Mediation analysis in longitudinal study with high-dimensional methylation mediators.

Mediation analysis has been widely utilized to identify potential pathways connecting exposures and outcomes. However, there remains a lack of analytical methods for high-dimensional mediation analysis in longitudinal data. To tackle this concern, we proposed an effective and novel approach with variable selection and the indirect effect (IE) assessment based on both linear mixed-effect model and generalized estimating equation. Initially, we employ sure independence screening to reduce the dimension of candidate mediators. Subsequently, we implement the Sobel test with the Bonferroni correction for IE hypothesis testing. Through extensive simulation studies, we demonstrate the performance of our proposed procedure with a higher F$_{1}$ score (0.8056 and 0.9983 at sample sizes of 150 and 500, respectively) compared with the linear method (0.7779 and 0.9642 at the same sample sizes), along with more accurate parameter estimation and a significantly lower false discovery rate. Moreover, we apply our methodology to explore the mediation mechanisms involving over 730 000 DNA methylation sites with potential effects between the paternal body mass index (BMI) and offspring growing BMI in the Shanghai sleeping birth cohort data, leading to the identification of two previously undiscovered mediating CpG sites.

A novel mRNA multi-epitope vaccine of Acinetobacter baumannii based on multi-target protein design in immunoinformatic approach.

Acinetobacter baumannii is a gram-negative bacillus prevalent in nature, capable of thriving under various environmental conditions. As an opportunistic pathogen, it frequently causes nosocomial infections such as urinary tract infections, bacteremia, and pneumonia, contributing to increased morbidity and mortality in clinical settings. Consequently, developing novel vaccines against Acinetobacter baumannii is of utmost importance. In our study, we identified 10 highly conserved antigenic proteins from the NCBI and UniProt databases for epitope mapping. We subsequently screened and selected 8 CTL, HTL, and LBL epitopes, integrating them into three distinct vaccines constructed with adjuvants. Following comprehensive evaluations of immunological and physicochemical parameters, we conducted molecular docking and molecular dynamics simulations to assess the efficacy and stability of these vaccines. Our findings indicate that all three multi-epitope mRNA vaccines designed against Acinetobacter baumannii are promising; however, further animal studies are required to confirm their reliability and effectiveness.

Genome-wide analysis of common and rare variants via multiple knockoffs at biobank scale, with an application to Alzheimer disease genetics.

Knockoff-based methods have become increasingly popular due to their enhanced power for locus discovery and their ability to prioritize putative causal variants in a genome-wide analysis. However, because of the substantial computational cost for generating knockoffs, existing knockoff approaches cannot analyze millions of rare genetic variants in biobank-scale whole-genome sequencing and whole-genome imputed datasets. We propose a scalable knockoff-based method for the analysis of common and rare variants across the genome, KnockoffScreen-AL, that is applicable to biobank-scale studies with hundreds of thousands of samples and millions of genetic variants. The application of KnockoffScreen-AL to the analysis of Alzheimer disease (AD) in 388,051 WG-imputed samples from the UK Biobank resulted in 31 significant loci, including 14 loci that are missed by conventional association tests on these data. We perform replication studies in an independent meta-analysis of clinically diagnosed AD with 94,437 samples, and additionally leverage single-cell RNA-sequencing data with 143,793 single-nucleus transcriptomes from 17 control subjects and AD-affected individuals, and proteomics data from 735 control subjects and affected indviduals with AD and related disorders to validate the genes at these significant loci. These multi-omics analyses show that 79.1% of the proximal genes at these loci and 76.2% of the genes at loci identified only by KnockoffScreen-AL exhibit at least suggestive signal (p < 0.05) in the scRNA-seq or proteomics analyses. We highlight a potentially causal gene in AD progression, EGFR, that shows significant differences in expression and protein levels between AD-affected individuals and healthy control subjects.

Altered gut mycobiome in patients with end-stage renal disease and its correlations with serum and fecal metabolomes.

BACKGROUND: The relationship between the gut mycobiome and end-stage renal disease (ESRD) remains largely unexplored. METHODS: In this study, we compared the gut fungal populations of 223 ESRD patients and 69 healthy controls (HCs) based on shotgun metagenomic sequencing data, and analyzed their associations with host serum and fecal metabolites. RESULTS: Our findings revealed that ESRD patients had a higher diversity in the gut mycobiome compared to HCs. Dysbiosis of the gut mycobiome in ESRD patients was characterized by a decrease of Saccharomyces cerevisiae and an increase in various opportunistic pathogens, such as Aspergillus fumigatus, Cladophialophora immunda, Exophiala spinifera, Hortaea werneckii, Trichophyton rubrum, and others. Through multi-omics analysis, we observed a substantial contribution of the gut mycobiome to host serum and fecal metabolomes. The opportunistic pathogens enriched in ESRD patients were frequently and positively correlated with the levels of creatinine, homocysteine, and phenylacetylglycine in the serum. The populations of Saccharomyces, including the HC-enriched Saccharomyces cerevisiae, were frequently and negatively correlated with the levels of various toxic metabolites in the feces. CONCLUSIONS: Our results provided a comprehensive understanding of the associations between the gut mycobiome and the development of ESRD, which had important implications for guiding future therapeutic studies in this field.

Metagenomic analysis of the gut virome in patients with irritable bowel syndrome.

Irritable bowel syndrome (IBS), a chronic functional gastrointestinal disorder, is recognized for its association with alterations in the gut microbiome and metabolome. This study delves into the largely unexplored domain of the gut virome in IBS patients. We conducted a comprehensive analysis of the fecal metagenomic data set from 277 IBS patients and 84 healthy controls to characterize the gut viral community. Our findings revealed a distinct gut virome in IBS patients compared to healthy individuals, marked by significant variances in between-sample diversity and altered abundances of 127 viral operational taxonomic units (vOTUs). Specifically, 111 vOTUs, predominantly belonging to crAss-like, Siphoviridae, Myoviridae, and Quimbyviridae families, were more abundant in IBS patients, whereas the healthy control group exhibited enrichment of 16 vOTUs from multiple families. We also investigated the interplay between the gut virome and bacteriome, identifying a correlation between IBS-enriched bacteria like Klebsiella pneumoniae, Fusobacterium varium, and Ruminococcus gnavus, and the IBS-associated vOTUs. Furthermore, we assessed the potential of gut viral signatures in predicting IBS, achieving a notable area under the receiver operator characteristic curve (AUC) of 0.834. These findings highlight significant shifts in the viral diversity, taxonomic distribution, and functional composition of the gut virome in IBS patients, suggesting the potential role of the gut virome in IBS pathogenesis and opening new avenues for diagnostic and therapeutic strategies targeting the gut virome in IBS management.

Metagenomic analysis reveals altered gut virome and diagnostic potential in pancreatic cancer.

Pancreatic cancer (PC) is a highly aggressive malignancy with a poor prognosis, making early diagnosis crucial for improving patient outcomes. While the gut microbiome, including bacteria and viruses, is believed to be essential in cancer pathogenicity, the potential contribution of the gut virome to PC remains largely unexplored. In this study, we conducted a comparative analysis of the gut viral compositional and functional profiles between PC patients and healthy controls, based on fecal metagenomes from two publicly available data sets comprising a total of 101 patients and 82 healthy controls. Our results revealed a decreasing trend in the gut virome diversity of PC patients with disease severity. We identified significant alterations in the overall viral structure of PC patients, with a meta-analysis revealing 219 viral operational taxonomic units (vOTUs) showing significant differences in relative abundance between patients and healthy controls. Among these, 65 vOTUs were enriched in PC patients, and 154 were reduced. Host prediction revealed that PC-enriched vOTUs preferentially infected bacterial members of Veillonellaceae, Enterobacteriaceae, Fusobacteriaceae, and Streptococcaceae, while PC-reduced vOTUs were more likely to infect Ruminococcaceae, Lachnospiraceae, Clostridiaceae, Oscillospiraceae, and Peptostreptococcaceae. Furthermore, we constructed random forest models based on the PC-associated vOTUs, achieving an optimal average area under the curve (AUC) of up to 0.879 for distinguishing patients from controls. Through additional 10 public cohorts, we demonstrated the reproducibility and high specificity of these viral signatures. Our study suggests that the gut virome may play a role in PC development and could serve as a promising target for PC diagnosis and therapeutic intervention. Future studies should further explore the underlying mechanisms of gut virus-bacteria interactions and validate the diagnostic models in larger and more diverse populations.

A convolutional neural network-based system for identifying neuroendocrine neoplasm and multiple types of lesions in the pancreas via endoscopic ultrasound (with videos).

BACKGROUND AND AIMS: Endoscopic ultrasound (EUS) is sensitive in detecting pancreatic neuroendocrine neoplasm (pNEN). However, the endoscopic diagnosis of pNEN is operator-dependent and time-consuming since pNEN mimics normal pancreas and other pancreatic lesions. We intended to develop a convolutional neural network (CNN)-based system named iEUS for identifying pNEN and multiple types of pancreatic lesions via EUS. METHODS: Retrospective data of 12,200 EUS images obtained from pNEN and non-pNEN pancreatic lesions, including pancreatic ductal adenocarcinoma (PDAC), autoimmune pancreatitis (AIP), and pancreatic cystic neoplasm (PCN), were used to develop iEUS. It was composed of a two-category (pNEN/ non-pNEN pancreatic lesion) classification model (CNN1) and a four-category (pNEN/ PDAC/ AIP/ PCN) classification model (CNN2). Videos from consecutive patients were prospectively collected for a human-iEUS contest to evaluate the performance of iEUS. RESULTS: A total of 573 patients were enrolled in this study. In the human-iEUS contest containing 203 videos, CNN1 and CNN2 showed an accuracy of 84.2% and 88.2% for diagnosing pNEN, respectively, which were significantly higher than that of novices (75.4%) and comparable with intermediate endosonographers (85.5%) and experts (85.5%). In addition, CNN2 showed an accuracy of 86.2%, 97.0%, and 97.0% for diagnosing PDAC, AIP, and PCN, respectively. With the assistance of iEUS, the sensitivity of endosonographers at all three levels in diagnosing pNEN has significantly improved (64.6% vs. 44.8%, 87.5% vs. 71.9%, 74.0% vs. 57.6%, respectively). CONCLUSIONS: The iEUS precisely diagnosed pNEN and other confusing pancreatic lesions, thus could assist endosonographers in achieving more accessible and accurate endoscopic diagnoses via EUS.

Design of Cryptococcus neoformans multi-epitope vaccine based on immunoinformatics method.

Cryptococcus neoformans is a widely distributed opportunistic pathogenic fungus. While C. neoformans commonly infects immunocompromised individuals, it can also affect those who are immunocompetent. Transmission of C. neoformans primarily occurs through the respiratory tract, leading to the development of meningitis. The mortality rate of Cryptococcal meningitis is high, and treatment options are limited. Cryptococcus neoformans infections pose a significant public health threat and currently lack targeted and effective response strategies. This study aimed to screen T lymphocyte (cytotoxic T lymphocyte and helper T lymphocyte) and B lymphocyte epitopes derived from four C. neoformans antigens and develop two multi-epitope vaccines by combining them with various adjuvants. Molecular docking results demonstrated that the vaccines bind stably to Toll-like receptor 4 ( and induce innate immunity. The credibility of the molecular docking results was validated through subsequent molecular dynamics simulations. Furthermore, the results of immune simulation analyses underscored the multi-epitope vaccine's capability to effectively induce robust humoral and cellular immune responses within the host organism. These two vaccines have demonstrated theoretical efficacy against C. neoformans infection as indicated by computer analysis. Nevertheless, additional experimental validation is essential to substantiate the protective efficacy of the vaccines.

A multi-epitope Cryptococcus neoformans vaccine covering the most common A and D phenotypes was designed using bioinformatics methods.

Powerful gene-based testing by integrating long-range chromatin interactions and knockoff genotypes.

Gene-based tests are valuable techniques for identifying genetic factors in complex traits. Here, we propose a gene-based testing framework that incorporates data on long-range chromatin interactions, several recent technical advances for region-based tests, and leverages the knockoff framework for synthetic genotype generation for improved gene discovery. Through simulations and applications to genome-wide association studies (GWAS) and whole-genome sequencing data for multiple diseases and traits, we show that the proposed test increases the power over state-of-the-art gene-based tests in the literature, identifies genes that replicate in larger studies, and can provide a more narrow focus on the possible causal genes at a locus by reducing the confounding effect of linkage disequilibrium. Furthermore, our results show that incorporating genetic variation in distal regulatory elements tends to improve power over conventional tests. Results for UK Biobank and BioBank Japan traits are also available in a publicly accessible database that allows researchers to query gene-based results in an easy fashion.

The association between air pollutant exposure and cerebral small vessel disease imaging markers with modifying effects of PRS-defined genetic susceptibility.

Studies have highlighted a possible link between air pollution and cerebral small vessel disease (CSVD) imaging markers. However, the exact association and effects of polygenic risk score (PRS) defined genetic susceptibility remains unclear. This cross-sectional study used data from the UK Biobank. Participants aged 40-69 years were recruited between the year 2006 and 2010. The annual average concentrations of NOX, NO2, PM2.5, PM2.5-10, PM2.5 absorbance, and PM10, were estimated, and joint exposure to multiple air pollutants was reflected in the air pollution index (APEX). Air pollutant exposure was classified into the low (T1), intermediate (T2), and high (T3) tertiles. Three CSVD markers were used: white matter hyper-intensity (WMH), mean diffusivity (MD), and fractional anisotropy (FA). The first principal components of the MD and FA measures in the 48 white matter tracts were analysed. The sample consisted of 44,470 participants from the UK Biobank. The median (T1-T3) concentrations of pollutants were as follows: NO2, 25.5 (22.4-28.7) µg/m3; NOx, 41.3 (36.2-46.7) µg/m3; PM10, 15.9 (15.4-16.4) µg/m3; PM2.5, 9.9 (9.5-10.3) µg/m3; PM2.5 absorbance, 1.1 (1.0-1.2) per metre; and PM2.5-10, 6.1 (5.9-6.3) µg/m3. Compared with the low group, the high group's APEX, NOX, and PM2.5 levels were associated with increased WMH volumes, and the estimates (95 %CI) were 0.024 (0.003, 0.044), 0.030 (0.010, 0.050), and 0.032 (0.011, 0.053), respectively, after adjusting for potential confounders. APEX, PM10, PM2.5 absorbance, and PM2.5-10 exposure in the high group were associated with increased FA values compared to that in the low group. Sex-specific analyses revealed associations only in females. Regarding the combined associations of air pollutant exposure and PRS-defined genetic susceptibility with CSVD markers, the associations of NO2, NOX, PM2.5, and PM2.5-10 with WMH were more profound in females with low PRS-defined genetic susceptibility, and the associations of PM10, PM2.5, and PM2.5 absorbance with FA were more profound in females with higher PRS-defined genetic susceptibility. Our study demonstrated that air pollutant exposure may be associated with CSVD imaging markers, with females being more susceptible, and that PRS-defined genetic susceptibility may modify the associations of air pollutants.

Bone mesenchymal stromal cell-derived small extracellular vesicles inhibit inflammation and ameliorate sepsis via delivery of microRNA-21a-5p.

BACKGROUND AIMS: Sepsis is a potentially life-threatening disease that results from a severe systemic inflammatory response due to infection. Mesenchymal stromal cell-derived small extracellular vesicles (MSC sEVs) are able to transfer bioactive molecules and have been demonstrated to play an important role in the pathophysiological process of sepsis. Herein the authors aimed to investigate the potential role and downstream molecular mechanism of MSC sEVs in sepsis. METHODS: MSC sEVs were acquired by ultracentrifugation and then injected into a cecal ligation and puncture mouse model. The efficacy of MSC sEVs in both in vitro and in vivo models of sepsis was evaluated. RESULTS: MSC sEV therapy improved survival, reduced sepsis-induced inflammation, attenuated pulmonary capillary permeability and improved liver and kidney function in septic mice. In addition, the authors found that microRNA-21a-5p (miR-21a-5p) was highly enriched in MSC sEVs, could be transferred to recipient cells, inhibited inflammation and increased survival in septic mice. Furthermore, the authors demonstrated that MSC sEV miR-21a-5p suppressed inflammation by targeting toll-like receptor 4 and programmed cell death 4. The therapeutic efficacy of MSC sEVs was partially abrogated by transfection with miR-21a-5p inhibitors. CONCLUSIONS: Collectively, the authors' data suggest that miR-21a-5p-bearing MSC sEVs may be a prospective and effective sepsis therapeutic strategy.

The optimal pre-post allocation for randomized clinical trials.

BACKGROUND: In pre-post designs, analysis of covariance (ANCOVA) is a standard technique to detect the treatment effect with a continuous variable measured at baseline and follow-up. For measurements subject to a high degree of variability, it may be advisable to repeat the pre-treatment and/or follow-up assessments. In general, repeating the follow-up measurements is more advantageous than repeating the pre-treatment measurements, while the latter can still be valuable and improve efficiency in clinical trials. METHODS: In this article, we report investigations of using multiple pre-treatment and post-treatment measurements in randomized clinical trials. We consider the sample size formula for ANCOVA under general correlation structures with the pre-treatment mean included as the covariate and the mean follow-up value included as the response. We propose an optimal experimental design of multiple pre-post allocations under a specified constraint, that is, given the total number of pre-post treatment visits. The optimal number of the pre-treatment measurements is derived. For non-linear models, closed-form formulas for sample size/power calculations are generally unavailable, but we conduct Monte Carlo simulation studies instead. RESULTS: Theoretical formulas and simulation studies show the benefits of repeating the pre-treatment measurements in pre-post randomized studies. The optimal pre-post allocation derived from the ANCOVA extends well to binary measurements in simulation studies, using logistic regression and generalized estimating equations (GEE). CONCLUSIONS: Repeating baselines and follow-up assessments is a valuable and efficient technique in pre-post design. The proposed optimal pre-post allocation designs can minimize the sample size, i.e., achieve maximum power.

Effectiveness of Water-Assisted Colonoscopy without Sedation in Patients with Ulcerative Colitis.

BACKGROUND: Studies have found that water-assisted colonoscopy (WAC) including water immersion colonoscopy (WIC) and water exchange colonoscopy (WEC) is superior to air insufflation colonoscopy (AIC) in terms of the cecal intubation rate. However, the application of WAC in ulcerative colitis (UC) has rarely been reported. This study aimed to explore the effectiveness of WAC without sedation in patients with UC. METHODS: One hundred and seventy-two UC patients were randomly divided into the AIC group (n = 56), WIC group (n = 58), and WEC group (n = 58). The cecal intubation rate, abdominal pain score, operator difficulty, bowel cleanliness, insertion, and total time were compared. RESULTS: The cecal intubation rate was higher in the WIC (91.4% vs. 75.0%; mean difference = 16.4%; 95% CI: 3.0-29.8%) and WEC (93.1% vs. 75.0%; mean difference = 18.1%; 95% CI: 5.0-31.2%) compared to the AIC group, while there was no difference between the WIC and WEC groups. The abdominal pain score and operator difficulty were lower in the WIC and WEC groups than in the AIC group, while there was no difference between the WIC and WEC groups. The bowel cleanliness during withdrawal was higher in the WIC and WEC groups than in the AIC group, while the WEC was superior to WIC. Compared with the AIC and WIC groups, the insertion time and total time were longer in the WEC group, and there was no difference in the AIC group and WIC group. CONCLUSION: In comparison with AIC, WAC can increase the cecal intubation rate, reduce abdominal pain scores and improve bowel cleanliness in patients with UC.

Clinical Features and Blood Indicators for Severity and Prognosis in COVID-19 Patients.

BACKGROUND: This study aimed to analyze the clinical manifestations and blood indicators to deepen the understanding of Coronavirus disease 2019 (COVID-19). METHODS: COVID-19 patients admitted to C10 West Ward, Tongji Hospital in Wuhan City ("West Ward") between January 31 and March 28, 2020, were retrospectively analyzed. RESULTS: A total of 61 COVID-19 patients were hospitalized, wherein the non-critical Group had 30 cases, while the critical group had 31 (including 14 survivors and 17 deaths). Age, the proportion of fever cases, white blood cell (WBC), basophils, red blood cell (RBC), hemoglobin, lactate dehydrogenase (LDH), C-reactive protein (CRP), high-sensitivity troponin, pro-BNP (brain natriuretic peptide), prothrombin time (PT), and D-dimer were higher in the critical group while lymphocytes, eosinophils, albumin were lower compared with those of the non-critical group (all p < 0.05). WBC (p = 0.008), basophils (p = 0.034), and LDH (p = 0.005) of the death subgroup climbed remarkably in comparison with those of the survival subgroup. CONCLUSIONS: Advanced age, high fever, increases in indicators such as WBC, basophils, CRP, LDH, high-sensitivity troponin, pro-BNP, and D-dimer, and decreases in indicators, including lymphocytes, eosinophils, and albumin, might forebode a critical condition.

Human umbilical cord mesenchymal stromal cell small extracellular vesicle transfer of microRNA-223-3p to lung epithelial cells attenuates inflammation in acute lung injury in mice.

BACKGROUND: Acute lung injury (ALI), manifested as strong pulmonary inflammation and alveolar epithelial damage, is a life-threatening disease with high morbidity and mortality. Small extracellular vesicles (sEVs), secreted by multiple types of cells, are critical cellular communication mediators and can inhibit inflammation by transferring bioactive molecules, such as microRNAs (miRNAs). Thus, we hypothesized that sEVs derived from mesenchymal stromal cells (MSC sEVs) could transfer miRNAs to attenuate inflammation of lung epithelial cells during ALI. METHODS: C57BL/6 male mice were intratracheally administered LPS (10 mg/kg). Six hours later, the mice were randomly administered with MSC sEVs (40 µg per mouse in 150 µl of saline), which were collected by ultracentrifugation. Control group received saline administration. After 48 h, the mice were sacrificed to evaluate pulmonary microvascular permeability and inflammatory responses. In vitro, A549 cells and primary human small airway epithelial cells (SAECs) were stimulated with LPS with or without MSC sEVs treatment. RESULTS: In vitro, MSC sEVs could also inhibit the inflammation induced by LPS in A549 cells and SAECs (reducing TNF-α, IL-1ß, IL-6 and MCP-1). Moreover, MSC sEV treatment improved the survival rate, alleviated pulmonary microvascular permeability, and inhibited proinflammatory responses (reducing TNF-α, IL-1ß, IL-6 and JE-1) in ALI mice. Notably, miR-223-3p was found to be served as a critical mediator in MSC sEV-induced regulatory effects through inhibition of poly (adenosine diphosphate-ribose) polymerase-1 (PARP-1) in lung epithelial cells. CONCLUSIONS: Overall, these findings suggest that MSC sEVs may offer a novel promising strategy for ALI.

Feasibility of salvage colonoscopy by water exchange for failed air-insufflated patients: a prospective, randomized, controlled trial.

BACKGROUND: A complete colonoscopy is crucial for screening colorectal diseases and colorectal cancer. However, a failure rate of up to 43% still exists. Several studies have indicated that the water exchange method can enhance the cecal intubation rate while reducing discomfort of the patient. Water exchange colonoscopy (WEC) might be a salvage treatment for the patients who failed from air insufflation colonoscopy (AIC). We aimed to assess the feasibility of WEC as a salvage measure following the failure of conventional AIC. METHODS: Patients willing to undergo unsedated colonoscopy at a tertiary-care referral center in China were randomly assigned 1:1 to WEC or AIC group for salvage after the initial AIC attempt failed. Patients were blinded to group assignment. The primary outcome was cecal intubation rate, the secondary outcomes included time to the cecum, maximum pain scores, and technical difficulty level. RESULTS: Recruited 104 patients were randomized to the WEC (n = 52) or AIC (n = 52) group. WEC significantly increased the cecal intubation rate (92.3% vs 73.1%; p = .02). The maximum pain scores and technical difficulty level in the WEC group were significantly lower than the AIC group during salvage procedure (p < .001). CONCLUSIONS: This randomized, controlled trial confirms that the WEC significantly enhanced cecal intubation rate in difficult colonoscopy in unsedated patients after the failure of standard AIC. The increased cecal intubation rate, lower pain scores and technical difficulty level suggest WEC is a good alternative for incomplete unsedated colonoscopy. Clinical trial registration number: ChiCTR2100051483.

Underwater endoscopic mucosal resection for rectal neuroendocrine tumors (with videos): a single center retrospective study.

BACKGROUND: Underwater endoscopic mucosal resection (UMER) is a new method of endoscopic resection to completely remove the lesion without submucosal injection. But few attempts have been carried out for rectal neuroendocrine tumors (rectal NETs). METHODS: We retrospectively investigated data on the tumor characteristics and outcomes of patients with ≤ 10 mm rectal NETs who underwent UEMR or endoscopic submucosal dissection (ESD) from January 2019 to June 2021 in our institute. RESULTS: The endoscopic resection rate was 100% in both UEMR and ESD groups. The histological complete resection rate of the UEMR group (95.5%) was lower than that of the ESD group (96.4%) with no significant difference. The average operation time, hospitalization time and operation cost of UEMR group were less than those of ESD group (P < 0.05). The incidence of postoperative abdominal pain and abdominal distention in the UEMR group was lower than that in the ESD group (P < 0.05). There was no significant difference in the incidence of delayed bleeding and perforation between the two groups. There was no local recurrence or distant metastasis in the two groups during the follow-up period. CONCLUSIONS: Both the UEMR and ESD can effectively treat ≤ 10 mm rectal NETs with invasion depth confined to the mucosa and submucosa. UEMR is superior to ESD in operation time, hospitalization time, operation cost, postoperative abdominal pain and abdominal distention.

Adaptive dose-response studies to establish proof-of-concept in learning-phase clinical trials.

In learning-phase clinical trials in drug development, adaptive designs can be efficient and highly informative when used appropriately. In this article, we extend the multiple comparison procedures with modeling techniques (MCP-Mod) procedure with generalized multiple contrast tests (GMCTs) to two-stage adaptive designs for establishing proof-of-concept. The results of an interim analysis of first-stage data are used to adapt the candidate dose-response models and the dosages studied in the second stage. GMCTs are used in both stages to obtain stage-wise p -values, which are then combined to determine an overall p -value. An alternative approach is also considered that combines the t -statistics across stages, employing the conditional rejection probability principle to preserve the Type I error probability. Simulation studies demonstrate that the adaptive designs are advantageous compared to the corresponding tests in a nonadaptive design if the selection of the candidate set of dose-response models is not well informed by evidence from preclinical and early-phase studies.

A meta-analysis of the watch-and-wait strategy versus total mesorectal excision for rectal cancer exhibiting complete clinical response after neoadjuvant chemoradiotherapy.

BACKGROUND: Some clinical researchers have reported that patients with cCR (clinical complete response) status after neoadjuvant chemoradiotherapy (nCRT) could adopt the watch-and-wait (W&W) strategy. Compared with total mesorectal excision (TME) surgery, the W&W strategy could achieve a similar overall survival. Could the W&W strategy replace TME surgery as the main treatment option for the cCR patients? By using the meta-analysis method, we evaluated the safety and efficacy of the W&W strategy and TME surgery for rectal cancer exhibiting cCR after nCRT. METHODS: We evaluated two treatment strategies for rectal cancer with cCR after nCRT up to July 2021 by searching the Cochrane Library, PubMed, Wanfang, and China National Knowledge Infrastructure (CNKI) databases. Clinical data for primary outcomes (local recurrence, cancer-related death and distant metastasis), and secondary outcomes (disease-free survival (DFS) and overall survival (OS)) were collected to evaluate the efficacy and safety in the two groups. RESULTS: We included nine studies with 818 patients in the meta-analysis, and there were five moderate-quality studies and four high-quality studies. A total of 339 patients were in the W&W group and 479 patients were in the TME group. The local recurrence rate in the W&W group was greater than that in the TME group in the fixed-effects model (OR 8.54, 95% CI 3.52 to 20.71, P < 0.001). The results of other outcomes were similar in the two groups. CONCLUSION: The local recurrence rate of the W&W group was greater than that in the TME group, but other results were similar in the two groups. With the help of physical examination and salvage therapy, the W&W strategy could achieve similar treatment effects with the TME approach. TRIAL REGISTRATION: Protocol registration number: CRD42021244032 .

Generalized multiple contrast tests in dose-response studies.

In the process of developing drugs, proof-of-concept studies can be helpful in determining whether there is any evidence of a dose-response relationship. A global test for this purpose that has gained popularity is a component of the multiple comparisons procedure with modeling techniques (MCP-Mod), which involves the specification of a candidate set of several plausible dose-response models. For each model, a test is performed for significance of an optimally chosen contrast among the sample means. An overall P-value is obtained from the distribution of the maximum of the contrast statistics. This is equivalent to basing the test on the minimum of the P-values arising from these contrast statistics and, hence, can be viewed as a method for combining dependent P-values. We generalize this idea to the use of different statistics for combining the dependent P-values, such as Fisher's combination method or the inverse normal combination method. Simulation studies show that the generalized multiple contrast tests (GMCTs) based on the Fisher and inverse normal methods are generally more powerful than the MCP-Mod procedure based on the minimum of the P-values except for cases where the true dose-response model is, in a sense, near the extremes of the candidate set of dose-response models. The proposed GMCTs can also be used for model selection and dosage selection by employing a closed testing procedure.