DHGE: Dual-View Hyper-Relational Knowledge Graph Embedding for Link Prediction and Entity Typing

In the field of representation learning on knowledge graphs (KGs), a hyper-relational fact consists of a main triple and several auxiliary attribute-value descriptions, which is considered more comprehensive and specific than a triple-based fact. However, currently available hyper-relational KG embedding methods in a single view are limited in application because they weaken the hierarchical structure that represents the affiliation between entities. To overcome this limitation, we propose a dual-view hyper-relational KG structure (DH-KG) that contains a hyper-relational instance view for entities and a hyper-relational ontology view for concepts that are abstracted hierarchically from the entities. This paper defines link prediction and entity typing tasks on DH-KG for the first time and constructs two DH-KG datasets, JW44K-6K, extracted from Wikidata, and HTDM based on medical data. Furthermore, we propose DHGE, a DH-KG embedding model based on GRAN encoders, HGNNs, and joint learning. DHGE outperforms baseline models on DH-KG, according to experimental results. Finally, we provide an example of how this technology can be used to treat hypertension. Our model and new datasets are publicly available.Comment: Accepted by AAAI 202

CD97 stabilises the immunological synapse between dendritic cells and T cells and is targeted for degradation by the Salmonella effector SteD.

The Salmonella enterica effector SteD depletes mature MHC class II (mMHCII) molecules from the surface of infected antigen-presenting cells through ubiquitination of the cytoplasmic tail of the mMHCII β chain. This requires the Nedd4 family HECT E3 ubiquitin ligase Wwp2 and a tumor-suppressing transmembrane protein adaptor Tmem127. Here, through a proteomic screen of dendritic cells, we found that SteD targets the plasma membrane protein CD97 for degradation by a similar mechanism. SteD enhanced ubiquitination of CD97 on K555 and mutation of this residue eliminated the effect of SteD on CD97 surface levels. We showed that CD97 localises to and stabilises the immunological synapse between dendritic cells and T cells. Removal of CD97 by SteD inhibited dendritic cell-T cell interactions and reduced T cell activation, independently of its effect on MHCII. Therefore, SteD suppresses T cell immunity by two distinct processes

Text2NKG: Fine-Grained N-ary Relation Extraction for N-ary relational Knowledge Graph Construction

Beyond traditional binary relational facts, n-ary relational knowledge graphs (NKGs) are comprised of n-ary relational facts containing more than two entities, which are closer to real-world facts with broader applications. However, the construction of NKGs still significantly relies on manual labor, and n-ary relation extraction still remains at a course-grained level, which is always in a single schema and fixed arity of entities. To address these restrictions, we propose Text2NKG, a novel fine-grained n-ary relation extraction framework for n-ary relational knowledge graph construction. We introduce a span-tuple classification approach with hetero-ordered merging to accomplish fine-grained n-ary relation extraction in different arity. Furthermore, Text2NKG supports four typical NKG schemas: hyper-relational schema, event-based schema, role-based schema, and hypergraph-based schema, with high flexibility and practicality. Experimental results demonstrate that Text2NKG outperforms the previous state-of-the-art model by nearly 20\% points in the $F_1$ scores on the fine-grained n-ary relation extraction benchmark in the hyper-relational schema. Our code and datasets are publicly available.Comment: Preprin

Allosteric Inhibition of Human Ribonucleotide Reductase by dATP Entails the Stabilization of a Hexamer

Ribonucleotide reductases (RNRs) are responsible for all de novo biosynthesis of DNA precursors in nature by catalyzing the conversion of ribonucleotides to deoxyribonucleotides. Because of its essential role in cell division, human RNR is a target for a number of anticancer drugs in clinical use. Like other class Ia RNRs, human RNR requires both a radical-generation subunit (β) and nucleotide-binding subunit (α) for activity. Because of their complex dependence on allosteric effectors, however, the active and inactive quaternary forms of many class Ia RNRs have remained in question. Here, we present an X-ray crystal structure of the human α subunit in the presence of inhibiting levels of dATP, depicting a ring-shaped hexamer (α[subscript 6]) where the active sites line the inner hole. Surprisingly, our small-angle X-ray scattering (SAXS) results indicate that human α forms a similar hexamer in the presence of ATP, an activating effector. In both cases, α[subscript 6] is assembled from dimers (α[subscript 2]) without a previously proposed tetramer intermediate (α[subscript 4]). However, we show with SAXS and electron microscopy that at millimolar ATP, the ATP-induced α[subscript 6] can further interconvert with higher-order filaments. Differences in the dATP- and ATP-induced α[subscript 6] were further examined by SAXS in the presence of the β subunit and by activity assays as a function of ATP or dATP. Together, these results suggest that dATP-induced α[subscript 6] is more stable than the ATP-induced α6 and that stabilization of this ring-shaped configuration provides a mechanism to prevent access of the β subunit to the active site of α.National Institutes of Health (U.S.) (GM100008)National Institutes of Health (U.S.) (Grant GM29595)Massachusetts Institute of Technology. Undergraduate Research Opportunities Progra

A generalized approach to photon avalanche upconversion in luminescent nanocrystals

Photon avalanching nanoparticles (ANPs) exhibit extremely nonlinear upconverted emission valuable for sub-diffraction imaging, nanoscale sensing, and optical computing. Avalanching has been demonstrated with Tm3+, Nd3+ or Pr3+-doped nanocrystals, but their emission is limited to 600 and 800 nm, restricting applications. Here, we utilize Gd3+-assisted energy migration to tune the emission wavelengths of Tm3+-sensitized ANPs and generate highly nonlinear emission of Eu3+, Tb3+, Ho3+, and Er3+ ions. The upconversion intensities of these spectrally discrete ANPs scale with the nonlinearity factor s = 10-17 under 1064 nm excitation at power densities as low as 6 kW/cm2. This strategy for imprinting avalanche behavior on remote emitters can be extended to fluorophores adjacent to ANPs, as we demonstrate with CdS/CdSe/CdS core/shell/shell quantum dots. ANPs with rationally designed energy transfer networks provide the means to transform conventional linear emitters into a highly nonlinear ones, expanding the use of photon avalanching in biological, chemical, and photonic applications.Comment: 13 pages, 5 figure

Anomalous metamagnetism in the low carrier density Kondo lattice YbRh3Si7

We report complex metamagnetic transitions in single crystals of the new low carrier Kondo antiferromagnet YbRh3Si7. Electrical transport, magnetization, and specific heat measurements reveal antiferromagnetic order at T_N = 7.5 K. Neutron diffraction measurements show that the magnetic ground state of YbRh3Si7 is a collinear antiferromagnet where the moments are aligned in the ab plane. With such an ordered state, no metamagnetic transitions are expected when a magnetic field is applied along the c axis. It is therefore surprising that high field magnetization, torque, and resistivity measurements with H||c reveal two metamagnetic transitions at mu_0H_1 = 6.7 T and mu_0H_2 = 21 T. When the field is tilted away from the c axis, towards the ab plane, both metamagnetic transitions are shifted to higher fields. The first metamagnetic transition leads to an abrupt increase in the electrical resistivity, while the second transition is accompanied by a dramatic reduction in the electrical resistivity. Thus, the magnetic and electronic degrees of freedom in YbRh3Si7 are strongly coupled. We discuss the origin of the anomalous metamagnetism and conclude that it is related to competition between crystal electric field anisotropy and anisotropic exchange interactions.Comment: 23 pages and 4 figures in the main text. 7 pages and 5 figures in the supplementary materia

Latexin expression is downregulated in human gastric carcinomas and exhibits tumor suppressor potential

<p>Abstract</p> <p>Background</p> <p>Latexin, also known as endogenous carboxypeptidase inhibitor (CPI), has been found to inhibit mouse stem cell populations and lymphoma cell proliferation, demonstrating its potential role as a tumor suppressor. Our previous study also suggested a correlation between latexin expression and malignant transformation of immortalized human gastric epithelial cells. Here, we examined latexin expression in human gastric carcinomas and investigated the effect of differential latexin expression on proliferation of gastric cancer cells <it>in vitro </it>and <it>in vivo</it>.</p> <p>Methods</p> <p>Monoclonal antibody against human latexin was prepared and immunohistochemical analysis was performed to detect latexin expression in 41 paired gastric carcinomas and adjacent normal control tissues. Human gastric cancer cells MGC803 (latexin negative) stably transfected with LXN gene and BGC823 cells (latexin positive) stably transfected with antisense LXN gene were established for anchorage-dependent colony formation assay and tumorigenesis assay in nude mice. Differentially expressed genes in response to exogeneous latexin expression were screened using microarray analysis and identified by RT-PCR. Bisulfite sequencing was performed to analyze the correlation of the methylation status of LXN promoter with latexin expression in cell lines.</p> <p>Results</p> <p>Immunohistochemical analysis showed significantly reduced latexin expression in gastric carcinomas (6/41, 14.6%) compared to control tissues (31/41, 75.6%) (<it>P </it>< 0.05). Overexpression of LXN gene in MGC803 cells inhibited colony formation and tumor growth in nude mice. Conversely, BGC823 cells transfected with antisense LXN gene exhibited enhanced tumor growth and colony formation. Additionally, several tumor related genes, including Maspin, WFDC1, SLPI, S100P, and PDGFRB, were shown to be differentially expressed in MGC803 cells in response to latexin expression. Differential expression of Maspin and S100P was also identified in BGC823 cells while latexin expression was downregulated. Further bisulfite sequencing of the LXN gene promoter indicated CpG hypermethylation was correlated with silencing of latexin expression in human cells.</p> <p>Conclusions</p> <p>Latexin expression was reduced in human gastric cancers compared with their normal control tissues. The cellular and molecular evidences demonstrated the inhibitory effect of latexin in human gastric cancer cell growth and tumorigenicity. These results strongly suggest the possible involvement of latexin expression in tumor suppression.</p

MTSS1/Src family kinase Dysregulation Underlies Multiple Inherited Ataxias

The genetically heterogeneous spinocerebellar ataxias (SCAs) are caused by Purkinje neuron dysfunction and degeneration, but their underlying pathological mechanisms remain elusive. The Src family of nonreceptor tyrosine kinases (SFK) are essential for nervous system homeostasis and are increasingly implicated in degenerative disease. Here we reveal that the SFK suppressor Missing-in-metastasis (MTSS1) is an ataxia locus that links multiple SCAs. MTSS1 loss results in increased SFK activity, reduced Purkinje neuron arborization, and low basal firing rates, followed by cell death. Surprisingly, mouse models for SCA1, SCA2, and SCA5 show elevated SFK activity, with SCA1 and SCA2 displaying dramatically reduced MTSS1 protein levels through reduced gene expression and protein translation, respectively. Treatment of each SCA model with a clinically approved Src inhibitor corrects Purkinje neuron basal firing and delays ataxia progression in MTSS1 mutants. Our results identify a common SCA therapeutic target and demonstrate a key role for MTSS1/SFK in Purkinje neuron survival and ataxia progression

Systematic assessment of long-read RNA-seq methods for transcript identification and quantification

The Long-read RNA-Seq Genome Annotation Assessment Project (LRGASP) Consortium was formed to evaluate the effectiveness of long-read approaches for transcriptome analysis. The consortium generated over 427 million long-read sequences from cDNA and direct RNA datasets, encompassing human, mouse, and manatee species, using different protocols and sequencing platforms. These data were utilized by developers to address challenges in transcript isoform detection and quantification, as well as de novo transcript isoform identification. The study revealed that libraries with longer, more accurate sequences produce more accurate transcripts than those with increased read depth, whereas greater read depth improved quantification accuracy. In well-annotated genomes, tools based on reference sequences demonstrated the best performance. When aiming to detect rare and novel transcripts or when using reference-free approaches, incorporating additional orthogonal data and replicate samples are advised. This collaborative study offers a benchmark for current practices and provides direction for future method development in transcriptome analysis