Soluble urokinase plasminogen activator receptor is associated with cardiovascular calcification in peritoneal dialysis patients.

BACKGROUND: Cardiovascular disease (CVD) is an important cause of morbidity and mortality in peritoneal dialysis (PD) patients. Cardiovascular calcification (CVC) is highly prevalent in PD patients and could predict their cardiovascular mortality. Soluble urokinase plasminogen activator receptor (suPAR) is closely associated with coronary artery calcification in hemodialysis patients and is an important predictor of CVD. However, the role of suPAR in PD patients is poorly understood. We investigated the relationship between serum suPAR and CVC in PD patients. METHODS: Abdominal aortic calcification (AAC) was assessed by lateral lumbar radiography, coronary artery calcification (CAC) by multi-slice computed tomography, and cardiac valvular calcification (ValvC) by echocardiography. CVC was defined as confirmed presence of calcification in one site (AAC, CAC, or ValvC). Patients were divided into CVC group and non-CVC group. Demographic characteristics, biochemical variables, comorbidities, PD regimen, serum suPAR, and medication were compared between the two groups. Logistic regression was conducted to determine association between serum suPAR and presence of CVC. The receiver-operator curve (ROC) was plotted to calculate the area under the curve (AUC) for suPAR to identify CVC and ValvC. RESULTS: Of 226 PD patients, 111 (49.1%) had AAC, 155 (68.6%) had CAC, and 26 (11.5%) had ValvC. There were significant differences in age, BMI, diabetes, white blood cell, phosphorus, hs-CRP, suPAR, time on dialysis, total volume of dialysate, ultrafiltration, volume of urine, and Kt/V between CVC and non-CVC group. Serum suPAR was associated with CVC by multivariate logistic regression analysis in PD patients, especially in elderly patients. The levels of serum suPAR were closely related to the degree of AAC, CAC, and ValvC in PD patients. The incidence of CVC was higher in patients with higher levels of suPAR. The ROC curve showed that serum suPAR had a predictive value for CVC (AUC = 0.651), especially for ValvC (AUC = 0.828). CONCLUSION: Cardiovascular calcification is prevalent in PD patients. High levels of serum suPAR are associated with cardiovascular calcification in PD patients, especially in elderly patients.

Cardiac valve calcification as a predictor of cardiovascular outcomes in peritoneal dialysis patients: an inverse probability of treatment weighting analysis.

BACKGROUND: Cardiovascular events (CVE) are the leading cause of death in peritoneal dialysis (PD) patients. The predictive value of cardiac valve calcification (CVC) for CVE in dialysis patients remains controversial. In particular, such studies are limited in PD patients. We aimed to examine the predictive role of CVC for CVE and cardiovascular mortality in PD patients. METHODS: A retrospective analysis was performed on patients who initiated PD in our hospital. According to the result of echocardiography, patients were divided into CVC group and non-CVC group. The differences in baseline demographic characteristics, biochemical variables, comorbidities, and clinical outcomes between the two groups were compared. Kaplan-Meier method was used to obtain survival curves. The Cox regression model was used to evaluate the influence of CVC for cardiovascular outcomes. The inverse probability of treatment weighting (IPTW) was used to eliminate influence of the confounders in the groups. RESULTS: 458 peritoneal dialysis patients were enrolled in this study. 77 patients were in CVC group and 381 patients in non-CVC group. The average follow-up time was (32 ± 21) months. At baseline, the absolute standardized difference (ASD) of age, BMI, history of CVE, diabetes, LVEF, LVMI, albumin, calcium, phosphorus, triglycerides, hsCRP, urine volume, Kt/V, statins and vitamin D intake rate were greater than 0.1 between the two groups. All of ASD dropped to less than 0.1 after IPTW, which meant that the balance had been reached between the two groups. Multivariable logistic analysis showed that advanced age, diabetes, and hyperphosphatemia were associated with CVC. The Kaplan-Meier survival curve showed the cumulative CVE-free survival rate and cardiovascular survival rate of CVC group were significantly lower than that of non-CVC group before and after IPTW (log-rank P < 0.05). After IPTW was used to eliminate the effect of confounders, multivariate Cox regression analysis still showed CVC was an independent risk factor for CVE (HR = 2.383, 95% CI 1.331~4.264, P = 0.003) and cardiovascular mortality (HR = 2.347, 95% CI 1.211~4.548, P = 0.012) in PD patients. CONCLUSION: The prevalence of CVC is high in peritoneal dialysis patients. CVC is an independent risk factor for CVE and cardiovascular mortality in peritoneal dialysis patients.

Self-Supervised Molecular Pretraining Strategy for Low-Resource Reaction Prediction Scenarios.

In the face of low-resource reaction training samples, we construct a chemical platform for addressing small-scale reaction prediction problems. Using a self-supervised pretraining strategy called MAsked Sequence to Sequence (MASS), the Transformer model can absorb the chemical information of about 1 billion molecules and then fine-tune on a small-scale reaction prediction. To further strengthen the predictive performance of our model, we combine MASS with the reaction transfer learning strategy. Here, we show that the average improved accuracies of the Transformer model can reach 14.07, 24.26, 40.31, and 57.69% in predicting the Baeyer-Villiger, Heck, C-C bond formation, and functional group interconversion reaction data sets, respectively, marking an important step to low-resource reaction prediction.

Modified methods obtain high-quality DNA and RNA from anaerobic activated sludge at a wide range of temperatures.

Anaerobic activated sludge is rich in humic substances and water, leading to significant differences in the stability of metagenomic DNA and metatranscriptomic RNA. Thus, it is of great difficulty to exact high-quality and high-yield DNA and RNA from them, especially those cultured at a wide range of temperatures. Here, we established fast and effective DNA and RNA extraction methods based on current commercial kits. The modified methods combined liquid nitrogen grinding with kits, achieving notable improvements in concentrations, yields, purity and integrities for both DNA and RNA. The ratios of OD260/280 of the metagenomic DNA were between 1.81 ± 0.03 and 1.83 ± 0.02, while OD260/280 and OD260/230 of the metatranscriptomic RNA ranged from 1.96 ± 0.01 to 2.13 ± 0.03 and from 1.94 ± 0.02 to 2.30 ± 0.03 respectively. Metagenomic DNA and metatranscriptomic RNA obtained by the modified methods perfectly met the requirements of second- and third-generation sequencing, providing valuable reference for extracting high-quality metagenomic DNA and metatranscriptomic RNA from environmental samples of high water content and humic substances under temperatures ranging from 18 °C to 52 °C.

Bacteria and archaea involved in anaerobic mercury methylation and methane oxidation in anaerobic sulfate-rich reactors.

The identification of dominant microbes in anaerobic mercury (Hg) methylation, methylmercury (MeHg) demethylation, and methane oxidation as sulfate-reducing bacteria, methanogens or, probably, anaerobic methanotrophic archaea (ANMEs) is of great interest. To date, however, the interrelationship of bacteria and archaea involved in these processes remains unclear. Here, we demonstrated the dynamics of microorganisms participating in these processes. Anaerobic fixed-bed reactors were operated with swine manure and sludge to produce methane stably, and then, sulfate (reactor C), sulfate and Hg(II) (reactor H), and sulfate and MeHg (reactor M) were added, and the reactors were operated for 120 d, divided equally into four periods, P1-P4. The bacterial compositions changed nonsignificantly, whereas Methanosaeta in reactors H and M decreased significantly, revealing that it was irrelevant for Hg transformation. The abundances of Syntrophomonadaceae, Methanoculleus, Candidatus Methanogranum and Candidatus Methanoplasma increased continuously with time; these species probably functioned in these processes, but further evidence is needed. Desulfocella and Desulfobacterium dominated first but eventually almost vanished, while the dominant archaeal genera Methanogenium, Methanoculleus and Methanocorpusculum were closely related to ANME-1 and ANME-2. PLS-DA results indicated that both bacteria and archaea in different periods in the three reactors were clustered separately, implying that the microbial compositions in the same periods were similar and changed markedly with time.

PacBio Long Reads Improve Metagenomic Assemblies, Gene Catalogs, and Genome Binning.

PacBio long reads sequencing presents several potential advantages for DNA assembly, including being able to provide more complete gene profiling of metagenomic samples. However, lower single-pass accuracy can make gene discovery and assembly for low-abundance organisms difficult. To evaluate the application and performance of PacBio long reads and Illumina HiSeq short reads in metagenomic analyses, we directly compared various assemblies involving PacBio and Illumina sequencing reads based on two anaerobic digestion microbiome samples from a biogas fermenter. Using a PacBio platform, 1.58 million long reads (19.6 Gb) were produced with an average length of 7,604 bp. Using an Illumina HiSeq platform, 151.2 million read pairs (45.4 Gb) were produced. Hybrid assemblies using PacBio long reads and HiSeq contigs produced improvements in assembly statistics, including an increase in the average contig length, contig N50 size, and number of large contigs. Interestingly, depth-based hybrid assemblies generated a higher percentage of complete genes (98.86%) compared to those based on HiSeq contigs only (40.29%), because the PacBio reads were long enough to cover many repeating short elements and capture multiple genes in a single read. Additionally, the incorporation of PacBio long reads led to considerable advantages regarding reducing contig numbers and increasing the completeness of the genome reconstruction, which was poorly assembled and binned when using HiSeq data alone. From this comparison of PacBio long reads with Illumina HiSeq short reads related to complex microbiome samples, we conclude that PacBio long reads can produce longer contigs, more complete genes, and better genome binning, thereby offering more information about metagenomic samples.

Differential gene expression profiling analysis in Pleurotus ostreatus during interspecific antagonistic interactions with Dichomitus squalens and Trametes versicolor.

This study provided analysis of differentially expressed genes (DEGs) in Pleurotus ostreatus under the interaction with Dichomitus squalens and Trametes versicolor, which is valuable for exploration on the fungal defence system against stressful condition caused by interspecific antagonistic interaction. Our result showed significant upregulation of abundant defence-related genes encoding laccase, manganese peroxidase, aldo-keto reductase, and glutathione S-transferase, which all play important roles in oxidative stress-resistant response. Importantly, Lacc2 and Lacc10 were found to be dominantly induced laccase genes in P. ostreatus under interspecific interaction. Meanwhile, a large number of carbohydrate metabolism-related and energy production-related genes involved in nutrient and territory competition were also enhanced. These genes were annotated as glycoside hydrolase, citrate synthase, malate dehydrogenase, succinate dehydrogenase, succinyl-CoA synthetase, NADH dehydrogenase, cytochrome c reductase/oxidase, and ATP synthase. Also, 12 DEGs were selected for validation by quantitative real-time PCR (qRT-PCR), all these genes showed consistent expression between the result of qRT-PCR and RNA-seq.

[Influence of Temperature on the Anaerobic Packed Bed Reactor Performance and Methanogenic Community].

This study aimed to analyze the effect of temperature on performance and microbial community structure of an anaerobic packed bed reactor (APBR). The temperature was increased step-wise from room temperature (22 degrees C ± 1 degrees C) to psychrophilic (15 degrees C ± 1 degrees C), mesophilic (37 degrees C ± 1 degrees C) and thermophilic (55 degrees C ± 1 degrees C). The results showed that, in the temperature changing process, the higher the temperature of APBR was, the higher COD removal rate and daily gas production were. After temperature changed to psychrophilic, mesophilic and thermophilic, COD removal rate and daily gas production were 25%, 45%, 60% and 2.3 L x d(-1), 4.0 L x d(-1), 8.5 L x d(-1) respectively. However, there was no significant change in biogas composition (-60%). A sudden temperature change caused a simultaneous increase in the concentration of volatile fatty acids (VFA), which had been fluctuating. Using 16S rRNA gene clone library screening, Euryarchaeota was commonly found, including important methanogens: MBT (Methanobacteriales), Mst (Methanosaetaceae) , Msc (Methanosarcinaceae) and MMB (Methanomicrobiales), as well as thermophilic bacteria and few spring Archaea. However, the diversity of methanogenic groups was reduced, especially at mesophilic. The results of quantitative PCR showed that the 16S rRNA gene concentrations of Mst, MMB and Msc were reduced by temperature changes. Although the relative proportion of every kind of methanogen was significantly affected, Mst was the dominant methanogen.

Intraperitoneal Perfusion Therapy of Endostar Combined with Platinum Chemotherapy for Malignant Serous Effusions: A Meta-analysis.

BACKGROUND: Malignant serous effusions (MSE) are one complication in patients with advanced cancer. Endostar is a new anti-tumor drug targeting vessels which exerts potent inhibition of neovascularization. This study aimed to systematically evaluate the efficacy and safety of intraperitoneal perfusion therapy of Endostar combined with platinum chemotherapy for malignant serous effusions (MSE). MATERIALS AND METHODS: Randomized controlled trials (RCTs) on intraperitoneal perfusion therapy of Endostar combined with platinum chemotherapy for malignant serous effusions were searched in the electronic data of PubMed, EMBASE, Web of Science, CNKI, VIP, CBM and WanFang. The quality of RCTs was evaluated by two independent researchers and a meta-analysis was performed using RevMan 5.3 software. RESULTS: The total of 25 RCTs included in the meta-analysis covered 1,253 patients, and all literature quality was evaluated as "B" grade. The meta-analysis showed that Endostar combined with platinum had an advantage over platinum alone in terms of response rate of effusions (76% vs 48%, RR=1.63, 95%CI: 1.50-1.78, P<0.00001) and improvement rate in quality of life (69% vs 44%, RR=1.57, 95%CI: 1.42-1.74, P<0.00001). As for safety, there was no significant difference between the two groups in the incidences of nausea and vomiting (35% vs 34%, RR=1.01, 95%CI: 0.87-1.18, P=0.88), leucopenia (38% vs 38%, RR=1, 95%CI: 0.87-1.15, P=0.99), and renal impairment (18% vs 20%, RR=0.86, 95%CI: 0.43-1.74, P=0.68). CONCLUSIONS: Endostar combined with platinum by intraperitoneal perfusion is effective for malignant serous effusions, and patient quality of life is significantly improved without the incidence of adverse reactions being obviously increased.

Laparoscopic versus open catheter placement in peritoneal dialysis patients: a systematic review and meta-analysis.

BACKGROUND: Peritoneal dialysis has been proven to be a safe and effective mode of renal replacement therapy for patients with end-stage renal disease. The usage of laparoscopic catheter placement technique was increased in recent years. But the advantages and disadvantages between the laparoscopic catheter placement technique and open laparotomy technique were still http://in controversy. The objective of this study is to access the operation-related data and complications of catheter placement for peritoneal dialysis (PD) patients, Then to determine the better method for catheter insertion. METHODS: We performed a systematic review and meta-analysis on published studies identified by the databases PubMed, EMBASE, Highwire, and the Cochrane Library. Analysis was performed using the statistical software Review Manager Version 5.0. RESULTS: We assessed the operation-related data and complications of four randomized controlled trials (RCTs) and ten observational studies. The available data showed that laparoscope prolonged the time for catheter insertion in PD patients, however, the two groups did not significantly differ in hospital stays, early and late complications, including infection, dialysate leaks, catheter migration, pericannular bleeding, blockage and hernia. CONCLUSIONS: The data showed that Laparoscopic catheter placement had no superiority to open surgery. However, this treatment still needs to be confirmed in a large, multi-center, well-designed RCT.

Quantitative structure-activity relationship analysis of aryl alkanol piperazine derivatives with antidepressant activities.

Quantitative structure-activity relationship analysis for recently synthesized aryl alkanol piperazine derivatives was studied for their antidepressant activities. The statistically significant 2D-QSAR models (r(2)>0.924, r(-CV)(2)>0.870, r(-pred)(2)>0.890) were developed using genetic function approximation (GFA) when the number of descriptors in equation was set to four, indicating the descriptors of Atype_C_6, Dipole-mag, S_sssCH and Jurs-PNSA-3 mainly influence the 5-hydroxytryptamine (5-HT) reuptake inhibition activity while the descriptors of HOMO, PMI-mag, S_sssN and Shadow-XZ may chiefly control the noradrenaline (NA) reuptake inhibition activity. The results of the 2D-QSAR models were further compared with 3D-QSAR models generated by molecular field analysis (MFA), investigating the substitutional requirements for the favorable receptor-drug interaction and providing useful information in the characterization and differentiation of their binding sites. The results derived may be useful in further designing novel antidepressants prior to synthesis.

Quantitative structure-property relationship studies on amino acid conjugates of jasmonic acid as defense signaling molecules.

Jasmonates and related compounds, including amino acid conjugates of jasmonic acid, have regulatory functions in the signaling pathway for plant developmental processes and responses to the complex equilibrium of biotic and abiotic stress. But the molecular details of the signaling mechanism are still poorly understood. Statistically significant quantitative structure-property relationship models (r(2) > 0.990) constructed by genetic function approximation and molecular field analysis were generated for the purpose of deriving structural requirements for lipophilicity of amino acid conjugates of jasmonic acid. The best models derived in the present study provide some valuable academic information in terms of the 2/3D-descriptors influencing the lipophilicity, which may contribute to further understanding the mechanism of exogenous application of jasmonates in their signaling pathway and designing novel analogs of jasmonic acid as ecological pesticides.

Expression of human insulin gene wrapped with chitosan nanoparticles in NIH3T3 cells and diabetic rats.

AIM: To study the expression of human insulin gene wrapped with chitosan nanoparticles in NIH3T3 cells and diabetic rats. METHODS: pCMV.Ins, an expression plasmid of the human insulin gene, was constructed. In total, 100 microg pCMV.Ins wrapped with chitosan nanoparticles (chitosan-pCMV.Ins) was transfected to NIH3T3 cells and diabetes rats through lavage and coloclysis, respectively. The transfected cells were grown in Dulbecco's modified Eagle's medium, containing G418, for 72 h after transfection. The clones were selected and continued to grow in G418 medium for 24 d. The expression of human insulin was detected by immunohistochemistry. Human insulin in the culture medium of transfected cells was measured. Fasting blood glucose and plasma human insulin of diabetic rats were measured for 5 d after transfection. RT-PCR and Western blotting were performed to confirm the expression of the human insulin gene in diabetic rats. RESULTS: Approximately 10% of NIH3T3 cells transfected by chitosan-pCMV.Ins expressed human insulin. Human insulin in the culture medium of NIH3T3 cells transfected by chitosan-pCMV.Ins significantly increased compared with that of the control group (P<0.01). Fasting blood glucose levels of the lavage group and the coloclysis group decreased significantly in 5 d (P<0.01) in comparison, while plasma insulin levels were much higher (P<0.01). The human insulin gene mRNA and human insulin were only detected in the lavage and the coloclysis groups. CONCLUSION: The human insulin gene can be transfected and expressed successfully by chitosan- pCMV.Ins in NIH3T3 cells and diabetes rats, which indicates that chitosan is a promising, non-viral vector for gene expression.

Quantitative structure-activity relationship studies on 1-aryl-tetrahydroisoquinoline analogs as active anti-HIV agents.

Predictive quantitative structure-activity relationship analysis was developed for a diverse series of recently synthesized 1-aryl-tetrahydroisoquinoline analogs with anti-HIV activities in this study. The conventional 2D-QSAR models were developed by genetic function approximation (GFA) and stepwise multiple linear regression (MLR) with acceptable explanation of 94.9% and 95.5% and good predicted power of 91.7% and 91.7%, respectively. The results of the 2D-QSAR models were further compared with 3D-QSAR model generated by molecular field analysis (MFA), investigating the substitutional requirements for the favorable receptor-drug interaction and quantitatively indicating the important regions of molecules for their activities. The results obtained by combining these methodologies give insights into the key features for designing more potent analogs against HIV.

Laparoscopic hepatic left lateral lobectomy combined with fiber choledochoscopic exploration of the common bile duct and traditional open operation.

AIM: To investigate the possibilities and advantages of laparoscopic hepatic left lateral lobectomy combined with fiber choledochoscopic exploration of the common bile duct compaired with traditional open operation. METHODS: Laparoscopic hepatic left lateral lobectomy combined with fiber choledochoscopic exploration of the common bile duct and traditional open operation were performed in two groups of patients who had gallstones in the left lobe of liver and in the common bile duct. The hospitalization time, hospitalization costs, operation time, operative complications and post-operative liver functions of the two groups of patients were studied. RESULTS: The operation time and post-operative liver functions of the two groups of patients had no significant differences, while the hospitalization time, hospitalization costs and operative complications of the laparoscopic hepatic left lateral lobectomy combined with fiber choledochoscopic exploration in the common bile duct group were significantly lower than those in the traditional open operation group. CONCLUSION: For patients with gallstones in the left lobe of liver and in the common bile duct, laparoscopic hepatic left lateral lobectomy combined with fiber choledochoscopic exploration of the common bile duct can significantly shorten the hospitalization time, reduce the hospitalization costs and the post-operative complications, without prolonging the operation time and bringing about more liver function damages compared with traditional open operation. This kind of operation has more advantages than traditional open operation.

[Correlation of polycyclic aromatic hydrocarbons (PAHs) in PM10- phoenix tree leaves-soil system of a coking & chemical factory in Shanghai].

In order to study the distributions characteristics, sources and relationship of PAHs in PM10- phoenix tree leaves-soil system of a coking & chemical factory in Shanghai, the samples of PM10, phoenix tree leaves and soil around the factory were collected for a year. The concentration of PAHs were analyzed according to the USEPA method 8 000 series. The results showed that the average concentration of PAHs in PM10, phoenix tree leaves and soil were 101.11 ng/m3, 79.45 ng/g and 121.53 microg/g, respectively. Particulate phase (PM10) contained mainly carcinogenic and mutagenic PAHs, among which BaA, BghiP, Flu and BaP were found at significant concentrations. In phoenix tree leaves, Nap,Chy, BaP and BghiP presented a higher level of concentration. In soil, 3 and 4-ring PAHs presented a higher level. PAHs concentrations of phoenix tree leaves were very lower in May. Only Ace (0.16 ng/g) and Pyr (0.63 ng/g) were detected. In July and August the concentrations (39.19 ng/g and 150.94 ng/g, respectively) were uplifted significantly. It could be concluded PAHs was from petroleum and coal-fired compound source. There were very strong positive relationships of 16 PAHs level among phoenix tree leaves, soil and PM10 (p < 0.01).

Polychlorinated biphenyls (PCBs) in PM10 surrounding a chemical industrial zone in Shanghai, China.

In order to gain comprehensive understanding of status, properties and sources of PCBs pollution at an industrial area in Shanghai, PM10 were collected during the period November 2004-September 2005. The results showed that the mean value of total PCBs in the industrial area was 2,017.22 pg m(-3). Three dioxin-like PCB congeners had a mean value of TEQ of 0.24 pg-TEQ m(-3). The concentrations of PCBs at all sites were higher in colder months than in warmer months. SigmaPCB concentrations were correlated positively with SO2, NO2 and OCPs, while negatively with polycyclic aromatic hydrocarbons (PAHs), ambient temperature, rainfall and wind speed. It could be concluded that the area had been contaminated by PCBs from a local source.