Data-driven identification of SARS-CoV-2 subpopulations using PhenoGraph and binary-coded genomic data.

For epidemic prevention and control, the identification of SARS-CoV-2 subpopulations sharing similar micro-epidemiological patterns and evolutionary histories is necessary for a more targeted investigation into the links among COVID-19 outbreaks caused by SARS-CoV-2 with similar genetic backgrounds. Genomic sequencing analysis has demonstrated the ability to uncover viral genetic diversity. However, an objective analysis is necessary for the identification of SARS-CoV-2 subpopulations. Herein, we detected all the mutations in 186 682 SARS-CoV-2 isolates. We found that the GC content of the SARS-CoV-2 genome had evolved to be lower, which may be conducive to viral spread, and the frameshift mutation was rare in the global population. Next, we encoded the genomic mutations in binary form and used an unsupervised learning classifier, namely PhenoGraph, to classify this information. Consequently, PhenoGraph successfully identified 303 SARS-CoV-2 subpopulations, and we found that the PhenoGraph classification was consistent with, but more detailed and precise than the known GISAID clades (S, L, V, G, GH, GR, GV and O). By the change trend analysis, we found that the growth rate of SARS-CoV-2 diversity has slowed down significantly. We also analyzed the temporal, spatial and phylogenetic relationships among the subpopulations and revealed the evolutionary trajectory of SARS-CoV-2 to a certain extent. Hence, our results provide a better understanding of the patterns and trends in the genomic evolution and epidemiology of SARS-CoV-2.

Transcriptome analysis reveals gene expression changes of the basidiomycetous yeast Apiotrichum mycotoxinivorans in response to ochratoxin A exposure.

Ochratoxin A (OTA) is one of the most common and deleterious mycotoxins found in food and feedstuffs worldwide; however, Apiotrichum mycotoxinivorans can detoxify OTA. Our results show that A. mycotoxinivorans GUM1709 efficiently degraded OTA, but it caused the accumulation of intracellular reactive oxygen species. The main aim of this study was to identify potential OTA-detoxifying enzymes and to explore the effects of OTA on A. mycotoxinivorans GMU1709. RNA-seq data revealed that 1643 and 1980 genes were significantly upregulated and downregulated, respectively, after OTA exposure. Functional enrichment analyses indicated that OTA exposure enhanced defense capability, protein transport, endocytosis, and energy metabolism; caused ribosomal stress; suppressed DNA replication and transcription; inhibited cell growth and division; and promoted cell death. The integration of secretome, gene expression, and molecular docking analyses revealed that two carboxypeptidase homologues (members of the metallocarboxypeptidase family) were most likely responsible for the detoxification of both extracellular and intracellular OTA. Superoxide dismutase and catalase were the main genes activated in response to oxidative stress. In addition, analysis of key genes associated with cell division and apoptosis showed that OTA exposure inhibited mitosis and promoted cell death. This study revealed the possible OTA response and detoxification mechanisms in A. mycotoxinivorans.

Transcriptomic responses of the zearalenone (ZEN)-detoxifying yeast Apiotrichum mycotoxinivorans to ZEN exposure.

Zearalenone (ZEN) is a potent oestrogenic mycotoxin that is mainly produced by Fusarium species and is a serious environmental pollutant in animal feeds. Apiotrichum mycotoxinivorans has been widely used as a feed additive to detoxify ZEN. However, the effects of ZEN on A. mycotoxinivorans and its detoxification mechanisms remain unclear. In this study, transcriptomic and bioinformatic analyses were used to investigate the molecular responses of A. mycotoxinivorans to ZEN exposure and the genetic basis of ZEN detoxification. We detected 1424 significantly differentially expressed genes (DEGs), of which 446 were upregulated and 978 were downregulated. Functional and enrichment analyses showed that ZEN-induced genes were significantly associated with xenobiotic metabolism, oxidative stress response, and active transport systems. However, ZEN-inhibited genes were mainly related to cell division, cell cycle, and fungal development. Subsequently, bioinformatic analysis identified candidate ZEN-detoxification enzymes. The Baeyer-Villiger monooxygenases and carboxylesterases, which are responsible for the formation and subsequent hydrolysis of a new ZEN lactone, respectively, were significantly upregulated. In addition, the expression levels of genes related to conjugation and transport involved in the xenobiotic detoxification pathway were significantly upregulated. Moreover, the expression levels of genes encoding enzymatic antioxidants and those related to growth and apoptosis were significantly upregulated and downregulated, respectively, which made it possible for A. mycotoxinivorans to survive in a highly toxic environment and efficiently detoxify ZEN. This is the first systematic report of ZEN tolerance and detoxification in A. mycotoxinivorans. We identified the metabolic enzymes that were potentially involved in detoxifying ZEN in the GMU1709 strain and found that ZEN-induced transcriptional regulation of genes is key to withstanding highly toxic environments. Hence, our results provide valuable information for developing enzymatic detoxification systems or engineering this detoxification pathway in other species.

Pan-genomic analysis provides novel insights into the association of E.coli with human host and its minimal genome.

MOTIVATION: Bacteria can usually acquire certain advantageous genes that enable the bacteria to adapt to rapidly changing niches, thereby leading to a wide range of intraspecific genome content and genetic redundancy. The minimal genome of Escherichia coli, which is the most important bacterial species, and the association between E.coli and its human host are worthy of further exploration. RESULTS: We used gene prediction and phylogenetic analysis to reveal a rich phylogenetic diversity among 491 E.coli strains and to reveal substantial differences between these strains with respect to gene number and genome length. We used pan-genomic analysis to accurately identify 867 core genes, in which only 243 genes are shared by essential genes. This analysis revealed that core genes mainly provide essential functions to the basic lifestyle of E.coli, and accessory genes are likely to confer selective advantages such as niche adaptation or the ability to colonize specific hosts. By association analysis, we found that E.coli strains in non-human hosts may more easily utilize foreign genetic materials to adapt to their surroundings, but the population in human hosts has higher demands for the control of population density, indicating that highly accurate quorum-sensing behavior is very important for harmony between E.coli and its human host. By considering core genes and previous deletions together, we proposed a potential direction for further reduction of the E.coli genome. AVAILABILITY AND IMPLEMENTATION: The data, analysis process and detailed information on software tools used in this study are all available in the supplementary material. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

The systematic analysis of ultraconserved genomic regions in the budding yeast.

Motivation: In the evolution of species, a kind of special sequences, termed ultraconserved sequences (UCSs), have been inherited without any change, which strongly suggests those sequences should be crucial for the species to survive or adapt to the environment. However, the UCSs are still regarded as mysterious genetic sequences so far. Here, we present a systematic study of ultraconserved genomic regions in the budding yeast based on the publicly available genome sequences, in order to reveal their relationship with the adaptability or fitness advantages of the budding yeast. Results: Our results indicate that, in addition to some fundamental biological functions, the UCSs play an important role in the adaptation of Saccharomyces cerevisiae to the acidic environment, which is backed up by the previous observation. Besides that, we also find the highly unchanged genes are enriched in some other pathways, such as the nutrient-sensitive signaling pathway. To facilitate the investigation of unique UCSs, the UCSC Genome Browser was utilized to visualize the chromosomal position and related annotations of UCSs in S.cerevisiae genome. Availability and implementation: For more details on UCSs, please refer to the Supplementary information online, and the custom code is available on request. Contact: fgao@tju.edu.cn. Supplementary information: Supplementary data are available at Bioinformatics online.

Recombinational DSBs-intersected genes converge on specific disease- and adaptability-related pathways.

Motivation: The budding yeast Saccharomyces cerevisiae is a model species powerful for studying the recombination of eukaryotes. Although many recombination studies have been performed for this species by experimental methods, the population genomic study based on bioinformatics analyses is urgently needed to greatly increase the range and accuracy of recombination detection. Here, we carry out the population genomic analysis of recombination in S.cerevisiae to reveal the potential rules between recombination and evolution in eukaryotes. Results: By population genomic analysis, we discover significantly more and longer recombination events in clinical strains, which indicates that adverse environmental conditions create an obviously wider range of genetic combination in response to the selective pressure. Based on the analysis of recombinational double strand breaks (DSBs)-intersected genes (RDIGs), we find that RDIGs significantly converge on specific disease- and adaptability-related pathways, indicating that recombination plays a biologically key role in the repair of DSBs related to diseases and environmental adaptability, especially the human neurological disorders. By evolutionary analysis of RDIGs, we find that the RDIGs highly prevailing in populations of yeast tend to be more evolutionarily conserved, indicating the accurate repair of DSBs in these RDIGs is critical to ensure the eukaryotic survival or fitness. Supplementary information: Supplementary data are available at Bioinformatics online.

Cognitive Changes in Peritoneal Dialysis Patients: A Multicenter Prospective Cohort Study.

RATIONALE & OBJECTIVE: Cognitive impairment is an independent predictor of technique failure and mortality in patients on peritoneal dialysis (PD) therapy. We investigated changes in cognitive function and factors associated with it in this population. STUDY DESIGN: Multicenter prospective cohort study. SETTING & PARTICIPANTS: 458 PD patients were enrolled and followed up for 2 years. PREDICTORS: Global and specific domains of cognitive function were measured at baseline and after 2 years. The Modified Mini-Mental State Examination (3MS) was used for assessment of global cognitive function; Trail-Making Tests A and B, for executive function; and subtests of the Battery for the Assessment of Neuropsychological Status, for immediate and delayed memory, visuospatial skill, and language ability. OUTCOMES: The primary outcome was change in cognitive function. Secondary outcomes included all-cause mortality, cardiovascular mortality, hospitalization, and transition to hemodialysis therapy. ANALYTICAL APPROACH: Multivariable linear regression models. RESULTS: The prevalence of cognitive impairment increased from 19.8% to 23.9%. 3MS scores significantly decreased (84.8 to 83.1), although executive function, immediate memory, and visuospatial skill improved over time. Delayed memory capacity and language ability were unchanged. Lower serum albumin level was associated with deteriorated delayed memory, visuospatial skill, and language ability, as well as with the decline in general cognitive function (ß values of 0.64, 0.90, 0.80, and 0.44, respectively). Advanced age, lower education, and depression were also correlated with deterioration in general and specific cognitive function. After multivariable adjustment, both global and specific cognitive impairment at baseline were associated with a greater rate of hospitalization, and memory dysfunction was associated with a lower dialysis modality survival rate. LIMITATIONS: A relatively short observation period, small number of deaths, and potential selection bias due to patients unavailable for the second assessment. CONCLUSIONS: In a PD population, global cognitive function declined over 2 years, though some specific cognitive domains improved. Besides well-recognized factors, hypoalbuminemia and depression were also risk factors for cognitive impairment.

Novel Equations for Estimating Lean Body Mass in Patients With Chronic Kidney Disease.

OBJECTIVE: Simplified methods to estimate lean body mass (LBM), an important nutritional measure representing muscle mass and somatic protein, are lacking in nondialyzed patients with chronic kidney disease (CKD). We developed and tested 2 reliable equations for estimation of LBM in daily clinical practice. DESIGN AND METHODS: The development and validation groups both included 150 nondialyzed patients with CKD Stages 3 to 5. Two equations for estimating LBM based on mid-arm muscle circumference (MAMC) or handgrip strength (HGS) were developed and validated in CKD patients with dual-energy x-ray absorptiometry as referenced gold method. RESULTS: We developed and validated 2 equations for estimating LBM based on HGS and MAMC. These equations, which also incorporated sex, height, and weight, were developed and validated in CKD patients. The new equations were found to exhibit only small biases when compared with dual-energy x-ray absorptiometry, with median differences of 0.94 and 0.46 kg observed in the HGS and MAMC equations, respectively. Good precision and accuracy were achieved for both equations, as reflected by small interquartile ranges in the differences and in the percentages of estimates that were 20% of measured LBM. The bias, precision, and accuracy of each equation were found to be similar when it was applied to groups of patients divided by the median measured LBM, the median ratio of extracellular to total body water, and the stages of CKD. CONCLUSIONS: LBM estimated from MAMC or HGS were found to provide accurate estimates of LBM in nondialyzed patients with CKD.

Cognitive Impairment and Structural Neuroimaging Abnormalities Among Patients with Chronic Kidney Disease.

BACKGROUND/AIMS: Cognitive impairment and abnormal structural neuroimaging is common in chronic kidney disease patients. We aimed to explore its association with dialysis modality and the relationship between cognitive impairment and abnormal structural neuroimaging. METHODS: Sixty peritoneal dialysis patients and 30 hemodialysis and 30 non-dialyzed stage 3-5 chronic kidney disease patients without history of stroke were enrolled for the study. Participants were matched for age, gender, education, diabetes status, and dialysis duration (if appropriate). Cognitive functions were measured using a battery of recognized instruments. Brain features were examined with 3-dimensional magnetic resonance imaging. RESULTS: Cognitive impairment was significantly more severe in dialysis patients than in non-dialyzed patients. The global and specific cognitive function were not significantly different between patients on peritoneal dialysis and hemodialysis. Hemodialysis patients had more severe white matter hyperintensity, sulcal and ventricular atrophy, and SVIs than other patients. In all groups, higher white matter grade, ventricular grade, and hippocampal atrophy were significantly associated with global cognitive impairment, with hazard ratios of 1.80 (1.22-2.64), 1.67 (1.09-2.57), and 2.49 (1.07-5.77), respectively. White matter grade was also significantly associated with delayed memory (hazard ratio 1.63; 1.12-2.39). CONCLUSION: Dialysis modality showed no association with cognitive impairment, although hemodialysis patients had more severe neuroimaging abnormalities. For the whole group, white matter hyperintensity, and ventricular and hippocampal atrophy, were independently associated with global cognitive impairment in chronic kidney disease patients.

Systems-level analysis of the metabolic responses of the diatom Phaeodactylum tricornutum to phosphorus stress.

Phosphorus is an important macronutrient. To understand the molecular and cellular responses to phosphorus stress better, transcriptome profiling in combination with biochemical investigations was conducted in the model diatom Phaeodactylum tricornutum. Out of 10 402 predicted genes, 2491 and 405 genes were significantly upregulated or downregulated respectively. Unsurprisingly, genes associated with phosphate uptake were upregulated, such as the phosphate transporters and alkaline phosphatases. Genes encoding stress-shock proteins were accordingly upregulated, including genes associated with stress-responsive proteins, signal transduction and secondary metabolism. Additionally, genes related to protein translation, carbon fixation, glycolysis and the citric acid cycle were also upregulated. Genes associated with gene transcription were downregulated, thereby resulting in the upregulation of translation to compensate for the limited supply of messenger RNA. The downregulation of genes related to ß-oxidation could contribute to the accumulation of fatty acids. Accordingly, triacylglycerols, which are important for energy storage, were determined to increase by 1.65-fold. Intracellular membranes, other than chloroplast membranes, tended to be dispersed; this finding was in accordance with the increased transcription of a total of 11 genes encoding putative phospholipases. Taken together, this work revealed the coordination of multiple metabolic pathways and certain key genes in the adaptation of P. tricornutum to phosphorus stress.

Antisense knockdown of pyruvate dehydrogenase kinase promotes the neutral lipid accumulation in the diatom Phaeodactylum tricornutum.

BACKGROUND: Microalgae have been an emerging biofuel resource; however, the germplasm improvement has been slow due to the lack of molecular tools. Pyruvate dehydrogenase kinase (PDK) deactivates the pyruvate dehydrogenase complex (PDC) which catalyzes the oxidative decarboxylation of pyruvate. Acetyl-CoA production via PDC is important in plant tissues that are active in fatty acid synthesis. RESULTS: A 1261-bp cDNA of a putative PDK gene (PtPDK) was cloned from a diatom Phaeodactylum tricornutum, and PtPDK antisense knockdown transgenic diatoms were generated. Both PtPDK transcript abundance and enzyme activity were reduced significantly due to antisense knockdown of PtPDK. Neutral lipid content of transgenic diatom cells increased up to 82% as determined by Nile red staining, and fatty acid composition was not altered. Transgenic cells showed slightly lower growth rate but similar cell size with the wild type, hence retaining similar biomass productivity. CONCLUSIONS: This work first obtained a successful engineered diatom regulating a key gene involved in lipid metabolism. Our findings also provide powerful indications in enhancing microalgal lipid production by metabolic engineering for biofuel industry.

Oral vitamin D supplementation on the prevention of peritoneal dialysis-related peritonitis: A pilot randomised controlled trial.

OBJECTIVE: Peritoneal dialysis (PD)-related peritonitis is independently associated with low serum 25-hydroxy vitamin D [25(OH)D] levels. Our objective is to examine the feasibility of conducting a large, randomised controlled trial to determine the effects of vitamin D supplementation on the risk of PD-related peritonitis. DESIGN: Pilot, prospective, open-label randomised controlled trial. SETTING: Peking University First Hospital, China. PARTICIPANTS: Patients receiving PD who had recovered from a recent episode of peritonitis between 30 September 2017 and 28 May 2020. INTERVENTIONS: Oral natural vitamin D supplementation (2000 IU per day) versus no vitamin D supplementation for 12 months. PRIMARY AND SECONDARY OUTCOME MEASURES: Primary outcomes were feasibility (recruitment success, retention, adherence, safety) and fidelity (change in serum 25(OH)D level during follow-up) for a large, randomised controlled trial in the future to determine the effects of vitamin D on PD-related peritonitis. Secondary outcomes were time to peritonitis occurrence and outcome of subsequent peritonitis. RESULTS: Overall, 60 among 151 patients were recruited (recruitment rate was 39.7%, 95% CI 31.9-47.5%, recruitment rate among eligible patients was 61.9%, 95% CI 52.2-71.5%). Retention and adherence rates were 100.0% (95% CI 100.0-100.0%) and 81.5% (95% CI 66.8-96.1%), respectively. During follow-up, serum 25(OH)D levels increased in the vitamin D (VD) group (from 19.25 ± 10.11 nmol/L to 60.27 ± 23.29 nmol/L after 6 months, p < 0.001, n = 31), and remained higher (p < 0.001) than those in the control group (n = 29). No differences were observed between the two groups with respect to time to subsequent peritonitis (hazard ratio 0.85, 95% CI 0.33-2.17) or any of the peritonitis outcomes. Adverse events were uncommon. CONCLUSIONS: A randomised controlled trial of the effect of vitamin D supplementation on peritonitis occurrence in patients receiving PD is feasible, safe and results in adequate serum 25(OH)D levels.

Point-of-care ultrasound diagnosis of skull fracture in Chinese children 0-6 years old with scalp hematoma from minor head trauma: A preliminary prospective observational study.

Background: Previous studies have suggested that point-of-care ultrasound could help to evaluate and diagnose pediatric skull fracture for the closed scalp hematoma from blunt trauma. However, relevant data in Chinese children are missing, especially in children 0-6 years old. Objectives: Our study aimed to evaluate the efficacy of point-of-care ultrasound to diagnose skull fracture in children 0-6 years old with scalp hematoma in China. Methods: We performed a prospective observational study and screened children 0-6 years old with closed scalp hematoma and a Glasgow coma scale of 14-15 at Hospital in China. Enrolled children (N = 152) were first evaluated for skull fracture with point-of-care ultrasound by the emergency physician and then received a head computed tomography scan. Results: The point-of-care ultrasound examination and computed tomography scan revealed skull fracture in 13 (8.6%) and 12 (7.9%) children, respectively. The kappa test showed a satisfactory agreement between two examinations (P < 0.0001), with kappa = 0.87 (95% confidence interval, i.e., 95% CI, [0.69, 1.00]) and area under the curve = 0.95 (95% CI [0.86, 1], P < 0.0001). The point-of-care ultrasound examination had the sensitivity of 91.7% (95% CI [62.5%, 100%]), specificity of 98.6% (95% CI [94.6%, 100%]), positive predictive value of 84.6% (95% CI [56.5%, 96.9%]), negative predictive value of 99.2% (95% CI [95.6%, 100%]), and accuracy of 98.0% (95% CI [94.1%, 99.6%]). Conclusions: While our study is preliminary in nature, our findings may guide future larger studies in assessing the utility of point-of-care ultrasound examination in diagnosing skull fractures in children with scalp hematoma from minor head trauma.

Estimation of Left Ventricular Ejection Fraction Using Cardiovascular Hemodynamic Parameters and Pulse Morphological Characteristics with Machine Learning Algorithms.

It is estimated that 360,000 patients have suffered from heart failure (HF) in Taiwan, mostly those over the age of 65 years, who need long-term medication and daily healthcare to reduce the risk of mortality. The left ventricular ejection fraction (LVEF) is an important index to diagnose the HF. The goal of this study is to estimate the LVEF using the cardiovascular hemodynamic parameters, morphological characteristics of pulse, and bodily information with two machine learning algorithms. Twenty patients with HF who have been treated for at least six to nine months participated in this study. The self-constructing neural fuzzy inference network (SoNFIN) and XGBoost regression models were used to estimate their LVEF. A total of 193 training samples and 118 test samples were obtained. The recursive feature elimination algorithm is used to choose the optimal parameter set. The results show that the estimating root-mean-square errors (ERMS) of SoNFIN and XGBoost are 6.9 ± 2.3% and 6.4 ± 2.4%, by comparing with echocardiography as the ground truth, respectively. The benefit of this study is that the LVEF could be measured by the non-medical image method conveniently. Thus, the proposed method may arrive at an application level for clinical practice in the future.

An Effective Preprocessing Method for High-Quality Pan-Genome Analysis of Bacillus subtilis and Escherichia coli.

Bacillus subtilis and Escherichia coli, as widely used microbial species, are of great significance in studying microbial community relationships, adaptive evolution in various niches, engineering cell factories that produce specific products, and designing genome reduction. The pan-genome analysis is an effective method for studying the characteristics and functions of genes among and within species. Many research directions and conclusions usually depend on accurate gene identification and reliable pan-genome results. However, there currently lack enough studies showing how to achieve high-quality pan-genome results between or within certain species. This chapter will take Bacillus subtilis as an example to introduce a stepwise manner for improving the quality of the pan-genome by gradually removing confounding strains step-by-step, and ultimately obtaining a reliable high-quality pan-genome landscape of Bacillus subtilis, which could be used as a quality control protocol in pan-genome analysis pipeline. Finally, we suggest further improving the pan-genome analysis results of Escherichia coli to prove the feasibility and credibility of the quality control protocol for obtaining high-quality pan-genome landscape.

Complete Genome Sequencing and Comparative Analysis of the Clinically-Derived Apiotrichum mycotoxinivorans Strain GMU1709.

Over the past decade, Apiotrichum mycotoxinivorans has been recognized globally as a source of opportunistic infections. It is a yeast-like fungus, and its association as an uncommon pulmonary pathogen with cystic fibrosis patients has been previously reported. Immunocompromised patients are at the highest risk of A. mycotoxinivorans infections. Therefore, to investigate the genetic basis for the pathogenicity of A. mycotoxinivorans, we performed whole-genome sequencing and comparative genomic analysis of A. mycotoxinivorans GMU1709 that was isolated from sputum specimens of a pneumonia patient receiving cardiac repair surgery. The assembly of Oxford Nanopore reads from the GMU1709 strain and its subsequent correction using Illumina paired-end reads yielded a high-quality complete genome with a genome size of 30.5 Mb in length, which comprised six chromosomes and one mitochondrion. Subsequently, 8,066 protein-coding genes were predicted based on multiple pieces of evidence, including transcriptomes. Phylogenomic analysis indicated that A. mycotoxinivorans exhibited the closest evolutionary affinity to A. veenhuisii, and both the A. mycotoxinivorans strains and the formerly Trichosporon cutaneum ACCC 20271 strain occupied the same phylogenetic position. Further comparative analysis supported that the ACCC 20271 strain belonged to A. mycotoxinivorans. Comparisons of three A. mycotoxinivorans strains indicated that the differences between clinical and non-clinical strains in pathogenicity and drug resistance may be little or none. Based on the comparisons with strains of other species in the Trichosporonaceae family, we identified potential key genetic factors associated with A. mycotoxinivorans infection or pathogenicity. In addition, we also deduced that A. mycotoxinivorans had great potential to inactivate some antibiotics (e.g., tetracycline), which may affect the efficacy of these drugs in co-infection. In general, our analyses provide a better understanding of the classification and phylogeny of the Trichosporonaceae family, uncover the underlying genetic basis of A. mycotoxinivorans infections and associated drug resistance, and provide clues into potential targets for further research and the therapeutic intervention of infections.

[Faster decline of total fluid removal is an independent risk factor for increased motality in patients on peritoneal dialysis].

OBJECTIVE: To explore the relationship between the rate of decline of total fluid removal (TFR), the sum of 24-hour urine and ultrafiltration and all-cause mortality in patients undergoing peritoneal dialysis (PD) through a prospective cohort study. METHODS: The study included 297 incident patients, starting PD between July 2002 and February 2007. All the patients were followed up until death, transfering to hemodialysis, or kidney transplant by February 2008. Demographics, biochemical data and dialysis adequacy were collected at the baseline. The TFR, urine and ultrafiltration before each clinic day were averaged every 3 months throughout the follow-up. The slope of TFR (k-TFR) was calculated for each patient over time by a simple linear regression analysis. RESULTS: The median age was 62 years, and 42.4% of the 297 incident PD patients were male and 71 patients (23.9%) died during the median 30-month follow-up. By multivariate Cox regression analysis, k-TFR rather than the baseline TFR was a significant risk factor of mortality after being adjusted for age, presence of diabetes mellitus, baseline hemoglobin and serum albumin. In another multivariate model including all the above covariates, k-TFR was superior to the baseline TFR for prediction of mortality. CONCLUSION: Faster decline of total fluid removal is significantly associated with higher risk of all-cause mortality.

Associations between small and middle molecules clearance and the change of cognitive function in peritoneal dialysis.

BACKGROUND: Uremic toxins have been suspected as potential contributors for cognitive impairment in peritoneal dialysis (PD) patients. However, associations between the clearance of serum small and middle molecules and the change of cognitive function were not fully explored and then we explored this issue in the present study. METHOD: A total of clinically-stable 222 patients on PD were enrolled and then followed up for 2 years in this single-center prospective cohort study. Small and middle molecules clearances were examined by urea clearance (Kt/V), creatinine clearance (Ccr) and beta-2 microglobulin (B2M) clearance via dialysate and urine at baseline and after 2 years. Global and specific cognitive impairment were measured at baseline and after 2 years. Modified Mini-Mental State Examination (3MS) was assessed for global cognitive function, trail-making tests A and B for executive function and subtests of the battery for the assessment of neuropsychological status for immediate and delayed memory, visuospatial skills and language ability. RESULTS: The median of total Kt/V, Ccr and B2M clearance were 1.89, 53.2 l/w/1.73 m2 and 17.5 l/w/1.73 m2, respectively at baseline. The prevalence of global cognitive impairment was 12.3% for 222 patients and 15.4% for the remained 130 patients after 2 years. At baseline, total Kt/V was independently positively associated with delayed memory function. Total and dialysate beta-2 microglobulin clearance was positively associated with 3MS scores and negatively with completion time on trail A after multivariate adjustment. At 2 years, we observed a significant difference in the changing trend of 3MS scores between groups divided by total B2M clearance (P = 0.033), which still maintained to be meaningful after multivariate adjustment (P = 0.024). Patients with total B2M clearance > 19.0 l/w/1.73 m2 got significant improvement on their 3MS scores (P = 0.005). Patients divided by total Kt/V or Ccr were not significantly different in the trends of general and any specific cognitive function during the follow up. CONCLUSION: The higher middle molecules clearance independently correlated to better performance on general cognitive and executive function in PD patients, which also predict an improvement in general cognitive function during the follow up.