Synteny analysis in Rosids with a walnut physical map reveals slow genome evolution in long-lived woody perennials.

BackgroundMutations often accompany DNA replication. Since there may be fewer cell cycles per year in the germlines of long-lived than short-lived angiosperms, the genomes of long-lived angiosperms may be diverging more slowly than those of short-lived angiosperms. Here we test this hypothesis.ResultsWe first constructed a genetic map for walnut, a woody perennial. All linkage groups were short, and recombination rates were greatly reduced in the centromeric regions. We then used the genetic map to construct a walnut bacterial artificial chromosome (BAC) clone-based physical map, which contained 15,203 exonic BAC-end sequences, and quantified with it synteny between the walnut genome and genomes of three long-lived woody perennials, Vitis vinifera, Populus trichocarpa, and Malus domestica, and three short-lived herbs, Cucumis sativus, Medicago truncatula, and Fragaria vesca. Each measure of synteny we used showed that the genomes of woody perennials were less diverged from the walnut genome than those of herbs. We also estimated the nucleotide substitution rate at silent codon positions in the walnut lineage. It was one-fifth and one-sixth of published nucleotide substitution rates in the Medicago and Arabidopsis lineages, respectively. We uncovered a whole-genome duplication in the walnut lineage, dated it to the neighborhood of the Cretaceous-Tertiary boundary, and allocated the 16 walnut chromosomes into eight homoeologous pairs. We pointed out that during polyploidy-dysploidy cycles, the dominant tendency is to reduce the chromosome number.ConclusionSlow rates of nucleotide substitution are accompanied by slow rates of synteny erosion during genome divergence in woody perennials

UHPLC-HRMS–based serum lipisdomics reveals novel biomarkers to assist in the discrimination between colorectal adenoma and cancer

The development of a colorectal adenoma (CA) into carcinoma (CRC) is a long and stealthy process. There remains a lack of reliable biomarkers to distinguish CA from CRC. To effectively explore underlying molecular mechanisms and identify novel lipid biomarkers promising for early diagnosis of CRC, an ultrahigh-performance liquid chromatography tandem high-resolution mass spectrometry (UHPLC-HRMS) method was employed to comprehensively measure lipid species in human serum samples of patients with CA and CRC. Results showed significant differences in serum lipid profiles between CA and CRC groups, and 85 differential lipid species (P < 0.05 and fold change > 1.50 or < 0.67) were discovered. These significantly altered lipid species were mainly involved in fatty acid (FA), phosphatidylcholine (PC), and triacylglycerol (TAG) metabolism with the constituent ratio > 63.50%. After performance evaluation by the receiver operating characteristic (ROC) curve analysis, seven lipid species were ultimately proposed as potential biomarkers with the area under the curve (AUC) > 0.800. Of particular value, a lipid panel containing docosanamide, SM d36:0, PC 36:1e, and triheptanoin was selected as a composite candidate biomarker with excellent performance (AUC = 0.971), and the highest selected frequency to distinguish patients with CA from patients with CRC based on the support vector machine (SVM) classification model. To our knowledge, this study was the first to undertake a lipidomics profile using serum intended to identify screening lipid biomarkers to discriminate between CA and CRC. The lipid panel could potentially serve as a composite biomarker aiding the early diagnosis of CRC. Metabolic dysregulation of FAs, PCs, and TAGs seems likely involved in malignant transformation of CA, which hopefully will provide new clues to understand its underlying mechanism

TorchAudio 2.1: Advancing speech recognition, self-supervised learning, and audio processing components for PyTorch

TorchAudio is an open-source audio and speech processing library built for PyTorch. It aims to accelerate the research and development of audio and speech technologies by providing well-designed, easy-to-use, and performant PyTorch components. Its contributors routinely engage with users to understand their needs and fulfill them by developing impactful features. Here, we survey TorchAudio's development principles and contents and highlight key features we include in its latest version (2.1): self-supervised learning pre-trained pipelines and training recipes, high-performance CTC decoders, speech recognition models and training recipes, advanced media I/O capabilities, and tools for performing forced alignment, multi-channel speech enhancement, and reference-less speech assessment. For a selection of these features, through empirical studies, we demonstrate their efficacy and show that they achieve competitive or state-of-the-art performance

Is dataset condensation a silver bullet for healthcare data sharing?

Safeguarding personal information is paramount for healthcare data sharing, a challenging issue without any silver bullet thus far. We study the prospect of a recent deep-learning advent, dataset condensation (DC), in sharing healthcare data for AI research, and the results are promising. The condensed data abstracts original records and irreversibly conceals individual-level knowledge to achieve a bona fide de-identification, which permits free sharing. Moreover, the original deep-learning utilities are well preserved in the condensed data with compressed volume and accelerated model convergences. In PhysioNet-2012, a condensed dataset of 20 samples can orient deep models attaining 80.3% test AUC of mortality prediction (versus 85.8% of 5120 original records), an inspiring discovery generalised to MIMIC-III and Coswara datasets. We also interpret the inhere privacy protections of DC through theoretical analysis and empirical evidence. Dataset condensation opens a new gate to sharing healthcare data for AI research with multiple desirable traits

Carbon Nanoparticles Inhibit Α-Glucosidase Activity and Induce a Hypoglycemic Effect in Diabetic Mice

New, improved therapies to reduce blood glucose are required for treating diabetes mellitus (DM). Here, we investigated the use of a new nanomaterial candidate for DM treatment, carbon nanoparticles (CNPs). CNPs were prepared by carbonization using a polysaccharide from Arctium lappa L. root as the carbon source. The chemical structure and morphology of the CNPs were characterized using Fourier-transform infrared spectroscopy, X-ray photoelectron spectroscopy, elemental analysis, and transmission electron microscopy. CNPs were spherical, 10-20 nm in size, consisting of C, H, O, and N, and featuring various functional groups, including C=O, C=C, C–O, and C–N. In vitro, the as-prepared CNPs could inhibit α-glucosidase with an IC50 value of 0.5677 mg/mL, which is close to that of the reference drug acarbose. Moreover, in vivo hypoglycemic assays revealed that the CNPs significantly reduced fasting blood-glucose levels in mice with diabetes induced by high-fat diet and streptozocin, lowering blood glucose after intragastric administration for 42 days. To the best of our knowledge, this is the first report of CNPs exhibiting α-glucosidase inhibition and a hypoglycemic effect in diabetic mice. These findings suggest the therapeutic potential of CNPs for diabetes

Confinement-Induced Deviation of Chain Mobility and Glass Transition Temperature for Polystyrene/Au Nanoparticles

The mobility and glass transition temperature (<i>T</i>_g) for polymers under nanoscale confinement differ substantially from the bulk. Whereas many studies have focused on the one-dimensional confinement, it has great significance to extend studies to higher geometries. Here, we systematically investigate the mobility by dipolar-filter sequence in solid-state NMR and <i>T</i>_g by DSC for thiolated polystyrene (PS-SH) on gold nanoparticles. The increase in <i>T</i>_g and signal suppression in NMR spectra clearly indicate that the surface confinement dominates molecular mobility as well as <i>T</i>_g. The molecular weight of PS-SH and nanoparticles size show significant influence on the immobilization and <i>T</i>_g. Our results can be fitted with a core–two shell model; the inner shell is under strong constraints while the outer shell with less confinement. This work is essential to better understand the confinement effect and also provides a step toward the ultimate desire to tailor the properties of nanomaterials

Fabrication, Evaluation, and Antioxidant Properties of Carrier-Free Curcumin Nanoparticles

Curcumin (Cur), a natural hydrophobic polyphenolic compound, exhibits multiple beneficial biological activities. However, low water solubility and relative instability hinder its application in food fields. In this study, carrier-free curcumin nanoparticles (CFC NPs) were prepared by adding the DMSO solution of Cur into DI water under continuous rapid stirring. The morphology of CFC NPs was a spherical shape with a diameter of 65.25 &plusmn; 2.09 nm (PDI = 0.229 &plusmn; 0.107), and the loading capacity (LC) of CFC NPs was as high as 96.68 &plusmn; 0.03%. The thermal property and crystallinity of CFC NPs were investigated by XRD. Furthermore, the CFC NPs significantly accelerated the release of Cur in vitro owing to its improved water dispersibility. Importantly, CFC NPs displayed significantly improved DPPH radical scavenging activity. Overall, all these results suggested that CFC NPs would be a promising vehicle to widen the applications of Cur in food fields

Investigation on the Mechanism of the Synthesis of Gold(I) Thiolate Complexes by NMR

In this article, we characterized the polymeric gold­(I) thiolates that precipitated from the intermediate solutions during the synthesis process of gold nanoparticles (GNPs) by the Brust–Schiffrin two-phase method and investigated the formation mechanism of the polymeric gold­(I) thiolates. The solution ¹H NMR confirmed the complete reduction from Au­(III) to Au­(I) with the addition of the first two equivalents of thiols, while only the third and fourth equivalents of thiols were found to participate in forming gold­(I) thiolates. Gold­(I) thiolates, [Au­(I)­SR]_<i>n</i>, precipitated from these solutions were further characterized by ¹H solid-state NMR spectroscopy under fast magic angle spinning (MAS), Raman spectroscopy, and thermogravimetric analysis. Further quantitative studies revealed that the composition of [Au­(I)­SR]_<i>n</i> could be controlled by changing the order of addition of the third and fourth equivalents of thiols. This work has great significance to better understand the mechanism of gold nanoparticle formation and thus to tailor the properties of the final products

Fabrication, Evaluation, and Antioxidant Properties of Carrier-Free Curcumin Nanoparticles

Curcumin (Cur), a natural hydrophobic polyphenolic compound, exhibits multiple beneficial biological activities. However, low water solubility and relative instability hinder its application in food fields. In this study, carrier-free curcumin nanoparticles (CFC NPs) were prepared by adding the DMSO solution of Cur into DI water under continuous rapid stirring. The morphology of CFC NPs was a spherical shape with a diameter of 65.25 ± 2.09 nm (PDI = 0.229 ± 0.107), and the loading capacity (LC) of CFC NPs was as high as 96.68 ± 0.03%. The thermal property and crystallinity of CFC NPs were investigated by XRD. Furthermore, the CFC NPs significantly accelerated the release of Cur in vitro owing to its improved water dispersibility. Importantly, CFC NPs displayed significantly improved DPPH radical scavenging activity. Overall, all these results suggested that CFC NPs would be a promising vehicle to widen the applications of Cur in food fields

New Insight into Intermediate Precursors of Brust–Schiffrin Gold Nanoparticles Synthesis

There is an ongoing intensive debate on the mechanism of gold nanoparticles formation regarding the intermediate precursors prior to the addition of reducing agent. A new detailed view of the widely used Brust–Schiffrin two-phase method to prepare gold nanoparticles is presented here. Precursor species of these reactions have been identified and quantified by NMR, UV–visible, Fourier-transform Raman spectroscopy, etc. We demonstrate that tetraalkylammonium gold complexes ([TOA]­[AuX₂]) and soluble gold thiolate ([TOA]­[AuSRX] and [TOA]­[Au­(SR)₂]) were detectable as the precursors by NMR spectroscopy. Their relative contents depend on the concentration of reactants. Higher concentration of the reactants is favorable for the formation of soluble thiolate. Polymeric gold thiolate [Au­(I)­SR]_<i>n</i> could eventually precipitate from the solution under specific conditions. The clear mechanism presented here is of great significance to tailor the size and properties of the final products