Haplotype-resolved de novo assembly is the ultimate solution to the study of sequence variations in a genome. However, existing algorithms either collapse heterozygous alleles into one consensus copy ...or fail to cleanly separate the haplotypes to produce high-quality phased assemblies. Here we describe hifiasm, a de novo assembler that takes advantage of long high-fidelity sequence reads to faithfully represent the haplotype information in a phased assembly graph. Unlike other graph-based assemblers that only aim to maintain the contiguity of one haplotype, hifiasm strives to preserve the contiguity of all haplotypes. This feature enables the development of a graph trio binning algorithm that greatly advances over standard trio binning. On three human and five nonhuman datasets, including California redwood with a ~30-Gb hexaploid genome, we show that hifiasm frequently delivers better assemblies than existing tools and consistently outperforms others on haplotype-resolved assembly.
The recent advances in sequencing technologies enable the assembly of individual genomes to the quality of the reference genome. How to integrate multiple genomes from the same species and make the ...integrated representation accessible to biologists remains an open challenge. Here, we propose a graph-based data model and associated formats to represent multiple genomes while preserving the coordinate of the linear reference genome. We implement our ideas in the minigraph toolkit and demonstrate that we can efficiently construct a pangenome graph and compactly encode tens of thousands of structural variants missing from the current reference genome.
In the metagenomic assembly of a microbial community, abundant species are often thought to assemble well given their deeper sequencing coverage. This conjuncture is rarely tested or evaluated in ...practice. We often do not know how many abundant species are missing and do not have an approach to recover them.
Here, we propose k-mer based and 16S RNA based methods to measure the completeness of metagenome assembly. We show that even with PacBio high-fidelity (HiFi) reads, abundant species are often not assembled, as high strain diversity may lead to fragmented contigs. We develop a novel reference-free algorithm to recover abundant metagenome-assembled genomes (MAGs) by identifying circular assembly subgraphs. Complemented with a reference-free genome binning heuristics based on dimension reduction, the proposed method rescues many abundant species that would be missing with existing methods and produces competitive results compared to those state-of-the-art binners in terms of total number of near-complete genome bins.
Our work emphasizes the importance of metagenome completeness, which has often been overlooked. Our algorithm generates more circular MAGs and moves a step closer to the complete representation of microbial communities.
Multitopic organic linkers can provide a means to organize metal cluster nodes in a regular three‐dimensional array. Herein, we show that isonicotinic acid N‐oxide (HINO) serves as the linker in the ...formation of a metal–organic framework featuring Dy2 single‐molecule magnets as nodes. Importantly, guest solvent exchange induces a reversible single‐crystal to single‐crystal transformation between the phases Dy2(INO)4(NO3)2⋅2 solvent (solvent=DMF (Dy2‐DMF), CH3CN (Dy2‐CH3CN)), thereby switching the effective magnetic relaxation barrier (determined by ac magnetic susceptibility measurements) between a negligible value for Dy2‐DMF and 76 cm−1 for Dy2‐CH3CN. Ab initio calculations indicate that this difference arises not from a significant change in the intrinsic relaxation barrier of the Dy2 nodes, but rather from a slowing of the relaxation rate of incoherent quantum tunneling of the magnetization by two orders of magnitude.
Guest swap: Exchange of the guest molecules within the pores of a metal–organic framework (MOF) featuring Dy2 single‐molecule magnets as nodes imparts major changes in the magnetization relaxation dynamics (see picture; spectra recorded from 2 K (blue plots) to 9 K (red)). As a result of guest exchange, significantly different effective relaxation barriers (Ueff) for the compound are measured. Atom colors: Dy=green, O=red, N=blue, C=gray.
Neutrophil-to-lymphocyte ratio (NLR) and platelet-to-lymphocyte ratio (PLR) have been emerging as the novel inflammatory biomarkers for determining the prognosis of various diseases. This study aimed ...to investigate the individual and joint effects of NLR and PLR on functional outcomes of acute ischemic stroke (AIS).
Our study involved 448 eligible patients with first-ever AIS. Clinical and laboratory data were collected on admission within 72 h from stroke onset. Unfavorable functional outcome was defined as a modified Rankin Scale score of 3-6 at 3 months after AIS. Cox proportional hazard model and spline regression models was used to estimate the effect of NLR and PLR on risk of adverse outcomes after the last patient who completed a 3-months follow-up was enrolled.
After adjusting confounders, NLR were significantly associated with the unfavorable functional outcomes (
-trend < 0.001). So were PLR (
-trend < 0.001). NLR was discovered to have higher predictive value than PLR (AUC = 0.776, 95%CI = 0.727-0.825,
< 0.001; AUC = 0.697, 95%CI = 0.641-0.753,
< 0.001). The optimal cutoff values for NLR and PLR was 3.51 and 141.52, respectively. Stratified analysis performed by cox proportional hazard model showed that high level of NLR and PLR (NLR ≥ 3.51, PLR ≥ 141.52) presented the highest risk of unfavorable functional outcomes (adjusted HR, 3.77; 95% CI: 2.38-5.95;
< 0.001). Followed by single high level of NLR (adjusted HR, 2.32; 95% CI: 1.10-4.87;
= 0.027). Single high level of PLR (NLR < 3.51, PLR ≥ 141.52) also showed higher risk than low level of the combination, but it did not reach statistical significance (adjusted HR, 1.42; 95% CI: 0.75-2.70;
= 0.285). No obvious additive relative excess risk due to interaction (RERI) not significant or multiplicative (adjusted HR, 0.71; 95%CI: 0.46-1.09;
= 0.114) interaction was found between the effects of NLR and PLR on the risk of unfavorable functional outcomes.
This study demonstrated that both NLR and PLR were independent predictors of 3-months functional outcomes of AIS. They may help to identify high-risk patients more forcefully when combined together.
Phosphors that exhibit tunable broadband emissions are highly desired in multi-functional LEDs, including pc-WLEDs and pc-NIR LEDs. In this work, broadband emissions were obtained and modulated in ...the unexpectedly wide spectral range of 517–609 nm for (Lu0.99−xGdxBi0.01)2WO6 phosphors by tuning the Gd3+ content (x = 0–0.99). The effects of Gd3+ doping on phase constituents, particle morphology, crystal structure, and photoluminescence were systematically investigated. Broadband green emission was obtained from Gd3+-free (Lu0.99Bi0.01)2WO6 phosphors (x = 0), whose emission intensity was enhanced by 50% with 5 at% Gd3+ (x = 0.05). The phase transition happened when x > 0.50 and the broadband red-NIR emission was obtained when x = 0.75–0.99. Three luminescence centers were proved to be responsible for the broadband green emissions via crystal structure, spectral fitting and fluorescence decay analysis. A pc-WLED with a high color rendering index (Ra = 91.3), a stable emission color, and a low color temperature (3951 K) was fabricated from the (Lu0.94Gd0.05Bi0.01)2WO6 broadband green phosphor, and an LED device that simultaneously emits high color rendering index white light and NIR light was obtained with the (Gd0.99Bi0.01)2WO6 broadband red-NIR phosphor. Night vision and noninvasive imaging were also demonstrated using the latter LED device.
In low-dimensional systems, the combination of reduced dimensionality, strong interactions and topology has led to a growing number of many-body quantum phenomena. Thermal transport, which is ...sensitive to all energy-carrying degrees of freedom, provides a discriminating probe of emergent excitations in quantum materials and devices. However, thermal transport measurements in low dimensions are dominated by the phonon contribution of the lattice, requiring an experimental approach to isolate the electronic thermal conductance. Here we measured non-local voltage fluctuations in a multi-terminal device to reveal the electronic heat transported across a mesoscopic bridge made of low-dimensional materials. Using two-dimensional graphene as a noise thermometer, we measured the quantitative electronic thermal conductance of graphene and carbon nanotubes up to 70 K, achieving a precision of ~1% of the thermal conductance quantum at 5 K. Employing linear and nonlinear thermal transport, we observed signatures of energy transport mediated by long-range interactions in one-dimensional electron systems, in agreement with a theoretical model.
Molecules exhibiting bistability have been proposed as elementary binary units (bits) for information storage, potentially enabling fast and efficient computing. In particular, transition metal ...complexes can display magnetic bistability via either spin-crossover or single-molecule magnet behavior. We now show that the octahedral iron(II) complexes in the molecular salt Fe(1-propyltetrazole)6(BF4)2, when placed in its high-symmetry form, can combine both types of behavior. Light irradiation under an applied magnetic field enables fully reversible switching between an S = 0 state and an S = 2 state with either up (M S = +2) or down (M S = −2) polarities. The resulting tristability suggests the possibility of using molecules for ternary information storage in direct analogy to current binary systems that employ magnetic switching and the magneto-optical Kerr effect as write and read mechanisms.
Alzheimer's disease (AD) is characterized by the accumulation of β-amyloid peptide (Aβ) and loss of neurons. Recently, a growing body of evidences have indicated that as a herbal compound naturally ...derived from grapes, resveratrol modulates the pathophysiology of AD, however, with a largely unclear mechanism. Therefore, we aimed to investigate the protection of resveratrol against the neurotoxicity of β-amyloid peptide 25-35 (Aβ(25-35)) and further explore its underlying mechanism in the present study. PC12 cells were injuried by Aβ(25-35), and resveratrol at different concentrations was added into the culture medium. We observed that resveratrol increased cell viability through the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) and lactate dehydrogenase (LDH) colorimetric assays. Flow cytometry indicated the reduction of cell apoptosis by resveratrol. Moreover, resveratrol also stabilized the intercellular Ca(2+) homeostasis and attenuated Aβ(25-35) neurotoxicity. Additionally, Aβ(25-35)-suppressed silent information regulator 1 (SIRT1) activity was significantly reversed by resveratrol, resulting in the downregulation of Rho-associated kinase 1 (ROCK1). Our results clearly revealed that resveratrol significantly protected PC12 cells and inhibited the β-amyloid-induced cell apoptosis through the upregulation of SIRT1. Moreover, as a downstream signal molecule, ROCK1 was negatively regulated by SIRT1. Taken together, our study demonstrated that SIRT1-ROCK1 pathway played a critical role in the pathomechanism of AD.
Cholestatic liver fibrosis was achieved by bile duct ligation (BDL) in mice. Liver injury associated with BDL for 15 days included significant reactive oxygen/nitrogen species generation, liver ...inflammation, cell death and fibrosis. Administration of Epigallocatechin 3-Gallate (EGCG) in animals reduced liver fibrosis involving parenchymal cells in BDL model. EGCG attenuated BDL-induced gene expression of pro-fibrotic markers (Collagen, Fibronectin, alpha 2 smooth muscle actin or SMA and connective tissue growth factor or CTGF), mitochondrial oxidative stress, cell death marker (DNA fragmentation and PARP activity), NFκB activity and pro-inflammatory cytokines (TNFα, MIP1α, IL1β, and MIP2). EGCG also improved BDL induced damages of mitochondrial electron transport chain complexes and antioxidant defense enzymes such as glutathione peroxidase and manganese superoxide dismutase. EGCG also attenuated hydrogen peroxide induced cell death in hepatocytes in vitro and alleviate stellate cells mediated fibrosis through TIMP1, SMA, Collagen 1 and Fibronectin in vitro. In conclusion, the reactive oxygen/nitrogen species generated from mitochondria plays critical pathogenetic role in the progression of liver inflammation and fibrosis and this study indicate that EGCG might be beneficial for reducing liver inflammation and fibrosis.
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