Resolving single-cell copy number profiling for large datasets.

The advances of single-cell DNA sequencing (scDNA-seq) enable us to characterize the genetic heterogeneity of cancer cells. However, the high noise and low coverage of scDNA-seq impede the estimation of copy number variations (CNVs). In addition, existing tools suffer from intensive execution time and often fail on large datasets. Here, we propose SeCNV, an efficient method that leverages structural entropy, to profile the copy numbers. SeCNV adopts a local Gaussian kernel to construct a matrix, depth congruent map (DCM), capturing the similarities between any two bins along the genome. Then, SeCNV partitions the genome into segments by minimizing the structural entropy from the DCM. With the partition, SeCNV estimates the copy numbers within each segment for cells. We simulate nine datasets with various breakpoint distributions and amplitudes of noise to benchmark SeCNV. SeCNV achieves a robust performance, i.e. the F1-scores are higher than 0.95 for breakpoint detections, significantly outperforming state-of-the-art methods. SeCNV successfully processes large datasets (>50 000 cells) within 4 min, while other tools fail to finish within the time limit, i.e. 120 h. We apply SeCNV to single-nucleus sequencing datasets from two breast cancer patients and acoustic cell tagmentation sequencing datasets from eight breast cancer patients. SeCNV successfully reproduces the distinct subclones and infers tumor heterogeneity. SeCNV is available at https://github.com/deepomicslab/SeCNV.

DeepHost: phage host prediction with convolutional neural network.

Next-generation sequencing expands the known phage genomes rapidly. Unlike culture-based methods, the hosts of phages discovered from next-generation sequencing data remain uncharacterized. The high diversity of the phage genomes makes the host assignment task challenging. To solve the issue, we proposed a phage host prediction tool-DeepHost. To encode the phage genomes into matrices, we design a genome encoding method that applied various spaced $k$-mer pairs to tolerate sequence variations, including insertion, deletions, and mutations. DeepHost applies a convolutional neural network to predict host taxonomies. DeepHost achieves the prediction accuracy of 96.05% at the genus level (72 taxonomies) and 90.78% at the species level (118 taxonomies), which outperforms the existing phage host prediction tools by 10.16-30.48% and achieves comparable results to BLAST. For the genomes without hits in BLAST, DeepHost obtains the accuracy of 38.00% at the genus level and 26.47% at the species level, making it suitable for genomes of less homologous sequences with the existing datasets. DeepHost is alignment-free, and it is faster than BLAST, especially for large datasets. DeepHost is available at https://github.com/deepomicslab/DeepHost.

Risk factors for postoperative nausea and vomiting in patients undergoing thoracic surgery / 中华麻醉学杂志

Objective:To identify the risk factors for postoperative nausea and vomiting (PONV) in the patients undergoing thoracic surgery.Methods:The medical records of patients of either sex, aged 18-80 yr, of American Society of Anesthesiologists physical status Ⅰ-Ⅲ, underwent elective thoracic surgery from January 2018 to January 2020, were collected retrospectively.The age, gender, educational background, American Society of Anesthesiologists physical status, motion sickness, history of smoking, history of drinking, history of heart disease, history of hypertension, history of diabetes, preoperative blood routine, liver function, parameters of electrolytes; operation method, type of operation, operation time, intraoperative nerve block, consumption of dexamethasone before anesthesia induction and intraoperative sufentanil and dexmedetomidine, use of postoperative patient-controlled intravenous analgesia (PCIA), and postoperative rescue opioid analgesics and antiemetics were recorded.The patients were divided into PONV group and non-PONV group depending on the occurrence of nausea and vomiting within 24 h after operation.PONV group was further divided into nausea group (PON group) and vomiting group (POV group) according to whether vomiting occurred.Logistic regression analysis was used to identify the risk factors for PONV.Results:A total of 3 791 patients were enrolled in this study, with 144 cases in PONV group and 3 647 cases in non-PONV group.The incidence of PONV was 3.80%.There were 38 patients in POV group, and the incidence was 26.4%.The results of logistic regression analysis showed that motion sickness, female, pulmonary wedge resection, postoperative PCIA and increased use of postoperative rescue opioid analgesics were risk factors for PONV in the patients undergoing thoracic surgery, intraoperative use of dexmedetomidine was a protective factor for PONV; motion sickness, female and history of hypertension were risk factors for postoperative vomiting in the patients at risk for PONV ( P<0.05). Conclusions:Motion sickness, female, pulmonary wedge resection, postoperative PCIA, and increased use of postoperative rescue opioid analgesics are risk factors and intraoperative use of dexmedetomidine is a protective factor for PONV in the patients undergoing thoracic surgery; motion sickness, female and history of hypertension are risk factors for postoperative vomiting in the patients at risk for PONV.

Risk factors for postoperative sleep disturbances in elderly patients undergoing thoracic surgery / 中华麻醉学杂志

Objective:To identify the risk factors for postoperative sleep disturbances in elderly patients undergoing thoracic surgery.Methods:A total of 200 elderly patients of both sexes, aged>65 yr, of American Society of Anesthesiology physical status Ⅱ or Ⅲ, scheduled for elective thoracic surgery, were enrolled in the study.Data regarding patient age, gender, body mass index (BMI), American Society of Anesthesiologists physical status, history of hypertension, history of diabetes mellitus, operation method, type of operation, operation time, intraoperative blood loss, use of intraoperative nerve block and use of dexmedetomidine in patient-controlled intravenous analgesia (PCIA) were collected.The patients were followed up after operation, the occurrence of postoperative pain at 48 h after operation was recorded, and patients′ subjective sleep quality at 48 h after operation was assessed using the Pittsburgh Sleep Quality Index Questionnaire (PSQI). Patients were divided into 2 groups according to PSQI score: non-postoperative sleep disturbances group (PSQI score<5) and postoperative sleep disturbances group (PSQI score≥5). A multivariate logistic regression was used to identify the risk factors for postoperative sleep disturbances in elderly patients undergoing thoracic surgery.Results:A total of 169 patients were included in this study, and the incidence of postoperative sleep disturbances was 45%.The results of logistic regression analysis showed that history of preoperative insomnia, BMI≥24 kg/m 2, diabetes mellitus, thoracic surgery, radical resection of lung cancer, radical resection of esophageal cancer, operation time≥120 min and moderate and severe postoperative pain were risk factors for postoperative sleep disturbances in elderly patients undergoing thoracic surgery, and use of intraoperative nerve block and use of dexmedetomidine during PCIA were protective factors for postoperative sleep disturbances in elderly patients ( P<0.05). Conclusion:History of preoperative insomnia, BMI≥24 kg/m 2, diabetes mellitus, thoracic surgery, radical resection of lung cancer, radical resection of esophageal cancer, operation time≥120 min, moderate and severe postoperative pain are risk factors and use of intraoperative nerve block and use of dexmedetomidine during PCIA are protective factors for postoperative sleep disturbances in elderly patients undergoing thoracic surgery.

Recombinant human brain myelin basic protein and its antibody preparation / 中国组织工程研究

BACKGROUND: Central nervous system (CNS) myelin is made up of 70% lipids and 30% proteins with human brain myelin basic protein (hMBP) constituting 1/3 of the proteins. MBP is a family of proteinswith four isoforms only in human brain. OBJECTIVE: To investigate the expression of MBP and its immunological function. DESIGN: Single sample study. SETTING: Department of Biochemistry and Molecule Biology, Huaxi College of Priclinical Medicine and Forensic Medicine, Sichuan University. MATERIALS: This experiment was conducted at Department of Bio chemistry and Molecule Biology, Huaxi College of Priclinical Medicine and Forensic Medicine, Sichuan University from August 2003 to March 2004. Relative molecular weight was 215000 hMBP cDNA clone pGEMP,prokaryotic expression recombinant vector pGEX-5T, T4 DNA Ligase,calf intestine alkaline phosphates, X-gal, IPTG, 123 Ladder (BRL), nitrocellu lose ,4-chloro-1-Naphthol;MBP and Anti- MBP ELISA kit. INTERVENTIONS: ①hBMP gene cDNA clone segment was digested with EcoR1 and BamH1; ②Construction and transformation of the recombinant expression vector p5TMP; ③ The growth and induced expression of the recombinant expression vector transformed bacteria; ④ Preparation of the antibody of recombinant hMBP. MAIN OUTCOME MEASURES: ① Detection and identification of the expressed protein product; ② Detection and identification of hMBP anti body. RESULTS: ① Screening and identification of recombinant MBP: The 4 999 bp pGEX-5T DNA and 557 bp MBP inserted fragment were obtained, indicating that the white colonies contained recombinant expression plasmid of exogenous DNA; ② A dense band disappeared from the control plasmid while a new special polypeptide band with apparent molecular weight 42 000 was detected in recombinant cell lysate; ③After 5 subcutaneous injections, antibody was obtained at 1:16 titer. The specificity of the antibody to MBP was confirmed.CONCLUSION: Compared with the original expression vector, the new constructed expression vector containing 215 000 MBP exons Ⅰ-Ⅶ coding sequence was not only without the coding area defects of 34 bp in 5' sequence but also expressed more highly in prokaryote obviously. In addition, the recombinant MBP antibody prepared successfully.

Recombinant human brain myelin basic protein and its antibody / 生物医学工程学杂志

We constructed the expression vector by inserting 21.5 KDa MBP human brain full-length cDNA coding sequence digested with restriction enzyme EcoR I and Sal I into downstream of pGEX-5T expression vector. The recombinant vector p5TMP was transformed into E. coli and the positive clonies were selected and incubated in LB medium induced by IPTG (isopropyl- -D-thiogalactoside). A new polypeptide band with apparent molecular weight 42 KDa was detected in transformed cell lysates by SDS-PAGE. Western blotting analysis confirmed that this fusion protein reacted specifically with antibodies to MBP, the expression level of MBP was about 414.6 mg/L medium estimated by immuno-dot blot, ELISA and absorbance scanning. Newzealand rabbits were immunized by subcutaneous injection of the purified recombinant MBP. The titer was obtained at 1:16 after 5 injections. The specificity of the antibody to MBP was confirmed by immuno-blot and Western blotting.

The cloning and sequencing of H-2Kk gene cDNA of 615 mice / 华西口腔医学杂志

<p><b>OBJECTIVE</b>The purposes of this study were to clone and sequence the major histocompatibility complex type I (MHC I) molecular antigen recognizing gene (H-2Kk) of 615 mice, and to provide the functional gene for transgenic therapy.</p><p><b>METHODS</b>The 1.4 kb full-length fragment of H-2Kk gene complementary DNA (cDNA) was amplified from the total RNA of 615 mouse liver by using reverse transcription polymerase chain reaction (RT-PCR). The cDNA was inserted into PGEM3Zf(+) vector directionally, and the competent E. coli JM109 was transformed with the ligated product. The recombinant PGEM3Zf(+)-H-2Kk cDNA plasmid was obtained using restricted enzyme analysis of the transfectants. The complete sequence of 615 mouse H-2Kk cDNA was determined by using Sanger's method.</p><p><b>RESULTS</b>The sequences of 615 mouse H-2Kk cDNA were 99% similar with those of H-2Kk cDNA which were reported by other researchers, and the sequences encoding antigen recognizing regions (ARS) were identical with each other.</p><p><b>CONCLUSION</b>The authors cloned the MHC I molecular antigen recognizing gene (H-2Kk) of 615 mice successfully and got the functional gene of MHC I.</p>