The single-cell transcriptome and chromatin accessibility datasets of peripheral blood mononuclear cells in Chinese holstein cattle

OBJECTIVES

This study was performed in the frame of a more extensive study dedicated to the integrated analysis of the single-cell transcriptome and chromatin accessibility datasets of peripheral blood mononuclear cells (PBMCs) with a large-scale GWAS of 45 complex traits in Chinese Holstein cattle. Lipopolysaccharide (LPS) is a crucial mediator of chronic inflammation to modulate immune responses. PBMCs include primary T and B cells, natural killer (NK) cells, monocytes (Mono), and dendritic cells (DC). How LPS stimulates PBMCs at the single-cell level in dairy cattle remains largely unknown.

DATA DESCRIPTION

We sequenced 30,756 estimated single cells and mapped 26,141 of them (96.05%) with approximately 60,075 mapped reads per cell after quality control for four whole-blood treatments (no, 2 h, 4 h, and 8 h LPS) by single-cell RNA sequencing (scRNA-seq) and single-cell sequencing assay for transposase-accessible chromatin (scATAC-seq). Finally, 7,107 (no), 9,174 (2 h), 6,741 (4 h), and 3,119 (8 h) cells were generated with ~ 15,000 total genes in the whole population. Therefore, the single-cell transcriptome and chromatin accessibility datasets in this study enable a further understanding of the cell types and functions of PBMCs and their responses to LPS stimulation in vitro.

Predictions of Milk Fatty Acid Contents by Mid-Infrared Spectroscopy in Chinese Holstein Cows

Genetic improvement of milk fatty acid content traits in dairy cattle is of great significance. However, chromatography-based methods to measure milk fatty acid content have several disadvantages. Thus, quick and accurate predictions of various milk fatty acid contents based on the mid-infrared spectrum (MIRS) from dairy herd improvement (DHI) data are essential and meaningful to expand the amount of phenotypic data available. In this study, 24 kinds of milk fatty acid concentrations were measured from the milk samples of 336 Holstein cows in Shandong Province, China, using the gas chromatography (GC) technique, which simultaneously produced MIRS values for the prediction of fatty acids. After quantification by the GC technique, milk fatty acid contents expressed as g/100 g of milk (milk-basis) and g/100 g of fat (fat-basis) were processed by five spectral pre-processing algorithms: first-order derivative (DER1), second-order derivative (DER2), multiple scattering correction (MSC), standard normal transform (SNV), and Savitzky-Golsy convolution smoothing (SG), and four regression models: random forest regression (RFR), partial least square regression (PLSR), least absolute shrinkage and selection operator regression (LassoR), and ridge regression (RidgeR). Two ranges of wavebands (4000~400 cm^-1 and 3017~2823 cm^-1/1805~1734 cm^-1) were also used in the above analysis. The prediction accuracy was evaluated using a 10-fold cross validation procedure, with the ratio of the training set and the test set as 3:1, where the determination coefficient (R²) and residual predictive deviation (RPD) were used for evaluations. The results showed that 17 out of 31 milk fatty acids were accurately predicted using MIRS, with RPD values higher than 2 and R² values higher than 0.75. In addition, 16 out of 31 fatty acids were accurately predicted by RFR, indicating that the ensemble learning model potentially resulted in a higher prediction accuracy. Meanwhile, DER1, DER2 and SG pre-processing algorithms led to high prediction accuracy for most fatty acids. In summary, these results imply that the application of MIRS to predict the fatty acid contents of milk is feasible.

[Predictive value of D-dimer for deep venous thrombosis of lower extremity in adult burn patients]

Objective: To investigate the predictive value of D-dimer for deep venous thrombosis (DVT) of lower extremity in adult burn patients. Methods: A retrospective case series study was conducted. The clinical data of 3 861 adult burn patients who met the inclusion criteria and were admitted to the Department of Burns of Zhengzhou First People's Hospital from January 1, 2015 to December 31, 2019 were collected. The patients were divided into DVT group (n=77) and non-DVT group (n=3 784) according to whether DVT of lower extremity occurred during hospitalization or not. Data of patients in the two groups were collected and compared, including the gender, age, total burn area, D-dimer level, with lower limb burn and inhalation injury or not on admission, with sepsis/septic shock, femoral vein indwelling central venous catheter (CVC), history of surgery, and infusion of concentrated red blood cells or not during hospitalization. Data were statistically analyzed with independent sample t test, Mann-Whitney U test, and chi-square test. The indicators with statistically significant differences between the two groups were analyzed with multivariate logistic regression analysis to screen the independent risk factors for DVT of lower extremity in 3 861 adult burn patients. The receiver operating characteristic (ROC) curve of the independent risk factors predicting DVT of lower extremity in 3 861 adult burn patients were drawn, and the area under the curve (AUC), the optimal threshold value, and the sensitivity and specificity under the optimal threshold value were calculated. The quality of the AUC was compared by Delong test, and the sensitivity and specificity under the optimal threshold value were compared using chi-square test. Results: There were no statistically significant differences in gender, occurrence of sepsis/septic shock or history of surgery during hospitalization between patients in the two groups (P>0.05), while there were statistically significant differences in age, total burn area, D-dimer level, lower limb burn and inhalation injury on admission, and femoral vein indwelling CVC and infusion of concentrated red blood cells during hospitalization between patients in the two groups (t=-8.17, with Z values of -5.04 and -10.83, respectively, χ2 values of 21.83, 5.37, 7.75, and 4.52, respectively, P<0.05 or P<0.01). Multivariate logistic regression analysis showed that age, total burn area, and D-dimer level were the independent risk factors for DVT of lower extremity in 3 861 adult burn patients (with odds ratios of 1.05, 1.02, and 1.14, respectively, 95% confidence intervals of 1.04-1.06, 1.00-1.03, and 1.10-1.20, respectively, P<0.05 or P<0.01). The AUCs of ROC of age, total burn area, and D-dimer level for predicting DVT of lower extremity in 3 861 adult burn patients were 0.74, 0.67, and 0.86, respectively (with 95% confidence intervals of 0.68-0.80, 0.60-0.74, and 0.83-0.89, respectively, P values<0.01), the optimal threshold values were 50.5 years old, 10.5% total body surface area, and 1.845 mg/L, respectively, the sensitivity under the optimal threshold values were 71.4%, 70.1%, and 87.0%, respectively, and the specificity under the optimal threshold values were 66.8%, 67.2%, and 72.9%, respectively. The AUC quality and sensitivity and specificity under the optimal threshold value of D-dimer level were significantly better than those of age (z=3.29, with χ2 values of 284.91 and 34.25, respectively, P<0.01) and total burn area (z=4.98, with χ2 values of 326.79 and 29.88, respectively, P<0.01), while the AUC quality and sensitivity and specificity under the optimal threshold values were similar between age and total burn area (P>0.05). Conclusions: D-dimer level is an independent risk factor for DVT of lower extremity in adult burn patients, its AUC quality and sensitivity and specificity under the optimal threshold value are better than those of age and total burn area, and it has good predictive value for DVT of lower extremity in adult burn patients.

LeGO-LOAM-SC: An Improved Simultaneous Localization and Mapping Method Fusing LeGO-LOAM and Scan Context for Underground Coalmine

Simultaneous localization and mapping (SLAM) is one of the key technologies for coal mine underground operation vehicles to build complex environment maps and positioning and to realize unmanned and autonomous operation. Many domestic and foreign scholars have studied many SLAM algorithms, but the mapping accuracy and real-time performance still need to be further improved. This paper presents a SLAM algorithm integrating scan context and Light weight and Ground-Optimized LiDAR Odometry and Mapping (LeGO-LOAM), LeGO-LOAM-SC. The algorithm uses the global descriptor extracted by scan context for loop detection, adds pose constraints to Georgia Tech Smoothing and Mapping (GTSAM) by Iterative Closest Points (ICP) for graph optimization, and constructs point cloud map and an output estimated pose of the mobile vehicle. The test with KITTI dataset 00 sequence data and the actual test in 2-storey underground parking lots are carried out. The results show that the proposed improved algorithm makes up for the drift of the point cloud map, has a higher mapping accuracy, a better real-time performance, a lower resource occupancy, a higher coincidence between trajectory estimation and real trajectory, smoother loop, and 6% reduction in CPU occupancy, the mean square errors of absolute trajectory error (ATE) and relative pose error (RPE) are reduced by 55.7% and 50.3% respectively; the translation and rotation accuracy are improved by about 5%, and the time consumption is reduced by 2~4%. Accurate map construction and low drift pose estimation can be performed.

Impact of the Order of Legendre Polynomials in Random Regression Model on Genetic Evaluation for Milk Yield in Dairy Cattle Population

The random regression test-day model has become the most commonly adopted model for routine genetic evaluations in dairy populations, which allows accurately accounting for genetic and environmental effects over lactation. The objective of this study was to explore appropriate random regression test-day models for genetic evaluation of milk yield in a Holstein population with a relatively small size, which is the common situation in regional or independent breeding companies to preform genetic evaluation. Data included 419,567 test-day records from 54,417 cows from the first lactation. Variance components and breeding values were estimated using a random regression test-day model with different orders (from first to fifth) of Legendre polynomials (LP) and accounted for homogeneous or heterogeneous residual variance across the lactation. Models were compared based on Akaike information criterion (AIC), Bayesian information criterion (BIC), and predictive ability. In general, models with a higher order of LP showed better goodness of fit based on AIC and BIC values. However, models with third, fourth, and fifth order of LP led to similar estimates of genetic parameters and predictive ability. Models with assumption of heterogeneous residual variances achieved better goodness of fit but yielded similar predictive ability compared with those with assumption of homogeneous residual variances. Therefore, a random regression model with third order of LP is suggested to be an appropriate model for genetic evaluation of milk yield in local Chinese Holstein populations.

Rapid and visual detection of 2019 novel coronavirus (SARS-CoV-2) by a reverse transcription loop-mediated isothermal amplification assay

OBJECTIVE

To evaluate a reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and compare it with RT-PCR.

METHODS

We designed primers specific to the orf1ab and S genes of SARS-CoV-2. Total viral RNA was extracted using the QIAamp Viral RNA Mini Kit. We optimized the RT-LAMP assay, and evaluated it for its sensitivity and specificity of detection using real-time turbidity monitoring and visual observation.

RESULTS

The primer sets orf1ab-4 and S-123 amplified the genes in the shortest times, the mean (±SD) times were 18 ± 1.32 min and 20 ± 1.80 min, respectively, and 63°C was the optimum reaction temperature. The sensitivities were 2 × 10¹ copies and 2 × 10² copies per reaction with primer sets orf1ab-4 and S-123, respectively. This assay showed no cross-reactivity with 60 other respiratory pathogens. To describe the availability of this method in clinical diagnosis, we collected 130 specimens from patients with clinically suspected SARS-CoV-2 infection. Among them, 58 were confirmed to be positive and 72 were negative by RT-LAMP. The sensitivity was 100% (95% CI 92.3%-100%), specificity 100% (95% CI 93.7%-100%). This assay detected SARS-CoV-2 in a mean (±SD) time of 26.28 ± 4.48 min and the results can be identified with visual observation.

CONCLUSION

These results demonstrate that we developed a rapid, simple, specific and sensitive RT-LAMP assay for SARS-CoV-2 detection among clinical samples. It will be a powerful tool for SARS-CoV-2 identification, and for monitoring suspected patients, close contacts and high-risk groups.

[Clinical analysis between trefoil factor 3 gene polymorphsims and susceptibility to papillary thyroid carcinoma]

Objective:To explore the relationships between trefoil factor 3（TFF3） gene polymorphisms and susceptibility to papillary thyroid carcinoma（PTC） in Han population of northern China. Method:A case-control study was performed in 123 PTC patients and 108 healthy controls. Four SNPs in the TFF3 gene, including rs225361, rs533093, rs9981660 and rs225439, were detected by gene sequencing. Result:Compared with healthy people, there was no significant difference in the genotype frequencies of rs225361, rs9981660, rs533093 and rs225439 alleles in the PTC group（P>0.05）. The CGTC and CGTT haploids of TFF3 gene were positively correlated with the occurrence of PTC, and CGCC and TGTC haploids were negatively correlated with the occurrence of PTC. TT genotype of rs9981660 had significant differences in the distribution of PTC with and without lymph node metastasis（P<0.05）. Conclusion:Polymorphisms in 4 SNP loci in the TFF3 gene may be unrelated to the occurrence of PTC. The CGTC, CGTT, CGCC and TGTC haploids in the TFF3 gene might be related to the development of PTC. The TT genotype at rs9981660 may be associated with lymph node metastasis of PTC.

[Diagnostic performance of ultrasound-based risk stratification systems for indeterminate thyroid nodules: comparison of the 2015ATA guidelines with the 2016 KTA/KSThR and 2017ACR guidelines]

Objective: To evaluate the diagnostic value of the 2015ATA, 2017ACR and 2016KTA/KSThR ultrasound model for indeterminate thyroids nodules. Method: Four hundred and sixty-four patients with thyroid nodules that were initially diagnosed as indeterminate thyroids nodules by fine needle aspiration(FNA) cytology were included in this study. The clinical data and two-dimensional ultrasonographic features were compared between the benign and malignant nodules. The two-dimensional ultrasound images of all nodules were sorted by the 2015ATA, 2017ACR and 2016KTA/KSThR guideline ultrasound model grading criteria, and the malignant risk of different grading were calculated. In order to calculate the diagnosis and other indicators, the optimal threshold drawing from ROC curve was drawn to obtain the cut-off value of 2015ATA, 2017ACR and 2016KTA/KSThR. Result: ①There was no significant difference in age, sex and nodule size between benign and malignant nodules(P>0.05), and there also was no significant difference in irregular margin, microcalcification between benign and malignant nodules.②The sensitivity of the 2015ATA ultrasound model was 87.9%, slightly lower than that of the 2016KTA/KSThR and 2017ACR guidelines(P>0.05).The specificity of 2015ATA was 63.9%, which was significantly higher than that of 2016KTA/KSThR and 2017ACR guidelines(P<0.05). There was no significant difference between 2015ATA ultrasound model and 2016KTA/KSThR guide ultrasound for the accuracy(P>0.05), but the accuracy of 2015ATA ultrasound model was significantly higher than that of 2017ACR guide(P<0.05).③The area under the curve of 2015ATA was slightly lower than that of 2016KTA/KSThR(0.889 VS 0.902, P>0.05) and significantly higher than that of 2017ACR(0.889 VS 0.854, P<0.05). Conclusion: 2015ATA has high specificity and accuracy and moderate sensitivity for the diagnosis of benign and malignant indeterminate thyroids nodules, which is helpful for the clinical evaluation and management of such nodules.

[The role of ATA (2015) guidelines, superb microvascular imaging, and spectral Doppler in differentiation between malignant and benign thyroid nodules]

Objective:To evaluate the diagnostic value of ultrasound patterns of 2015 American Thyroid Association (ATA) guidelines, color Doppler flow imaging (CDFI), superb microvascular imaging (SMI), and spectral Doppler in the differentiation of benign and malignant thyroid nodules.Method:The study included 254 thyroid nodules confirmed by fine needle aspiration cytology (FNAC) or histopathologic examination. All nodules were detected by ultrasonography, SMI, CDFI and spectral Doppler respectively. Blood flow detection technologies (CDFI and SMI) were used to classify flow distribution characteristics of thyroid nodules according to Kim's grading criteria. The optimal threshold drawing from ROC curve is calculated to obtain the cut-off value of spectral Doppler.Result:①For benign solid nodules with peripheral flow distribution and malignant solid nodules with central blood flow distribution, the display rates of SMI are higher than those of the CDFI, the differences were statistically significant (P< 0.05). ②There was a significance difference in detecting benign and malignant nodules using spectral Doppler (P< 0.05). ③The specificity and accuracy of combinative modality 2015 ATA+SMI was significantly higher than that of ATA, SMI, and spectral Doppler. There was no significant difference between ATA+SMI and ATA+SMI+spectral Doppler for the sensitivity, specificity, and accuracy.Conclusion:SMI had a better detection rate of blood vessels than CDFI and contribute a certain value in differential diagnosis of benign and malignant thyroid nodules. The combination of 2015 ATA and SMI can improve diagnostic value in the differentiation between benign and malignant thyroid nodules.

[The effects of PM 2.5 and air quality index on the emergency of otolaryngology]

Objective:To discuss the effects of PM 2.5 and air quality index on the emergency of otolaryngology. Method:Collect in 2015 Beijing tongren hospital emergency department patients with acute otitis media, epistaxis, acute epiglottitis as well as the same time Beijing AQI value and the PM 2.5 density data as the experimental group 1, chooses in 2015 first Affiliated Hospital of Hebei North University similar patient as well as the same time Zhangjiakou AQI value and the PM 2.5 density as the experimental group 2. Statistics the quantity of each sickness of two groups, and the relationships with PM 2.5 and AQI value; Group all data by AQI value and statistics the differences in the incidence rates of each group. Result:The number of cases of acute otitis media and epistaxis in the 2 experimental group were all correlated with the change of PM 2.5 and AQI value, and the correlation was positive between the two groups, However, the incidence of acute epiglottitis was not significantly correlated with the concentration of PM 2.5 and AQI, and there was no significant correlation between the two. The air quality when severe and more pollution when the number of the cases of acute otitis media and epistaxis compared with good air quality for the number of P<0.05, the difference was statistically significant. Conclusion:The increase of PM 2.5 concentration and AQI index is a health risk factor for acute otitis media and epistaxis.

[Expression and clinical significance of Nrf2 and ERK pathway in papillary thyroid carcinoma]

Objective:To explore the expression and clinical significance of nuclear factor erythroid-2 related factor 2 (Nrf2) and ERK sinal in papillary thyroid carcinoma (PTC). Method:PTC microassy were detected by immunohistochemical method (IHC). The expression of Nrf2, ERK₂ and p-ERK½ in PTC, para-carcimoma and normal thyroid tissue were detected by Western blot. The transcriptional level of Nrf2 mRNA in PTC, para-carcimoma and normal thyroid tissue were detected by real-time quantitative PCR (qPCR) method. Result:Nrf2, ERK₂, p-ERK½ protein were high expression in group of lymph node metastasis PTC and negative or weak positive expression in para-carcinoma tissue (P<0.01). And the proteins of clinical stage Ⅲ-Ⅳ of PTC groups express higher than without lymph node metastasis group and clinical stage Ⅰ-Ⅱ of PTC group (P<0.05). The expression of Nrf2 protein was positively correlated with ERK₂ and p-ERK½ protein in PTC (r=0.723 2,r=0.668 6,P<0.05). The Western blot results of Nrf2, ERK₂, p-ERK½ had a higher level in PTC than those of paracarcinoma and normal thyroid tissue (P<0.01). The level of Nrf2 mRNA were higher than those of paracarcinoma and normal thyroid tissue (P<0.01). Conclusion:High expresion of Nrf2 may be associated with the progression of papillary thyroid carcinoma, and may relate to the high expression and activity of ERK pathway.

[Assess the diagnostic value of MicroPure system with ultrasonography combined with mSMI in diagnosing thyroid nodules in TI-RADS 3 and 4]

Objective:To assess the diagnostic value of MicroPure system with ultrasonography combined with mSMI in diagnosing thyroid nodules inTI-RADS3 and 4; to compare the testing capability in thyroid nodules micro salcifications between MicroPure system and grey-scale ultrasonography; and to compare the diagnostic efficiency between mSMI and color doppler flow imaging (CDFI).Method:Exerting gery-scale ultrasonography and CDFI to choose 86 patients with 106 nodules (64 TI-RADS3 class nodules; 42 TI-RADS4 class nodules). These thyroid nodules were detected by grey-scale ultrasonography, CDFI, MicroPure system with ultrasonography, mSMI, and they were graded by TI-RADS. Then the ultrasound diagnosis value were compared with their FNA and surgical pathology results by gery-scale ultrasonography and CDFI; grey-scale ultrasonography and CDFI and MicroPure system; grey-scale ultrasonography and mSMI and MicroPure system, and diagnostic efficiency between mSMI and CDFI were compared, and the detectability of thyroid nodules micro salcifications between MicroPure system and grey-scale ultrasonography.Result:The results showed that combination of MicroPure system and mSMI had a higher sensitivity (91.44%, P< 0.05); The MicroPure system showed a higher testing capability compare to grey-scale ultrasonography in thyroid nodules micro salcifications (P< 0.05); The mSMI showed a higher sensitivity compared to the CDFI (P< 0.05).Conclusion:Combining mSMI and MicroPure system could improve the discreminability of TI-RADS3, 4 class thyroid nodules, then provide evidence to assess,diagnosis and treat the patients in clinical.

[Investigation of CXCR4 mediated chemoresistance in nasopharyngeal carcinoma cell line CNE2]

Objective:Since nasopharyngeal carcinoma is easy to develop resistance during cisplatin-based chemotherapy,CXCR4 expression levels were elevated in mang tumors,and the factor to do with tumor metastasis and chemotherapy drug resistance,and so on has a very important link.We established cisplatin-resistant nasopharyngeal carcinoma cell line, named as CNE2/DDP, and investigated the function of CXCR4 in molecular mechanism behind this resistance.Method:CNE2/DDP was firstly build up by increasing concentration of cisplatin. And then afterwards,MTT assay, RNA interference techniques, microRNA overexpresion techniques, quantative PCR and western blotting were applied to analyze the function of CXCR4 and its downstream effectors.Result:①the expression of CXCR4 was increased in CNE2/DDP and downregulation of CXCR4 with CXCR4 siRNA was able to decrease the resistance of CNE/DDP to cisplatin; ②the expression of let-7a was decrease in CNE2/DDP, while the expression of bcl-2 was increased. Upregulation of let-7a via transfection of let-7a mimics could downregulate the expression of bcl-2 and damage the resistance of CNE2/DDP to cisplation;③downregulation of CXCR4 through CXCR4 siRNA transfection was capable of improving the expression of let-7a. Conclusion:We were the first to found that CXCR4 was related to chemoresistance of CNE2/DPP to cisplatin. Meanwhile, we confirmed that CXCR4 affected the expression of bcl-2 through regulating the expression of let-7a to modulate the chemoresistance of CNE2/DPP to cisplatin.

[Study on anti-oxidase in smoking-related laryngeal squamous cell carcinoma]

Objective:To investigate the role of oxidative stress in smoking-related laryngeal squamous carcinoma through detecting the expression of antioxidant enzymes in smoking patients. Method:A total of 138 cases with laryngeal squamous cell carcinoma enrolled in the first hospital affiliated the northern he bei college from 2012 to 2015 and forty five volunteers were conducted. All participants were divided into three groups according to smoking index: group A(heavy smoking, 88 cases of laryngeal cancer patients) and group B(no smoking 50 cases of laryngeal cancer patients) and C group(45 heavy smoking volunteers).Catalase(CAT), glutathione peroxidase(GSH-px) and malondialdehyde(MDA) and the expression of NRF2 in serum, tissue adjacent to carcinoma, and carcinoma tissues from each groups were measured, respectively. Result:①the expression of the CAT and GSH-px in group A were significantly lower than that of group B(P <0.05), but higher than that of group C(P <0.05); ②the MDA level of group A is significantly higher than group B(P <0.05) and C group(P <0.01);③NRF2 was highly expressed in carcinoma tissues, and the expression level was negatively correlated with degree of carcinoma differentiation (P <0.05). Conclusion:Compared with nonsmoking patients, heavy smoking patients with laryngeal cancer were under more severe oxidative stress. NRF2 expression level in patients with laryngeal squamous cell carcinomas was associated with pathological stage.

Assessment of biodiversity in Chilean cattle using the distribution of major histocompatibility complex class II BoLA-DRB3 allele

Bovine leukocyte antigens (BoLAs) are used extensively as markers for bovine disease and immunological traits. In this study, we estimated BoLA-DRB3 allele frequencies using 888 cattle from 10 groups, including seven cattle breeds and three crossbreeds: 99 Red Angus, 100 Black Angus, 81 Chilean Wagyu, 49 Hereford, 95 Hereford × Angus, 71 Hereford × Jersey, 20 Hereford × Overo Colorado, 113 Holstein, 136 Overo Colorado, and 124 Overo Negro cattle. Forty-six BoLA-DRB3 alleles were identified, and each group had between 12 and 29 different BoLA-DRB3 alleles. Overo Negro had the highest number of alleles (29); this breed is considered in Chile to be an 'Old type' European Holstein Friesian descendant. By contrast, we detected 21 alleles in Holstein cattle, which are considered to be a 'Present type' Holstein Friesian cattle. Chilean cattle groups and four Japanese breeds were compared by neighbor-joining trees and a principal component analysis (PCA). The phylogenetic tree showed that Red Angus and Black Angus cattle were in the same clade, crossbreeds were closely related to their parent breeds, and Holstein cattle from Chile were closely related to Holstein cattle in Japan. Overall, the tree provided a thorough description of breed history. It also showed that the Overo Negro breed was closely related to the Holstein breed, consistent with historical data indicating that Overo Negro is an 'Old type' Holstein Friesian cattle. This allelic information will be important for investigating the relationship between major histocompatibility complex (MHC) and disease.

Ultra-wideband all-fiber tunable Tm/Ho-co-doped laser at 2 μm

We demonstrate an all-fiber tunable Tm/Ho-codoped laser operating in the 2 μm wavelength region. The wavelength tuning range of the Tm/Ho-codoped fiber laser (THFL) with 1-m length of Tm/Ho-codoped fiber (THDF) was from 1727 nm to 2030 nm. Efficient short wavelength operation and ultra-wide wavelength tuning range of 303 nm were both achieved. To the best of our knowledge, this is the broadest tuning range that has been reported for an all-fiber rare-earth-doped laser to date. By increasing the THDF length to 2 m, the obtainable wavelength of the THFL was further red-shifted to the range from 1768 nm to 2071 nm. The output power of the THFL was scaled up from 1810 nm to 2010 nm by using a stage of Tm/Ho-codoped fiber amplifier (THFA), which exhibited the maximum slope efficiency of 42.6% with output power of 408 mW at 1910 nm.

High-power all-fiber wavelength-tunable thulium doped fiber laser at 2 μm

Power scaling of an all-fiber wavelength-tunable thulium doped fiber laser (TDFL) based on a monolithic master oscillator power amplifier (MOPA) system is presented. The whole configuration is comprised of a low-power seed oscillator and two stages of double-cladding thulium doped fiber amplifiers (TDFAs). The tuning of the operating wavelength is realized by inserting a spectral tunable filter into the seed oscillator. Maximum average output power of 115 W is obtained at 1950 nm with a linearly fitted slope efficiency of 51.7%. This laser has superior spectral characteristics with wavelength tunable from 1940 nm to 2070 nm. To the best of our knowledge, this is the first demonstration of an all-fiber wavelength-tunable TDFL at 2 μm with output power exceeding 100 W. The results are of great interest for many application areas.

Gasification of torrefied Miscanthus × giganteus in an air-blown bubbling fluidized bed gasifier

Torrefaction is suggested to be an effective method to improve the fuel properties of biomass and gasification of torrefied biomass should provide a higher quality product gas than that from unprocessed biomass. In this study, both raw and torrefied Miscanthus × giganteus (M×G) were gasified in an air-blown bubbling fluidized bed (BFB) gasifier using olivine as the bed material. The effects of equivalence ratio (ER) (0.18-0.32) and bed temperature (660-850°C) on the gasification performance were investigated. The results obtained suggest the optimum gasification conditions for the torrefied M × G are ER 0.21 and 800°C. The product gas from these process conditions had a higher heating value (HHV) of 6.70 MJ/m(3), gas yield 2m(3)/kg biomass (H2 8.6%, CO 16.4% and CH4 4.4%) and cold gas efficiency 62.7%. The comparison between raw and torrefied M × G indicates that the torrefied M × G is more suitable BFB gasification.

c-Myc-mediated repression of miR-15-16 in hypoxia is induced by increased HIF-2α and promotes tumor angiogenesis and metastasis by upregulating FGF2

Previous studies have established the link between aberrant microRNA (miRNA) expression and hypoxia in various neoplasms. However, how these hypoxia-related miRNAs modulate tumor progression is still unclear. Therefore, the patterns of miRNA in colorectal carcinoma cell lines in response to hypoxia or not were first screened and the hypoxia-induced repression of the miR-15-16 cluster was confirmed. Then, this repression was found to be associated with high tumor stage and poor prognosis in colorectal carcinoma and is shown to promote tumor angiogenesis and metastasis by the loss of restriction of its target gene, fibroblast growth factor-2 (FGF2). Moreover, the general and alterative promoters of the miR-15-16 host (deleted in lymphocytic leukemia 2, DLEU2) were mapped, and three c-Myc/Max binding sites in response to the hypoxia-induced repression of miR-15-16 were further identified. Finally, an enhanced stability of c-Myc/Max heterodimer promoted by increased hypoxia-inducible factor-2α (HIF-2α) was validated, and we also verified that the enhancement contributed to the hypoxia-induced repression of miR-15-16. In brief, the c-Myc-mediated transcriptional repression of miR-15-16 in hypoxia is induced by increased HIF-2α and promoted tumor angiogenesis and hematogenous metastasis by the further loss of post-transcriptional inhibition of FGF2. Our study provides a better understanding of the coping mechanisms in response to tumor hypoxia and may be helpful in developing an effective prognostic marker or treatment target against solid tumors.

Thirteen watt all-fiber mid-infrared supercontinuum generation in a single mode ZBLAN fiber pumped by a 2 μm MOPA system

All-fiber-integrated mid-infrared (mid-IR) supercontinuum (SC) generation in a single mode ZBLAN (ZrF4-BaF2-LaF3-AlF3-NaF) fiber with 13 W average output power and a spectrum extending from ∼1.9 to 4.3 μm is reported, which we believe is the highest output power for mid-IR SC generation in ZBLAN fibers. The overall optical conversion efficiency from the 790 nm pump light of the last stage Tm-doped fiber (TDF) amplifier to the total SC output was 20%, and the SC power for wavelengths longer than 2.5 μm was 6.85 W with a power ratio of 52.69% with respect to the total SC power. The mid-IR SC generation in ZBLAN fiber was pumped by a 2 μm master oscillator power amplifier (MOPA) system, which is also very appropriate for high power 2-2.5 μm region SC generation. We also demonstrate high efficiency SC generation in the TDF amplifier with 62.1 W average power, 39.8% optical efficiency, and a spectrum extending from 1.9 to 2.7 μm.

Expression and localization of trefoil factor family genes in rat submandibular glands

The trefoil factor (TFF) family, which comprises TFF1, TFF2 and TFF3, plays an essential role in epithelial regeneration within the gastrointestinal tract. All three TFFs are present in human saliva; TFF3 is the predominant trefoil peptide. Little is known about the expression and tissue distribution of TFFs in rats, which are commonly used as a model system for human studies. We investigated the localization of the TFF genes that encode secretory peptides in rat submandibular glands (SMG). All three TFFs were expressed in rat SMG, although their location varied. Substantial amounts of TFF1 were detected only in the cytoplasm of epithelial cells in the SMG granular convoluted tubules (GCT), while TFF2 and TFF3 were widely distributed in the cytoplasm of epithelial cells of intercalated ducts (ID), striated ducts (SD) and interlobular ducts (ILD). The three TFFs also were detected especially in the lumens of the SD and ILD. Semi-quantitative RT-PCR and in situ hybridization experiments confirmed TFF1, TFF2 and TFF3 mRNA expressions in the SMG. Greater expression of TFF peptides and mRNA was observed in male rats than in females. The broad expression of TFFs in rat SMG cells and lumens suggests that TFFs function in this organ by their secretion into the duct lumens. We also found differences in TFF expression profiles between rat and human SMG; therefore, caution should be exercised when using rats as a model for human TFF studies.

COMT rs4680 Met is not always the 'smart allele': Val allele is associated with better working memory and larger hippocampal volume in healthy Chinese

Catechol-O-methyltransferase (COMT) Val158Met (rs4680) polymorphism plays a crucial role in regulating brain dopamine level. Converging evidence from Caucasian samples showed that, compared with rs4680 Val allele, the Met allele was linked to lower COMT activity, which in turn was linked to better cognitive performance such as working memory (WM) and to a larger hippocampus (a brain region important for WM). However, some behavioral studies have shown that the function of rs4680 appears to vary across different ethnic groups, with Chinese subjects showing an opposite pattern as that for Caucasians (i.e. the Val allele is linked to better cognitive functions related to WM in Chinese). Using a sample of healthy Han Chinese college students (ages from 19 to 21 years), this study investigated the association of COMT Val158Met genotype with behavioral data on a two-back WM task (n = 443, 189M/254F) and T1 MRI data (n = 320, 134M/186F). Results showed that, compared to the Met allele, the Val allele was associated with larger hippocampal volume (the right hippocampus: β = -0.118, t = -2.367, P = 0.019, and the left hippocampus: β = -0.099, t = -1.949, P = 0.052) and better WM performance (β = -0.110, t = -2.315, P = 0.021). These results add to the growing literature on differentiated effects of COMT rs4680 polymorphism on WM across populations and offer a brain structural mechanism for such population-specific genetic effects.

Germline hMSH2 promoter mutation in a Chinese HNPCC kindred: evidence for dual role of LOH

Hereditary non-polyposis colorectal cancer (HNPCC) is a dominantly inherited cancer predisposition syndrome that is caused by germline mutations in mismatch repair genes. By screening the core promoters of hMSH2, hMLH1, and hMSH6 in 37 Chinese suspected HNPCC families, a novel germline mutation c.-78_-79delGT was found in the hMSH2 promoter. Its pathogenic effects were supported by the following findings: (a) it co-segregated with HNPCC-related cancers and was not present in the 220 control subjects, (b) tumors harboring the mutation lacked the expression of hMSH2 and showed high microsatellite instability, (c) it significantly decreased the promoter activity, and (d) it abolished the binding ability of the transcription factor E1A-F. Loss of heterozygosity (LOH) was found in three of the tumors studied. Intriguingly, in the tumors from patients II:1 and III:1, LOH occurred in the wild-type allele and agreed well with the traditional 'two-hit' model. In contrast, in the tumor from patient III:3, LOH occurred in the mutant allele. A pathogenic somatic mutation (c.2210+1G>A) was also found in this tumor; therefore, we proposed that the 'second hit' was inactivated by somatic mutation, and the mutant allele was lost during tumor progression; this provided evidence for the new hypothesis for the dual role of LOH.

Role of extracellular exopolymers in biological phosphorus removal

Three sequencing batch reactors (SBRs) supplied with different carbon sources were investigated. The system supplied with glucose gained the best enhanced biological phosphorus removal (EBPR), although all of them were seeded from the same sludge. With the measurement of poly-beta-hydroxyalkanoate (PHA) concentration, phosphorus content in sludge and extracellular exopolymers (EPs) with scanning electron microscopy (SEM) combined with energy dispersive spectrometry (EDS), it was found that the biosorption effect of EPs played an important role in phosphorus removal and that the amount of PHA at the end of anaerobic phase was not the only key factor to determine the following phosphorus removal efficiency.

Crystal structure of 2,3-bis(2-cyanoethylthio)-6,7-vinylenedithiotetrathiafulvalene, C14H10N2S8

C14H10N2S8, triclinic, P1̅ (no. 2), a = 7.753(2) Å, b = 11.403(3) Å, c = 12.371(5) Å, α = 64.10(2)°, β = 84.62(2)°, γ = 77.34(2)°, V = 959.9 Å3, Z = 2, Rgt(F) = 0.061, wRref(F2) = 0.168, T = 293 K.

Crystal structure of tricalcium tantalum trigallium disilicon oxide, Ca3TaGa3Si2O14

Ca3Ga3O14Si2Ta, trigonal, P321 (No. 150), a = 8.1081(4) Å, c = 4.9850(4) Å, V = 283.8 Å3, Z = 1, Rgt(F) = 0.025, wRref(F2) = 0.064, T = 293 K.

Crystal structure of 4,5-(ethoxyethylenedithio)-1,3-dithiole-2-thione, C7H8OS5

C7H8OS5, monoclinic, P121/c1 (No. 14), a = 8.3699(7) Å, b = 17.573(2) Å, c = 7.5305(7) Å, β = 103.584(7)°, V = 1076.6 Å3, Z=4, Rgt(F) = 0.033, wRref(F2) = 0.082, T = 293 K.

Crystal structure of tetra-n-butylammonium (1,3-dithiol-2-thione-4,5-dithiolato)-( diethyldithiocarbamato-S,S')-nickelate(II), (C16H36N)(C8H10NNiS7)

C24H46N2NiS7, monoclinic, C1c1 (No. 9), a = 8.846(2) Å, b = 24.702(6) Å, c = 15.392(3) Å, β = 95.12(1)°, V = 3349.9Å3, Z = 4, Rgt(F) = 0.059, wRref(F2) = 0.166, T = 293 K.

Depletion effect on partial organization of atactic polymer chain segments in microcells

Glass transition for atactic poly(methyl methacrylate) (a-PMMA) prepared in nano-cells by microemulsion polymerization was measured at a faster heating rate after slow cooling of the sample from a temperature above Tg. An additional enthalpy relaxation and glass transition were observed at higher temperatures for the a-PMMA sample due to the partial organization of the chain segments which occurred during microemulsion polymerization. The re-precipitated a-PMMA did not show any self-organization under the same thermal conditions, although there are no changes in molecular weight or tacticity of the polymer chains. A depletion-interaction phenomenon was understood to provide entropic force for the self-organization of polymer chains inside the walls of the microemulsion cells.

Fluorescence detection in capillary arrays based on galvanometer step scanning

A computer-controlled galvanometer scanner is adapted for scanning a focused laser beam across a 96-capillary array for laser-induced fluorescence detection. The signal at a single photomultiplier tube is temporally sorted to distinguish among the capillaries. The limit of detection for fluoresceins is 3 x 10(-11) M (S/N = 3) for 5 mW of total laser power scanned at 4 Hz. The observed cross-talk among capillaries is 0.2%. Advantages include the efficient utilization of light due to the high duty-cycle of step scan, good detection performance due to the reduction of stray light, ruggedness due to the small mass of the galvanometer mirror, low cost due to the simplicity of components, and flexibility due to the independent paths for excitation and emission.

Rubbing-induced molecular reorientation on an alignment surface of an aromatic polyimide containing cyanobiphenyl side chains

Surface lamellar decoration (SLD), surface enhanced Raman scattering (SERS) and optical second harmonic generation (SHG) experiments have been utilized to study the molecular orientation and conformation changes at a rubbed polyimide alignment-layer surface. This aromatic polyimide containing pendent cyanobiphenyl mesogens was synthesized via a polycondensation of 2,2'-bis(3,4-dicarboxy-phenyl)hexafluoropropane dianhydride (6FDA) with bis[omega-[4-(4-cyanophenyl)phenoxy]hexyl] 4,4'-diamino-2,2'-biphenyldicarboxylate (nCBBP, n = 6), abbreviated as 6FDA--6CBBP. Uniform alignment layers, possessing high pretilt angles ranging from 39 degrees to 43 degrees, have been achieved after mechanical rubbing of the polyimide thin film surface at room temperature and subsequent annealing. This is the first time that high pretilt angles have been detected to possess a negative angle (-theta(c)) with respect to the rubbing direction (i.e., opposite to the rubbing direction), considerably different from the conventional pretilt angle (theta(c)) observed along the rubbing direction. This observation is confirmed using magnetic null and SHG methods. Combined polyethylene (PE) SLD and atomic force microscopy experiments reveal that the azimuthal orientation distribution of the long axis of the edge-on PE lamellar crystals is oriented normal to the rubbing direction, indicating that the PE chains are aligned parallel to the rubbing direction. This SLD technique probes the anisotropic surface orientation of the outermost molecules of the rubbed polyimide layer. The SERS results show that prior to rubbing the surface, both the pendent cyanobiphenyls in the side chains and backbones possess nearly planar chain conformations at the polyimide surface. Mechanical rubbing causes not only tilting of the backbone moieties, such as imide-phenylene structure, but also significant conformational rearrangements of the pendent side chains at the surfaces. The molecular mechanism of this unusual alignment is due to the fact that the pendent cyanobiphenyls forms a uniformly tilted conformation on the rubbed surface, and the polar cyano groups point down toward the layer surface deduced from SHG phase measurements. This conformational rearrangement of the side chains results in the formation of fold-like bent structures on the surface, which directly leads to the long axis of cyanobiphenyls having the -theta(c) pretilt angle with respect to the rubbing direction.

Selective detection of individual DNA molecules by capillary polymerase chain reaction

On-line capillary polymerase chain reaction (PCR) coupled with laser-induced fluorescence detection was successfully demonstrated for individual DNA molecules. A single 30-microm-i.d. fused-silica capillary was used both as the reaction vessel and for isolating single molecules. SYBR green I dye was added into the reaction mixture for dynamic fluorescent labeling. Because of the small inside diameter of the capillary, PCR-amplified DNA fragments from single molecules were localized in the capillary, providing discrete product zones with concentrations at readily detectable levels. By counting the number of peaks in the capillary via electromigration past a detection window, the number of starting DNA molecules could be determined. With selective primer design, only the molecule of interest was detected. Amplification of the 110-bp fragment from an individual human beta-globin gene and the 142-bp fragment from an individual HIV-1 DNA was demonstrated. This opens the possibility of highly selective and sensitive disease diagnosis at a very early stage.

On-line nanoliter cycle sequencing reaction with capillary zone electrophoresis purification for DNA sequencing

An integrated system for DNA sequencing based on a nanoreactor for cycle-sequencing reaction coupled with on-line capillary zone electrophoresis (CZE) for purification and capillary gel electrophoresis (CGE) for separation is presented. Less than 100 nl of premixed reagent solution, which includes dye-labeled terminator pre-mix, bovine serum albumin and template, was hydrodynamically injected into a fused-silica capillary (75 microm I.D.) inside a laboratory-made microthermocycler for cycle sequencing reaction. In the same capillary, the reaction products were purified by CZE followed by on-line injection of the DNA fragments into another capillary for CGE. Over 540 base pairs (bp) of DNA can be separated and the bases called for single-standed DNA with 0.9% error rate. The total time was about 3.5 h, or a cycle time of 2 h with staggered operation. For double-stranded DNA, a longer reaction time was required and base calling up to 490 bp with 1.2% error rate was achieved. The whole system is readily adaptable to automated multiplex operation for DNA sequencing or polymerase chain reaction analysis.

Multiplexed capillary zone electrophoresis and micellar electrokinetic chromatography with internal standardization

Although liquid chromatography and gas chromatography are the main workhorses in the analytical laboratory, samples can only be analyzed consecutively in an instrument. In this study, capillary zone electrophoresis and micellar electrokinetic chromatography separations are performed in a 96-capillary array system with laser-induced fluorescence detection. Migration times of four kinds of fluoresceins and six polyaromatic hydrocarbons (PAHs) are normalized to one of the capillaries using two internal standards. The relative standard deviations after normalization are 0.6-1.4% for the fluoresceins and 0.1-1.5% for the PAHs. Quantitative calibration of the separations based on peak areas is also performed, again with substantial improvement over the raw data. This opens up the possibility of performing massively parallel separations for high-throughput chemical analysis for process monitoring, combinatorial synthesis, and clinical diagnosis.

[Compatible leaching effect of Concha Ostreae and some commonly-used Chinese medicinal materials]

OBJECTIVE

Based on a study of Concha Ostreae, to provide some reference for the rational approach to leaching mineral drugs.

METHOD

Taking the change rates of compatible leaching and value of A as targets, the compatible leaching effect of Concha Ostreae with Radix et Rhizoma Rhei Praeparata, Radix Scutellariae, Pollen Typhae and Fructus Aurantii lmmaturus was studied.

RESULT

If Concha Ostreae and the above cited medicinal herbs are decocted together, the yield of extract may be reduced to a certain extent, but the target composition of Radix et Rhizoma Rhei Praeparata and Fructus Aurantii lmmaturus remains intact, only the content of Radix Scutellariae baicalin may be influenced.

CONCLUSION

The relationship of technology with preparation must be taken into consideration when making choice of the proper way to leach Concha Ostreae.

[Variation of female migraine after menopause and its prophylaxis and treatment]

320 cases of female migraine after menopause according to the diagnostic criteria were studied by using 1:1 matched analysis. It was found that the additional symptoms increased after menopause. Eighty cases available for follow-up were divided into two groups, on which the treatment tests were done. Each patient in group I took Nilestrioli 2 mg twice a month and Perphenazine 12 mg and Doxepin 75 mg per day, while each patient in group II took Tolfenamic acid 300 mg a day. Two months after treatment, the cure rates were 57.58% in group I and 27.78% in group II. Two monthes after the cessation of therapy, 2 cases had relapses in group I. These data indicate that the decrease of estrin disorder and the additional symptoms after monopause play important roles in the change of migraine physiology, and the corresponding treatment methods are rational.

[Separation and preparation of indole alkaloids in Lycorma delicatula White. by HPLC]

A HPLC method for separating and preparing indole alkaloids is described. HPLC conditions for analysis: BIO-RAD series 700 HPLC, model 700 data station, UV: model 1749 UV-VIS monitor, column: BIO-RAD Hi-pore RP318, 250 mm x 10 mm, mobile phase: 80% methanol-H2O(gradient), flow rate: 1.5 ml/min, detection wavelength: 254 nm. On the basis of spectral (1HNMR, 13CNMR, H-H COSY, MS, DEPT) and chemical evidence, the structures of two compounds were elucidated as beta-yohimbine (yohimban-16-carboxylic acid-17-hydroxy methylester (3 alpha, 16 alpha, 17 beta)) and ajmalicine (oxayohimban-16-carboxylic acid-16,17-didehydro-19-ethyl methyl ester (19 alpha)).