alpha-helical membrane proteins. A high overall accuracy of 97.8% was observed in the 5-fold cross-validation test. In addition, the current method distinguished OMPs from globular proteins and alpha-helical membrane proteins with overall accuracies of 98.2 and 96.4%, respectively. The prediction performance is superior to the state-of-the-art methods in the literature. It is anticipated that the current method might be a powerful tool for the discrimination of OMPs.

Prediction of nuclear receptors with optimal pseudo amino acid composition.

Nuclear receptors are involved in multiple cellular signaling pathways that affect and regulate processes such as organ development and maintenance, ion transport, homeostasis, and apoptosis. In this article, an optimal pseudo amino acid composition based on physicochemical characters of amino acids is suggested to represent proteins for predicting the subfamilies of nuclear receptors. Six physicochemical characters of amino acids were adopted to generate the protein sequence features via web server PseAAC. The optimal values of the rank of correlation factor and the weighting factor about PseAAC were determined to get the appropriate descriptor of proteins that leads to the best performance. A nonredundant dataset of nuclear receptors in four subfamilies is constructed to evaluate the method using support vector machines. An overall accuracy of 99.6% was achieved in the fivefold cross-validation test as well as the jackknife test, and an overall accuracy of 98.4% was reached in a blind dataset test. The performance is very competitive with that of some previous methods.

EZ-Entry: a clinical data management system.

In this paper, a new data management system named EZ-Entry is introduced. Five major functions are enclosed in this system: (1) user authentication; (2) database construction; (3) double data entry with instant alignment; (4) revision tracking; (5) query management. The practical application performed on two clinical trials indicates that EZ-Entry meets the requirements of clinical data management with high efficiency and security. This software is freely available on request from the authors for academic purposes.

[Research progress on induced membrane technique for the treatment of segmental bone defect].

Treatment of large bone defects caused by trauma, osteomyelitis, and tumors has been a major challenge in clinical. In the past, there have been many ways to repair and reconstruct the large bone defects. However, there is a long period of treatment, high technical requirement and complications such as ununion. After Masquelet reported the induced membrane technology in 2000, the technique was widely used in treatment of trauma, osteomyelitis, and large bone defects caused by tumors. It has been obtained good results. It has the advantages of short course, high healing rate, easy operation and easy to master. The induced membrane has unique structural characteristics and biological characteristics. There are many kinds of osteogenic factors that are included in the membrane, such as vascular endothelial growth factor, and morphogenetic protein-2, transforming growth factor-ß1, etc. These osteogenic factors contribute to accelerate bone healing. With the development of induced membrane technology. The technology of Reamer Irrigator Aspirator technology, engineering tissue technology and internal fixation is used in clinic.It can provide bone source, promote bone defect reconstruction, improve long-term limb function and reduce complications.This paper retrospectively summarizes the experimental research and clinical progress of Masquelet technique in the treatment of large bone defects.

Steroids in the treatment of IgA nephropathy to the improvement of renal survival: a systematic review and meta-analysis.

BACKGROUND: Studies have shown that steroids can improve kidney survival and decrease the risk of proteinuria in patients with Immunoglobulin A nephropathy, but the overall benefit of steroids in the treatment of Immunoglobulin A nephropathy remains controversial. The aim of this study was to evaluate the benefits and risks of steroids for renal survival in adults with Immunoglobulin A nephropathy. METHODOLOGY AND PRINCIPAL FINDINGS: We searched the Cochrane Renal Group Specialized Register, Cochrane Controlled Trial Registry, MEDLINE and EMBASE databases. All eligible studies were measuring at least one of the following outcomes: end-stage renal failure, doubling of serum creatinine and urinary protein excretion. Fifteen relevant trials (n = 1542) that met our inclusion criteria were identified. In a pooled analysis, steroid therapy was associated with statistically significant reduction of the risk in end-stage renal failure (RR: 0.46, 95% CI: 0.27 to 0.79), doubling of serum creatinine (RR = 0.34, 95%CI = 0.15 to 0.77) and reduced urinary protein excretion (MD = -0.47 g/day, 95%CI = -0.64 to -0.31). CONCLUSIONS/SIGNIFICANCE: We identified that steroid therapy was associated with a decrease of proteinuria and with a statistically significant reduction of the risk in end-stage renal failure. Moreover, subgroup analysis also suggested that long-term steroid therapy had a higher efficiency than standard and short term therapy.

Improving the classification of nuclear receptors with feature selection.

Nuclear receptors are involved in multiple cellular signaling pathways that affect and regulate processes. Because of their physiology and pathophysiology significance, classification of nuclear receptors is essential for the proper understanding of their functions. Bhasin and Raghava have shown that the subfamilies of nuclear receptors are closely correlated with their amino acid composition and dipeptide composition [29]. They characterized each protein by a 400 dimensional feature vector. However, using high dimensional feature vectors for characterization of protein sequences will increase the computational cost as well as the risk of overfitting. Therefore, using only those features that are most relevant to the present task might improve the prediction system, and might also provide us with some biologically useful knowledge. In this paper a feature selection approach was proposed to identify relevant features and a prediction engine of support vector machines was developed to estimate the prediction accuracy of classification using the selected features. A reduced subset containing 30 features was accepted to characterize the protein sequences in view of its good discriminative power towards the classes, in which 18 are of amino acid composition and 12 are of dipeptide composition. This reduced feature subset resulted in an overall accuracy of 98.9% in a 5-fold cross-validation test, higher than 88.7% of amino acid composition based method and almost as high as 99.3% of dipeptide composition based method. Moreover, an overall accuracy of 93.7% was reached when it was evaluated on a blind data set of 63 nuclear receptors. On the other hand, an overall accuracy of 96.1% and 95.2% based on the reduced 12 dipeptide compositions was observed simultaneously in the 5-fold cross-validation test and the blind data set test, respectively. These results demonstrate the effectiveness of the present method.