Continuous spin excitations in the three-dimensional frustrated magnet K2Ni2(SO4)3

Continuous spin excitations are widely recognized as one of the hallmarks of novel spin states in quantum magnets, such as quantum spin liquids (QSLs). Here, we report the observation of such kind of excitations in K2Ni2(SO4)3, which consists of two sets of intersected spin-1 Ni2+ trillium lattices. Our inelastic neutron scattering measurement on single crystals clearly shows a dominant excitation continuum, which exhibits a distinct temperature-dependent behavior from that of spin waves, and is rooted in strong quantum spin fluctuations. Further using the self-consistent-gaussian-approximation method, we determined the fourth- and fifth-nearest neighbor exchange interactions are dominant. These two bonds together form a unique three-dimensional network of corner-sharing tetrahedra, which we name as ''hyper-trillium'' lattice. Our results provide direct evidence for the existence of QSL features in K2Ni2(SO4)3 and highlight the potential for the hyper-trillium lattice to host frustrated quantum magnetism.Comment: 6 pages and 5 figures, plus several pages of supplemental material, comments are welcom

ParaBTM: A Parallel Processing Framework for Biomedical Text Mining on Supercomputers

A prevailing way of extracting valuable information from biomedical literature is to apply text mining methods on unstructured texts. However, the massive amount of literature that needs to be analyzed poses a big data challenge to the processing efficiency of text mining. In this paper, we address this challenge by introducing parallel processing on a supercomputer. We developed paraBTM, a runnable framework that enables parallel text mining on the Tianhe-2 supercomputer. It employs a low-cost yet effective load balancing strategy to maximize the efficiency of parallel processing. We evaluated the performance of paraBTM on several datasets, utilizing three types of named entity recognition tasks as demonstration. Results show that, in most cases, the processing efficiency can be greatly improved with parallel processing, and the proposed load balancing strategy is simple and effective. In addition, our framework can be readily applied to other tasks of biomedical text mining besides NER

GTZ: a fast compression and cloud transmission tool optimized for FASTQ files

Abstract Background The dramatic development of DNA sequencing technology is generating real big data, craving for more storage and bandwidth. To speed up data sharing and bring data to computing resource faster and cheaper, it is necessary to develop a compression tool than can support efficient compression and transmission of sequencing data onto the cloud storage. Results This paper presents GTZ, a compression and transmission tool, optimized for FASTQ files. As a reference-free lossless FASTQ compressor, GTZ treats different lines of FASTQ separately, utilizes adaptive context modelling to estimate their characteristic probabilities, and compresses data blocks with arithmetic coding. GTZ can also be used to compress multiple files or directories at once. Furthermore, as a tool to be used in the cloud computing era, it is capable of saving compressed data locally or transmitting data directly into cloud by choice. We evaluated the performance of GTZ on some diverse FASTQ benchmarks. Results show that in most cases, it outperforms many other tools in terms of the compression ratio, speed and stability. Conclusions GTZ is a tool that enables efficient lossless FASTQ data compression and simultaneous data transmission onto to cloud. It emerges as a useful tool for NGS data storage and transmission in the cloud environment. GTZ is freely available online at: https://github.com/Genetalks/gtz

Protection against Metabolic Associated Fatty Liver Disease by Protocatechuic Acid

ABSTRACTGut microbiota–diet interaction has been identified as a key factor of metabolic associated fatty liver disease (MAFLD). Recent studies suggested that dietary polyphenols may protect against MAFLD by regulating gut microbiota; however, the underlying mechanisms remain elusive. We first investigated the effects of cyanidin 3-glucoside and its phenolic metabolites on high-fat diet induced MAFLD in C57BL/6J mice, and protocatechuic acid (PCA) showed a significant positive effect. Next, regulation of PCA on lipid metabolism and gut microbiota were explored by MAFLD mouse model and fecal microbiota transplantation (FMT) experiment. Dietary PCA reduced intraperitoneal and hepatic fat deposition with lower levels of transaminases (AST & ALT) and inflammatory cytokines (IL-1β, IL-2, IL-6, TNF-α & MCP-1), but higher HDL-c/LDL-c ratio. Characterization of gut microbiota indicated that PCA decreased the Firmicutes/Bacteroidetes ratio mainly by reducing the relative abundance of genus Enterococcus, which was positively correlated with the levels of LDL-c, AST, ALT and most of the up-regulated hepatic lipids by lipidomics analysis. FMT experiments showed that Enterococcus faecalis caused hepatic inflammation, fat deposition and insulin resistance with decreased expression of carnitine palmitoyltransferase-1 alpha (CPT1α), which can be reversed by PCA through inhibiting Enterococcus faecalis. Transcriptomics analysis suggested that Enterococcus faecalis caused a significant decrease in the expression of fibroblast growth factor 1 (Fgf1), and PCA recovered the expression of Fgf1 with insulin-like growth factor binding protein 2 (Igfbp2), insulin receptor substrate 1 (Irs1) and insulin receptor substrate 2 (Irs2). These results demonstrated that high proportion of gut Enterococcus faecalis accelerates MAFLD with decreased expression of CPT1α and Fgf1, which can be prevented by dietary supplementation of PCA

Molecular co-assembled strategy tuning protein conformation for cartilage regeneration

Abstract The assembly of oligopeptide and polypeptide molecules can reconstruct various ordered advanced structures through intermolecular interactions to achieve protein-like biofunction. Here, we develop a “molecular velcro”-inspired peptide and gelatin co-assembly strategy, in which amphiphilic supramolecular tripeptides are attached to the molecular chain of gelatin methacryloyl via intra-/intermolecular interactions. We perform molecular docking and dynamics simulations to demonstrate the feasibility of this strategy and reveal the advanced structural transition of the co-assembled hydrogel, which brings more ordered β-sheet content and 10-fold or more compressive strength improvement. We conduct transcriptome analysis to reveal the role of co-assembled hydrogel in promoting cell proliferation and chondrogenic differentiation. Subcutaneous implantation evaluation confirms considerably reduced inflammatory responses and immunogenicity in comparison with type I collagen. We demonstrate that bone mesenchymal stem cells-laden co-assembled hydrogel can be stably fixed in rabbit knee joint defects by photocuring, which significantly facilitates hyaline cartilage regeneration after three months. This co-assembly strategy provides an approach for developing cartilage regenerative biomaterials

Nanofibrous polypeptide hydrogels with collagen-like structure as biomimetic extracellular matrix

Abstract Supramolecular peptides exhibit obvious similarities with collagen fibers in terms of self-assembly characteristics, nanofibrous structure, and responsiveness to external stimuli. Here, a series of supramolecular peptides were developed by altering the amino acid sequence, enabling the self-assembly of three types of 4-biphenylacetic acid (BPAA)-tripeptides into fibrous hydrogel through hydrogen bonding and π–π stacking under the influence of ion induction. Transmission electron and scanning electron microscopies revealed that the diameter of the fiber within nanofibrous hydrogels was ~ 10 and ~ 40 nm, respectively, which was similar with the self-assembled collagen fibers. For this reason, these hydrogels could be considered as a biomimetic extracellular substitute. Meanwhile, the gelation concentration induced by ions was even lower than 0.66 wt%, with an elastic modulus of ~ 0.27 kPa, corresponding to a water content of 99.34 wt%. In addition, the three supramolecular hydrogels were found to be good substrates for L929 cell adhesion and MC-3T3 cell proliferation. The overall results implied that BPAA-based hydrogels have a lucrative application potential as cell carriers. Graphical Abstrac