Imputation of missing milk Fourier transform mid-infrared spectra using existing milk spectral databases: A strategy to improve the reliability of breeding values and predictive models.

The use of milk Fourier transform mid-infrared (FT-MIR) spectrometry to develop management and breeding tools for dairy farmers and industry is growing and supported by the availability of numerous new predicted phenotypes to assess the nutritional quality of milk and its technological properties, but also the animal health and welfare status and its environmental fingerprint. For genetic evaluations, having a long-term and representative spectral dairy herd improvement (DHI) database improves the reliabilities of estimated breeding values (EBV) from these phenotypes. Unfortunately, most of the time, the raw spectral data used to generate these estimations are not stored. Moreover, many reference measurements of those phenotypes, needed during the FT-MIR calibration step, are available from past research activities but lack spectra records. So, it is impossible to use them to improve the FT-MIR models. Consequently, there is a strong interest in imputing those missing spectra. The innovative objective of this study was to use the existing large spectral DHI database to estimate missing spectra by selecting probable spectra using, as the match criteria, common dairy traits recorded for a long time by DHI organizations. We tested 4 match criteria combinations. Combination 1 required to have equal fat and protein contents between the sample for which a spectrum was to be estimated and the reference samples in the DHI database. Combination 2 also required an equal urea content. Combination 3 requested equal fat, protein, and lactose contents. Finally, combination 4 included all criteria. When more than one spectrum was found during the search, their average was the estimated spectrum for the query sample. Concretely, this study estimated missing spectra for 1,700 samples using 2,000,000 spectral DHI records. For assessing the effect of this spectral estimation on the prediction quality, FT-MIR equations were used to predict 11 phenotypes, selected as their quantification used different FT-MIR regions. They were related to the milk fat and mineral composition, lactoferrin content, quantity of eructed methane, body weight (BW), and dry matter intake. The accuracy between predictions obtained from actual and estimated spectra was evaluated by calculating the mean absolute error (MAE). The criteria in the fourth and second combinations were too strict to estimate a spectrum for most samples. Indeed, for many samples, no spectra with the same values for those matching criteria was found. The third match criteria combination had a poorer prediction performance for all studied traits and spectral absorptions than the first combination due to fewer matched samples available to compute the missing spectrum. By allowing a range for matching lactose content (±0.1 g/dL milk), we showed that this new combination increased the number of selected samples to compute missing spectra and predict better the infrared absorption at different wavenumbers, especially those related to the lactose quantification. The prediction performance was further improved by performing queries on the entire Walloon DHI spectral database (6,625,570 spectra), and it varied among the studied phenotypes. Without considering the traits used for the matching, the best predictions were obtained for the content of saturated fatty acids (MAE = 0.15 g/dL milk) and BW (MAE = 12.80 kg). Yet, the predictions for the unsaturated fatty acids were less accurate (MAE = 0.13 and 0.018 g/dL milk for monounsaturated and polyunsaturated fatty acids), likely because of the poorer predictions of spectral regions related to long-chain fatty acids. Similarly, poorer predictions were observed for the amount of methane eructed by dairy cows (MAE = 47.02 g/d), likely because it is not directly related to fat content or composition. Prediction accuracies for the remaining traits were also low. In conclusion, we observed that increasing the number of relevant matching criteria helps improve the quality of FT-MIR predicted phenotypes and the number of spectra used during the search. So, it would be of great interest to test in the future the suitability of the developed methodology with large-scale international spectral databases to improve the reliability of EBV from these FT-MIR-based phenotypes and the robustness of FT-MIR predictive models.

[A comparative analysis of the clinical symptoms of benign paroxysmal positional vertigo between older and young and middle-aged patients].

Objective: To compare the differences in clinical symptoms and the time required for diagnosis of benign paroxysmal positional vertigo (BPPV) between older patients and young and middle-aged patients in the structured inquiry of dizziness history. Methods: The medical records of 6 807 patients diagnosed with BPPV from the Vertigo Database of Vertigo Clinical Diagnosis, Treatment, and Research Center of Beijing Tiantan Hospital, Capital Medical University, between January 2019 and October 2021 were retrospectively analyzed. The data included basic demographic information, clinical symptoms in a structured medical history questionnaire, and the time interval from the appearance of BPPV symptoms to diagnosis consultation. The patients were divided into the young and middle-aged group (<65 years old) and the older group (≥65 years old). The differences in clinical symptoms and consultation time were compared between these two groups. Categorical variables were represented by numbers (%), and compared using Chi-squared tests or Fisher's exact probability test for analysis; whereas, continuous variables conforming to normal distribution were represented by mean±standard deviation. Both data groups were compared and analyzed by Student's t-test. Results: The mean age of the older group was 65-92 (71±5) years, while the mean age of the middle-aged group was 18-64 (49±12) years. The incidence of vertigo (42.5% vs. 49.1%, χ2=23.69, P<0.001); vertigo triggered by changes in position of the head or body (52.4% vs. 58.7%, χ2=22.31, P<0.001); and autonomic symptoms (10.1% vs. 12.4%, χ2=7.09, P=0.008) were lower, but hearing loss (11.8% vs. 7.8%, χ2=27.36, P<0.001) and sleep disorders (18.5% vs. 15.2%, χ2=11.13, P=0.001) were higher in the older group than in the young and middle-aged group. The time from the appearance of dizziness to diagnosis was commonly longer in the older patient group than the other group (55.0% vs. 38.5%, χ2=55.95, P<0.001). Conclusions: Older patients with BPPV have more atypical symptoms and complex concomitant symptoms than young and middle-aged patients. For older patients with dizziness, positional testing is needed to confirm the possibility of BPPV even if the clinical symptoms are atypical.

[Scimitar syndrome with pulmonary sequestration containing carcinoma: a case report].

We reported the manifestations, auxiliary examination, and treatment courses of a case of scimitar syndrome with pulmonary sequestration containing carcinoma. The clinical characteristics of scimitar syndrome with pulmonary sequestration, pulmonary sequestration containing carcinoma were summarized based on the data of this case and the related literatures before January 2022. Scimitar syndrome can coexist with ipsilateral pulmonary sequestration. Because sequestered lung tissue has a risk of malignant transformation, a cancer screening test is useful for early diagnosis and timely treatment.

[Establishment and analysis of prediction model for invasive subsolid pulmonary nodules based on radiomics].

Objective: To evaluate the best radiomic features based prediction model for identifying the histopathological subtypes of invasive adenocarcinoma or noninvasive pulmonary nodules appearing as subsolid nodules. Methods: A total of 352 patients (108 males and 244 females, median age was [M(Q1,Q3)]57 (50,65), underwent high-resolution chest CT and appearing as subsolid nodules and further treated by surgical resection whose subsequently pathological results were classified as atypical adenomatous hyperplasia (AAH), carcinoma in situ (AIS), microinvasive carcinoma (MIA), invasive adenocarcinoma (IA), from January 2015 to September 2019, in Radiology Department of Zhongda Hospital Affiliated to Southeast University and Jinling Hospital, Medical School of Nanjing University were retrospectively collected. They were divided into non-invasive group (n=233) and invasive group (n=119) according to pathological findings. According to the ratio of training set: internal test set: external test set, which is about 3∶1∶1,the patients in Zhongda Hospital Affiliated to Southeast University were randomly divided into training set (n=215, non-IA∶IA 155∶60) and internal test set(n=69, non-IA∶IA 52∶17), meanwhile a certain number of patients in Jinling Hospital, Medical School of Nanjing University(n=68, non-IA∶IA 26∶42)were randomly selected as an independent external test set. Particular quantitative parameters of the nodules, radiomic features, morphological characteristics, clinical data, and serum tumor markers were recorded. Radiomic label was constructed using LASSO regression method. The morphological model, CT model and comprehensive model were constructed by binary logistic regression and were verified in test sets, respectively. Results: Shape_MinorAxis(Gradient),Glszm_ZoneEntropy(LBP) were selected as the two most significant features based on training set. Radiomic tag=1.065 75×Shape_MinorAxis(Gradient)+0.030 58×Glszm_ZoneEntropy(LBP). Comparing the prediction performance of all models in each data cohort, the CT model (Ln(P/1-P)=-2.417 11+1.031 60×Radimic tag+1.203 06×Diameter+1.614 21×(Pleural indentation sign = Y) constructed by radiomic label, pleural depression, and quantitative parameters (diameter, average density) was much better than other models and was chosen as the optimal model, with an AUC of CT models in training cohort and test cohort was 0.954 (95%CI: 0.927-0.981), 0.865 (95%CI:0.764-0.966), better than morphological model 0.857 (95%CI:0.796-0.918), 0.818(95%CI: 0.686-0.949) and comprehensive model 0.951(95%CI: 0.921-0.981), 0.856(95%CI: 0.730-0.982), respectively. Conclusion: The integrative CT model has a better prediction efficiency for identifying invasive or noninvasive nodules appearing as subsolid nodules.

[Establishment of quality evaluation criteria for out-patient medical records of cancer pain and assessment of its application effect].

Objective: To establish the quality evaluation criteria for out-patient medical records of cancer pain and evaluate the effect of its application. Methods: The evaluation criterion was established based on Delphi method for out-patient medical records of cancer pain in the Affiliated Huai'an No.1 People's Hospital of Nanjing Medical University. Firstly, the weight of each evaluation indicator was calculated by the method of Attribute Hierarchical Model in combination with technique for order preference by similarity to solution (AHM-TOPSIS), and out-patient medical records of 50 cancer pain patients (group A, 150 records) received in June 2020 were assessed comprehensively. Secondly, the relative closeness (Ci value) between the writing quality and the ideal solution was calculated, as well as the proportion of evaluation indicators which were lack of standardization. Thirdly, the corresponding countermeasures were adapted based on the results of assessment. Finally, another 50 medical records (156 records) received in October 2021 were re-evaluated by the same method, and the differences of quality of medical record and proportion of each evaluation indicator which was lack of standardization before and after the intervention were compared. Results: A specific criterion which contained integrity of materials required for the medical records, documents of the complaints and medical history of cancer pain, description of the previous medical treatment for cancer pain, regular assessment of cancer pain and its' document, quantitative assessment and its' document, comprehensive assessment and its' document, dynamic assessment and its' document, reasonable of pain medication, reasonable of the drug usage and dosage, reasonable adjustment of the drug variety or dosage, prevention of adverse reactions of analgesic drugs and its' document, evaluation and management of adverse reactions of analgesic drugs and its' document (12 indicators) was established to evaluate the out-patient medical records of cancer pain. The proportion of medical records which Ci≥0.6 was 62.0% (93/150) in group A before the intervention. It was increased to 84.6% (132/156) in group B after the intervention and the difference was statistically significant (P<0.001). Furthermore, the proportions of comprehensive assessment of cancer pain which were lack of standardization, prevention of adverse reaction, quantitative evaluation and dynamic assessment of cancer pain accounted for a higher level, which was 64.0% (96/150), 55.3% (83/150), 54.7% (93/150) and 52.7% (79/150) respectively in group A before the intervention. However, proportions of such records were decreased to 50.6% (79/156), 35.9% (56/156), 32.1% (50/156) and 39.7% (62/156) respectively in group B after the intervention and the differences were statistically significant (all P<0.05). Conclusions: A specific quality evaluation criterion is established based on Delphi method and AHM-TOPSIS for the out-patient medical records of cancer pain. The quality of medical records has been improved in a certain level after adapting comprehensive evaluation and intervention on the out-patient medical records of cancer pain.

[Clinical analysis of pulmonary nocardiosis associated with bronchiectasis].

Objective: To better understand the clinical characteristics of pulmonary nocardiosis associated with bronchiectasis. Methods: Patients diagnosed as bronchiectasis complicated with pulmonary nocardiosis in 9 tertiary general hospitals in China were enrolled from March 2016 to March 2020, with the record of general data, imaging performance and pathogen. The literature was reviewed. Results: Totally 17 patients were included. There were 12 females and 5 males. The ages ranged from 45 to 79 years, with an average of (63±9) years. There were 15 nonsmokers and 2 smokers, all of whom with chronic course. The clinical manifestations were mostly cough, expectoration, hemoptysis, fever, and dyspnea. The imaging manifestation was bronchiectasis in both lungs, with the most common involvement in the left lower lung, right middle lobe and left lingual lobe. Sputum cultures were positive in 10 cases, bronchoalveolar lavage fluid (BALF) cultures were positive in 6 cases, and next generation gene sequencings were positive in 4 cases, including 2 cases of Nocardia gelsenkii, 2 cases of Nocardia abscess, 2 cases of Nocardia stellate, 1 case of Nocardia mexicana, 1 case of Nocardia otitis caviae, and 9 cases of undetermined Nocardia. There were 3 cases of Klebsiella pneumoniae, 2 cases of Pseudomonas aeruginosa and 2 cases of Aspergillus. The symptoms and imaging of all patients were improved after anti Nocardia therapy. Conclusions: Bronchiectasis combined with nocardiosis is more common in middle-aged and elderly women without smoking, which is similar to the clinical manifestations of Lady Windermere syndrome. Bronchiectasis often involves the left lower lobe, right middle lobe and left lingual lobe. Nocardia infection might further precipitate the initiation and progression of bronchiectasis.

Genome-wide association study of milk production traits in a crossbred dairy sheep population using three statistical models.

Milk production is one of the most important characteristics of dairy sheep, and the identification of genes affecting milk production traits is critical to understanding the genetics and improve milk production in future generations. Three statistical techniques, namely GWAS, ridge-regression BLUP and BayesC π , were used to identify SNPs in significant association with three milk production traits (milk yield, fat yield and protein yield) in a crossbred dairy sheep population. The results suggested that chromosomes 1, 3, 4, 5, 7 and 11 were likely to harbor genes important to milk production because these chromosomes had the greatest top-100-SNP variance contributions on the three milk production traits. The GWAS analysis identified between 74 and 288 genome-wide significant SNP (P < 0.05) whereas the BayesCπ model revealed between six and 63 SNPs, each with >95% posterior probability of inclusion as having a non-zero association effect on at least one of the three milk production traits. Positional candidate genes for milk production in sheep were searched, based on the sheep genomic assembly OAR version 3.1, such as those which map position coincided with or was located within 0.1 Mbp of a genome-wide suggestive or significant SNP. These identified SNPs and candidate genes supported some previous findings and also added new information about genetic markers for genetic improvement of lactation in dairy sheep, but keeping in mind that the majority of these positional candidate genes are not necessarily true causative loci for these traits and future validations are thus necessary.

Estimation of genomic breed composition of individual animals in composite beef cattle.

Three statistical models (an admixture model, linear regression, and ridge-regression BLUP) and two strategies for selecting SNP panels (uniformly spaced vs. maximum Euclidean distance of SNP allele frequencies between ancestral breeds) were compared for estimating genomic-estimated breed composition (GBC) in Brangus and Santa Gertrudis cattle, respectively. Animals were genotyped with a GeneSeek Genomic Profiler bovine low-density version 4 SNP chip. The estimated GBC was consistent among the uniformly spaced SNP panels, and values were similar between the three models. However, estimated GBC varied considerably between the three methods when using fewer than 10 000 SNPs that maximized the Euclidean distance of allele frequencies between the ancestral breeds. The admixture model performed most consistently across various SNP panel sizes. For the other two models, stabilized estimates were obtained with an SNP panel size of 20 000 SNPs or more. Based on the uniformly spaced 20K SNP panel, the estimated GBC was 69.8-70.5% Angus and 29.5-30.2% Brahman for Brangus, and 63.9-65.3% Shorthorn and 34.7-36.1% Brahman in Santa Gertrudis. The estimated GBC of ancestries for Santa Gertrudis roughly agreed with the pedigree-expected values. However, the estimated GBC in Brangus showed a considerably larger Angus composition than the pedigree-expected value (62.5%). The elevated Angus composition in the Brangus could be due to the mixture of some 1/2 Ultrablack animals (Brangus × Angus). Another reason could be the consequences of selection in Brangus cattle for phenotypes where the Angus breed has advantages.

A unified local objective function for optimally selecting SNPs on arrays for agricultural genomics applications.

Over the years, ad-hoc procedures were used for designing SNP arrays, but the procedures and strategies varied considerably case by case. Recently, a multiple-objective, local optimization (MOLO) algorithm was proposed to select SNPs for SNP arrays, which maximizes the adjusted SNP information (E score) under multiple constraints, e.g. on MAF, uniformness of SNP locations (U score), the inclusion of obligatory SNPs and the number and size of gaps. In the MOLO, each chromosome is split into equally spaced segments and local optima are selected as the SNPs having the highest adjusted E score within each segment, conditional on the presence of obligatory SNPs. The computation of the adjusted E score, however, is empirical, and it does not scale well between the uniformness of SNP locations and SNP informativeness. In addition, the MOLO objective function does not accommodate the selection of uniformly distributed SNPs. In the present study, we proposed a unified local function for optimally selecting SNPs, as an amendment to the MOLO algorithm. This new local function takes scalable weights between the uniformness and informativeness of SNPs, which allows the selection of SNPs under varied scenarios. The results showed that the weighting between the U and the E scores led to a higher imputation concordance rate than the U score or E score alone. The results from the evaluation of six commercial bovine SNP chips further confirmed this conclusion.

[Bivariate heritability estimation of resting heart rate and common chronic disease based on extended pedigrees].

OBJECTIVE: To estimate the univariate heritability of resting heart rate and common chronic disease such as hypertension, diabetes, and dyslipidemia based on extended pedigrees in Fujian Tulou area and to explore bivariate heritability to test for the genetic correlation between resting heart rate and other relative phenotypes. METHODS: The study was conducted in Tulou area of Nanjing County, Fujian Province from August 2015 to December 2017. The participants were residents with Zhang surname and their relatives from Taxia Village, Qujiang Village, and Nanou Village or residents with Chen surname and their relatives from Caoban Village, Tumei Village, and Beiling Village. The baseline survey recruited 1 563 family members from 452 extended pedigrees. The pedigree reconstruction was based on the family information registration and the genealogy booklet. Univariate and bivariate heritability was estimated using variance component models for continuous variables, and susceptibility-threshold model for binary variables. RESULTS: The pedigree reconstruction identified 1 seven-generation pedigree, 2 five-generation pedigrees, 23 four-generation pedigrees, 186 three-generation pedigrees, and 240 two-generation pedigrees. The mean age of the participants was 57.2 years and the males accounted for 39.4%. The prevalence of hypertension, diabetes, dyslipidemia in this population was 49.2%, 10.0%, and 45.2%, respectively. The univariate heritability estimation of resting heart rate, hypertension, and dyslipidemia was 0.263 (95%CI: 0.120－0.407), 0.404 (95%CI: 0.135－0.673), and 0.799 (95%CI: 0.590－1), respectively. The heritability of systolic blood pressure, diastolic blood pressure, fasting glucose, total cholesterol, triglyceride, high-density lipoprotein cholesterol, and low-density lipoprotein cholesterol was 0.379, 0.306, 0.393, 0.452, 0.568, 0.852, and 0.387, respectively. In bivariate analysis, there were phenotypic correlations between resting heart rate with hypertension, diabetes, diastolic blood pressure, fasting glucose, and triglyceride. After taking resting heart rate into account, there were strong genetic correlations between resting heart rate with fasting glucose (genetic correlation 0.485, 95%CI: 0.120－1, P<0.05) and diabetes (genetic correlation 0.795, 95%CI: 0.181－0.788, P<0.05). CONCLUSION: Resting heart rate was a heritable trait and correlated with several common chronic diseases and related traits. There was strong genetic correlation between resting heart rate with fasting glucose and diabetes, suggesting that they may share common genetic risk factors.

[Effect of cognitive impairment on social function and quality of life in chronic schizophrenia].

Objective: To clarify the effect of cognitive impairment on social function and quality of life of chronic schizophrenia, and provide clinical cognitive strategies for improving the social function and quality of life of patients with schizophrenia. Methods: Atotal of 158 patients with chronic schizophrenia were selected from May 2017 to October 2017 in the Psychiatry Department of the Third Affiliated Hospital of Sun Yat-sen University received psychological assessments, such as, MATRICS Consensus Cognitive Battery(MCCB), the Brief Psychiatric Rating Scale(BPRS), the Personal and Social Performance scale(PSP), and Schizophrenia Quality of Life Scale(SQLS). We further explored the effects of neurocognitive and social cognitive functions on their individual and social performance and quality of life in patients with schizophrenia. Results: (1) The scores of SQLS in the group with impaired social cognitive function were higher than those with good social function(101±46 vs 76±40, P=0.002). (2) The digital sequence and continuous performance test of the socially functional group were higher than the defect group. (3) There was a significant correlation between the years of education(R(2)=0.334, F=25.542), continuous performance (R(2)=0.316, F=35.647), BPRS (R(2)=0.280, F=60.386) and social function (P<0.001). (4) BPRS (R(2)=0.486, F=228.28), and emotional management (MSCEIT) (R(2)=0.510, F=124.789), education (R(2)=0.531, F=90.161), age (R(2)=0.539, F=69.644) significantly affected the SQLS score of patients with schizophrenia(P<0.001). Conclusion: The social function and quality of life of patients with schizophrenia are significantly correlated with their years of education and disease severity. Continuous performance in neurocognition significantly affects the social function of patients with schizophrenia, and emotional management in social cognition significantly affects their quality of life. Socially functional schizophrenia patients have higher digital sequences (working memory) and continuous performance (attention/alertness) scores.

[Calculation Method of Incubation Period of Infectious Diseases and Its Epidemiological Significance].

Based on the practical application, this paper introduced the basic calculation conditions, methods and epidemiological significance of incubation period. The real data were used for calculations of the incubation period by lognormal, gamma, Weibull and Erlang distribution methods. Both of the complete and incomplete observation data were demonstrated.

[Value of serum alpha-fetoprotein for the prognostic evaluation of hepatitis B virus-related acute-on-chronic liver failure treated with artificial liver].

Objective: To investigate the value of alpha-fetoprotein (AFP) level on survived hepatitis B virus-related acute-on-chronic liver failure (HBV-ACLF) patients treated with artificial liver. Methods: Clinical indicators of HBV-ACLF patients who were previously treated with plasma exchange-based artificial liver at our department were retrospectively collected. The difference of serum AFP level between the survival and the death group was compared at 30, 90 and 180 days after artificial liver treatment. The ROC curves of the subjects were plotted, and the sensitivity and specificity of AFP for the survival prediction of the patients at 30, 90 and 180 days after artificial liver surgery were calculated. AFP was divided into a high AFP group and a low AFP group using median value. AFP and postoperative survival predictive value at 30, 90, and 180 days were analyzed. Results: A total of 93 cases were included in this study. The AFP of the survival group at 30, 90, and 180 days was (231.0 ± 286.2) ng / ml, (237.69 ± 297) ng / ml, (229.44 ± 286.46) ng/ml, and the death group was (76.4 ± 104.7) ng/ml, (103.13 ± 116.99) ng / ml, (136.34 ± 2.9.29) ng/ml, respectively. AFP of the death group was significantly lower than the corresponding survival group (P < 0.05). Receiver operating characteristic (ROC) curve analyses indicated that the area under the curve (AUC) and its 95% confidence interval at 30, 90, and 180 days after artificial liver surgery were 0.739 (0.611 ~ 0.867), 0.675 (0.550 ~ 0.80), 0.653 (0.524 ~ 0.781), respectively. The median serum AFP value was 110 ng/ml, and the survival analysis showed that the survival time of the high AFP group was significantly higher than the low AFP group at 30 d (P = 0.01), 90 d (P = 0.04) and 180 d (P = 0.03) after artificial liver surgery. Conclusion: Serum AFP can be used as a predictor of survival for HBV-ACLF patients after artificial liver therapy and its clinical value needs to be further verified by the larger sample size.

[Suggestions for thoracic surgery clinical practice in non-epidemic area of 2019 coronavirus disease].

In this paper, the mechanism of destroying human alveolar epithelial cells and pulmonary tissue by 2019 novel coronavirus (2019-nCoV) was discussed firstly. There may be multiple mechanisms including killing directly the target cells and hyperinflammatory responses. Secondly, the clinical features, CT imaging, short-term and long-term pulmonary function damage of the 2019 coronavirus disease (COVID-19) was analyzed. Finally, some suggestions for thoracic surgery clinical practice in non-epidemic area during and after the epidemic of COVID-19 were provided, to help all the thoracic surgery patients receive active and effective treatment.

Evaluation of genotyping concordance for commercial bovine SNP arrays using quality-assurance samples.

SNP arrays are widely used in genetic research and agricultural genomics applications, and the quality of SNP genotyping data is of paramount importance. In the present study, SNP genotyping concordance and discordance were evaluated for commercial bovine SNP arrays based on two types of quality assurance (QA) samples provided by Neogen GeneSeek. The genotyping discordance rates (GDRs) between chips were on average between 0.06% and 0.37% based on the QA type I data and between 0.05% and 0.15% based on the QA type II data. The average genotyping error rate (GER) pertaining to single SNP chips, based on the QA type II data, varied between 0.02% and 0.08% per SNP and between 0.01% and 0.06% per sample. These results indicate that genotyping concordance rate was high (i.e. from 99.63% to 99.99%). Nevertheless, mitochondrial and Y chromosome SNPs had considerably elevated GDRs and GERs compared to the SNPs on the 29 autosomes and X chromosome. The majority of genotyping errors resulted from single allotyping errors, which also included the opposite instances for allele 'dropout' (i.e. from AB to AA or BB). Simultaneous allotyping errors on both alleles (e.g. mistaking AA for BB or vice versa) were relatively rare. Finally, a list of SNPs with a GER greater than 1% is provided. Interpretation of association effects of these SNPs, for example in genome-wide association studies, needs to be taken with caution. The genotyping concordance information needs to be considered in the optimal design of future bovine SNP arrays.

[The correlation between functional magnetic resonance imaging features and expression of Her-2 in breast cancer].

Objective: To explore the correlation between dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI), magnetic resonance diffusion-weighted imaging (DWI) images of breast cancer and human epidermal growth factor receptor-2 (Her-2) expression. Methods: A retrospective analysis of 84 patients with breast cancer confirmed by biopsy from January 2012 to December 2016 in Zhejiang University Lishui Hospital was conducted. The data of DCE-MRI, DWI scanning were collected before surgery and Her-2 was detected by immunohistochemistry (IHC). Then, all the patients were divided into Her-2 positive group and Her-2 negative group according to Her-2 expression. There were 44 cases in the Her-2 positive group and 40 cases in the Her-2 negative group. The differences in the characteristics of the lesion morphology, time-signal intensity curve (TIC), early enhancement rate and apparent diffusion coefficient (ADC) were compared, and their correlation with Her-2 expression was analyzed. Results: Of the 84 lesions, 12 were orthotopic ductal carcinoma, 6 were lobular carcinoma, and 66 were invasive ductal carcinoma. There were significant differences in lesion morphology (P=0.012) and TIC curve morphology (P=0.038) between Her-2 positive group and negative group. At the same time, the early enhancement rate (P=0.012) and ADC value (P=0.038) of Her-2 positive group were significantly higher than those of negative group. Except morphology of segmental lesions and TIC curve morphology, other characteristic parameters were correlated to Her-2 (all P<0.05). The correlation coefficients between early enhancement rate, ADC value and Her-2 expression were as high as 0.758 and 0.809 (all P<0.05). Conclusions: The morphology of breast cancer lesions, time-signal intensity curve, early enhancement rate and ADC value are all correlated with Her-2 expression.The early enhancement rate and ADC value are significantly positively correlated with Her-2 expression.

[Effects of hypoxic exosomes on the proliferation, migration and invasion of hepatocellular carcinoma Huh7 cells].

Objective: To explore the effects of hypoxic exosomes secreted from hepatocellular carcinoma Huh7 cells on the proliferation, migration and invasion under co-cultured normoxic condition. Methods: Hypoxic exosomes secreted from Huh7 cells under hypoxic conditions were extracted by differential ultracentrifugation. Transmission electron microscopy, nanoparticles tracking analysis and western blot were used for the identification of hypoxic exosomes. Hypoxic exosomes were co-cultured with Huh7 cells under normoxic conditions. CCK8, cell scratch and transwell assay were used to detect the changes of cell proliferation, migration and invasion. Statistical analysis was performed by one-way ANOVA and t-test. Results: Hypoxic exosomes secreted from Huh7 cells ranged in size from 30 to 150 nm in diameter, and expressed exosome surface markers CD9, CD63 and TSG101. Hypoxic exosomes significantly enhanced the proliferation of normoxic Huh7 cells (A value of hypoxic exosomes and control group at 48 and 72 h were 2.131 ± 0.092 and 1.760 ± 0.104,t= 3.740,P<0.01, 3.121 ± 0.157 and 2.298 ± 0.085,t= 8.289,P< 0.01). The migration distance between hypoxic exosome and control group at 48 and 72 h were (0.37 ± 0.06 cm)and(0.19 ± 0.05 cm),t= 4.813,P< 0.05, (1.15 ± 0.07 cm) and(0.62 ± 0.08 cm),t= 8.874,P< 0.05, and invasion ability [hypoxic exosomes and control group were (123 ± 18), (44 ± 12),t= 6.203,P< 0.01]. Conclusion: Hypoxic exosomes secreted from hepatocellular carcinoma Huh7 cells can promote cell proliferation, migration and invasion in hypoxic environment, suggesting that intercellular information transmission mediated by hypoxic exosomes may be one of the key mechanisms for the amplification of malignancy of hepatocellular carcinoma cells in hypoxic microenvironment.

Improving accuracy of genomic prediction in Brangus cattle by adding animals with imputed low-density SNP genotypes.

Reliable genomic prediction of breeding values for quantitative traits requires the availability of sufficient number of animals with genotypes and phenotypes in the training set. As of 31 October 2016, there were 3,797 Brangus animals with genotypes and phenotypes. These Brangus animals were genotyped using different commercial SNP chips. Of them, the largest group consisted of 1,535 animals genotyped by the GGP-LDV4 SNP chip. The remaining 2,262 genotypes were imputed to the SNP content of the GGP-LDV4 chip, so that the number of animals available for training the genomic prediction models was more than doubled. The present study showed that the pooling of animals with both original or imputed 40K SNP genotypes substantially increased genomic prediction accuracies on the ten traits. By supplementing imputed genotypes, the relative gains in genomic prediction accuracies on estimated breeding values (EBV) were from 12.60% to 31.27%, and the relative gain in genomic prediction accuracies on de-regressed EBV was slightly small (i.e. 0.87%-18.75%). The present study also compared the performance of five genomic prediction models and two cross-validation methods. The five genomic models predicted EBV and de-regressed EBV of the ten traits similarly well. Of the two cross-validation methods, leave-one-out cross-validation maximized the number of animals at the stage of training for genomic prediction. Genomic prediction accuracy (GPA) on the ten quantitative traits was validated in 1,106 newly genotyped Brangus animals based on the SNP effects estimated in the previous set of 3,797 Brangus animals, and they were slightly lower than GPA in the original data. The present study was the first to leverage currently available genotype and phenotype resources in order to harness genomic prediction in Brangus beef cattle.

Identifying the germ cells during embryogenesis and gametogenesis by germ-line gene vasa in an anadromous fish, American shad Alosa sapidissima.

American shad Alosa sapidissima, an anadromous clupeid, exhibits variation in reproductive strategies, including semelparity and iteroparity. It provides an excellent model for studying the behaviour of germ cells in anadromous fish during their migration from sea to river. The vasa gene was characterized in A. sapidissima as a germ-cell marker to elaborate the process of germ-cell development and differentiation in anadromous species. A complementary (c)DNA fragment of 819 bp, partial open reading frame (ORF), was cloned by degenerate PCR and named as ASvas. In adult A. sapidissima, vasa transcript was exclusively detected in gonads by reverse-transcription (RT)-PCR. Through chromogenic in situ hybridization, the vasa messenger (m)RNA was specifically detected in primordial germ cells (PGC) in embryos and germ cells at early stages in ovary and testis. Besides, the cellular distribution profile of Vasa protein also proved that vasa gene could be used as a germ-line marker to trace the PGCs migration during embryogenesis and the germ-cell differentiation during gametogenesis in A. sapidissima. During embryogenesis, the migrating PGCs were clearly detected at tail-bud stage and the PGCs reached the genital ridge at the stage of pre-hatching stage in A. sapidissima embryos. During gametogenesis, the Vasa protein was dynamically expressed in differentiating germ cells at different stages in adult gonads. As far as we know, this is the first report to demonstrate the PGCs migration and germ-cell differentiation through vasa gene expression in the anadromous species. The findings will pave a way for investigating germ-cell development and maturation in the A. sapidissima and other anadromous fish.

[Correlation between postoperative neutrophil to lymphocyte ratio and recurrence and prognosis of hepatocellular carcinoma after radical liver resection].

Objective: To investigate the correlation between postoperative peripheral blood neutrophil to lymphocyte ratio (NLR) and recurrence and prognosis of patients with hepatocellular carcinoma (HCC). Methods: The clinicopathological and follow-up data of 344 patients with HCC who underwent radical liver resection from May 2010 to April 2014 were analyzed retrospectively. Results: Of the 344 patients, 104 had early recurrence and 84 had late recurrence. Receiver operating characteristic (ROC) curve analysis showed that the NLR predicted area under the curve (AUC) of early recurrence was 0.622 (P<0.001), the optimal cut-off value was 2.41. The AUC of late recurrence was 0.634 (P=0.001), the optimal cut-off value was 2.15. Cox multivariate analysis showed the serum concentration of hepatitis B surface antigen (HR=2.508, 95% CI: 1.311-4.798), microvascular invasion (HR=2.422, 95% CI: 1.239-4.734), Milan criteria (HR=2.373, 95% CI: 1.427-3.948) and postoperative NLR (HR=2.285, 95% CI: 1.379-3.788) were independent risk factors of early recurrence after HCC resection. Postoperative NLR (HR=2.927, 95% CI: 1.630-5.255), liver cirrhosis (HR=2.531, 95% CI: 1.291-4.962) and serum concentration of albumin (HR=2.257, 95% CI: 1.251-4.073) were independent risk factors of late recurrence after HCC resection. The median recurrence-free survival (RFS) of the 344 patients was 45.0 months, and the median overall survival (OS) was 63.2 months. ROC curve analysis showed that the postoperative NLR predicted 5-year survival AUC was 0.689 (P<0.05), with an optimal cutoff of 2.29. Cox multivariate analysis showed microvascular invasion (HR=2.247, 95% CI: 1.534-3.291), postoperative NLR (HR=2.217, 95% CI: 1.653-2.974), and liver cirrhosis (HR=1.685, 95% CI: 1.168-2.431), Milan criteria (HR=1.679, 95% CI: 1.238-2.277), serum concentration of hepatitis B surface antigen (HR=1.623, 95% CI: 1.102-2.392), serum concentration of albumin (HR=1.43, 95% CI: 1.066-1.918) were independent factors of RFS after HCC resection, while microvascular invasion (HR=3.862, 95% CI: 2.407-6.197), Barcelona staging (HR=2.864, 95% CI: 1.600-5.125), postoperative NLR (HR=2.688, 95% CI: 1.782-4.055), liver cirrhosis (HR=2.039, 95% CI: 1.184-3.514), serum concentration of albumin (HR=1.81, 95% CI: 1.204-2.720) were independent factors of OS. Conclusions: For HCC patients who receive radical liver resection, postoperative NLR ≥2.29 implicates poor prognosis. Moreover, postoperative NLR ≥2.41 suggests early recurrence, while NLR ≥2.15 suggests late recurrence.