[Efficacy and initial clinical evaluation of optical genome mapping in the diagnosis of structural variations]

To investigate the efficacy and value of optical genome mapping (OGM) in detecting chromosomal structural variations. In a clinical study about high-precision analysis of genomic structural variation for complex genetic diseases, a retrospective study was performed on the cases with karyotyping at the department of Obstetrics and Gynecology, and Endocrinology of Peking Union Medical College Hospital from January to December 2021. Ten cases with abnormal karyotype was detected by OGM. Partial cases were verified by fluorescence in situ hybridization (FISH), SNP array or CNV-seq. Results of ten cases, nine were detected with abnormality by OGM, including unbalanced chromosomal rearrangements (n=3), translocation (n=5) and paracentric inversion (n=1), and the results were in concordance with other standard assays. However, one case with breakpoint and reconnected at centromere has not been detected. In conclusion, ten samples were comprehensively analyzed by karyotyping, FISH, SNP array or CNV-seq, and OGM, and results demonstrated that optical genome mapping as a new technology can not only detect unbalanced rearrangements such as copy number variants as well as balanced translocations and inversions, but more importantly, it can refine breakpoints and orientation of duplicated segments or insertions. So it can contribute to the diagnosis of genetic diseases and prevent birth defect. However, the current technology is not yet capable of detecting breakpoints of balanced structural variations lying within unmapped regions.

[Clinical significance of No.11p posterior lymph nodes dissection in gastric cancer surgery]

Objective: To analyze the association of No.11p posterior lymph node metastasis with clinicopathological features and its prognostic significance in gastric cancer. Methods: A single-center retrospective cohort study was conducted. Clinicopathological data of patients with primary gastric cancers undergoing No.11p posterior lymph node dissection from January 2016 to December 2020 were retrieved from the Database of Gastric Cancer, West China Hospital, Sichuan University. Case inclusion criteria: (1) gastric cancer proved by pathology; (2) radical resection with intraoperative No.11p posterior lymph node dissection; (3) operations performed by the same surgical team; (4) no previous history of other malignant tumors and no concurrent malignant tumors. Those with stump gastric cancer, history of gastrectomy, neoadjuvant chemotherapy, incomplete clinicopathological data and lost to follow-up were excluded. During the operation, the upper edge of the pancreas was retracted forward to expose the area between the upper edge of the pancreas and the splenic vessels. The proximal segment of the splenic artery was skeletonized to remove lymphatic tissue anterior and superior to the splenic artery for No.11p lymph node dissection. For patients with lymphadenopathy in the area between the splenic artery and the splenic vein, dissection was performed. The enlarged lymph nodes were labeled with titanium clips and named as No.11p posterior lymph node. Pathological examination was performed separately after the specimen was isolated. Statistical analysis was performed using R software. Results: A total of 127 gastric cancer patients, who underwent No.11p posterior lymph nodes dissection were included in this study, of which 120 patients without No.11p posterior lymph nodes metastasis (No.11p posterior lymph nodes negative) and 7 patients with No.11p posterior lymph nodes metastasis (No.11p posterior lymph nodes positive). A total of 8 metastatic No.11p posterior lymph nodes were detected in 7 patients, metastasis rate and with a ratio of 5.5% (7/127) and 6.8% (8/127), respectively. In the subgroup analysis of T3-4 stage patients, the metastasis rate and ratio of No.11p posterior lymph nodes were 9.0% (7/78) and 10.7% (8/75), respectively. Compared to negative cases, patients with No.11p posterior lymph nodes metastasis had larger tumor (P=0.002), higher proportion of Borrmann type Ⅲ and Ⅳ tumors (P=0.005), more metastatic lymph nodes (P<0.001), more advanced T stage (P=0.043), N stage (P=0.004) and TNM stage (P=0.015). In survival analysis, patients with No.11p posterior lymph node metastasis had a significantly worse prognosis than those without metastasis after adjusting for TNM stage (hazard ratio=3.009, 95% confidence interval: 1.824-4.964, P<0.001). Conclusions: The No.11p posterior lymph node metastasis in gastric cancer is associated with worse prognosis. For patients of T3-4 stage gastric cancer, No.11p posterior lymph node dissection should be emphasized during radical operation.

Significance of miRNA in enhancement of flavonoid biosynthesis

Flavonoid metabolism shows very strong plasticity in plant development and coping with the changing environment. Flavonoid biosynthesis is regulated by many metabolic pathways, including transcriptional regulation, post-transcriptional control, post-translational regulationand epigenetic regulation. miRNA is a form of endogenous noncoding single-strand small molecule RNA that primarily regulates the expression of target genes horizontally after transcription through splicing and translational suppression. It also plays an important role in regulating plant growth and development, secondary metabolism and biotic and abiotic stress. miRNA can regulate the formation of flavonoids by acting on structural genes or indirectly by using an MBW transcription complex comprising MYB-bHLH-WD40. This study summarizes the biosynthesis and mechanisms of miRNA, and provides a summary of the mechanisms of miRNAs involved in production of flavonoids, in order to elucidate the biosynthesis pathway and complex regulatory network of plant flavonoids. We aim to provide new insights into improving the content of flavonoid active ingredients in plants.

[Investigation on awareness of schistosomiasis control knowledge among residents going to Africa in Taizhou City]

OBJECTIVE

To understand the awareness of schistosomiasis control knowledge among people going to Africa in Taizhou City, to provide insights into the development of control measures for imported schistosomiasis.

METHODS

During the period from July to October, 2019, a face-to-face questionnaire survey was conducted among people that had gone to African countries between 2015 and 2018 and return to China now, including awareness of schistosomiasis control knowledge, type of living and drinking water and contact with river and lake water.

RESULTS

A total of 573 peoples going to Africa were investigated, and 572 eligible questionnaires were recovered. Among the 572 people interviewed, senior high school and above was the predominant education level (509 people, 89.0%), labor was the predominant aim (543 people, 94.9%), and Angola (52.3%) and Algeria (15.9%) were predominant destiny countries. There were 7.2% of the interviewees hearing about African schistosomiasis, 19.8% knowing infections by contact with infested water, and 36 people with a history of contact with river and lake water. In addition, 270 interviewees used running water as drinking water and 276 used running water as living water.

CONCLUSIONS

The awareness rate of schistosomiasis control knowledge is low among people going to Africa in Taizhou City. Health education pertaining to schistosomiasis control is required to be improved among those going to Africa in Taizhou City to increase the awareness of schistosomiasis prevention and avoid parasitic infections.

An application research for near-surface repository of strontium-90 sorption kinetic model on mudrocks

In this study,90Sr was used as the test radionuclide to characterize the sorption kinetics and effects of initial 90Sr activity and remaining 90Sr in solid concentration were simulated for a near-surface repository. The study focused on the sorption characteristics of radionuclides in unsaturated groundwater environment (or vadose zone) is the important information for investigating the near-surface disposal of intermediate and low-level radioactive waste (ILLW). Moreover, the 90Sr sorption experiments reached equilibrium within 56 h, which fit to the first order sorption kinetic model, and the remaining 90Sr in mudrock samples showed obvious sorption equilibrium hysteresis, which fit to the second order sorption kinetic model. Before reaching the maximum sorption capacity, the sorption rate constant increases with 90Sr increasing; the distribution coefficient (Kd) of 56 h decreases with the remaining 90Sr decreasing. In addition, it showed that the slow sorption process dominated before the sorption reaches equilibrium. In fact, a reliable safety assessment methodology for on-going near-surface repository required a lot of the radionuclides parameters with local environment including the radionuclides sorption/desorption rate constant and maximum sorption capacity.

[Insular infraorbital neurovascular pedicle labial salivary gland transplantation for severe dry eye: a case report]

A 52-year-old male presented to Beijing Tongren Hospital with a 5-year history of bilateral dry eyes. He had been diagnosed with Steven-Johnson syndrome due to allergy to cold medication. On examination, the Schirmer I test value was 0 mm, the tear break-up time was 0 s, and corneal fluorescein staining showed corneal epithelial erosion with partial fusion in both eyes. The clinical diagnosis was dry eyes (severe) and Steven-Johnson syndrome. No significant effect was observed after use of artificial tears and anti-inflammatory eye drops and tear punctal embolization. Then an insular infraorbital neurovascular pedicle labial salivary gland transplantation was performed in the right eye. During the 1-year postoperative follow-up, the symptoms and signs were significantly improved in the operated eye, and the surgical results were satisfactory. (Chin J Ophthalmol, 2021, 57: 946-948).

Pan-Asian adaptation of the EHNS-ESMO-ESTRO Clinical Practice Guidelines for the diagnosis, treatment and follow-up of patients with squamous cell carcinoma of the head and neck

The most recent version of the European Society for Medical Oncology (ESMO) Clinical Practice Guidelines for the diagnosis, treatment and follow-up of squamous cell carcinoma (SCC) of the oral cavity, larynx, oropharynx and hypopharynx was published in 2020. It was therefore decided by both the ESMO and the Korean Society of Medical Oncology (KSMO) to convene a special, virtual guidelines meeting in July 2021 to adapt the ESMO 2020 guidelines to consider the potential ethnic differences associated with the treatment of SCCs of the head and neck (SCCHN) in Asian patients. These guidelines represent the consensus opinions reached by experts in the treatment of patients with SCCHN (excluding nasopharyngeal carcinomas) representing the oncological societies of Korea (KSMO), China (CSCO), India (ISMPO), Japan (JSMO), Malaysia (MOS), Singapore (SSO) and Taiwan (TOS). The voting was based on scientific evidence and was independent of the current treatment practices and drug access restrictions in the different Asian countries. The latter was discussed when appropriate. This manuscript provides a series of expert recommendations (Clinical Practice Guidelines) which can be used to provide guidance to health care providers and clinicians for the optimisation of the diagnosis, treatment and management of patients with SCC of the oral cavity, larynx, oropharynx and hypopharynx across Asia.

[Establishment of a deep learning-based visual model for intelligent recognition of Oncomelania hupensis]

OBJECTIVE

To establish a deep learning-based visual model for intelligent recognition of Oncomelania hupensis, the intermediate host of Schistosoma japonicum, and evaluate the effects of different training strategies for O. hupensis image recognition.

METHODS

A total of 2 614 datasets of O. hupensis snails and 4 similar snails were generated through field sampling and internet capture, and were divided into training sets and test sets. An intelligent recognition model was created based on deep learning, and was trained and tested. The precision, sensitivity, specificity, accuracy, F1 score and Youden index were calculated. In addition, the receiver operating characteristic (ROC) curve of the model for snail recognition was plotted to evaluate the effects of "new learning", "transfer learning" and "transfer learning + data enhancement" training strategies on the accuracy of the model for snail recognition.

RESULTS

Under the "transfer learning + data enhancement" strategy, the precision, sensitivity, specificity, accuracy, Youden index and F1 score of the model were 90.10%, 91.00%, 97.50%, 96.20%, 88.50% and 90.51% for snail recognition, which were all higher than those under both "new learning" and "transfer learning" strategies. There were significant differences in the sensitivity, specificity and accuracy of the model for snail recognition under "new learning", "transfer learning" and "transfer learning + data enhancement" training strategies (all P values < 0.001). In addition, the area under the ROC curve of the model was highest (0.94) under the "transfer learning + dataenhancement" training strategy.

CONCLUSIONS

This is the first visual model for intelligent recognition of O. hupensis based on deep learning, which shows a high accuracy for snail image recognition. The "transfer learning + data enhancement" training strategy is helpful to improve the accuracy of the model for snail recognition.

[Development of a fluorescent recombinase-aided isothermal amplification-based nucleic acid assay for detection of Leishmania]

OBJECTIVE

To develop a fluorescent recombinase-aided isothermal amplification (RAA)-based nucleic acid assay for detection of Leshimania.

METHODS

Specific primers and probes were designed targeting Leishmania internal transcribed spacer 1 (ITS1) gene for RAA assay, and a fluorescent RAA assay was developed for detection of Leishmania following screening of primer pairs and optimization of primer and probe concentrations. The sensitivity of RAA assay for detection of Leishmania was evaluated using recombinant plasmid containing Leishmania ITS1 gene sequences at different copies and Leshimania genomic DNA at different concentrations as templates, and the specificity of RAA assay for detection of Leishmania was evaluated using the genomic DNA of transfusion-transmitted parasites, including Babesia microti, Toxoplasma gondii, Plamodium vivax, P. ovale, P. falciparum, P. malariae, L. donovani and L. infantum.

RESULTS

After the optimal primer pair was screened from 9 pairs of primer combinations, the final primer and probe concentrations were optimized as 0.3 μmol/L and 0.08 μmol/L, respectively. Nucleic acid detection of Leishmania was completed by the fluorescent RAA assay at an isothermal temperature of 39 °C within 20 min. Remarkable florescent signals were seen within 5 min following RAA detection of genomic DNA of L. donovani and L. infantum, and no cross-reactions were observed with B. microti, T. gondii, P. vivax, P. ovale, P. falciparum or P. malariae. The lowest limitation of detection of the fluorescent RAA assay was 10 copies/μL recombinant plasmid containing Leishmania ITS1 gene sequences and 1 fg/μL Leishmania genomic DNA.

CONCLUSIONS

A rapid, simple, sensitive and specific fluorescent RAA assay is successfully developed for detection of L. donovani and L. infantum, which is effective for field screening of leishmaniasis.

Genome-wide single nucleotide polymorphism array and whole-genome sequencing reveal the inbreeding progression of Banna minipig inbred line

Inbred pigs are promising animal models for biomedical research and xenotransplantation. Established in 1980, the Banna minipig inbred (BMI) line originated from a sow and its own male offspring. It was selected from a small backcountry minority Lahu village, where records show that no other pig breed has ever been introduced. During the inbreeding process, we perfomed extreme inbreeding over 23 consecutive generations using full-sibling or parent-offspring mating. In order to investigate the inbreeding effects in BMI pigs across generations over the past 40 years, in this study we conducted a genome-wide SNP genotyping of the last 10 generations, representing generations 14-23. In total, we genotyped 57,746 SNPs, corresponding to an average decrease in heterozygosity rate of 0.0078 per generation. Furthermore, we were only able to identify 18,216 polymorphic loci with a MAF larger than 0.05, which is substantially lower than the values in previous reports on other pig breeds. In addition, we sequenced the genome of the first pig in the twenty-third generation (inbreeding coefficient 99.28%) to an average coverage of 12.4× to evaluate at the genome level the impact of advanced inbreeding. ROH analysis indicates that BMI pigs have longer ROHs than Wuzhishan and Duroc pigs. Those long ROH regions in BMI pigs are enriched for distinct functions compared with the highly polymorphic regions. Our study reveals a genome-wide allele diversity loss during the progress of inbreeding in BMI pigs and characterizes ROH and polymorphic regions as a result of inbreeding. Overall, our results indicate the successful establishment of the BMI line, which paves the way for further in-depth studies.