[Research progress on the impact of public health and social measures on influenza during the COVID-19 pandemic].

Public health and social measures (PHSMs) are one of the most important measures in the prevention and control of COVID-19 and have also been effective in suppressing the spread of influenza viruses, but their effectiveness has not been fully investigated. This study aimed to review the progress of research on the impact of PHSMs on influenza during the COVID-19 pandemic based on the latest evidence of the effectiveness of various PHSMs in controlling transmission of influenza viruses, to provide scientific evidence for optimizing influenza prevention and control strategies.

[Genetic expression differences of 11 beta-hydroxysteroid dehydrogenase in the bone microvascular endothelial cells derived from different regions of the human femoral head].

Objective: To investigate the expression levels and activation differences of 11beta-hydroxysteroid dehydrogenase (11beta-HSD) gene in bone microvascular endothelial cells (BMECs) in different regions of human femoral head. Methods: Tissue specimens of femoral heads were obtained from hip arthroplasty carried out in China-Japan Friendship Hospital from January 2017 to June 2018. And the BMECs we isolated, purified, identified and cultured from different regions of the human femoral head: in the subchondral and cancellous bone regions. The BMECs from the two regions were intervened by hydrocortisone with a series of low concentration gradients (0, 0.03, 0.06, 0.10 mg/ml) respectively. The cell phenotype and functional status of BMECs and cell migration were detected by scratch experiments, and the angiogenesis in different regions of the femoral head was observed. The mRNA and protein expression of 11beta-HSD1, 11beta-HSD2 in BMECs were detected by real-time fluorescence quantitative polymerase chain reaction (RT-PCR) and Western-blot method, respectively. Results: With the increase of the concentration of hydrocortisone, the 11beta-HSD1 mRNA and protein expression of BMECs in the subchondral and cancellous bone regions of the femoral head increased significantly, and the 11beta-HSD1 mRNA and protein expression of BMECs in the subchondral bone region was significantly lower than those in cancellous bone region (all P<0.05). The 11beta-HSD2 mRNA and protein expression of BMECs in the cancellous bone region showed a slow decrease first and then increased slightly at 0.10 mg/ml, while the expression in the subchondral bone region was the opposite. The 11beta-HSD2 mRNA and protein expression of BMECs in subchondral bone region was slightly higher than those in cancellous bone region (all P<0.05), but there was no significant statistical difference between the two regions at 0.10 mg/ml (0.123±0.018 vs 0.126±0.021, 0.577±0.231 vs 0.609±0.174, t=1.380, 0.409, both P>0.05). At different times of the 0.06 mg/ml hydrocortisone intervention, there was no significant differences in scratch closure rate, the number of BMECs lumen, the number of buds and the length of tubule branches in different regions of the femoral head (all P>0.05). Conclusion: The 11beta-HSD expression of BMECs in different regions of human femoral head is significantly different. The 11beta-HSD1 is high-expressed, but 11beta-HSD2 is low-expressed in BMECs of the cancellous bone region, and those are opposite in the subchondral bone region, which helps to explain the pathological characteristics and pathogenesis of hormonal osteonecrosis.

[Morphological changes of the central sulcus in children with complete growth hormone deficiency: a 3.0 T MRI study].

Objective: To analyze morphological changes in central sulcus of the cerebral cortex in children with complete growth hormone deficiency (CGHD). Methods: Patients attending the Shandong Provincial Hospital who were diagnosed with CGHD or idiopathic short stature were recruited from January 2015 to January 2019. Thirty children with CGHD (18 males and 12 females, 5 to 14 years old) and 30 children with idiopathic short stature (22 males and 8 females, 5 to 14 years old) were included. Measurements of the central sulcus, including the average width, maximum depth, average depth, top length, bottom length and depth position-based profiles (DPP), were obtained using Brain VISA software. The significant differences between groups were statistically analyzed. Results: The average width of bilateral central sulci in children with CGHD (left: (2.26±0.41) mm; right: (2.19±0.34) mm) were significantly higher than those in children with idiopathic short stature (left: (2.10±0.27) mm; right: (2.02±0.18) mm) (P<0.05) ; The maximum depth of the left central sulcus ((19.67±1.29) mm) and the average depth of the right central sulcus ((14.18±1.41) mm) were significantly lower than those in children with idiopathic short stature (left maximum depth: (20.69±1.43) mm; right average depth: (14.92±1.21) mm) (P<0.05) . Children with CGHD had significantly lower DPP at the middle part of the left central sulcus (sites: 46-54) and the inferior part of the right central sulcus(sites: 91-98). Conclusion: There are significant morphological changes of the central sulcus in children with CGHD, which may represent the structural basis of their relatively slower development in motor, cognitive and linguistic functional performance.

Relationship between Postmortem Interval and FTIR Spectroscopy Changes of the Rat Skin.

ABSTRACT: Objective To infer postmortem interval （PMI） based on spectral changes of the dorsal skin of rats within 15 days postmortem using Fourier transform infrared （FTIR） spectroscopy. Methods The rats were sacrificed by cervical dislocation after anesthesia, and then placed at 25 ℃ and relative humidity of 50%. The FTIR spectral data collected from the dorsal skin at PMI points were modeled with machine learning technique. Results There was no significant difference of absorption peak location among all the PMI groups but their peak intensities changed as a function of PMIs. The model for PMI estimation was constructed using partial least squares （PLS） regression, reaching a R2 of 0.92 and a root mean square error （RMSE） of 1.30 d. As shown in variable importance for projection （VIP）, four spectral bands including 1 760-1 700 cm-1, 1 660-1 640 cm-1, 1 580-1 540 cm-1 and 1 460-1 420 cm-1 were determined as important contributions to model prediction. Conclusion Application of the FTIR technique to detect postmortem spectral changes of the rat skin provides a novel proposal for PMI estimation.

Porous tantalum rods for treating osteonecrosis of the femoral head.

This study evaluated the outcomes of using porous tantalum rods for the treatment of osteonecrosis of the femoral head (ONFH). We performed core decompression and inserted porous tantalum implants in 149 patients (168 consecutive hips) with ONFH. Hips had large (65), medium (64), or small (39) lesions; 63 lesions were lateral, 68 were central, and 35 were medial. Conversion to total hip arthroplasty (THA) was the end point of this survey. A total of 130 cases (138 hips) were followed. The mean follow-up time was 38.46 ± 5.76 months; 43 hips (31%) were converted to or needed THA. Of the 43 hips requiring THA, 33 had large lesions, including 1 medial, 3 central, and 29 lateral lesions; 9 had medium, lateral lesions, and 1 hip had a small, lateral lesion. Bone grafting was used in 59 hips, with 3 hips failing; 40 of 79 hips without bone grafts failed. The sum distances between the tops of the rods and the lateral lesion boundaries (SDTL, mm) were measured in anteroposterior and lateral radiographs. In the failure and spared groups, the average SDTLs were 7.65 ± 2.759 and 0.83 ± 2.286 mm, respectively. The survival of porous tantalum rods used for treating early-stage ONFH was affected by the size and location of the lesion, whether or not a bone graft was used, as well as the distance between top of the rod and the lateral boundary of the lesion.

[Incidence of postoperative complications in Chinese patients with gastric or colorectal cancer based on a national, multicenter, prospective, cohort study].

Objective: To investigate the incidence of postoperative complications in Chinese patients with gastric or colorectal cancer, and to evaluate the risk factors for postoperative complications. Methods: This was a national, multicenter, prospective, registry-based, cohort study of data obtained from the database of the Prevalence of Abdominal Complications After Gastro- enterological Surgery (PACAGE) study sponsored by the China Gastrointestinal Cancer Surgical Union. The PACAGE database prospectively collected general demographic characteristics, protocols for perioperative treatment, and variables associated with postoperative complications in patients treated for gastric or colorectal cancer in 20 medical centers from December 2018 to December 2020. The patients were grouped according to the presence or absence of postoperative complications. Postoperative complications were categorized and graded in accordance with the expert consensus on postoperative complications in gastrointestinal oncology surgery and Clavien-Dindo grading criteria. The incidence of postoperative complications of different grades are presented as bar charts. Independent risk factors for occurrence of postoperative complications were identified by multifactorial unconditional logistic regression. Results: The study cohort comprised 3926 patients with gastric or colorectal cancer, 657 (16.7%) of whom had a total of 876 postoperative complications. Serious complications (Grade III and above) occurred in 4.0% of patients (156/3926). The rate of Grade V complications was 0.2% (7/3926). The cohort included 2271 patients with gastric cancer with a postoperative complication rate of 18.1% (412/2271) and serious complication rate of 4.7% (106/2271); and 1655 with colorectal cancer, with a postoperative complication rate of 14.8% (245/1655) and serious complication rate of 3.0% (50/1655). The incidences of anastomotic leakage in patients with gastric and colorectal cancer were 3.3% (74/2271) and 3.4% (56/1655), respectively. Abdominal infection was the most frequently occurring complication, accounting for 28.7% (164/572) and 39.5% (120/304) of postoperative complications in patients with gastric and colorectal cancer, respectively. The most frequently occurring grade of postoperative complication was Grade II, accounting for 65.4% (374/572) and 56.6% (172/304) of complications in patients with gastric and colorectal cancers, respectively. Multifactorial analysis identified (1) the following independent risk factors for postoperative complications in patients in the gastric cancer group: preoperative comorbidities (OR=2.54, 95%CI: 1.51-4.28, P<0.001), neoadjuvant therapy (OR=1.42, 95%CI:1.06-1.89, P=0.020), high American Society of Anesthesiologists (ASA) scores (ASA score 2 points:OR=1.60, 95% CI: 1.23-2.07, P<0.001, ASA score ≥3 points:OR=0.43, 95% CI: 0.25-0.73, P=0.002), operative time >180 minutes (OR=1.81, 95% CI: 1.42-2.31, P<0.001), intraoperative bleeding >50 mL (OR=1.29,95%CI: 1.01-1.63, P=0.038), and distal gastrectomy compared with total gastrectomy (OR=0.65,95%CI: 0.51-0.83, P<0.001); and (2) the following independent risk factors for postoperative complications in patients in the colorectal cancer group: female (OR=0.60, 95%CI: 0.44-0.80, P<0.001), preoperative comorbidities (OR=2.73, 95%CI: 1.25-5.99, P=0.030), neoadjuvant therapy (OR=1.83, 95%CI:1.23-2.72, P=0.008), laparoscopic surgery (OR=0.47, 95%CI: 0.30-0.72, P=0.022), and abdominoperineal resection compared with low anterior resection (OR=2.74, 95%CI: 1.71-4.41, P<0.001). Conclusion: Postoperative complications associated with various types of infection were the most frequent complications in patients with gastric or colorectal cancer. Although the risk factors for postoperative complications differed between patients with gastric cancer and those with colorectal cancer, the presence of preoperative comorbidities, administration of neoadjuvant therapy, and extent of surgical resection, were the commonest factors associated with postoperative complications in patients of both categories.

Dengue virus inactivation by minipool TnBP/Triton X-45 treatment of plasma and cryoprecipitate.

BACKGROUND AND OBJECTIVES: A minipool solvent/detergent (S/D; 1% TnBP/1% Triton X-45; 31°C) process was developed for viral inactivation of plasma and cryoprecipitate used for transfusion. The goal of this study was to determine the rate and extent of inactivation of dengue virus (DENV) during this process. MATERIALS AND METHODS: DENV-1 was propagated using C6/36 mosquito cells to an infectivity titre close to 9 log and spiked (10% v/v) into individual plasma and cryoprecipitate samples from two distinct donors. Samples were taken right after spiking and during viral inactivation treatment by 1% TnBP-1% Triton X-45 at 31°C. DENV-1 infectivity was assessed on Vero E6 cells by a focus-forming assay (FFA). Culture medium and complement-inactivated plasma were used as experimental controls. Experiments were done in duplicate. RESULTS: DENV-1 infectivity was 7·5 log in spiked plasma and 7·1 and 7·3 log in spiked cryoprecipitate. There was no loss of DENV-1 infectivity in the spiked materials, nor in the controls not subjected to S/D treatment. No infectivity was found in plasma and cryoprecipitate subjected to S/D treatment at the first time-point evaluated (10 min). CONCLUSION: DENV-1 was strongly inactivated in plasma and cryoprecipitate, respectively, within 10 min of 1% TnBP/1% Triton X-45 treatment at 31°C. These data provide a reassurance of the safety of such S/D-treated plasma and cryoprecipitate with regard to the risk of transmission of all DENV serotypes and other flaviviruses.

Update of PROFEAT: a web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence.

Sequence-derived structural and physicochemical features have been extensively used for analyzing and predicting structural, functional, expression and interaction profiles of proteins and peptides. PROFEAT has been developed as a web server for computing commonly used features of proteins and peptides from amino acid sequence. To facilitate more extensive studies of protein and peptides, numerous improvements and updates have been made to PROFEAT. We added new functions for computing descriptors of protein-protein and protein-small molecule interactions, segment descriptors for local properties of protein sequences, topological descriptors for peptide sequences and small molecule structures. We also added new feature groups for proteins and peptides (pseudo-amino acid composition, amphiphilic pseudo-amino acid composition, total amino acid properties and atomic-level topological descriptors) as well as for small molecules (atomic-level topological descriptors). Overall, PROFEAT computes 11 feature groups of descriptors for proteins and peptides, and a feature group of more than 400 descriptors for small molecules plus the derived features for protein-protein and protein-small molecule interactions. Our computational algorithms have been extensively tested and used in a number of published works for predicting proteins of specific structural or functional classes, protein-protein interactions, peptides of specific functions and quantitative structure activity relationships of small molecules. PROFEAT is accessible free of charge at http://bidd.cz3.nus.edu.sg/cgi-bin/prof/protein/profnew.cgi.

[Effect of jejunal feeding tube placement on complications after laparoscopic radical surgery in patients with incomplete pyloric obstruction by gastric antrum cancer].

Objective: To assess the effect of jejunal feeding tube placement on early complications of laparoscopic radical gastrectomy in patients with incomplete pyloric obstruction by gastric cancer. Methods: This was a retrospective cohort study. Perioperative clinical data of 151 patients with gastric antrum cancer complicated by incomplete pyloric obstruction who had undergone laparoscopic distal radical gastrectomy from May 2020 to May 2022 in the First Affiliated Hospital of Nanchang University were collected. Intraoperative jejunal feeding tubes had been inserted in 69 patients (nutrition tube group) and not in the remaining 82 patients (conventional group). There were no statistically significant differences in baseline characteristics between the two groups (all P>0.05). The operating time, intraoperative bleeding, time to first intake of solid food, time to passing first flatus, time to drainage tube removal, and postoperative hospital stay, and early postoperative complications (occurded within 30 days after surgery) were compared between the two groups. Results: Patients in both groups completed the surgery successfully and there were no deaths in the perioperative period. The operative time was longer in the nutritional tube group than in the conventional group [(209.2±4.7) minutes vs. (188.5±5.7) minutes, t=2.737, P=0.007], whereas the time to first postoperative intake of food [(2.7±0.1) days vs. (4.1±0.4) days, t=3.535, P<0.001], time to passing first flatus [(2.3±0.1) days vs. (2.8±0.1) days, t=3.999, P<0.001], time to drainage tube removal [(6.3±0.2) days vs. (6.9±0.2) days, t=2.123, P=0.035], and postoperative hospital stay [(7.8±0.2) days vs. (9.7±0.5) days, t=3.282, P=0.001] were shorter in the nutritional tube group than in the conventional group. There was no significant difference between the two groups in intraoperative bleeding [(101.1±9.0) mL vs. (111.4±8.7) mL, t=0.826, P=0.410]. The overall incidence of short-term postoperative complications was 16.6% (25/151). Postoperative complications did not differ significantly between the two groups (all P>0.05). Conclusion: It is safe and feasible to insert a jejunal feeding tube in patients with incomplete outlet obstruction by gastric antrum cancer during laparoscopic radical gastrectomy. Such tubes confer some advantages in postoperative recovery.

[The efficacy and safety of low-dose chemotherapy combined with tyrosine kinase inhibitors in the treatment of Philadelphia-chromosomal-positive acute lymphoblastic leukemia].

Objective: The study aims to explore the efficacy and safety of low-dose chemotherapy combined with tyrosine kinase inhibitor (TKI) as an induction therapy for Philadelphia-chromosomal-positive acute lymphoblastic leukemia (Ph(+) ALL) . Methods: The data of the consecutive newly diagnosed patients with Ph(+) ALL were reviewed. The efficacy and safety of low-dose chemotherapy and conventional-dose chemotherapy combined with TKI were compared. Results: A total of 217 patients with a median age of 38 (10-69) years old were included in this study. 78 patients were in the low-dose chemotherapy group, and 139 patients were in the conventional-dose chemotherapy group. There were no significant differences in the 4-week complete remission (CR) rate (98.7% vs 97.0%, P=0.766) and overall CR rate (100% vs 100%, P=1.000) between the two groups. Multivariate analyses showed that the chemotherapy intensity was not related to the disease-free survival rate and overall survival rate. However, the lower incidence of infection (P=0.017) , the shorter duration of neutropenia (P=0.001) and PLT<20 × 10(9)/L (P=0.057) , and the lower red blood cell transfusion volume (P=0.002) were more common in the low-dose chemotherapy group than in the conventional-dose chemotherapy group. Conclusions: The low-dose chemotherapy is superior to the conventional-dose chemotherapy combined with TKI as induction therapy in Ph(+) ALL with similar efficacy but is safer.

Risk factors for Clostridioides difficile infection in children: a systematic review and meta-analysis.

BACKGROUND: Clostridioides difficile is considered an urgent threat to human health by the US Centers for Disease Control and Prevention. In recent years, C. difficile has been reported increasingly as a cause of gastrointestinal disease in children, and the prevalence of hospital-acquired C. difficile infection and community-acquired CDI in children is increasing. AIM: To perform a systematic review and meta-analysis of risk factors for CDI in children. METHODS: MEDLINE/PubMed, EMBASE, Web of Science, Scopus, OVID, China National Knowledge Infrastructure, Wanfang (Chinese), SinoMed (Chinese) and Weipu (Chinese) were searched from inception to 12th January 2022. Observational studies (cohort, case-control and cross-sectional) on CDI in children were included in the analysis. Data were pooled using a fixed or random-effects model, and odds ratios (OR) were calculated. FINDINGS: In total, 25 observational studies were included in the analysis. Prior antibiotic exposure [OR 1.93, 95% confidence interval (CI) 1.25-2.97], prolonged hospitalization (OR 14.68, 95% CI 13.24-16.28), history of hospitalization (OR 3.67, 95% CI 1.91-7.06), gastric acid suppressants (OR 1.96, 95% CI 1.41-2.73), male gender (OR 1.18, 95% CI 1.05-1.32), neoplastic disease (OR 3.40, 95% CI, 2.85-4.07), immunodeficiency (OR 4.18, 95% CI 3.25-5.37), solid organ transplantation (OR 4.56, 95% CI 3.95-5.27) and enteral feeding (OR 2.21, 95% CI 1.05-4.62) were associated with increased risk of CDI. CONCLUSION: This systematic review and meta-analysis provides further evidence for the susceptibility factors of CDI to improve clinicians' awareness of CDI, and prevent C. difficile-associated diarrhoea in children.

Development and preliminary application of novel genomewide SSR markers for genetic diversity analysis of an economically important bio-control agent Platygaster robiniae (Hymenoptera: Platygastridae).

Platygaster robiniae Buhl and Duso (Hymenoptera: Platygastridae) is an egg-larvae parasitoid of the black locust gall midge (Obolodiplosis robiniae) (Haldeman) (Diptera: Cecidomyiidae) which is a serious invasive pest in China, where it attacks an important hardwood species, the black locust tree, Robini pseudoacacia L. (Fabales: Fabaceae). Despite the use of P. robiniae as an effective biocontrol agent, the absence of sequence data and other molecular markers have limited its genetic applications for pest management in forests. Simple-sequence repeats (SSRs) are valuable molecular markers for population genetic structure studies. In the present study, we identified 14,123 SSRs, of which 7799 SSR primer pairs were successfully designed. Subsequently, 240 SSR were chosen and tested with 48 P. robiniae accessions from two geographically separated populations in north and south China. Of these, 34 were polymorphic, with an average of three alleles (Na) and four genotypes (NG) each. The average values of observed heterozygosity (Ho) was 0.3514, expected heterozygosity (He) 0.4167, Shannon's information index (I) 0.7143, and polymorphism information content (PIC) 0.3558, respectively. Neighbour joining analysis (bootstrap 1000) revealed that Chengdu (CD) and Dangdong (DD) popluations clustered into two main divisions, and some individuals from two popluations clustered together as the third devision, which indicated the gene flow and genetic differentiation were present between two populations. Our finding indicates that these SSR markers will be useful for further studies on the genotype identification and genetic mapping of the genus Platygaster.

MiR-503-5p regulates cell epithelial-to-mesenchymal transition, metastasis and prognosis of hepatocellular carcinoma through inhibiting WEE1.

OBJECTIVE: To explore the role and underlying mechanism of MicroRNA-503-5p (miR-503-5p) in the metastasis and prognosis of hepatocellular carcinoma (HCC). MATERIALS AND METHODS: Sixty-three pairs of surgical HCC specimens and adjacent tissue samples were obtained, and Huh7, Hep3B, HCCLM3, MHCC-97H, MHCC-97L, LO2, and HEK293T cell lines were used for this study. The transwell assay was used to detect cell migration and invasion. Additionally, Western blot and quantitative Real Time-Polymerase Chain Reaction (qRT-PCR) were used to detect relative protein and mRNA expression levels, respectively. RESULTS: High miR-503-5p expression inhibited cell mobility in HCCLM3 cells, while low miR-503-5p expression promoted cell migration and invasion in HCCLM3 cells. The same effect of miR-503-5p on EMT was also observed in HCC through Western blot. We then performed a dual-luciferase assay to show that WEE1 is a direct target of miR-503-5p in HCC. Furthermore, WEE1 knockdown inhibited EMT and cell metastasis in HCC cells. WEE1 overexpression impaired the inhibitory effect of miR-503-5p in HCC CONCLUSIONS: MiR-503-5p inhibited cell EMT and metastasis through inhibiting WEE1, which predicted prognosis of HCC. MiR-503-5p and WEE1 may be used as potential biomarkers for the prognosis of HCC.

[Minimal residual disease in adults with Philadelphia chromosome negative acute lymphoblastic leukemia in high-risk].

Objective: To explore the significance of minimal residual disease (MRD) in predicting prognosis and guiding therapy of adults with Philadelphia-chromosome negative acute lymphoblastic leukemia (Ph(-) ALL) in high-risk. Methods: Data of newly diagnosed adults with Ph(-) ALL in high-risk who achieved CR were reviewed. Variables associated with outcome were identified by COX regression model and Landmark analysis. Results: A total of 177 patients, 99 (56%) cases male with a median age of 40 years (range, 16-65 years) were included in this study. Of them, 95 (54%) patients received allo-HSCT in CR(1). Multivariate analyses showed that MRD negativity after the first cycle of consolidation (HR=0.52, 95%CI 0.30-0.89, P=0.017) and achieving CR within 4 weeks (HR=0.43, 95%CI 0.24-0.79, P=0.006) were the factors significantly-associated with longer DFS, and allo-HSCT was associated with both longer DFS (HR=0.13, 95%CI 0.08-0.22, P<0.001) and OS (HR=0.24, 95%CI 0.15-0.41, P<0.001) . Landmark analysis was performed on 121 patients, of 85 patients achieving MRD negativity after the first cycle of consolidation, multivariate analyses showed that MRD negativity after the third cycle of consolidation was significantly-associated with longer DFS (HR=0.18, 95%CI 0.05-0.64, P=0.008) and OS (HR=0.14, 95%CI 0.04-0.50, P=0.003) . For the patients achieving MRD negativity after both the first and the third cycles of consolidation, the 3-year DFS rate in the allo-HSCT cohort had a higher trend compared with that in the chemotherapy cohort (75.2% vs 51.3%, P=0.082) , however, the 3-year OS rates in the 2 cohorts were similar (72.7% vs 68.7%, P=0.992) . In those with MRD positivity after the first and/or the third cycle of consolidation, 3-year DFS (64.8% vs 33.3%, P=0.006) and OS (77.0% vs 33.3%, P=0.028) rates in the allo-HSCT cohort were significantly higher than those in the chemotherapy cohort, and similar to those in the cohort achieving MRD negativity after both the first and the third cycles of consolidation and receiving allo-HSCT. Conclusions: MRD negativity after the first cycle of consolidation was a predictor for better outcome in adults with Ph(-) ALL in high-risk. The survival advantage of the allo-HSCT cohort was not pronounced compared with that in the chemotherapy cohort even in those with high-risk features but achieving MDR negativity after both the first and third cycles of consolidation. However, allo-HSCT could be a good option for the patients with MRD positivity after the first and/or the third cycle of consolidation.

A support vector machines approach for virtual screening of active compounds of single and multiple mechanisms from large libraries at an improved hit-rate and enrichment factor.

Support vector machines (SVM) and other machine-learning (ML) methods have been explored as ligand-based virtual screening (VS) tools for facilitating lead discovery. While exhibiting good hit selection performance, in screening large compound libraries, these methods tend to produce lower hit-rate than those of the best performing VS tools, partly because their training-sets contain limited spectrum of inactive compounds. We tested whether the performance of SVM can be improved by using training-sets of diverse inactive compounds. In retrospective database screening of active compounds of single mechanism (HIV protease inhibitors, DHFR inhibitors, dopamine antagonists) and multiple mechanisms (CNS active agents) from large libraries of 2.986 million compounds, the yields, hit-rates, and enrichment factors of our SVM models are 52.4-78.0%, 4.7-73.8%, and 214-10,543, respectively, compared to those of 62-95%, 0.65-35%, and 20-1200 by structure-based VS and 55-81%, 0.2-0.7%, and 110-795 by other ligand-based VS tools in screening libraries of >or=1 million compounds. The hit-rates are comparable and the enrichment factors are substantially better than the best results of other VS tools. 24.3-87.6% of the predicted hits are outside the known hit families. SVM appears to be potentially useful for facilitating lead discovery in VS of large compound libraries.

PROFEAT: a web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence.

Sequence-derived structural and physicochemical features have frequently been used in the development of statistical learning models for predicting proteins and peptides of different structural, functional and interaction profiles. PROFEAT (Protein Features) is a web server for computing commonly-used structural and physicochemical features of proteins and peptides from amino acid sequence. It computes six feature groups composed of ten features that include 51 descriptors and 1447 descriptor values. The computed features include amino acid composition, dipeptide composition, normalized Moreau-Broto autocorrelation, Moran autocorrelation, Geary autocorrelation, sequence-order-coupling number, quasi-sequence-order descriptors and the composition, transition and distribution of various structural and physicochemical properties. In addition, it can also compute previous autocorrelations descriptors based on user-defined properties. Our computational algorithms were extensively tested and the computed protein features have been used in a number of published works for predicting proteins of functional classes, protein-protein interactions and MHC-binding peptides. PROFEAT is accessible at http://jing.cz3.nus.edu.sg/cgi-bin/prof/prof.cgi.

Long noncoding RNA RUSC1-AS-N indicates poor prognosis and increases cell viability in hepatocellular carcinoma.

OBJECTIVE: This study aimed at exploring the expression and prognostic values of a novel long noncoding RNA RUSC1-AS-N in hepatocellular carcinoma (HCC), and to investigate the biological roles of RUSC1-AS-N in HCC cells. PATIENTS AND METHODS: RUSC1-AS-N expression in public available microarray data was analyzed. The expression of RUSC1-AS-N in our cohort containing 66 HCC tissues and paired adjacent non-cancerous hepatic tissues was measured by qRT-PCR. The correlation between RUSC1-AS-N expression and clinicopathological characteristics was evaluated by Pearson χ2-test. The prognostic value of RUSC1-AS-N was analyzed by Kaplan-Meier survival analysis. The biological roles of RUSC1-AS-N on HCC cell viability were evaluated by Glo cell viability assays and Ethynyl deoxyuridine incorporation assays. The effects of RUSC1-AS-N on HCC cell cycle were evaluated by fluorescence-activated cell sorting (FACS) analyses of propidium-iodide (PI) stained cells. The effects of RUSC1-AS-N on HCC cell apoptosis were evaluated by TdT-mediated dUTP nick end-labeling (TUNEL) assays. RESULTS: RUSC1-AS-N is upregulated in HCC tissues and associated with poor prognosis of HCC patients from GSE54238 and GSE40144. In our cohort, we further confirmed the upregulation of RUSC1-AS-N in HCC tissues. High expression of RUSC1-AS-N associates with large tumor size, vein invasion, encapsulation incompletion, advanced BCLC stage, and poor recurrence-free survival and overall survival. Functional assays revealed that RUSC1-AS-N knockdown markedly decreases cell viability, induces cell-cycle arrest and apoptosis of HCC cells. CONCLUSIONS: RUSC1-AS-N is upregulated and acts as an oncogene in HCC. RUSC1-AS-N may be a promising prognostic biomarker and therapeutic target for HCC.

Potentiation of irinotecan sensitivity by Se-methylselenocysteine in an in vivo tumor model is associated with downregulation of cyclooxygenase-2, inducible nitric oxide synthase, and hypoxia-inducible factor 1alpha expression, resulting in reduced angiogenesis.

Until recently, the use of Se-methylselenocysteine (MSC) as selective modulator of the antitumor activity and selectivity of anticancer drugs including irinotecan, a topoisomerase I poison, had not been evaluated. Therapeutic synergy between MSC and irinotecan was demonstrated by our laboratory in mice bearing human squamous cell carcinoma of the head and neck tumors. In FaDu xenografts, a poorly differentiated tumor-expressing mutant p53, the cure rate was increased from 30% with irinotecan alone to 100% with the combination of irinotecan and MSC. Cellular exposure to cytotoxic concentration of SN-38, the active metabolite of irinotecan (0.1 microM) alone and in combination with noncytotoxic concentration of MSC (10 microM) did not result in additional enhancement of chk2 phosphorylation and downregulation of specific DNA replication-associated proteins, cdc6, MCM2, cdc25A, nor increase in PARP cleavage, caspase activation and the 30-300 kb DNA fragmentation induced by SN-38 treatment. MSC did not alter significantly markers associated with apoptosis, nor potentiate irinotecan-induced apoptosis. These results indicate that apoptosis is unlikely to be one of the main mechanism associated with the observed in vivo therapeutic synergy. In contrast, significant downregulation of cyclooxygenase-2 (COX-2) expression and activity was observed in the cells exposed to SN-38 in combination with MSC compared to SN-38 alone. Moreover, the inhibition of PGE(2) production was also observed in the cells treated with the combination as compared with SN-38 alone. Analysis of tumor tissues at 24 h after treatment with synergistic modality of irinotecan and MSC revealed significant downregulation of COX-2, inducible nitric oxide synthase (iNOS) and hypoxia-induced factor-1alpha expression (HIF 1alpha). Moreover, decreased microvessel density was observed after irinotecan treatment with the addition of MSC. These results suggest that observed therapeutic synergy correlates with the inhibition of neoangiogenesis through the downregulation of COX-2, iNOS and HIF-1alpha expression.

Machine learning approaches for predicting compounds that interact with therapeutic and ADMET related proteins.

Computational methods for predicting compounds of specific pharmacodynamic and ADMET (absorption, distribution, metabolism, excretion and toxicity) property are useful for facilitating drug discovery and evaluation. Recently, machine learning methods such as neural networks and support vector machines have been explored for predicting inhibitors, antagonists, blockers, agonists, activators and substrates of proteins related to specific therapeutic and ADMET property. These methods are particularly useful for compounds of diverse structures to complement QSAR methods, and for cases of unavailable receptor 3D structure to complement structure-based methods. A number of studies have demonstrated the potential of these methods for predicting such compounds as substrates of P-glycoprotein and cytochrome P450 CYP isoenzymes, inhibitors of protein kinases and CYP isoenzymes, and agonists of serotonin receptor and estrogen receptor. This article is intended to review the strategies, current progresses and underlying difficulties in using machine learning methods for predicting these protein binders and as potential virtual screening tools. Algorithms for proper representation of the structural and physicochemical properties of compounds are also evaluated.