MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

MEGAHIT is a NGS de novo assembler for assembling large and complex metagenomics data in a time- and cost-efficient manner. It finished assembling a soil metagenomics dataset with 252Gbps in 44.1 hours and 99.6 hours on a single computing node with and without a GPU, respectively. MEGAHIT assembles the data as a whole, i.e., it avoids pre-processing like partitioning and normalization, which might compromise on result integrity. MEGAHIT generates 3 times larger assembly, with longer contig N50 and average contig length than the previous assembly. 55.8% of the reads were aligned to the assembly, which is 4 times higher than the previous. The source code of MEGAHIT is freely available at https://github.com/voutcn/megahit under GPLv3 license.Comment: 2 pages, 2 tables, 1 figure, submitted to Oxford Bioinformatics as an Application Not

Modified Glucose-Insulin-Potassium Regimen Provides Cardioprotection With Improved Tissue Perfusion in Patients Undergoing Cardiopulmonary Bypass Surgery

Background Laboratory studies demonstrate glucose-insulin-potassium (GIK) as a potent cardioprotective intervention, but clinical trials have yielded mixed results, likely because of varying formulas and timing of GIK treatment and different clinical settings. This study sought to evaluate the effects of modified GIK regimen given perioperatively with an insulin-glucose ratio of 1:3 in patients undergoing cardiopulmonary bypass surgery. Methods and Results In this prospective, randomized, double-blinded trial with 930 patients referred for cardiac surgery with cardiopulmonary bypass, GIK (200 g/L glucose, 66.7 U/L insulin, and 80 mmol/L KCl) or placebo treatment was administered intravenously at 1 mL/kg per hour 10 minutes before anesthesia and continuously for 12.5 hours. The primary outcome was the incidence of in-hospital major adverse cardiac events including all-cause death, low cardiac output syndrome, acute myocardial infarction, cardiac arrest with successful resuscitation, congestive heart failure, and arrhythmia. GIK therapy reduced the incidence of major adverse cardiac events and enhanced cardiac function recovery without increasing perioperative blood glucose compared with the control group. Mechanistically, this treatment resulted in increased glucose uptake and less lactate excretion calculated by the differences between arterial and coronary sinus, and increased phosphorylation of insulin receptor substrate-1 and protein kinase B in the hearts of GIK-treated patients. Systemic blood lactate was also reduced in GIK-treated patients during cardiopulmonary bypass surgery. Conclusions A modified GIK regimen administered perioperatively reduces the incidence of in-hospital major adverse cardiac events in patients undergoing cardiopulmonary bypass surgery. These benefits are likely a result of enhanced systemic tissue perfusion and improved myocardial metabolism via activation of insulin signaling by GIK. Clinical Trial Registration URL: clinicaltrials.gov. Identifier: NCT01516138

BASE: a practical de novo assembler for large genomes using long NGS reads

© 2016 The Author(s). Background: De novo genome assembly using NGS data remains a computation-intensive task especially for large genomes. In practice, efficiency is often a primary concern and favors using a more efficient assembler like SOAPdenovo2. Yet SOAPdenovo2, based on de Bruijn graph, fails to take full advantage of longer NGS reads (say, 150 bp to 250 bp from Illumina HiSeq and MiSeq). Assemblers that are based on string graphs (e.g., SGA), though less popular and also very slow, are more favorable for longer reads. Methods: This paper shows a new de novo assembler called BASE. It enhances the classic seed-extension approach by indexing the reads efficiently to generate adaptive seeds that have high probability to appear uniquely in the genome. Such seeds form the basis for BASE to build extension trees and then to use reverse validation to remove the branches based on read coverage and paired-end information, resulting in high-quality consensus sequences of reads sharing the seeds. Such consensus sequences are then extended to contigs. Results: Experiments on two bacteria and four human datasets shows the advantage of BASE in both contig quality and speed in dealing with longer reads. In the experiment on bacteria, two datasets with read length of 100 bp and 250 bp were used. Especially for the 250 bp dataset, BASE gives much better quality than SOAPdenovo2 and SGA and is simlilar to SPAdes. Regarding speed, BASE is consistently a few times faster than SPAdes and SGA, but still slower than SOAPdenovo2. BASE and Soapdenov2 are further compared using human datasets with read length 100 bp, 150 bp and 250 bp. BASE shows a higher N50 for all datasets, while the improvement becomes more significant when read length reaches 250 bp. Besides, BASE is more-meory efficent than SOAPdenovo2 when sequencing data with error rate. Conclusions: BASE is a practically efficient tool for constructing contig, with significant improvement in quality for long NGS reads. It is relatively easy to extend BASE to include scaffolding.published_or_final_versio

MTR4 drives liver tumorigenesis by promoting cancer metabolic switch through alternative splicing.

The metabolic switch from oxidative phosphorylation to glycolysis is required for tumorigenesis in order to provide cancer cells with energy and substrates of biosynthesis. Therefore, it is important to elucidate mechanisms controlling the cancer metabolic switch. MTR4 is a RNA helicase associated with a nuclear exosome that plays key roles in RNA processing and surveillance. We demonstrate that MTR4 is frequently overexpressed in hepatocellular carcinoma (HCC) and is an independent diagnostic marker predicting the poor prognosis of HCC patients. MTR4 drives cancer metabolism by ensuring correct alternative splicing of pre-mRNAs of critical glycolytic genes such as GLUT1 and PKM2. c-Myc binds to the promoter of the MTR4 gene and is important for MTR4 expression in HCC cells, indicating that MTR4 is a mediator of the functions of c-Myc in cancer metabolism. These findings reveal important roles of MTR4 in the cancer metabolic switch and present MTR4 as a promising therapeutic target for treating HCC

MegaGTA: A sensitive and accurate metagenomic gene-targeted assembler using iterative de Bruijn graphs

© 2017 The Author(s). Background: The recent release of the gene-targeted metagenomics assembler Xander has demonstrated that using the trained Hidden Markov Model (HMM) to guide the traversal of de Bruijn graph gives obvious advantage over other assembly methods. Xander, as a pilot study, indeed has a lot of room for improvement. Apart from its slow speed, Xander uses only 1 k-mer size for graph construction and whatever choice of k will compromise either sensitivity or accuracy. Xander uses a Bloom-filter representation of de Bruijn graph to achieve a lower memory footprint. Bloom filters bring in false positives, and it is not clear how this would impact the quality of assembly. Xander does not keep track of the multiplicity of k-mers, which would have been an effective way to differentiate between erroneous k-mers and correct k-mers. Results: In this paper, we present a new gene-targeted assembler MegaGTA, which attempts to improve Xander in different aspects. Quality-wise, it utilizes iterative de Bruijn graphs to take full advantage of multiple k-mer sizes to make the best of both sensitivity and accuracy. Computation-wise, it employs succinct de Bruijn graphs (SdBG) to achieve low memory footprint and high speed (the latter is benefited from a highly efficient parallel algorithm for constructing SdBG). Unlike Bloom filters, an SdBG is an exact representation of a de Bruijn graph. It enables MegaGTA to avoid false-positive contigs and to easily incorporate the multiplicity of k-mers for building better HMM model. We have compared MegaGTA and Xander on an HMP-defined mock metagenomic dataset, and showed that MegaGTA excelled in both sensitivity and accuracy. On a large rhizosphere soil metagenomic sample (327Gbp), MegaGTA produced 9.7-19.3% more contigs than Xander, and these contigs were assigned to 10-25% more gene references. In our experiments, MegaGTA, depending on the number of k-mers used, is two to ten times faster than Xander. Conclusion: MegaGTA improves on the algorithm of Xander and achieves higher sensitivity, accuracy and speed. Moreover, it is capable of assembling gene sequences from ultra-large metagenomic datasets. Its source code is freely available at https://github.com/HKU-BAL/megagta.Link_to_subscribed_fulltex

Synthesis and Mechanism of Tetracalcium Phosphate from Nanocrystalline Precursor

Tetracalcium phosphate (TTCP, Ca4(PO4)2O) was prepared by the calcination of coprecipitated mixture of nanoscale hydroxyapatite (HA, Ca10(PO4)6(OH)2) and calcium carbonate crystal (CaCO3), followed by cooling in the air or furnace. The effect of calcination temperature on crystal structure and phase composition of the coprecipitation mixture was characterized by transmission electron microscope (TEM), thermal analysis-thermogravimetry (DTA-TG), X-ray diffraction (XRD), Fourier transform-infrared spectroscopy (FT-IR), and Raman spectroscopy (RS). The obtained results indicated that the synthesized mixture consisted of nanoscale HA and CaCO3 with uniform distribution throughout the composite. TTCP was observed in the air quenching samples when the calcination temperature was above 1185°C. With the increase of the calcination temperature, the amount of the intermediate products in the air quenching samples decreased and cannot be detected when calcination temperature reached 1450°C. Unexpectedly, the mixture of HA and calcium oxide was observed in the furnace cooling samples. Clearly, the calcination temperature and cooling methods are critical for the synthesis of high-purity TTCP. The results indicate that the nanosize of precursors can decrease the calcination temperature, and TTCP can be calcinated by low temperature

Safety of HIF prolyl hydroxylase inhibitors for anemia in dialysis patients: a systematic review and network meta-analysis

Aim: We performed a systematic review and network meta-analysis evaluating the safety and efficacy of hypoxia-inducible factor prolyl hydroxylase inhibitors (HIF-PHIs) among dialysis chronic kidney disease patients.Methods: Safety was evaluated with any adverse events (AEs), serious adverse events (SAEs), and 12 common events. Efficacy was mainly analyzed with hemoglobin response. All reported results were summarized using mean difference and risk ratio (RR) with 95% confidence interval (CI). Publication bias was assessed through funnel plots.Results: Twenty trials (19 studies) with 14,947 participants were included, comparing six HIF-PHIs with erythropoiesis-stimulating agents (ESAs). No significant differences were indicated in overall AEs and SAEs between each HIF-PHI and ESA. The occurrence of gastrointestinal disorder was higher in enarodustat and roxadustat than in ESAs (RR: 6.92, 95% CI: 1.52–31.40, p = 0.01; RR: 1.30, 95% CI: 1.04–1.61, p = 0.02). The occurrence of hypertension was lower in vadadustat than in ESAs (RR: 0.81, 95% CI: 0.69–0.96, p = 0.01). The occurrence of vascular-access complications was higher in roxadustat (RR: 1.15, 95% CI: 1.04–1.27, p<0.01) and lower in daprodustat (RR: 0.78, 95% CI: 0.66–0.92, p<0.01) than in ESAs. In the risk of the other nine events, including cardiovascular events, no significant differences were observed between HIF-PHIs and ESAs. For hemoglobin response, network meta-analysis showed that compared with ESAs, significant increases were shown in roxadustat (RR: 1.04, 95% CI: 1.01–1.07, p<0.01) and desidustat (RR: 1.22, 95% CI: 1.01–1.48, p = 0.04), whereas noticeable reductions were indicated in vadadustat (RR: 0.88, 95% CI: 0.82–0.94, p<0.01) and molidustat (RR: 0.83, 95% CI: 0.70–0.98, p = 0.02). There was no significant difference between daprodustat and ESAs (RR: 0.97, 95% CI: 0.89–1.06, p = 0.47).Conclusion: Although HIF-PHIs did not show significant differences from ESAs in terms of overall AEs and SAEs, statistical differences in gastrointestinal disorder, hypertension, and vascular-access complications were observed between HIF-PHIs, which deserved to be noted in clinical decision making.Systematic review registration: This study is registered with PROSPERO (registration number CRD42022312252