SARS-CoV-2 variant of concern fitness and adaptation in primary human airway epithelia

The severe acute respiratory syndrome coronavirus 2 pandemic is characterized by the emergence of novel variants of concern (VOCs) that replace ancestral strains. Here, we dissect the complex selective pressures by evaluating variant fitness and adaptation in human respiratory tissues. We evaluate viral properties and host responses to reconstruct forces behind D614G through Omicron (BA.1) emergence. We observe differential replication in airway epithelia, differences in cellular tropism, and virus-induced cytotoxicity. D614G accumulates the most mutations after infection, supporting zoonosis and adaptation to the human airway. We perform head-to-head competitions and observe the highest fitness for Gamma and Delta. Under these conditions, RNA recombination favors variants encoding the B.1.617.1 lineage 3' end. Based on viral growth kinetics, Alpha, Gamma, and Delta exhibit increased fitness compared to D614G. In contrast, the global success of Omicron likely derives from increased transmission and antigenic variation. Our data provide molecular evidence to support epidemiological observations of VOC emergence.

[Research progress in functional regeneration methods and mechanisms of taste buds]

Gustation is one of the most important human senses. Taste dysfunctions, which may be due to aging, tongue cancer surgery, radiotherapy and chemotherapy, affect life quality. That is why the need for taste bud regeneration has received more attention. At present, research on development and renewal of taste cells provides a basis for taste bud regeneration; molecular mechanisms related to taste bud regeneration are being continuously uncoverd, aiding in the identification of more accurate targets for therapy. New methods such as nerve regeneration, tissue engineering, and cytokine therapy have emerged. The author reviews the mechanism and the latest methods of taste bud regeneration of lingual epithelium, aiming to open new horizions for the prevention and treatment of gustatory diseases, and provide theoretical references for its regeneration.

Saliva sampling method influences oral microbiome composition and taxa distribution associated with oral diseases

Saliva is a readily accessible and inexpensive biological specimen that enables investigation of the oral microbiome, which can serve as a biomarker of oral and systemic health. There are two routine approaches to collect saliva, stimulated and unstimulated; however, there is no consensus on how sampling method influences oral microbiome metrics. In this study, we analyzed paired saliva samples (unstimulated and stimulated) from 88 individuals, aged 7-18 years. Using 16S rRNA gene sequencing, we investigated the differences in bacterial microbiome composition between sample types and determined how sampling method affects the distribution of taxa associated with untreated dental caries and gingivitis. Our analyses indicated significant differences in microbiome composition between the sample types. Both sampling methods were able to detect significant differences in microbiome composition between healthy subjects and subjects with untreated caries. However, only stimulated saliva revealed a significant association between microbiome diversity and composition in individuals with diagnosed gingivitis. Furthermore, taxa previously associated with dental caries and gingivitis were preferentially enriched in individuals with each respective disease only in stimulated saliva. Our study suggests that stimulated saliva provides a more nuanced readout of microbiome composition and taxa distribution associated with untreated dental caries and gingivitis compared to unstimulated saliva.

[Analysis of the types and functions of CD34+ cells in full-thickness skin defect wounds of normal mice and diabetic mice by single-cell RNA sequencing]

Objective: To analyze the types and functions of CD34+ cells in full-thickness skin defect wounds of normal mice and diabetic mice by single-cell RNA sequencing. Methods: This study was an experimental study. The CD34+ cell lineage tracing mouse was produced, and the visualization of CD34+ cells under the fluorescent condition was realized. Six male CD34+ cell lineage tracing mice aged 7-8 weeks (designated as diabetic group) were intraperitoneally injected with streptozotocin to establish a diabetic model, and full-thickness skin defect wounds were prepared on their backs when they reached 13 weeks old. Another 6 male CD34+ cell lineage tracing mice aged 13 weeks (designated as control group) were also subjected to full-thickness skin defect wounds on their backs. On post-injury day (PID) 4, wound tissue was collected from 3 mice in control group and 2 mice in diabetic group, and digested to prepare single-cell suspensions. CD34+ cells were screened using fluorescence-activated cell sorting, followed by single-cell RNA sequencing. The Seurat 4.0.2 program in the R programming language was utilized for dimensionality reduction, visualization, and cell clustering analysis of CD34+ cell types, and to screen and annotate the marker genes for each CD34+ cell subpopulation. Kyoto encyclopedia of genes and genomes (KEGG) and gene ontology (GO) enrichment analysis was performed to analyze the differentially expressed genes (DEGs) of CD34+ fibroblasts (Fbs), smooth muscle cells (SMCs), keratinocytes (KCs), and chondrocyte-like cells (CLCs) in the wound tissue of two groups of mice for exploring cellular functions. Results: On PID 4, CD34+ cells in the wound tissue of both groups of mice were consisted of 7 cell types, specifically endothelial cells, Fbs, KCs, macrophages, T cells, SMCs, and CLCs. Among these, Fbs were further classified into 5 subpopulations. Compared with those in control group, the proportions of CD34+ endothelial cells, Fbs subpopulation 1, Fbs subpopulation 4, KCs, and CLCs in the wound tissue of mice were increased in diabetic group, while the proportions of CD34+ Fbs subpopulation 2, Fbs subpopulation 3, and SMCs were decreased. The marker genes for annotating CD34+ CLCs, endothelial cells, Fbs subpopulation 1, Fbs subpopulation 2, Fbs subpopulation 3, Fbs subpopulation 4, Fbs subpopulation 5, KCs, macrophages, SMCs, and T cells were respectively metastasis-associated lung adenocarcinoma transcript 1, fatty acid binding protein 4, Gremlin 1, complement component 4B, H19 imprinted maternally expressed transcript, Dickkopf Wnt signaling pathway inhibitor 2, fibromodulin, keratin 5, CD74 molecule, regulator of G protein signaling 5, and inducible T-cell co-stimulator molecule. KEGG and GO enrichment analysis revealed that, compared with those in control group, DEGs with significant differential expression (SDE) in CD34+ Fbs from the wound tissue of mice in diabetic group on PID 4 were significantly enriched in terms related to inflammatory response, extracellular matrix (ECM) organization, regulation of cell proliferation, and aging (with Pvalues all <0.05), DEGs with SDE in CD34+ SMCs were significantly enriched in terms related to cell migration, apoptotic process, positive regulation of transcription, and phagosome (with P values all <0.05), DEGs with SDE in CD34+ KCs were significantly enriched in terms related to mitochondrial function, transcription, and neurodegenerative diseases (with P values all <0.05), and DEGs with SDE in CD34+ CLCs were significantly enriched in terms related to rhythm regulation, ECM, and viral infection (with P values all <0.05). Conclusions: CD34+ cells display high heterogeneity in the healing process of full-thickness skin defect wounds in both normal mice and diabetic mice. The significantly enriched functions of DEGs with SDE in CD34+ cell subpopulations in the wound tissue of the two mouse groups are closely related to the wound healing process.

Neutron-gamma discrimination with broaden the lower limit of energy threshold using BP neural network

Neutron-gamma discrimination is a tough and significative in experimental neutrons measurements procedure, especially for low-energy neutrons signal discrimination. In this work, based on the Pulse Shape Discrimination (PSD) and Back-Propagation (BP) artificial neural networks, a neutron-gamma discrimination method is developed to broaden the lower limit of energy threshold with the hidden layer of 20 neurons. Compared with neutron-gamma discrimination method based on PSD only, the developed neutron-gamma discrimination method based on the PSD and BP-ANN can discriminate neutron and gamma-ray signals with low energy threshold, which can discriminate signals up to 99.93%. Moreover, this work can reduce the energy threshold from 350 keV to 70 keV, as well as the acquired data utilization increased from 60% to more than 99.9%, which overcome the hardware limitations and distinguish neutron and gamma-ray signals, effectively. The developed neutron-gamma discrimination method and the trained neural network can be directly used to other experimental neutrons measurements.

[Application of preoperative serum CYFRA 21-1 level in the prognosis of colorectal cancer]

To explore the predictive value of preoperative serum CYFRA 21-1 in colorectal cancer (CRC) resection patients. In this retrospective study, 456 patients with CRC who received surgical treatment in the Department of General Surgery, Affiliated Hospital of Nantong University from January 2016 to February 2018 were analyzed. Preoperative CYFRA 21-1, CEA, CA19-9 and pathological data of the study subjects were collected. Determine the cut-off value of CYFRA 21-1 based on the X-tile. Chi-square test or Fisher exact probability test were used to compare clinicopathological features in different CYFRA 21-1 level groups. Univariate and multivariate regression analysis of factors affecting 5-year overall survival (OS) and disease-free survival (DFS). Kaplan-Meier survival curves were used to analyze 5-year differences in OS and DFS in CRC patients with different levels of CYFRA 21-1, CEA and CA19-9. Receiver operating characteristic(ROC) was adopted. ROC curves were used to analyze the prognostic efficacy of CYFRA21-1 for CRC, and nomogram maps were used to predict 1, 3, and 5-year survival rates. The results showed that the optimal cut-off values of serum CYFRA 21-1, CEA and CA19-9 were 4.9 ng/ml, 29.2 ng/ml and 72.8 U/ml, respectively. Different gender, tumor size, location, degree of differentiation, depth of invasion, lymph node metastasis and tumor node metastasis (TNM) classification stage were significantly different between the two groups with high and low CYFRA 21-1, the P-values were 0.018,<0.001,<0.001,<0.001, 0.002, 0.001, 0.003, respectively. CYFRA 21-1 (≥4.9 ng/ml) was an independent risk factor for 5-year OS (HR: 4.008, 95%CI: 2.309-6.958, P<0.001) and DFS (HR: 3.75, 95%CI: 2.227-6.314, P<0.001) in CRC patients. CYFRA 21-1 predicts a 5-year AUC of 0.725 and 0.720 for OS and DFS, respectively, and 0.804 and 0.827 for the combination of CEA and CA19-9. Based on the results of multivariate Cox regression analysis, nomogram graphs of OS and DFS were established, the C-indexes were 0.799 and 0.803, respectively. In conclusion, preoperative serum CYFRA 21-1 level may be an independent risk factor affecting the prognosis of patients with colorectal cancer. The prognostic model established by CYFRA 21-1 combined with CEA, CA19-9 and TNM stages may provide references for the prevention of CRC recurrence and clinical decision-making.

Polishing De Novo Nanopore Assemblies of Bacteria and Eukaryotes With FMLRC2

As the accuracy and throughput of nanopore sequencing improve, it is increasingly common to perform long-read first de novo genome assemblies followed by polishing with accurate short reads. We briefly introduce FMLRC2, the successor to the original FM-index Long Read Corrector (FMLRC), and illustrate its performance as a fast and accurate de novo assembly polisher for both bacterial and eukaryotic genomes.

[Feasibility of ultrasound radiomics-based models for classification of hepatic echinococcosis]

OBJECTIVE

To investigate the feasibility of establishment of ultrasound radiomics-based models for classification of hepatic echinococcosis, so as to provide insights into precision ultrasound diagnosis of hepatic echinococcosis.

METHODS

The ultrasonographic images were retrospectively collected from 200 patients with hepatic echinococcosis in Shiqu County, Ganzi Tibetan Autonomous Prefecture, Sichuan Province in October 2014, and the regions of interest were plotted in ultrasonographic images of hepatic echinococcosis lesions. The ultrasound radiomics features of hepatic echinococcosis were extracted with 25 methods, and screened using pre-selection and the least absolute shrinkage and selection operator. Then, all ultrasonographic images were randomly assigned into the training and independent test sets according to the type of lesions at a ratio of 7:3. Machine learning models for classification of hepatic echinococcosis were created based on two classifiers, including kernel logistic regression (KLR) and medium Gaussian support vector machine (MGSVM). The receiver operating characteristic (ROC) curves were plotted, and the sensitivity, specificity and areas under the curves (AUC) of the created machine learning models for classification of hepatic echinococcosis were calculated.

RESULTS

A total of 5 005 ultrasound radiomics features were extracted from 200 patients with hepatic echinococcosis using 25 methods, and 36 optimal radiomics features were screened through feature selection, based on which two machine learning models were created, including KLR and MGSVM. ROC curve analysis showed that MGS-VM presented a higher efficacy for hepatic echinococcosis classification than KLR in the training set, with a sensitivity of 0.82, a specificity of 0.78 and AUC of 0.88, while KLR presented a higher efficacy for hepatic echinococcosis classification than MGSVM in the independent test set, with a sensitivity of 0.82, a specificity of 0.72 and AUC of 0.86, respectively.

CONCLUSIONS

Ultrasound radiomics-based machine learning models are feasible for hepatic echinococcosis classification.

[Analyses on the quantity, structure and allocation equity of stomatologists in China]

Objective: To study the quantity, structure and allocation equity of stomatologists, in order to provide bases and advices for improving the allocation of stomatologists in China. Methods: On the basis of data from China Health Statistics Yearbooks and Brief Book of Administrative Divisions of the People's Republic of China, the general situation of stomatologists was analyzed by descriptive analysis. Gini coefficient was used to evaluate the allocation equity in 2010 and 2020. Results: The total number of stomatologists reached 2 780 hundred in 2020, which increased by 150.5% compared with that in 2010. The overall quality structure of stomatologists had improved. The gender proportion was balanced and the age distribution was reasonable. The team was mainly composed by the young people, in which the numbers under 44 years old accounted for 71.6% (1 991 hundred/2 780 hundred). The proportion of personnel with senior professional titles decreased to 7.9% (220 hundred/2 780 hundred) while the total number increased to 220 thousand. The distribution of stomatologists by population was fair. Gini coefficients of the whole country as well as the eastern, central and western regions were less than 0.3. Conclusions: The quantity, quality and allocation equity of stomatologists were still insufficient in China. It is necessary to optimize the human resources allocation for stomatologists. It is suggested to increase the talents supply through supply-side reform, medicine-education collaboration and multi-agent participation. And it is suggested to optimize criterions to improve the quality of stomatologists.

[Use of oral anticoagulants and related factors among new-onset acute ischemic stroke patients with nonvalvular atrial fibrillation: A report from the China Atrial Fibrillation Registry Study]

Objective: This study aimed to investigate the oral anticoagulant (OAC) usage among new-onset acute ischemic stroke (AIS) patients with nonvalvular atrial fibrillation (NVAF) in China, and to explore the possible influencing factors of influent anticoagulant therapy in these patients. Methods: The NVAF patients who experienced new-onset and non-fatal AIS from August 2011 to December 2018 in the China Atrial Fibrillation Registry (China-AF), were enrolled. The follow-up ended in December 2019. Information including patients' demographic characteristics, medical history, medication usage, which were collected before and after the index stroke, were analyzed. Patients were classified into OAC group or non-OAC group according to OAC usage within 3 months post stroke. Multivariate logistic regression analysis were conducted to calculate the odds ratios (ORs) of factors which might be associated with OAC usage within 3 months post stroke. Results: A total of 957 new-onset AIS patients were enrolled, 39.4% (377/957) patients were treated with OAC within 3 months after AIS. Covering by high-reimbursement-rate insurance (OR: 1.91, 95%CI: 1.28-2.86, P=0.002), higher number of concomitant drugs (1-2 types OR: 2.10, 95%CI: 1.36-3.23, P=0.001; ≥3 types OR: 2.31, 95%CI: 1.37-3.91, P=0.002) and 3-month-peri-stroke AF recurrence (OR: 3.34, 95%CI: 2.34-4.76, P<0.001) were associated with OAC usage within 3 months post stroke, while higher HASBLED score (OR: 0.49, 95%CI: 0.40-0.60, P<0.001) and pre-stroke antiplatelet usage (OR: 0.29, 95%CI: 0.20-0.43, P<0.001) were related to no OAC usage within 3 months post stroke. Conclusions: In China, the proportion of NVAF patients who initiated OAC therapy within 3 months after new-onset AIS is as low as about 39.4%. Factors related to the OAC usage within 3 months post stroke are 3-month-peri-stroke AF recurrence, number of concomitant drugs and patients with high-reimbursement-rate insurance coverage, but higher HASBLED score and pre-stroke antiplatelet usage are related to no OAC usage within 3 months post stroke.

[SWOT analysis of influenza vaccination promotion of primary care staff based on the perspective of the supplier, customer, and management]

Objective: To analyze the situation of influenza vaccination among primary healthcare workers, find out the problems, and explore the strategies and measures to promote influenza vaccination among grass-roots medical staff. Methods: From April to May 2021, key insider interviews and literature research were carried out based on the perspectives of influenza vaccine suppliers (influenza vaccine manufacturers), consumers (primary medical institutions and primary healthcare workers), and managers (governments at all levels, health administrative departments and disease prevention and control departments). The SWOT (strengths, weaknesses, opportunities, and threats) analysis technique was used to comprehensively evaluate the current situation of influenza vaccination among grass-roots healthcare workers, and a SWOT analysis matrix was established. Results: Influenza vaccination of grass-roots healthcare workers have advantages and opportunities, including primary medical and health institutions' vital influenza vaccination accessibility, influenza vaccine safety is higher, COVID-19 outbreak improves the public awareness of respiratory infectious diseases and vaccine production enthusiasm, coronavirus vaccination has strengthened the capacity of the vaccine distribution system. There are also disadvantages and threats such as the high price of influenza vaccine, insufficient supply, low awareness of influenza vaccine vaccination among grass-roots healthcare workers, lack of demand assessment mechanism on influenza vaccine, poor vaccine deployment, structural imbalance in vaccine supply in different areas, and severe vaccine waste. SWOT analysis matrix of the influenza vaccination status of grass-roots healthcare workers was established, forming dominant opportunity (SO) strategy, dominant threat (ST) strategy, inferior opportunity (WO) strategy, and inferior threat (WT) strategy. Conclusion: Measures should be taken by the supplier, the demand-side, and the management side to improve the influenza vaccine coverage rate of primary healthcare workers, but the emphasis should be on the coordination and management of the management side.

[Drug selection for simultaneous treatment of tuberculosis combined with hepatitis C virus infection]

Clinically, patients with tuberculosis (TB) combined with hepatitis C virus (HCV) infection often require simultaneous treatment. Consequently, when anti-HCV and TB drugs are used in combination drug-drug interactions (DDIs), anti-TB drug-induced hepatotoxicity, and liver disease states need to be considered. This paper focuses on discussing the metabolic mechanisms of commonly used anti-TB and HCV drugs and the selection options of combined drugs, so as to provide rational drug use for TB patients combined with HCV infection.

[Human bone marrow mesenchymal stem cells improve steroid resistance of human airway epithelial BEAS-2B cells in vitro]

Objective: To explore the effect of human bone marrow mesenchymal stem cells(MSC) on the steroid resistance of human airway epithelial cells. Methods: Ovalbumin (OVA)/lipopolysaccharide (LPS) were used to construct steroid resistant BEAS-2B cells, which were then co-cultured with MSC. Groups were set as follows: blank group, model group, Glucocorticoid group, MSC group, MSC+Glucocorticoid group (MSC+bud group). The expression of interleukin (IL)-8 in the cell supernatant was detected by enzyme-linked immunosorbent assay (ELISA); the expression of reactive oxygen species (ROS) in the cells was detected by flow cytometry; the expression of glucocorticoid receptor α (GRα) and histone deacetylase 2 (HDAC2) protein in the cell was detected by Western blotting; and the expression of GRα and HDAC2 mRNA was detected by reverse transcription-polymerase chain reaction (RTPCR). Results: The expression level of IL-8 in the MSC group was significantly lower than that in the Glucocorticoid group (31.7±0.7 vs. 49.8±3.6, P<0.01). The expression of ROS in the MSC group was significantly lower than that in the Glucocorticoid group (2754±154 vs.4624±228, P<0.05). The expression level of HDAC2 mRNA in the MSC group was significantly higher than that in the Glucocorticoid group(1.749±0.005 vs. 1.283±0.098, P<0.05). The expression level of GRα mRNA in the MSC group was significantly higher than that in the Glucocorticoid group (1.623±0.079 vs.1.047±0.220, P<0.01). The expression of HDAC2 protein in the MSC group was significantly higher than that in the Glucocorticoid group (1.067±0.100 vs. 0.620±0.083, P<0.01). The expression of GRα protein in the MSC group was significantly higher than that in the Glucocorticoid group (0.834±0.053 vs. 0.579±0.017, P<0.01). ROS was positively correlated with the IL-8 expression (r=0.796, P<0.01) and negatively correlated with the HDAC2 and GRα mRNA expression (r=-0.893 3, P<0.01; r=0.931 4, P<0.01, respectively), as well as the HDAC2 and GRα Protein expression (r=-0.929 5, P<0.01;r=-0.864 3, P<0.01, respectively). Conclusions: Human MSC can improve steroid resistance of airway epithelial cells in an exocrine manner. The mechanism may be related to the down-regulation of ROS and up-regulation of HDAC2, which lead to GRα overexpression. In addition, MSC may improve the steroid resistance by reducing the expression of IL-8.

[Investigation and analysis of a mass ammonia gas poisoning accident]

Objective: To investigation and analysis of ammonia gas leakage in a meat factory. Methods: In April 2013, Enterprise managers and workers were investigated, and clinical data of 24 patients were analyzed. Results: The company caused a leak in the ammonia pipeline maintenance operation, Among the patients, 20 had stimulus response and 4 had mild poisoning. Conclusion: To prevent group occupational ammonia poisoning, it is necessary to strengthen the awareness of occupational disease prevention of enterprise owners and the awareness of self-protection of workers.

Highly contiguous assemblies of 101 drosophilid genomes

Over 100 years of studies in Drosophila melanogaster and related species in the genus Drosophila have facilitated key discoveries in genetics, genomics, and evolution. While high-quality genome assemblies exist for several species in this group, they only encompass a small fraction of the genus. Recent advances in long-read sequencing allow high-quality genome assemblies for tens or even hundreds of species to be efficiently generated. Here, we utilize Oxford Nanopore sequencing to build an open community resource of genome assemblies for 101 lines of 93 drosophilid species encompassing 14 species groups and 35 sub-groups. The genomes are highly contiguous and complete, with an average contig N50 of 10.5 Mb and greater than 97% BUSCO completeness in 97/101 assemblies. We show that Nanopore-based assemblies are highly accurate in coding regions, particularly with respect to coding insertions and deletions. These assemblies, along with a detailed laboratory protocol and assembly pipelines, are released as a public resource and will serve as a starting point for addressing broad questions of genetics, ecology, and evolution at the scale of hundreds of species.

Urinary biomarkers of early renal injury in antiretroviral-naïve HIV-positive persons in Shanghai, China: comparison with the general population

Objectives

People living with HIV (PLWH) have a high risk of kidney injury. Measurement of serum creatinine, along with proteinuria, is not sensitive to detect early kidney injury. Here, we investigated novel urinary biomarkers of early renal injury in PLWH.

Methods

We performed a cross‐sectional study of 166 antiretroviral‐naïve PLWH and 99 HIV‐negative persons who all had an estimated glomerular filtration rate > 90 mL/min/1.73 m². We compared the levels of seven urinary biomarkers between the two groups using the propensity score matching (PSM) approach and explored the risk factors associated with elevated urinary biomarkers in PLWH.

Results

Eighty‐three pairs were successfully matched based on PSM. Compared with the HIV‐negative group, the HIV‐positive group had higher ratios of N‐acetyl‐β‐D‐glucosaminidase (NAG) to urine creatinine (UCr), alpha1‐microglobulin (α1‐M) to UCr, kidney injury marker‐1 (KIM‐1) to UCr, neutrophil gelatinase‐associated lipocalin to UCr, and epidermal growth factor to UCr, whereas the Tamm–Horsfall protein to UCr ratio and the abnormal albumin to UCr ratio were not significantly different. Positive correlations were observed between HIV RNA level and NAG: UCr (r_s = 0.32; P < 0.001) and α1‐M:UCr (r_s = 0.24; P = 0.002) ratios, and negative correlations were observed between CD4 cell count and NAG:UCr (r_s = –0.34; P < 0.001), KIM‐1:UCr (r_s = –0.16; P = 0.042) and α1‐M:UCr (r_s = –0.36; P < 0.001) ratios. In multivariate linear regression analyses, older age, lower total cholesterol and higher HIV RNA were independently associated with higher NAG:UCr; older age, lower total cholesterol and lower CD4 cell count were independently associated with higher α1‐M:UCr.

Conclusions

In comparioson with HIV‐negative participants, PLWH were more likely to have tubular injury. Early antiretroviral treatment might mitigate the development of kidney injury.

A vertebrate adaptive radiation is assembled from an ancient and disjunct spatiotemporal landscape

To investigate the origins and stages of vertebrate adaptive radiation, we reconstructed the spatial and temporal histories of adaptive alleles underlying major phenotypic axes of diversification from the genomes of 202 Caribbean pupfishes. On a single Bahamian island, ancient standing variation from disjunct geographic sources was reassembled into new combinations under strong directional selection for adaptation to the novel trophic niches of scale-eating and molluscivory. We found evidence for two longstanding hypotheses of adaptive radiation: hybrid swarm origins and temporal stages of adaptation. Using a combination of population genomics, transcriptomics, and genome-wide association mapping, we demonstrate that this microendemic adaptive radiation of novel trophic specialists on San Salvador Island, Bahamas experienced twice as much adaptive introgression as generalist populations on neighboring islands and that adaptive divergence occurred in stages. First, standing regulatory variation in genes associated with feeding behavior (prlh, cfap20, and rmi1) were swept to fixation by selection, then standing regulatory variation in genes associated with craniofacial and muscular development (itga5, ext1, cyp26b1, and galr2) and finally the only de novo nonsynonymous substitution in an osteogenic transcription factor and oncogene (twist1) swept to fixation most recently. Our results demonstrate how ancient alleles maintained in distinct environmental refugia can be assembled into new adaptive combinations and provide a framework for reconstructing the spatiotemporal landscape of adaptation and speciation.

A retrospective cohort study of early mortality among patients with HIV/TB co-infection in Shanghai municipality

OBJECTIVES

Tuberculosis (TB) is the most common and fatal opportunistic co-infection among HIV-infected individuals. While TB-associated mortality predominantly occurs in the first 90 days after admission, such a correlation remains unclear in HIV/TB co-infected patients. Thus, we aimed to investigate the 90-day mortality and associated risk factors among HIV/TB co-infected patients in China.

METHODS

Adult patients with HIV and a newly confirmed TB diagnosis admitted to the Shanghai Public Health Clinical Center between September 2009 and August 2017 were enrolled. Clinical and laboratory characteristics, key treatments and outcomes were collected retrospectively. The associations between different factors and early mortality were analysed.

RESULTS

Of the 485 laboratory-confirmed HIV/TB patients [median (range) age = 39 (19-79) years], 413 (85.15%) were male. Diagnosis was confirmed by culture, pathology and acid-fast bacilli smear alone in 362 (74.6%), 6 (1.2%) and 117 (24.1%) patients, respectively. Multiple drug-/rifampin-resistant TB was detected in 21 (5.8%) of the 367 patients with a positive culture. Rifampin or rifabutin was administered to 402 (82.9%) patients. Additionally, 66 (13.6%) and 86 (17.7%) died within 90 days and 1 year of admission, respectively. Of the 64 TB-related deaths, 59 (92.2%) occurred within 90 days of admission. In Cox regression, central nervous system (CNS) TB [odds ratio (OR) = 2.49, 95% confidence interval (CI): 1.46-4.23, P < 0.001], no antiretroviral therapy (ART) within 3 months after admission (OR = 11, 95% CI: 6.4-18.9, P < 0.001), and plasma albumin level < 25 g/L (OR = 1.91, 95% CI: 1.07-3.40, P = 0.021) were associated with early death.

CONCLUSIONS

Tuberculosis co-infection was prevalent and fatal in HIV-infected patients, with most deaths occurring within 90 days of admission. Early mortality was associated with CNS-TB, no ART, and serum albumin level < 25 g/L.

Glycyrrhizin improves bone metabolism in ovariectomized mice via inactivating NF-κB signaling

OBJECTIVES

Postmenopausal osteoporosis (PMO) is a prevalent metabolic bone disease with high morbidity and serious complications. Here, we studied the effect of glycyrrhizin on bone metabolism using the ovariectomized (OVX) mouse model.

METHODS

Osteoclast-related gene expression and osteoclastic function were evaluated in RAW264.7 cells and bone marrow-derived monocytes (BMMs) by real-time polymerase chain reaction and bone resorption assay. For animal studies, female C57BL/6J mice were randomly divided into sham operated, OVX and OVX with glycyrrhizin groups. Bone mass and trabecular microarchitecture were analyzed by micro-computed tomography, dual X-ray absorptiometry, and histomorphometric analysis. Receptor activator of nuclear factor-κB (NF-κB) ligand-induced osteoclastogenesis and the NF-κB signaling pathway were studied by tartrate-resistant acid phosphatase staining and western blotting, respectively.

RESULTS

Glycyrrhizin inhibits RANKL-induced expression of Nfatc-1, c-Fos, Trap, Ds-stamp, and Ctsk in RAW264.7 cells. Also, fewer bone resorption pits form when BMMs are incubated in the presence of glycyrrhizin. Glycyrrhizin ameliorates bone loss and improves trabecular bone parameters in OVX mice. BMMs isolated from OVX mice show higher ability of RANKL-induced osteoclastogenesis, which is tremendously reversed by glycyrrhizin. There is significantly higher phosphorylation of IκB-α at Ser32 and NF-κB p65 at Ser536, as well as increased protein levels of c-FOS and NFATc-1 in BMMs of OVX mice, which are all greatly suppressed by glycyrrhizin.

CONCLUSIONS

Our findings imply that glycyrrhizin is a potential efficient adjuvant therapeutic for PMO.

[Sex Characteristics and Distribution of External Ear in Uygur Population of Xinjiang]

Objective To analyze the characteristics of the bilateral external ears of Uygur adults by directly observing the morphological characteristics of the external ears of Uygur adults and classifying each feature. The frequency distribution of the characteristics was calculated to provide reference for forensic identification. Methods The 210 cases （75 males and 135 females） of bilateral external ear photos of Uygur adults in Xinjiang that met the inclusion criteria were collected. The frequencies of the features of the external ear were recorded and distinguished between the two sexes and the different sides. The data were statistically analyzed by SPSS 21.0 statistical software. Results The shapes of the external ears of males and females were commonly oblique or rectangular （34.67% of the left external ear of males and 41.33% of the right were oblique; 30.37% of the left and right external ear of females were rectangular）, while triangular ears were the rare variants and the least common. Sex and bilateral differences were observed as regards the form of the helix in the subjects. Normally rolled helix was the most common （58.67% males and 61.48% females for the left ear; 60.00% males and 72.59% females for the right ear）. Wide covering scapha helix was the most rare for the male left ear and flat helix was the most rare for the female right ear. Square and free earlobes were the most common （49.33% males and 62.96% females for the left ear; 40.00% males and 54.81% females for the right ear）, whereas triangular earlobes were rarely seen. Single knob tragus （40.00% males and 37.78% females for the left ear; 37.33% males and 33.33% females for the right ear） and projection type of Darwin's tubercle （50.67% males and 40.00% females for the left ear; 48.00% males and 39.26% females for the right ear） were found to be common. Conclusion The characteristics of the bilateral external ears of male and female Uygur adults have differences, which can be used for forensic identification.

Crohn's Disease Differentially Affects Region-Specific Composition and Aerotolerance Profiles of Mucosally Adherent Bacteria

BACKGROUND

The intestinal microbiota play a key role in the onset, progression, and recurrence of Crohn disease (CD). Most microbiome studies assay fecal material, which does not provide region-specific information on mucosally adherent bacteria that directly interact with host systems. Changes in luminal oxygen have been proposed as a contributor to CD dybiosis.

METHODS

The authors generated 16S rRNA data using colonic and ileal mucosal bacteria from patients with CD and without inflammatory bowel disease. We developed profiles reflecting bacterial abundance within defined aerotolerance categories. Bacterial diversity, composition, and aerotolerance profiles were compared across intestinal regions and disease phenotypes.

RESULTS

Bacterial diversity decreased in CD in both the ileum and the colon. Aerotolerance profiles significantly differed between intestinal segments in patients without inflammatory bowel disease, although both were dominated by obligate anaerobes, as expected. In CD, high relative levels of obligate anaerobes were maintained in the colon and increased in the ileum. Relative abundances of similar and distinct taxa were altered in colon and ileum. Notably, several obligate anaerobes, such as Bacteroides fragilis, dramatically increased in CD in one or both intestinal segments, although specific increasing taxa varied across patients. Increased abundance of taxa from the Proteobacteria phylum was found only in the ileum. Bacterial diversity was significantly reduced in resected tissues of patients who developed postoperative disease recurrence across 2 independent cohorts, with common lower abundance of bacteria from the Bacteroides, Streptococcus, and Blautia genera.

CONCLUSIONS

Mucosally adherent bacteria in the colon and ileum show distinct alterations in CD that provide additional insights not revealed in fecal material.

[Clinical analysis of seven cases of myeloid sarcoma]

Objective: To investigate the clinical manifestations, pathological features, diagnosis and treatment of myeloid sarcoma, and to improve the understanding of myeloid sarcoma. Methods: The clinical data, diagnosis and treatment of 7 patients with myeloid sarcoma were retrospectively analyzed. Results: Of the 7 patients with myeloid sarcoma, 1 was male and 6 were female. In most patients, the local compression symptoms caused by painless local masses or masses were the first manifestations. One patient had lesions involving the cervix and vaginal bleeding was the first symptom. The lesions were extensive with 19 sites involved. The positive proportion of immunohistochemical staining was 6/6 for CD43, 6/7 for MPO, 4/5 for CD117, 4/4 for LCA, 3/5 for CD34 and 2/2 for CD99. Lymphocyte markers CD3 and CD20 were negative in all 7 patients. Conclusions: Myeloid sarcoma is a rare hematological malignancy. Early diagnosis and active treatment are the key to improve prognosis. Current treatments include systemic chemotherapy, surgical resection, radiation therapy, and hematopoietic stem cell transplantation.

Nonlinear sequence similarity between the Xist and Rsx long noncoding RNAs suggests shared functions of tandem repeat domains

The marsupial inactive X chromosome expresses a long noncoding RNA (lncRNA) called Rsx that has been proposed to be the functional analog of eutherian Xist Despite the possibility that Xist and Rsx encode related functions, the two lncRNAs harbor no linear sequence similarity. However, both lncRNAs harbor domains of tandemly repeated sequence. In Xist, these repeat domains are known to be critical for function. Using k-mer based comparison, we show that the repeat domains of Xist and Rsx unexpectedly partition into two major clusters that each harbor substantial levels of nonlinear sequence similarity. Xist Repeats B, C, and D were most similar to each other and to Rsx Repeat 1, whereas Xist Repeats A and E were most similar to each other and to Rsx Repeats 2, 3, and 4. Similarities at the level of k-mers corresponded to domain-specific enrichment of protein-binding motifs. Within individual domains, protein-binding motifs were often enriched to extreme levels. Our data support the hypothesis that Xist and Rsx encode similar functions through different spatial arrangements of functionally analogous protein-binding domains. We propose that the two clusters of repeat domains in Xist and Rsx function in part to cooperatively recruit PRC1 and PRC2 to chromatin. The physical manner in which these domains engage with protein cofactors may be just as critical to the function of the domains as the protein cofactors themselves. The general approaches we outline in this report should prove useful in the study of any set of RNAs.

[The study of using cordyceps-astragalus-salvia miltiorrhiza to treat acute lung injury induced by paraquat poisoning in rats]

Objective: To study the therapy of cordyceps-astragalus-salvia miltiorrhiza in treating acute lung injury and pulmonary interstitial fibrosis induced by paraquat poisoning. Methods: All 120 adult Wister male rats were randomly assigned to three groups, the paraquat poisoning group (rats were intragastric administration paraquat 50 mg/kg body weight once at the beginning) , the cordyceps-astragalus-salvia miltiorrhiza therapy group (rats were given cordyceps-astragalus-salvia miltiorrhiza 90 mg/kg body weight intragastric administration half an hour after paraquat was given, then the same dose was given once a day) ; control group (rats were intragastric administration with physiological saline) . At 7th, 14th, 21st, and 28th day rats were sacrificed postanesthetic respectively after paraquat exposure, sample of lung tissue, bronchoalveolar lavage (BAL) , and venous blood were collected. GSH, SOD, TNF-α, TGF-β1, and HYP in plasma, bronchoalveolar lavage (BAL) , and the lung homogenates were determined. Optical microscope was performed to examine pathological changes in lung. Results: Each experimental time point paraquat group and the treatment group rats serum SOD content significantly lower than the control group (P<0.05) . Each experimental time point the treatment group rats serum SOD levels increased significantly than that of paraquat group (P<0.05) . Each experimental time point paraquat group rats serum GSH content significantly lower than that of the control group (P<0.05) . Treatment group rats 7 days time GSH content significantly lower than that of the control group (P<0.05) . Treatment group 21 days, 28 days GSH content was increased significantly than that of the paraquat group (P<0.05) . Each experimental time point paraquat group rats alveolar lavage SOD content was significantly lower than that of the control group (P<0.05) . Treatment group 7 days, 14 days time SOD content was significantly lower than that of the control group (P<0.05) , Treatment group 21 days, 28 days SOD content was increased significantly than that of the paraquat group (P<0.05) . Each experimental time point paraquat group and the treatment group rats alveolar lavage GSH content significantly were lower than that of the control group (P<0.05) . Treatment group days 14 and 21 days, 28 days GSH content was increased significantly than that of the paraquat group (P<0.05) . Each experimental time point paraquat group rats alveolar lavage TNF α levels was higher than that of the control group (P<0.05) . Treatment group 7 days, 14 days the rat alveolar lavage TNF α levels was higher than that of the control group (P<0.05) . Treatment group 21 days, 28 days TNF α content significantly was decreased than that of paraquat group (P<0.05) . Paraquat group days 14 and 21 days, 28 days HYP content was significantly higher than that of control group (P<0.05) . Treatment group 21 days HYP content was significantly higher than that of control group (P<0.05) . Treatment group 28 days time HYP content in lung tissue of rats was significantly decreased than that of the paraquat group (P<0.05) . Each experimental time point paraquat group rat lung tissue (tissue homogenate) TGF-β1 content was higher than that of the control group, the difference was statistically significant (P<0.05) . Under optical microscope, the tissue damage of lung was aggravated, and reduced after cordyceps-astragalus-salvia miltiorrhiza was administrated. Conclusion: Cordyceps-astragalus-salvia miltiorrhiza can reduce inflammation factor releasing, and relieve lung injury. It has therapeutic effect on lung injury induced by paraquat poisoning.

[Xanthogranulonatous pyelonephritis: report of 5 cases]

Xanthogranulomatous pyelonephritis (XGP) is an unusual form of chronic pyelonephritis in which the renal parenchyma is destroyed and replaced by lipid-laden foamy macrophages. It usually affects middle-aged women with a history of recurrent urinary tract infection, diabetes, or kidney stones. The inflammatory process is usually diffuse and can extend beyond the kidney. The rare focal forms may simulate primary renal tumours. The preoperative imaging diagnosis may be difficult. We reported five cases of XGP, The findings of ours were recorded including kidney size, shape, contour, the echogenecity of the renal parenchyma, the internal echoes of the dilate collecting system, the presence of perinephric fluid accumulation and obstruction. One of the 5 cases was a male patient, and the other four were female, with a mean age of 53 years. He affected kidneys of the 5 cases swelled in different degrees, and one of them was found with line-like anechoic fluid. Among the 5 cases, one kidney appeared as diffusely reducing of the parenchyma echogenicity, multiple hypoechoic areas, disappearance of corticomedullary differentiation and multiple hyperecho with shadow. A round cystic anechoic lesion was found in one kidney, with internal punctate echo and peripheral fluid. Ultrasonographic finding of 1 case was extremely hypoechoic lesion on the left kidney, protruding from the outline of the kidney, with the partial renal capsule discontinuous, the less clear boundary, and a little blood flow in it. Ultrasonographic demonstration of 2 cases was mild dilatation of the collecting system with irregular wall thickening and internal hypoechogenicity, and 1 case was solid lesion with less clear boundary to the pelvic wall and a small amount of blood flow signal, the another 1 case was showed floccule without internal blood flow. Three cases were caused by chronic obstruction verified by operation, of which one was staghorn calculi, one was poorly differentiated squamous cell carcinoma in the middle part of the ureter, and one was inflammatory stricture of upper ureteral. Through analysis of the above five cases and review of related literature, we explored diagnoses and management of the patients with XGP. Xanthogranulomatous pyelonephritis (XGP) is a rare chronic variant of pyelonephritis characterized by destruction of the renal parenchyma. Combining ultrasonographic features of XGP with clinical recurrent urinary infection and chronic obstruction, XGP can be included in the differentiation. The diagnosis of XGP suspected by ultrasound can be clarified by CT, MRI, contrast-enhanced ultrasound.

FMLRC: Hybrid long read error correction using an FM-index

Background

Long read sequencing is changing the landscape of genomic research, especially de novo assembly. Despite the high error rate inherent to long read technologies, increased read lengths dramatically improve the continuity and accuracy of genome assemblies. However, the cost and throughput of these technologies limits their application to complex genomes. One solution is to decrease the cost and time to assemble novel genomes by leveraging “hybrid” assemblies that use long reads for scaffolding and short reads for accuracy.

Results

We describe a novel method leveraging a multi-string Burrows-Wheeler Transform with auxiliary FM-index to correct errors in long read sequences using a set of complementary short reads. We demonstrate that our method efficiently produces significantly more high quality corrected sequence than existing hybrid error-correction methods. We also show that our method produces more contiguous assemblies, in many cases, than existing state-of-the-art hybrid and long-read only de novo assembly methods.

Conclusion

Our method accurately corrects long read sequence data using complementary short reads. We demonstrate higher total throughput of corrected long reads and a corresponding increase in contiguity of the resulting de novo assemblies. Improved throughput and computational efficiency than existing methods will help better economically utilize emerging long read sequencing technologies.

[Autophagy regulated by JWA influenced sensitivity of esophageal cancer to cisplatin]

Objective: To explore the effect of JWA on cisplatin sensitivity and its potential molecular mechanism in esophageal cancer. Methods: The siRNA was used to inhibit the JWA expression, then cisplatin sensitivity and LC3 (autophagy related protein) expression levels were observed in TE1 cells.Further, the effect of autophagy inhibitor tamoxifen (3-MA) on above process was determined.Cisplatin sensitivity of 20 fresh esophageal cancer samples was evaluated by histoculture drug response assay (HDRA). Result: Silencing JWA gene increased the sensitivity of TE1 cells to cisplatin (P<0.05), and decreased the LC3-Ⅰ and LC3-Ⅱ proteins induced by cisplatin.Furthermore, combined with 3-MA increased the inhibition rate of cisplatin in JWA silencing group (P<0.05). Additionally, the inhibition rate of cisplatin on tissues with low JWA expression were higher than those with high expression (45.6% vs 25.6%, P=0.005). Conclusions: JWA could influence the cisplatin sensitivity by regulating autophagy in esophageal cancer.

Measurement of diagnostic neutral beam parameters on J-TEXT

A Doppler frequency shift spectrum (DFSS) system composed of two spectrometers has been developed for the joint Texas experimental tokamak to measure diagnostic neutral beam parameters including the beam energy fractions, intensity distributions, and divergences. The beam energy fractions are derived from measurements of H-alpha (Hα) emission using collisional excitation cross sections. The beam intensity distributions are obtained using an 11-channel measurement with a reconstruction technique. The beam divergences are obtained from spectrum broadening and geometric calculations. The results of preliminary investigations indicate that the DFSS system works well and can be used to obtain all of these parameters simultaneously. According to the preliminary experiment, the one-third energy fraction has the largest proportion (about 45%) of the beam energy and the full energy fraction is about 10%. The beam diameter is about 8.1 cm at a distance of 2.04 m from the accelerator. The beam divergence angle is about 3.3°. The current beam parameters are insufficient for charge-exchange measurements.

Protective effects of naringin against gp120-induced injury mediated by P2X7 receptors in BV2 microglial cells

This study was aimed at exploring the effects of P2X7 receptors on gp120-induced injury and naringin's protective effects against gp120-induced injury in BV2 microglia. BV2 microglia injury model was established by gp120 treatment and MTS assay was used to verify whether naringin has a cell-protective effect against gp120-induced injury. Changes in P2X7 receptor expression were assayed using RT-PCR, qPCR, and western blot. Results showed that the ODs of the Ctrl, gp120, gp120+naringin, and gp120+BBG groups were 0.91 ± 0.10, 0.71 ± 0.09, 0.83 ± 0.10, and 0.83 ± 0.10, respectively. Compared to the control group, the gp120 group showed a significantly decreased cell survival rate. Cell survival rates of the gp120+naringin group increased significantly compared to those of the gp120 group, while no difference was observed when compared to the gp120+BBG group. The relative P2X7 mRNA expression levels in the Ctrl, gp120, gp120+naringin, and gp120+BBG groups were 0.73 ± 0.06, 1.05 ± 0.06, 0.78 ± 0.05, and 0.81 ± 0.04, respectively. The corresponding P2X7 protein expression levels were 0.46 ± 0.04, 0.79 ± 0.04, 0.38 ± 0.07, and 0.42 ± 0.06. P2X7 mRNA and protein expression in the gp120 group increased significantly compared to those in the control group, and declined in the gp120+naringin group compared to those in the gp120 group. Therefore, P2X7 receptors might be involved in gp120-induced injury in BV2 microglia, and naringin might play a protective role by inhibiting the up-regulated expression of P2X7 receptors.

The curative efficacy of arthroscopic therapy in treating anterior cruciate ligament rupture with secondary osteoarthritis

OBJECTIVE

To compare and analyze the clinical effects of arthroscopic therapy and drug therapy in treating anterior cruciate ligament (ACL) rupture with secondary osteoarthritis (OA).

PATIENTS AND METHODS

A total of 68 patients that were diagnosed as ACL rupture with secondary OA in our hospital from February 2014 to February 2015 were enrolled in our study. All of the patients were randomly divided into control group (n = 30) and observation group (n = 38) according to the order of admission. The patients in the control group were given analgesic, anti-inflammatory drugs + functional rehabilitation training whereas the patients in the observation group were given ACL reconstruction + OA debridement and functional rehabilitation training under arthroscopy.

RESULTS

The success rate of the observation group was 92.1%. After 3-month follow-up, the clinical total effective rate of the observation group was significantly higher than that of the control group, the prevalence of complications in the observation group was significantly lower than in the control group, and differences were statistically significant (p < 0.05). Lysholm scale scoring of observation group was significantly higher than of the control group, modified McGill pain scale score was significantly lower than that of the control group, and differences were statistically significant (p < 0.05). Quadriceps muscle peak torque, average power, and the optimal single work at 60°/s, 120°/s, and 180°/s were significantly higher than those of the control group, and differences were statistically significant (p < 0.05).

CONCLUSIONS

Arthroscopic operative therapy was safe and effective for the treatment of ACL with secondary OA. Compared with drug therapy, it can significantly improve the movement function of the knee joint, so it was worthy of clinical application.

Functional polymorphisms in microRNA gene and hepatitis B risk among Asian population: a meta-analysis

Genetic mutations in microRNA gene can alter expression, which may interact to increase the risk of developing various diseases, including hepatitis B. However, published results are inconclusive or ambiguous. The aim of this review and meta-analysis is to more precisely estimate the association between polymorphisms in microRNA genes and hepatitis B risk. A digital search was performed of the MEDLINE EMBASE, CNKI, and CBM databases to identify relevant articles published up to February 18, 2014. Ten case-control studies were included, with a total of 6042 patients with hepatitis B and 6834 healthy controls. Nine single-nucleotide polymorphisms in the miRNA gene were examined, including miR-34b/c [rs4938723 (T>C)], miR-196a-2 [rs11614913 (C>T)], miR-146a [rs2910164 (G>C)], miR-499 [rs3746444 (T>C)], miR-122 [rs3783553 (ins/del)], miR-149 [rs2292832 (C>T)], miR-106b-25 [rs999885 (A>G)], miR-let-7c [rs6147150 (ins/del)], and miR-218 [rs11134527 (A>G)]. The meta-analysis results indicated that the miR-196a-2*T, miR-122*del, miR-106b-25*A, and miR-let-7c*del alleles/carriers increase the risk of hepatitis B among the Asian population. However, the miR-146a, miR- 499, miR-149, miR-218, and miR-34b/c polymorphisms may not be linked with the risk of hepatitis B. Further investigations are warranted to determine the exact associations between microRNA mutations and hepatitis B susceptibility.

Analyses of allele-specific gene expression in highly divergent mouse crosses identifies pervasive allelic imbalance

Complex human traits are influenced by variation in regulatory DNA through mechanisms that are not fully understood. Since regulatory elements are conserved between humans and mice, a thorough annotation of cis regulatory variants in mice could aid in this process. Here we provide a detailed portrait of mouse gene expression across multiple tissues in a three-way diallel. Greater than 80% of mouse genes have cis regulatory variation. These effects influence complex traits and usually extend to the human ortholog. Further, we estimate that at least one in every thousand SNPs creates a cis regulatory effect. We also observe two types of parent-of-origin effects, including classical imprinting and a novel, global allelic imbalance in favor of the paternal allele. We conclude that, as with humans, pervasive regulatory variation influences complex genetic traits in mice and provide a new resource toward understanding the genetic control of transcription in mammals.

Design of charge exchange recombination spectroscopy for the joint Texas experimental tokamak

The old diagnostic neutral beam injector first operated at the University of Texas at Austin is ready for rejoining the joint Texas experimental tokamak (J-TEXT). A new set of high voltage power supplies has been equipped and there is no limitation for beam modulation or beam pulse duration henceforth. Based on the spectra of fully striped impurity ions induced by the diagnostic beam the design work for toroidal charge exchange recombination spectroscopy (CXRS) system is presented. The 529 nm carbon VI (n = 8 - 7 transition) line seems to be the best choice for ion temperature and plasma rotation measurements and the considered hardware is listed. The design work of the toroidal CXRS system is guided by essential simulation of expected spectral results under the J-TEXT tokamak operation conditions.

Regulation of autophagy by miR-30d impacts sensitivity of anaplastic thyroid carcinoma to cisplatin

miR-30d has been observed to be significantly down-regulated in human anaplastic thyroid carcinoma (ATC), and is believed to be an important event in thyroid cell transformation. In this study, we found that miR-30d has a critical role in modulating sensitivity of ATC cells to cisplatin, a commonly used chemotherapeutic drug for treatment of this neoplasm. Using a mimic of miR-30d, we demonstrated that miR-30d could negatively regulate the expression of beclin 1, a key autophagy gene, leading to suppression of the cisplatin-activated autophagic response that protects ATC cells from apoptosis. A reporter gene assay demonstrated that the binding sequences of miR-30d in the beclin 1-3' UTR was the region required for the inhibition of beclin 1 expression by this miRNA. We further showed that inhibition of the beclin 1-mediated autophagy by the miR-30d mimic sensitized ATC cells to cisplatin both in vitro (cell culture) and in vivo (animal xenograft model). These results suggest that dysregulation of miR-30d in ATC cells is responsible for the insensitivity to cisplatin by promoting autophagic survival. Thus, miR-30d may be exploited as a potential target for therapeutic intervention in the treatment of ATC.

Comparative analysis and visualization of multiple collinear genomes

Background

Genome browsers are a common tool used by biologists to visualize genomic features including genes, polymorphisms, and many others. However, existing genome browsers and visualization tools are not well-suited to perform meaningful comparative analysis among a large number of genomes. With the increasing quantity and availability of genomic data, there is an increased burden to provide useful visualization and analysis tools for comparison of multiple collinear genomes such as the large panels of model organisms which are the basis for much of the current genetic research.

Results

We have developed a novel web-based tool for visualizing and analyzing multiple collinear genomes. Our tool illustrates genome-sequence similarity through a mosaic of intervals representing local phylogeny, subspecific origin, and haplotype identity. Comparative analysis is facilitated through reordering and clustering of tracks, which can vary throughout the genome. In addition, we provide local phylogenetic trees as an alternate visualization to assess local variations.

Conclusions

Unlike previous genome browsers and viewers, ours allows for simultaneous and comparative analysis. Our browser provides intuitive selection and interactive navigation about features of interest. Dynamic visualizations adjust to scale and data content making analysis at variable resolutions and of multiple data sets more informative. We demonstrate our genome browser for an extensive set of genomic data sets composed of almost 200 distinct mouse laboratory strains.

Subspecific origin and haplotype diversity in the laboratory mouse

Here we provide a genome-wide, high-resolution map of the phylogenetic origin of the genome of most extant laboratory mouse inbred strains. Our analysis is based on the genotypes of wild-caught mice from three subspecies of Mus musculus. We show that classical laboratory strains are derived from a few fancy mice with limited haplotype diversity. Their genomes are overwhelmingly Mus musculus domesticus in origin, and the remainder is mostly of Japanese origin. We generated genome-wide haplotype maps based on identity by descent from fancy mice and show that classical inbred strains have limited and non-randomly distributed genetic diversity. In contrast, wild-derived laboratory strains represent a broad sampling of diversity within M. musculus. Intersubspecific introgression is pervasive in these strains, and contamination by laboratory stocks has played a role in this process. The subspecific origin, haplotype diversity and identity by descent maps can be visualized using the Mouse Phylogeny Viewer (see URLs).

Anti-inflammatory and analgesic effects and molecular mechanisms of JCICM-6, a purified extract derived from an anti-arthritic Chinese herbal formula

The anti-inflammatory and anti-nociceptive effects and the molecular mechanisms of JCICM-6, a purified extract derived from an anti-arthritic Chinese herbal formula composed of Caulis Sinomenii, Aconiti laterralis Preparata, Rhizoma Curcumae longae, Radix Paeoniae albae, and Cortex Moutan, were examined for the first time. JCICM-6 was prepared using pharmaceutical extraction technology, purified by Amberlite XAD-7HP polymeric resin. Pharmacologically, in carrageenan-induced edema and carrageenan-evoked thermal hyperalgesia in paws of rats, the oral administration of JCICM-6 at dosages of 0.4, 0.8, and 1.6g/kg demonstrated significant inhibition with a dose-dependent manner. Mechanistic studies showed that JCICM-6 effectively decreased the production of the pro-inflammatory cytokines of IL-6 and IL-1beta and expression of COX-2 and iNOS proteins, and simultaneously elevated the level of anti-inflammatory cytokine IL-4 in the carrageenan-injected rat paw tissues and exudates. The positive reference drug, indomethacin at a dosage of 10mg/kg, demonstrated inhibitory potency in both rat models, but it could not augment the production of IL-4, indicating JCICM-6 and indomethacin might possess different pharmacological properties and molecular mechanisms although both have anti-inflammatory and analgesic effects in rats. These results suggest that JCICM-6 would be a valuable candidate for further investigation as a new anti-arthritic drug.

Effects of dietary methionine and lysine sources on nutrient digestion, nitrogen utilization, and duodenal amino acid flow in growing goats

This study investigated the effects of supplementation of various sources of Met and Lys on nutrient digestion, N utilization, and duodenal AA flows in growing goats. Four 4-mo-old Liuyang Black wether goats were used in a 4 x 4 Latin square experiment and were assigned to 4 dietary treatments: (1) control, (2) control + lipid-coated Met-Zn chelate and Lys-Mn chelate (PML), (3) control + Met-Zn chelate and Lys-Mn chelate (CML), and (4) control + dl-Met, l-Lys-HCl, ZnSO(4).7H(2)O, and MnSO(4).H(2)O (FML). Compared with control, PML reduced (P < 0.05) ruminal NH(3) concentration, urinary N excretion, and plasma urea N concentration and increased (P < 0.05) the activity of ruminal endo-1,4-beta-d-glucanase and beta-glucosidase, the duodenal flow of N, N retention (g/d as well as % of absorbed N), the duodenal flows of Met, Lys, His, Val, and total essential AA, and plasma concentrations of Lys, Val, Phe, and total essential AA. Supplementing Zn-Met and Mn-Lys chelates had similar (P > 0.05) but lesser effects on these measures compared with PML, and the effects on most of the measures were not statistically significant (P > 0.05) when compared with control. Supplementing free-form Met and Lys had no effects compared with control (P > 0.05). The results indicate that lipid coating and chelating of AA provide a protection, and to a lesser extent by only chelating, of the AA from microbial degradation in the rumen and possibly has effects on rumen fermentation, which increases MP supply. This technology could improve productive performance and be of potential benefit to ruminant production if cost-effective products are developed.

The role of phytochelatins in arsenic tolerance in the hyperaccumulator Pteris vittata

•  Pteris vittata was the first identified arsenic (As) hyperaccumulator. Here we investigated whether phytochelatins (PCs) are involved in the hypertolerance of arsenic by P. vittata. •  P. vittata was exposed to 0-500 µm arsenate for 5 d, or to 50 µm arsenate for 0-7 d. In addition, l-buthionine-sulphoximine (BSO), an inhibitor of γ-glutamylcysteine synthetase, was used in combination with different arsenate exposures. The relationships between As accumulation and the concentrations of PCs and glutathione (GSH) were examined. •  PC synthesis was induced upon exposure to arsenate in P. vittata, with only PC₂ detected in the plant. The As concentration correlated significantly with PC₂ concentration in both roots and shoots, but not with GSH. The molar ratio of PC-SH to As was c. 0.09 and 0.03 for shoots and roots, respectively, suggesting that only a small proportion (1-3%) of the As in P. vittata can be complexed with PCs. In the presence of arsenate, addition of BSO decreased PC₂ concentrations in roots and shoots by 89-96% and 30-33%, respectively. BSO alone was found to inhibit root growth of P. vittata markedly. •  The results suggest that PCs play a limited role in the hypertolerance of As in P. vittata.

Complete genome analysis of enterovirus 71 isolated from an outbreak in Taiwan and rapid identification of enterovirus 71 and coxsackievirus A16 by RT-PCR

Hand, foot, and mouth disease (HFMD) and encephalomyelitis were two major clinical manifestations during the 1998 enterovirus 71 (EV71) epidemic in Taiwan. To investigate whether different clinical patterns were caused by alterations in EV71 genomes, the complete nucleotide sequences of four EV71 strains associated with HFMD or encephalomyelitis were compared. Among these viral strains, two or three nucleotide differences were found within the 5'-noncoding region, and two or four amino acid differences were found within the regions encoding viral polyproteins; however, none of these differences were correlated with either clinical manifestation. Because coxsackievirus A16 was another major causative agent of HFMD, a reverse transcription-polymerase chain reaction assay, with high sensitivity and specificity for identification of EV71 (both 100%) and coxsackievirus A16 (100 and 98.8%), was developed for the rapid differential identification of these two viruses in HFMD patients.

Cleaning method of the oil field wastewater treatment by UF process

This article introduces experiments and researches of polysulphone ultrafiltration membrane's effect on oil field polluted water and approaches renewing oil field polluted water and approaches renewing of membrane's flux by different detergents and cleaning method. Good result has been achieved by doing experiments and the renewal rate of membrane is over 90%.

The thermal environment of arboreal pools and its effects on the metabolism of the arboreal, oophagous tadpoles of a Taiwanese tree frog, Chirixalus eiffingeri (Anura: Rhacophoridae)

We have studied seasonal and diurnal fluctuations of water temperature in bamboo stumps and the effect of temperature on the energy metabolism of arboreal, oophagous tadpoles of Chirixalus eiffingeri. We collected tadpoles (Gosner stage 28-29) in February and August from Chitou, Taiwan and acclimated them to 12 and 22 degrees C. Using a closed system, we measured tadpole oxygen consumption (V.O(2)) at 12, 17 and 22 degrees C. The water temperature was lowest in February (11-13 degrees C), increased rapidly during March and April and was highest from May to August (20-24 degrees C). Diel fluctuations in the temperature of the pools of water in bamboo stumps mirrored fluctuations in air temperature. Tadpoles collected in February and August exhibited metabolic compensation in that tadpoles acclimated at 12 degrees C had significantly higher V.O(2) than those acclimated at 22 degrees C. There are at least two possible explanations for the presence of metabolic compensation in C. eiffingeri tadpoles. Firstly, the larval period of C. eiffingeri ranges from 40 to 78 days, a tadpole could experience relatively large fluctuations in body temperature (up to 10 degrees C) during the development. As a result, C. eiffingeri tadpoles most likely evolved metabolic compensation to maintain activity levels under different thermal environments. Secondly, because arboreal pools are small, thermally unstratified, aquatic microhabitats, tadpoles are unable to behaviorally select preferred temperatures. As a result, metabolic compensation allows tadpoles to regulate their physiological functions.

Molecular epidemiology of enterovirus 71 in Taiwan

Taiwan suffered a severe and widespread outbreak of enterovirus infection in 1998. More than 400 children were hospitalized, with seventy-eight fatalities due to central nerve system (CNS) involvement and cardiopulmonary collapse. Enterovirus 71 (EV71) was incriminated as the causative agent for the fatal cases. To understand the viral molecular epidemiology in this outbreak, fragments of 207-bp length of the VP4 region in 23 Taiwanese EV 71 isolates were sequenced. Pair-wise comparison revealed a 17.5-24.4% difference between the isolates and the prototype BrCr. However, all the changes in the VP4 region of the isolated strains were synonymous substitutions. Phylogenetic analysis was performed on these 23 isolates and 21 others deposited in GenBank. In this study, forty-four EV71 isolates from the world were separated into three distinct genotypes: A, B and C. The EV71 prototype strain, BrCr/70, is the only strain of genotype A. Group B included strains from the United States, Japan and Taiwan. Most strains in genotype B were isolated prior to 1990. Group C consisted of strains from Japan and Taiwan. Most strains of genotype C were isolated after 1990, they were further divided into 3 clusters: i.e. C-1, C-2 and C-3. In Taiwan, two genotypes, B and C-3, were co-circulating during the outbreak in 1998, although a minor group of genotype B may have appeared in Taiwan before 1986. The majority of the isolates clustered in genotype C-3. Genotype C showed a higher evolutionary rate than genotype B (3.9 x 10(-3) vs. 1.4 x 10(-3)) in the VP4 region. There seems to be a worldwide trend with strains of genotype B appearing earlier than strains of genotype C which took over later in the dominance.

Proteomic detection of changes in protein synthesis induced by NGX6 transfected in human nasopharyngeal carcinoma cells

In the previous study, we cloned a new gene, named NGX6, related to nasopharyngeal carcinoma (NPC) at 9p. To study its function in the pathogenesis of NPC, we have investigated changes in protein synthesis between NPC cell line HNE1 and that transfected with the gene. Using high-resolution two-dimensional electrophoresis, we found that 22 protein spots showed variations that were significant and reproducible. Analysis of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and database searches identified seven proteins that were upregulated and seven proteins that were downregulated. These proteins included Fas, zinc-finger protein (ZNF), RAB, and Ah receptor-interacting protein (AIP). The functional implications of the identified proteins are discussed.