A comprehensive assessment of exome capture methods for RNA sequencing of formalin-fixed and paraffin-embedded samples.

RNA-Seq analysis of Formalin-Fixed and Paraffin-Embedded (FFPE) samples has emerged as a highly effective approach and is increasingly being used in clinical research and drug development. However, the processing and storage of FFPE samples are known to cause extensive degradation of RNAs, which limits the discovery of gene expression or gene fusion-based biomarkers using RNA sequencing, particularly methods reliant on Poly(A) enrichment. Recently, researchers have developed an exome targeted RNA-Seq methodology that utilizes biotinylated oligonucleotide probes to enrich RNA transcripts of interest, which could overcome these limitations. Nevertheless, the standardization of this experimental framework, including probe designs, sample multiplexing, sequencing read length, and bioinformatic pipelines, remains an essential requirement. In this study, we conducted a comprehensive comparison of three main commercially available exome capture kits and evaluated key experimental parameters, to provide the overview of the advantages and limitations associated with the selection of library preparation protocols and sequencing platforms. The results provide valuable insights into the best practices for obtaining high-quality data from FFPE samples.

Perceived Constraints on Active Recreational Sport Participation among Residents in Urban China.

Recreational sport participation is an important pathway to improving the quality of life. While facilities for recreational sports are provided in many urban areas in China, how urban residents might be aware of or use these facilities for recreational sport participation is still a vague notion in the literature. This study explored the linkages between perceived leisure constraints and active participation in recreational sports among urban residents. We collected data samples from 2901 urban residents in China to identify their perceived constraints and the effects of the perceived constraints on active recreational sport participation by structural equation models. Five perceived constraints of active recreational sport participation were identified: intrapersonal, interpersonal, environmental condition, facility-service management, and leisure opportunity constraints. More specifically, leisure opportunity, intrapersonal, facility-service management, and interpersonal constraints were the four most important constraints limiting active recreational sport participation of urban residents. Theoretical and practical implications to facilitate the active recreational sport participation of Chinese urban residents were discussed.

Cost-effectiveness of artificial intelligence screening for diabetic retinopathy in rural China.

BACKGROUND: Diabetic retinopathy (DR) has become a leading cause of global blindness as a microvascular complication of diabetes. Regular screening of diabetic retinopathy is strongly recommended for people with diabetes so that timely treatment can be provided to reduce the incidence of visual impairment. However, DR screening is not well carried out due to lack of eye care facilities, especially in the rural areas of China. Artificial intelligence (AI) based DR screening has emerged as a novel strategy and show promising diagnostic performance in sensitivity and specificity, relieving the pressure of the shortage of facilities and ophthalmologists because of its quick and accurate diagnosis. In this study, we estimated the cost-effectiveness of AI screening for DR in rural China based on Markov model, providing evidence for extending use of AI screening for DR. METHODS: We estimated the cost-effectiveness of AI screening and compared it with ophthalmologist screening in which fundus images are evaluated by ophthalmologists. We developed a Markov model-based hybrid decision tree to analyze the costs, effectiveness and incremental cost-effectiveness ratio (ICER) of AI screening strategies relative to no screening strategies and ophthalmologist screening strategies (dominated) over 35 years (mean life expectancy of diabetes patients in rural China). The analysis was conducted from the health system perspective (included direct medical costs) and societal perspective (included medical and nonmedical costs). Effectiveness was analyzed with quality-adjusted life years (QALYs). The robustness of results was estimated by performing one-way sensitivity analysis and probabilistic analysis. RESULTS: From the health system perspective, AI screening and ophthalmologist screening had incremental costs of $180.19 and $215.05 but more quality-adjusted life years (QALYs) compared with no screening. AI screening had an ICER of $1,107.63. From the societal perspective which considers all direct and indirect costs, AI screening had an ICER of $10,347.12 compared with no screening, below the cost-effective threshold (1-3 times per capita GDP of Chinese in 2019). CONCLUSIONS: Our analysis demonstrates that AI-based screening is more cost-effective compared with conventional ophthalmologist screening and holds great promise to be an alternative approach for DR screening in the rural area of China.

Occurrence and ecological risk assessment of PPCPs in typical inflow rivers of Taihu lake, China.

The occurrence and ecological risks of ten typical pharmaceutical and personal care products (PPCPs) at 12 typical inflow rivers of Taihu lake was investigated in this study. Seven out of the ten typical PPCPs targeted were detected in all the water samples and sediment samples tested. The PPCPs concentration detected were 0-94.91 ng/L for water samples and 0-18.27 ng/g for sediment samples. Sulfamethoxazole (SMZ) and erythromycin (ERY) has relatively higher concentration than other PPCPs in surface water samples, ciprofloxacin (CIP) and ofloxacin (OFX) has relatively higher concentration in the sediment samples. Inflow river-Caoqiao river has a relatively highest contamination of TN and TP, the PPCPs concentration in the river channel, estuary, lake-body also shows high value. This occurs in both the surface water and sediment sample, implied a relatively high pollution input from Caoqiao river. SMZ holds high long-term ecological risks in both surface water and sediment of almost all the tested inflow rivers of Taihu lake. Only ERY has medium short-term risks in surface water, other analyzed PPCPs hold low or insignificant short-terms risks for both surface water and sediments. This study fills the gap of PPCPs ecological risk of surface water and sediment of 12 typical inflow rivers of Taihu Lake, and revealed the importance of control sulfanilamide of the economic belt around Taihu Lake. The results of the present study are useful in providing information for PPCPs control and sustainable water management in freshwater lakes.

[Assessment of Heavy Metal Pollution in Soil and Its Bioaccumulation by Dominant Plants in a Lead-Zinc Mining Area, Nanjing].

To identify plants with potential application in phytoremediation, the concentration of cadmium (Cd), chromium (Cr), copper (Cu), manganese (Mn), lead (Pb), and zinc (Zn) in soil and 14 dominant plants sampled from a lead-zinc mining area in Nanjing City was measured. Furthermore, the heavy metal contamination of soil, and bioaccumulation and translocation of the 6 heavy metals by the 14 plants were evaluated. The results showed that the principal contaminants were Cd, Mn, Zn, and Pb, and their single factor pollution index was 45.71, 11.68, 10.40, and 4.46, respectively. Furthermore, the Nemerow index of this area was 33.45, which indicated that the mining area was severely polluted. All the 14 dominant plant species were metal-tolerant, although the concentration of metal varied between different spices. Among them, Pteris multifida and Trachelospermum jasminoides significantly accumulated the heavy metals. The concentration of Zn in all the dominant plants was beyond the normal range; however, the bio-concentration factor (BCF) of only Digitaria sanguinalis for Zn was>1, while the BCF of the remaining species for the 6 heavy metals was<1. Furthermore, the heavy metal bio-transfer factor (BTF) of the 14 species was generally high. The BTF of Helianthus tuberosus and Dendranthema indicum for the 6 heavy metals was>1. According to the mechanism of heavy metal accumulation, the 14 plant species were classified into 3 types:accumulators (H. tuberosus, D. indicum, Phytolacca americana, Justicia procumbens, D. sanguinalis, Sonchus brachyotus, Solanum nigrum, and Setaria viridis), root compartment (P. multifida and T. jasminoides), and excluders (Solidago decurrens, Duchesnea indica, Carex breviculmis, and Cyrtomium fortunei).

Preoperative assessment of axillary lymph node status in breast cancer patients by ultrasonography combined with mammography: A STROBE compliant article.

Preoperative assessment of nodal stage is of importance in breast cancer treatment decision-making. This study was done to determine the power of combined mammography and ultrasonography in differentiating N0-N1 from N2-N3 breast cancer.We retrospectively reviewed clinical data of 3944 female patients with invasive breast cancer by preoperative mammography and ultrasonography between January 2006 and December 2013 at our hospital. Pathological diagnosis was available for each patient. Sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and accuracy of mammography alone, ultrasonography alone, and combination of them for assessment of axillary lymph node (ALN) status were calculated, using definitive histological results as the baseline.The sensitivity, specificity, PPV, NPV, and accuracy was 90.4%, 68.2%, 36.5%, 97.2%, and 71.9% for ultrasonography; was 66.9%, 80.8%, 41.3%, 92.3%, and 78.4% for mammography; and was 94.9%, 62.4%, 33.8%, and 98.4% for combined mammography and ultrasonography. For combination, accuracy and the area under the receiver operating characteristic curve was 67.9% and 0.85, respectively.In conclusion, combining ultrasonography and mammography improves the sensitivity in differentiating N0-N1 breast cancer from N2-N3 breast cancer, but leading to a reduced specificity. Addition of mammography to ultrasonography seems not to provide significant benefits in predicting ALN status in breast cancer patients.

A comparative proteomic characterization and nutritional assessment of naturally- and artificially-cultivated Cordyceps sinensis.

Cordyceps sinensis has gained increasing attention due to its nutritional and medicinal properties. Herein, we employed label-free quantitative mass spectrometry to explore the proteome differences between naturally- and artificially-cultivated C. sinensis. A total of 22,829 peptides with confidence ≥95%, corresponding to 2541 protein groups were identified from the caterpillar bodies/stromata of 12 naturally- and artificially-cultivated samples of C. sinensis. Among them, 165 proteins showed significant differences between the samples of natural and artificial cultivation. These proteins were mainly involved in energy production/conversion, amino acid transport/metabolism, and transcription regulation. The proteomic results were confirmed by the identification of 4 significantly changed metabolites, thus, lysine, threonine, serine, and arginine via untargeted metabolomics. The change tendencies of these metabolites were partly in accordance with changes in abundance of the proteins, which was upstream of their synthetic pathways. In addition, the nutritional value in terms of the levels of nucleosides, nucleotides, and adenosine between the artificially- and naturally-cultivated samples was virtually same. These proteomic data will be useful for understanding the medicinal value of C. sinensis and serve as reference for its artificial cultivation. SIGNIFICANCE: C. sinensis is a precious and valued medicinal product, the current basic proteome dataset would provide useful information to understand its development/infection processes as well as help to artificially cultivate it. This work would also provide basic proteome profile for further study of C. sinensis.

Spatial Regression and Prediction of Water Quality in a Watershed with Complex Pollution Sources.

Fast economic development, burgeoning population growth, and rapid urbanization have led to complex pollution sources contributing to water quality deterioration simultaneously in many developing countries including China. This paper explored the use of spatial regression to evaluate the impacts of watershed characteristics on ambient total nitrogen (TN) concentration in a heavily polluted watershed and make predictions across the region. Regression results have confirmed the substantial impact on TN concentration by a variety of point and non-point pollution sources. In addition, spatial regression has yielded better performance than ordinary regression in predicting TN concentrations. Due to its best performance in cross-validation, the river distance based spatial regression model was used to predict TN concentrations across the watershed. The prediction results have revealed a distinct pattern in the spatial distribution of TN concentrations and identified three critical sub-regions in priority for reducing TN loads. Our study results have indicated that spatial regression could potentially serve as an effective tool to facilitate water pollution control in watersheds under diverse physical and socio-economical conditions.

Simultaneous quantification of 11 active constituents in Shexiang Baoxin Pill by ultraperformance convergence chromatography combined with tandem mass spectrometry.

On account of the complexity of chemical constituents of Shexiang Baoxin Pill (SBP), a famous traditional Chinese medicine (TCM) formula, a novel and effective UPC2-MS/MS method was developed to simultaneously determine the content of 11 active compounds of SBP with outstanding separation ability. Eleven components in SBP, including 2 ginsenosides, 2 bile acids, 3 bufadienolides and 4 volatiles were detected by electrospray ionization tandem mass spectrometry in positive and negative ion modes with multiple reaction monitor (MRM). The analysis was performed at 30°C using an Acquity UPC2 Diol (3.0×50mm, 1.7µm) column with linear gradient elution (eluent A, CO2; eluent B, methanol containing 20mM ammonium acetate), back pressure of 2000 psi, flow rate of 1.2mL/min and the injection volume of 1.0µL. The method was extensively validated regarding the linearity (r≥0.9974), precision (≤3.11%), recovery (93.34-104.50%), repeatability (≤2.00%) and stability (≤4.20%). Using this method, 11 active compounds of SBP with different polarity were simultaneously quantified in one chromatography analysis within 8min. Statistical analysis of the effects of 11 compounds on the quality of SBP revealed that the content of cinnamaldehyde varied widely in different batches. This work presents an exemplary study for quality control of complex samples, especially for TCMs.

[Spatial Distribution, Source and Ecological Risk Assessment of Heavy Metals in the Coastal Sediments of Northern Dongying City].

Concentrations of seven heavy metals in the coastal sediments of the northern Dongying City were measured. The spatial distribution and sources of heavy metals were discussed and the ecological risk was assessed using sediment quality guidelines (SQGs) and the potential ecological risk index (PERI). The concentration ranges of Hg, As, Pb, Cd, Cr, Cu, and Zn were calculated as 0.005-0.092, 3.44-10.41, 6.59-19.00, 0.50-1.10, 32.42-60.25, 1.72-23.78, and 31.13-69.96 mg·kg-1, respectively. Higher metal concentrations were observed at site S10, which was close to the mouth of Tiaohe River and contained plenty of organic matter, silt, and clay. Principal component analysis (PCA) indicated that As and Pb in the sediments were derived from natural weathering processes, while other metals were mainly attributed to anthropogenic sources, i.e., land-sourced pollutants transported by runoff. Concentrations of As, Cd, Cr, and Cu at some sampling sites exceeded the threshold effect level (TEL) stated in the SQGs implying occasional harmful effects on biological life. PERI showed that the sediments in this area generally had a medium risk, except sites S10, S3, and S9 posing a considerable risk, and that Cd and Hg were the major contributors to the ecological risk. It is necessary to take effective measures to control heavy metal fluxes from rivers around this area and to reduce the risk.

Assessment of the Spatial and Temporal Variations of Water Quality for Agricultural Lands with Crop Rotation in China by Using a HYPE Model.

Many water quality models have been successfully used worldwide to predict nutrient losses from anthropogenically impacted catchments, but hydrological and nutrient simulations with limited data are difficult considering the transfer of model parameters and complication of model calibration and validation. This study aims: (i) to assess the performance capabilities of a new and relatively more advantageous model, namely, Hydrological Predictions for the Environment (HYPE), that simulates stream flow and nutrient load in agricultural areas by using a multi-site and multi-objective parameter calibration method and (ii) to investigate the temporal and spatial variations of total nitrogen (TN) and total phosphorous (TP) concentrations and loads with crop rotation by using the model for the first time. A parameter estimation tool (PEST) was used to calibrate parameters. Results show that the parameters related to the effective soil porosity were highly sensitive to hydrological modeling. N balance was largely controlled by soil denitrification processes. P balance was influenced by the sedimentation rate and production/decay of P in rivers and lakes. The model reproduced the temporal and spatial variations of discharge and TN/TP relatively well in both calibration (2006-2008) and validation (2009-2010) periods. Among the obtained data, the lowest Nash-Suttclife efficiency of discharge, daily TN load, and daily TP load were 0.74, 0.51, and 0.54, respectively. The seasonal variations of daily TN concentrations in the entire simulation period were insufficient, indicated that crop rotation changed the timing and amount of N output. Monthly TN and TP simulation yields revealed that nutrient outputs were abundant in summer in terms of the corresponding discharge. The area-weighted TN and TP load annual yields in five years showed that nutrient loads were extremely high along Hong and Ru rivers, especially in agricultural lands.

Quality assessment of clinical research on liver cancer treated by intra-arterial infusion of Chinese medicine.

OBJECTIVE: To assess the methodological quality of clinical research on Chinese medicine (CM) applied by intra-arterial infusion in treating primary liver cancer (PLC). METHODS: Cochrane Central Register of Controlled Trials (CENTRAL), PubMed, and three Chinese databases, including Chinese BioMedical Database (CBM), China National Knowledge Infrastructure (CNKI) and China Academic Journal (VIP) were searched. Chinese articles were also searched manually in 16 journals. Two reviewers independently selected studies, the quality of literatures were assessed according to the Cochrane Collaboration method of quality assessment. RESULTS: A total of 14 articles met the inclusion criteria for this review. Only three of these articles described the randomization method used. None of the studies was blinded. All of the articles didn't report the calculation of the sample size. Only six studies mentioned adverse reactions. All of the studies were of grade C according to the Cochrane Collaboration method. Six studies reported results of survival, and only two of these reported better efficacy in the treatment groups. CONCLUSIONS: The quality of studies concerned intra-arterial infusion of CM in treating with PLC was poor and the exact effect of these medicines still need evaluation. Well designed RCTs with large sample sizes, adequate follow-up data and reliable methods of assessment are needed to better appraise the real effect of CMs in the treatment of PLC patients.

An atom-economic route to thiophenes and 2,2'-bithiophenes by intramolecular transannulation of gem-dialkylthio enynes.

An atom-economic route to thiophenes and bithiophenes has been developed starting from the readily available gem-dialkylthio enynes. A range of functionalized thiophenes and bithiophenes, bearing a pendent vinylthio group, were obtained in good to high yields under mild conditions.

Dynamical behaviors of a stochastic delay logistic system with impulsive toxicant input in a polluted environment.

A stochastic delay logistic system with Markov switching and impulsive toxicant input in a polluted environment is proposed and studied. Some sufficient criteria for extinction, non-persistence in the mean and weak persistence of the solutions are established.

Effect of socioeconomic status on secondary prevention of stroke.

OBJECTIVE: Cardiovascular risk factors increase risk for stroke recurrence. Secondary prevention of stroke may be affected not only by established risk factors, but also socioeconomic status. This study evaluates relationships between socioeconomic status and cardiovascular and behavioral factors. DESIGN: Cross-section study. SETTING: Public Health and Education Institute, Peking University. PARTICIPANTS: Outpatients (n = 2354) with a past diagnosis of stroke or transient ischemic attack. INTERVENTION(S): The investigation consisted of a questionnaire regarding patients' socioeconomic and living status, and a clinical examination at the research center. MAIN OUTCOME MEASURE(S): Control rates of risk factors for cardiovascular disease. RESULTS: With regard to hypertension patients, 67.0% were aware of having hypertension, 63.6% were treated and 53.9% had controlled hypertension; for patients with hypercholesterolemia, 46.7% were aware of having hypercholesterolemia, 38.6% were treated and 3.8% had controlled hypercholesterolemia; for patients with diabetes mellitus, 28.0% were aware of having diabetes mellitus, 25.7% were treated and 3.5% had controlled diabetes mellitus. After multivariate analysis, education was the strongest associated factor for controls of hypertension and diabetes mellitus. After adjustment for sex and age, strong and graduated relationships were noted between the level of education and control of risk factors, with the odds ratios increasing at every increment. CONCLUSION: Education exerts the most important effect on the control of established cardiovascular risk factors; Successful intervention to reduce these risk factors will have to be addressed, not just with regard to specific risk factors, but also with the societal conditions that lead to the adoption and maintenance of high-risk behaviors.

The association between socioeconomic status of high-risk patients with coronary heart disease and the treatment rates of evidence-based medicine for coronary heart disease secondary prevention in China: Results from the Bridging the Gap on CHD Secondary Prevention in China (BRIG) Project.

BACKGROUND: In China, low socioeconomic status (SES) may be a barrier for patients with coronary heart disease (CHD) to receive adequate treatment because of their inadequate access to health resources. This study aims to evaluate whether and to what extent SES is associated with the treatment of CHD patients. METHODS: A cross-sectional survey was conducted among 2,803 CHD outpatients, a representative sample of China. An SES composite index was derived based on educational levels, monthly income, occupation, and access to medical insurance for each patient. The association between SES and treatment status of several key medications was analyzed. RESULTS: In total, 2,278 CHD outpatients with complete SES information were studied. The treatment rates of clopidogrel and statins were 6.7% and 34.2% in patients with the lowest SES and 41.7% and 75% in patients with the highest SES. In multiple logistic regression analyses, SES was independently associated with the use of aspirin, clopidogrel, statins and beta-blockers. Compared with the patients with the highest SES, the patients with the lowest SES had a 43.4% lower treatment rate for aspirin, a 76% lower rate for clopidogrel, a 70.2% lower rate for statins, and a 70.2% lower rate for beta-blockers after adjustment for various cofactors. CONCLUSIONS: Socioeconomic status is closely associated with the treatment status of secondary prevention in CHD high-risk patients in China. Policy makers and medical professionals urgently need to develop policies and strategies to improve medical care for patients of low SES.

A nitrogen budget of the Changjiang river catchment.

Based on 1997-1998 field investigations in the Changjiang river mouth, rain sampling from the river's upper reaches to the mouth, historical data, and relevant literature, the various sources of Total Nitrogen (TN) and Dissolved Inorganic Nitrogen (DIN) in the Changjiang river catchment and N transport in the Changjiang river mouth were estimated. The export fluxes of various form of N were mainly controlled by the river runoff, and the export fluxes of NO3-N, DIN and TN in 1998 (an especially heavy flood year) were 1438 10(3) tonnes (t) yr(-1) or 795.1 kg km(-2) yr(-1), 1746 10(3) t yr(-1) or 965.4 kg km(-2) yr(-1) and 2849 10(3) t yr(-1) or 1575.3 kg km(-2) yr(-1), respectively. The TN and DIN in the Changjiang river came mainly from precipitation, agricultural nonpoint sources, N lost from fertilizer and soil, and point sources of industrial waste and residential sewage discharge, which were about 56.2% and 62.3%, 15.4% and 18.5%, 17.1% and 14.4%, respectively, of the N outflow at the Changjiang river mouth; maximum transport being in the middle reaches.