Long nanopore reads are advantageous in de novo genome assembly. However, nanopore reads usually have broad error distribution and high-error-rate subsequences. Existing error correction tools cannot ...correct nanopore reads efficiently and effectively. Most methods trim high-error-rate subsequences during error correction, which reduces both the length of the reads and contiguity of the final assembly. Here, we develop an error correction, and de novo assembly tool designed to overcome complex errors in nanopore reads. We propose an adaptive read selection and two-step progressive method to quickly correct nanopore reads to high accuracy. We introduce a two-stage assembler to utilize the full length of nanopore reads. Our tool achieves superior performance in both error correction and de novo assembling nanopore reads. It requires only 8122 hours to assemble a 35X coverage human genome and achieves a 2.47-fold improvement in NG50. Furthermore, our assembly of the human WERI cell line shows an NG50 of 22 Mbp. The high-quality assembly of nanopore reads can significantly reduce false positives in structure variation detection.
Arsenic (As) contamination of rice (Oryza sativa) is a worldwide concern and elucidating the molecular mechanisms of As accumulation in rice may provide promising solutions to the problem. Previous ...studies using microarray techniques to investigate transcriptional regulation of plant responses to As stress have identified numerous differentially expressed genes. However, little is known about the metabolic and regulatory network remodelings, or their interactions with microRNA (miRNA) in plants upon As(III) exposure.
We used Illumina sequencing to acquire global transcriptome alterations and miRNA regulation in rice under As(III) treatments of varying lengths of time and dosages.
We found that the response of roots was more distinct when the dosage was varied, whereas that of shoots was more distinct when the treatment time was varied. In particular, the genes involved in heavy metal transportation, jasmonate (JA) biosynthesis and signaling, and lipid metabolism were closely related to responses of rice under As(III) stress. Furthermore, we discovered 36 new As(III)-responsive miRNAs, 14 of which were likely involved in regulating gene expression in transportation, signaling, and metabolism.
Our findings highlight the significance of JA signaling and lipid metabolism in response to As(III) stress and their regulation by miRNA, which provides a foundation for subsequent functional research.
High-performance pervaporation membranes have potential in industrial separation applications, but overcoming the permeability-selectivity trade-off is a challenge. We report a strategy to create ...highly flexible metal-organic framework nanosheet (MOF-NS) membranes with a faveolate structure on polymer substrates for alcohol-water separation. The controlled growth followed by a surface-coating method effectively produced flexible and defect-free superhydrophobic MOF-NS membranes. The reversible deformation of the flexible MOF-NS and the vertical interlamellar pathways were captured with electron microscopy. Molecular simulations confirmed the structure and revealed transport mechanism. The ultrafast transport channels in MOF-NS exhibited an ultrahigh flux and a separation factor of 8.9 in the pervaporation of 5 weight % ethanol-water at 40°C, which can be used for biofuel recovery. MOF-NS and polydimethylsiloxane synergistically contribute to the separation performance.
Honeycomb channels enhance separations
Pervaporation membranes use a combination of permeation and evaporation for energy-efficient separations of volatile compounds from solutions. Xu
et al
. designed a strategy to fabricate defect-free superhydrophobic metal-organic framework (MOF) nanosheet membranes. Instead of dispersing the MOFs into a polydimethylsiloxane (PDMS) matrix, the authors grew a continuous and uniform layer of embedded MOF seeds on polymeric substrates that were then sealed with PDMS. This procedure results in a honeycomb-like structure with high flexibility and fast molecular transport channels, thus enhancing the separation of alcohols from water. —MSL
Flexible metal-organic framework honeycombed nanosheet membranes are applied for alcohol-water separations.
Although long-read single-cell RNA isoform sequencing (scISO-Seq) can reveal alternative RNA splicing in individual cells, it suffers from a low read throughput. Here, we introduce HIT-scISOseq, a ...method that removes most artifact cDNAs and concatenates multiple cDNAs for PacBio circular consensus sequencing (CCS) to achieve high-throughput and high-accuracy single-cell RNA isoform sequencing. HIT-scISOseq can yield >10 million high-accuracy long-reads in a single PacBio Sequel II SMRT Cell 8M. We also report the development of scISA-Tools that demultiplex HIT-scISOseq concatenated reads into single-cell cDNA reads with >99.99% accuracy and specificity. We apply HIT-scISOseq to characterize the transcriptomes of 3375 corneal limbus cells and reveal cell-type-specific isoform expression in them. HIT-scISOseq is a high-throughput, high-accuracy, technically accessible method and it can accelerate the burgeoning field of long-read single-cell transcriptomics.
In this study, a 304/20MnSi stainless-steel clad rebar was prepared by single-pass compression process using the MMS-200 Thermal Mechanical Simulator. The impact of different degrees of deformation ...and deformation temperature on microstructure evolution and the mechanical properties of stainless steel clad rebars were investigated. The study indicated that with the increase of the degree of deformation, the content of pearlite in a carbon steel matrix was increased, and the grains refined. The metallurgical bonding of the bonded interface was formed under high temperature and high extrusion force. With the increase of the deformation temperature, more bainite was obtained on the side of carbon steel, and the grain size increased. The obvious diffusion of Fe, Cr and Ni elements near the bonding interface resulted in higher microhardness of the stainless steel side and smaller microhardness of the carbon steel side. Moreover, the engineering stress-strain curves obtained by the tensile test showed that the plastic deformation of stainless steel and carbon steel was more coordinated. With the increase of deformation temperature and the degree of deformation, the tensile strength of the stainless steel clad rebar was as high as 690 MPa and the elongation was 26%, which was superior to the properties of the clad rebar prepared by other process parameters.
Aberrant RNA splicing is recognized to contribute to cancer pathogenesis, but the underlying mechanisms remain mainly obscure. Here, we report that the splicing factor SRSF2 is upregulated frequently ...in human hepatocellular carcinoma (HCC), where this event is associated with poor prognosis in patients. RNA-seq and other molecular analyses were used to identify SRSF2-regulated alternative splicing events. SRSF2 binding within an alternative exon was associated with its inclusion in the RNA, whereas SRSF2 binding in a flanking constitutive exon was associated with exclusion of the alternative exon. Notably, cancer-associated splice variants upregulated by SRSF2 in clinical specimens of HCC were found to be crucial for pathogenesis and progression in hepatoma cells, where SRSF2 expression increased cell proliferation and tumorigenic potential by controlling expression of these variants. Our findings identify SRSF2 as a key regulator of RNA splicing dysregulation in cancer, with possible clinical implications as a candidate prognostic factor in patients with HCC.
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In this study, the impact of different surface treatment and degree of vacuum on the interface and mechanical properties of 304/Q345 stainless steel clad plate was investigated. The study indicated ...that more continuous or aggregated Al₂O₃ and Si-Mn composite oxides were formed at the interface after brush grinding. However, less inclusions such as Al₂O₃, MnS and Ca-Mg-Al-Si composite oxides were formed at the interface after pickling treatment. For the vacuum degrees of 10
Pa, 1 Pa and 105 Pa, the oxidation reaction became more intense with the decrease in vacuum degree. The interface inclusions were gradually changed from Al₂O₃ and Si-Mn complex oxides to oxide scale and MnCr₂O₄ spinel oxide. The interfacial bonding strength of stainless steel clad plate was improved with the increase in degree of vacuum. The bonding strength was 55 MPa at vacuum of 10⁵ Pa, but it was 484 MPa at vacuum of 10
Pa, which is far greater than that of the national standard, and an excellent performance was obtained.
Computed tomographic perfusion (CTP) can play an auxiliary role in the selection of patients with acute ischemic stroke for endovascular treatment. However, data on CTP in non-stroke patients with ...intracranial arterial stenosis are scarce. We aimed to investigate images in patients with asymptomatic intracranial arterial stenosis to determine the detection accuracy and interpretation time of large/medium-artery stenosis or occlusion when combining computed tomographic angiography (CTA) and CTP images.
We retrospectively reviewed 39 patients with asymptomatic intracranial arterial stenosis from our hospital database from January 2021 to August 2023 who underwent head CTP, head CTA, and digital subtraction angiography (DSA). Head CTA images were generated from the CTP data, and the diagnostic performance for each artery was assessed. Two readers independently interpreted the CTA images before and after CTP, and the results were analyzed.
After adding CTP maps, the accuracy (area under the curve) of diagnosing internal carotid artery (R1: 0.847 vs. 0.907, R2: 0.776 vs. 0.887), middle cerebral artery (R1: 0.934 vs. 0.933, R2: 0.927 vs. 0.981), anterior cerebral artery (R1: 0.625 vs. 0.750, R2: 0.609 vs. 0.750), vertebral artery (R1: 0.743 vs. 0.764, R2: 0.748 vs. 0.846), and posterior cerebral artery (R1: 0.390 vs. 0.575, R2: 0.390 vs. 0.585) occlusions increased for both readers (p < 0.05). Mean interpretation time (R1: 72.4 ± 6.1 s vs. 67.7 ± 6.4 s, R2: 77.7 ± 3.8 s vs. 72.6 ± 4.7 s) decreased when using a combination of both images both readers (p < 0.001).
The addition of CTP images improved the accuracy of interpreting CTA images and reduced the interpretation time in asymptomatic intracranial arterial stenosis. These findings support the use of CTP imaging in patients with asymptomatic intracranial arterial stenosis.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Interfacial bonding behavior of 7050 aluminum alloy clad plates during hot-roll cladding under different vacuum degrees was investigated. The results demonstrated that the bonding effect of the ...interface was positively correlated with the vacuum degree. Due to severe surface oxidation at 10
5
Pa, the metal on both sides of the interface did not undergo metallurgical bonding and mainly maintained physical contact, with an ultimate tensile strength (UTS) of only 209 MPa across the interface. At 10
2
Pa, the large-scale migration of original interfacial grain boundary was still inhibited and continuous dynamic recrystallization occurred mainly at the interface with bulging only locally, which directly led to brittle fracture. At 10
–1
Pa, significant discontinuous dynamic recrystallization (DDRX) occurred at the interface, resulting in the complete elimination of the original interface. And UTS across the interface was 338 MPa, reaching the level of the matrix. Therefore, interfacial metallurgical bonding could be achieved by reducing the oxidation of interface and further inducing DDRX during hot-roll cladding.
Graphical Abstract
In order to investigate interfacial oxide evolution of 7050 aluminum alloy clad plates during the subsequent heat treatment and the effect on mechanical properties, the clad plates were subjected to ...solution and aging treatment. The results indicated that the solution treatment had little effect on the evolution of Al2O3 film at the interface, and the shear properties at the interface with different reductions at 10−2 Pa were significantly improved after solution process, reaching the matrix level. However, Al2O3 film at the interface primarily evolved to MgO and became an interface inclusion during the aging process, which significantly reduced the interfacial bonding effect at rolling reductions of 60% and 70% and the vacuum degree of 105 Pa and 10 Pa. When the rolling reduction was 80% and the vacuum degree was 10−2 Pa, the bonding interface disappeared completely without any impurity element aggregation as well as defects. And the shear properties at the aged interface could be entirely restored to the matrix level. Therefore, increasing the rolling reduction and the vacuum degree contributed to eliminate the negative effect of evolution products during solution and aging process on the healing of the interface.
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