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.

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.

Risk Factors Associated with Inadequate Bowel Preparation in Patients with Functional Constipation.

BACKGROUND: Constipation is a common reason of poor bowel preparation, which negatively influences the quality of colonoscopy. Risk factors for inadequate bowel preparation in constipated patients remain unclear. AIMS: This study aimed to investigate the high-risk factors that might influence the quality of bowel preparation in patients with functional constipation. METHODS: Consecutive patients with functional constipation who underwent colonoscopy between June 2016 and April 2017 were enrolled. A standard split dose of 4 l polyethylene glycol was used for bowel preparation. Patient- and procedure-related parameters were recorded. The primary outcome was an adequate rate of bowel preparation. Risk factors for inadequate bowel preparation were screened by multivariate logistic regression analysis. RESULTS: A total of 199 patients were included. Adequate bowel preparation was found in 62.8% (125/199) of patients. At multivariate analysis, Bristol stool form scale (BSFS) 1 [odds ratio (OR) 2.73, 95% confidence interval (CI) 1.26-5.90; P = 0.011], rectal pain score during defecation < 2 (OR 4.14, 95% CI 1.22-13.97; P = 0.022), and starting-to-defecation interval ≥ 4 h (OR 3.83, 95% CI 1.34-10.91; P = 0.012) were risk factors for inadequate bowel preparation in patients with constipation. For patients with no, 1, 2, or 3 risk factors, the rates of inadequate bowel preparation were 11%, 23%, 49%, and 65%, respectively. CONCLUSIONS: With the standard preparation regime, > 1/3 of patients with functional constipation had inadequate bowel cleansing. BSFS 1, rectal pain score during defecation < 2, and starting-to-defecation interval ≥ 4 h were identified as independent risk factors for inadequate bowel preparation in constipated patients. TRIAL REGISTRATION: ClinicalTrials.gov number NCT02842411.

Circular stripes were more common in Barrett's esophagus after acetic acid staining.

BACKGROUND: The diagnosis of Barrett's esophagus (BE) is disturbed by numerous factors, including correct gastroesophageal junction judgment, the initial location of the Z-line and the biopsy result above it. The acetic acid (AA) could help to diagnose BE better than high resolution imaging technology or magnifying endoscopy, by providing enhanced contrast of different epithelium. We have noticed AA could produce multiple white circular lines, forming circular stripes (CS), at lower esophagus, which hasn't been reported by others. This study aimed to investigate whether the CS is a special marker in BE patients. METHODS: A total of 47 BE patients and 63 healthy people were enrolled from March 2016 to October 2016, and 2% AA staining had been operated routinely at lower esophagus under high resolution gastroscopy. We observed whether there were CS after AA staining and the images were compared between the two groups. RESULTS: CS were confirmed in 42 patients (89.36%) in the BE group and 5 (7.94) in the control group ((χ2 = 72.931, P < 0.001)). The average width of CS was 0.76 ± 0.25 cm in BE group, which was similar to that in the control group (0.88 ± 0.11 cm). Villous or punctate or reticular pattern usually existed above or below the CS. CONCLUSIONS: CS could be found at lower esophagus in most BE patients with AA staining, and this special feature might be valuable in diagnosing, evaluating and following up of BE patients.

Research on the inhibiting effect of tanshinone IIA on colon cancer cell growth via COX-2-Wnt/ß-catenin signaling pathway.

PURPOSE: To investigate the effects of tanshinone IIA (TSIIA) on the colon cancer cell growth and to explore the mechanism of TSIIA in regulating the colon cancer cell growth via cyclooxygenase (COX)-2-Wnt/ß-catenin signaling pathway. METHODS: Colon cancer cell line HC8693 was exposed to different concentrations of TSIIA. After 24-hr exposure, MTT assay was used to detect the lethal concentration of TSIIA on HC8693 cells. The expression levels of COX-2 and ß-catenin were detected by semi-quantitative PCR (sq-PCR). The protein expression levels of COX-2 and ß-catenin were detected by Western blot, and the expression of vascular endothelial growth factor (VEGF) was detected by enzyme-linked immunosorbent assay (ELISA). Celecoxib, a COX-2 selective inhibitor, was used to inhibit the COX-2 of HC8693 cells, and the inhibiting effect of TSIIA on HC8693 cell growth was assessed. RESULTS: MTT assay showed that TSIIA concentration of 20µM inhibited significantly the HC8693 cell growth (p<0.01). With reverse transcription after RNA extraction and (sq-PCR) detection the expression levels of COX-2 and ß-catenin were significantly decreased (p<0.01). Western blot showed that the protein expression levels of COX-2 and ß-catenin were significantly decreased (p<0.01). ELISA showed that the expression of VEGF was also significantly decreased (p<0.01); after celecoxib (10µM) was added, 20µM TSIIA had no inhibiting effect on the growth of HC8693 cells (p>0.05). Western blot showed no significant differences in the protein expression levels of COX-2 and ß-catenin compared with those in the control group (not exposed to TSIIA). CONCLUSIONS: TSIIA can inhibit the expression of COX-2 and activate the Wnt/ß-catenin signaling pathway, thus downregulating the level of VEGF, and resulting in growth inhibition of colon cancer cells.

Endoscopic ultrasonography for preoperative staging of esophageal carcinoma.

OBJECTIVE: To evaluate the diagnostic value of endoscopic ultrasonography (EUS) in preoperative staging of esophageal carcinoma (EC). MATERIAL AND METHODS: A total of 86 surgical patients with EC who were confirmed by endoscopy and biopsy underwent preoperative TN staging with EUS examination. The EUS findings were compared with surgical pathologic results. RESULTS: The accuracy of EUS in T and N staging of EC was 82.6% and 84.9%, respectively. While determining whether EC invades the muscularis propria or outer membrane, EUS had the favorable sensitivity, specificity, positive predictive value and negative predictive value. The short-axis diameter of lymph nodes of 5mm had high sensitivity and negative predictive value to determine malignance with low specificity and positive predictive value. The short-axis diameter of 10mm presented the satisfactory sensitivity, specificity, positive predictive value and negative predictive value. CONCLUSION: EUS can accurately determine the TN staging of EC and provide a reliable basis for the treatment of EC.

An evaluation of multiple algorithms for the measurement of the heart rate corrected JTpeak interval.

Interest in the effects of drugs on the heart rate-corrected JTpeak (JTpc) interval from the body-surface ECG has spawned an increasing number of scientific investigations in the field of regulatory sciences, and more specifically in the context of the Comprehensive in vitro Proarrhythmia Assay (CiPA) initiative. We conducted a novel initiative to evaluate the role of automatic JTpc measurement technologies by comparing their ability to distinguish multi- from single-channel blocking drugs. A set of 5232 ECGs was shared by the FDA (through the Telemetric and Holter ECG Warehouse) with 3 ECG device companies (AMPS, Mortara, and Philips). We evaluated the differences in drug-concentration effects on these measurements between the commercial and the FDA technologies. We provide a description of the drug-induced placebo-corrected changes from baseline for dofetilide, quinidine, ranolazine, and verapamil, and discuss the various differences across all technologies. The results revealed only small differences between measurement technologies evaluated in this study. It also confirms that, in this dataset, the JTpc interval distinguishes between multi- and single-channel (hERG) blocking drugs when evaluating the effects of dofetilide, quinidine, ranolazine, and verapamil. However, in the case of quinidine and dofetilide, we noticed a poor consistency across technologies because of the lack of standard definitions for the location of the peak of the T-wave (T-apex) when the T-wave morphology is abnormal.

Design of a cryptococcus neoformans vaccine by subtractive proteomics combined with immunoinformatics.

The emergence of Cryptococcus neoformans has posed an undeniable burden to many regions worldwide, with its strains mainly entering the lungs through the respiratory tract and spreading throughout the body. Limitations of drug regimens, such as high costs and limited options, have directed our attention toward the promising field of vaccine development. In this study, the subtractive proteomics approach was employed to select target proteins from databases that can accurately cover serotypes A and D of the Cryptococcus neoformans. Further, two multi-epitope vaccines consisting of T and B cell epitopes were demonstrated that they have good structural stability and could bind with immune receptor to induce desired immune responses in silico. After further evaluation, these vaccines show the potential for large-scale production and applicability to the majority of the population of the world. In summary, these two vaccines have been theoretically proven to combat Cryptococcus neoformans infections, awaiting further experimental validation of their actual protective effects.