Joint Language Semantic and Structure Embedding for Knowledge Graph Completion

The task of completing knowledge triplets has broad downstream applications. Both structural and semantic information plays an important role in knowledge graph completion. Unlike previous approaches that rely on either the structures or semantics of the knowledge graphs, we propose to jointly embed the semantics in the natural language description of the knowledge triplets with their structure information. Our method embeds knowledge graphs for the completion task via fine-tuning pre-trained language models with respect to a probabilistic structured loss, where the forward pass of the language models captures semantics and the loss reconstructs structures. Our extensive experiments on a variety of knowledge graph benchmarks have demonstrated the state-of-the-art performance of our method. We also show that our method can significantly improve the performance in a low-resource regime, thanks to the better use of semantics. The code and datasets are available at https://github.com/pkusjh/LASS.Comment: COLING 202

Adaptive neural network control of a robotic manipulator with unknown backlash-like hysteresis

This study proposes an adaptive neural network controller for a 3-DOF robotic manipulator that is subject to backlashlike hysteresis and friction. Two neural networks are used to approximate the dynamics and the hysteresis non-linearity. A neural network, which utilises a radial basis function approximates the robot's dynamics. The other neural network, which employs a hyperbolic tangent activation function, is used to approximate the unknown backlash-like hysteresis. The authors also consider two cases: full state and output feedback control. For output feedback, where system states are unknown, a high gain observer is employed to estimate the states. The proposed controllers ensure the boundedness of the control signals. Simulations are also performed to show the effectiveness of the controllers

catena-Poly[cobalt(II)-bis­(μ-3,7-dichloro­quinoline-8-carboxyl­ato-κ3 N,O:O′)]

In the crystal structure of the title compound, [Co(C10H4Cl2NO2)2]n, the CoII cation lies on a twofold rotation axis. Each cation is N,O-chelated by the carboxyl­ate anions of two 3,7-dichloro­quinoline-8-carboxyl­ate ligands. The second carboxyl­ate O atom of each ligand coordinates to the CoII cation of an adjacent mol­ecule, linking the cations into a linear chain. Strong inter­chain π–π stacking inter­actions are observed in the crystal structure (perpendicular distance 3.42 Å, centroid-to-centroid distance 3.874 Å

Depletion of pre-mRNA splicing factor Cdc5L inhibits mitotic progression and triggers mitotic catastrophe.

Disturbing mitotic progression via targeted anti-mitotic therapy is an attractive strategy for cancer treatment. Therefore, the exploration and elucidation of molecular targets and pathways in mitosis are critical for the development of anti-mitotic drugs. Here, we show that cell division cycle 5-like (Cdc5L), a pre-mRNA splicing factor, is a regulator of mitotic progression. Depletion of Cdc5L causes dramatic mitotic arrest, chromosome misalignments and sustained activation of spindle assembly checkpoint, eventually leading to mitotic catastrophe. Moreover, these defects result from severe impairment of kinetochore-microtubule attachment and serious DNA damage. Genome-wide gene expression analysis reveals that Cdc5L modulates the expression of a set of genes involved in the mitosis and the DNA damage response. We further found that the pre-mRNA splicing efficiency of these genes were impaired when Cdc5L was knocked down. Interestingly, Cdc5L is highly expressed in cervical tumors and osteosarcoma. Finally, we demonstrate that downregulation of Cdc5L decreases the cell viability of related tumor cells. These results suggest that Cdc5L is a key regulator of mitotic progression and highlight the potential of Cdc5L as a target for cancer therapy

Implementation of trait-based ozone plant sensitivity in the Yale interactive terrestrial biosphere model v1.0 to assess global vegetation damage

A major limitation in modeling global ozone (O3) vegetation damage has long been the reliance on empiri- cal O3 sensitivity parameters derived from a limited num- ber of species and applied at the level of plant functional types (PFTs), which ignore the large interspecific variations within the same PFT. Here, we present a major advance in large-scale assessments of O3 plant injury by linking the trait leaf mass per area (LMA) and plant O3 sensitivity in a broad and global perspective. Application of the new ap- proach and a global LMA map in a dynamic global veg- etation model reasonably represents the observed interspe- cific responses to O3 with a unified sensitivity parameter for all plant species. Simulations suggest a contemporary global mean reduction of 4.8 % in gross primary productivity by O3, with a range of 1.1 %–12.6 % for varied PFTs. Hotspots with damage > 10 % are found in agricultural areas in the eastern US, western Europe, eastern China, and India, accompanied by moderate to high levels of surface O3. Furthermore, we simulate the distribution of plant sensitivity to O3, which is highly linked with the inherent leaf trait trade-off strategies of plants, revealing high risks for fast-growing species with low LMA, such as crops, grasses, and deciduous trees

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Staufen1-Mediated mRNA Decay in Mammalian Cells

Thesis (Ph.D.)--University of Rochester. School of Medicine & Dentistry. Dept. of Biochemistry and Biophysics, 2012.Staufen1 (STAU1) is a double-stranded RNA-binding protein. In mammals, STAU1 binding to the 3'-untranslated region (3'UTR) of mRNAs that contain a STAU1- binding site (SBS) results in recruitment of the ATP-dependent helicase UPF1. As a consequence, STAU1-mediated mRNA decay (SMD) occurs when translation terminates normally. UPF1 also plays a key role in nonsense-mediated mRNA decay (NMD). NMD generally targets mRNAs that prematurely terminate translation as a means of quality control. However, NMD also provides for proper regulation of certain physiologic mRNAs. STAU1 binds to the CH domain of UPF1, which is the same region that binds the NMD factor UPF2. Various experiments have proved that STAU1 and UPF2 compete for UPF1 binding, which leads to competition between SMD and NMD. During the differentiation of C2C12 myoblasts (MBs) into myotubes (MTs), the STAU1-to-UPF2 ratio is increased. Due to competition between SMD and NMD, the SMD efficiency increases and, concomitantly, the NMD efficiency decreases in MTs compared to MBs. The increased efficiency of SMD contributes to the downregulation of the SMD target PAX3 mRNA, which encodes a transcriptional factor that maintains MBs in an undifferentiated status. The decreased efficiency of NMD contributes to the upregulation of the NMD target myogenin mRNA, which encodes another transcriptional factor that is essential for differentiation. Besides the physiological importance of SMD, defining the properties of SBSs is an open question. The best characterized SBS derives from the 3'UTR of mRNA encoding ADP-ribosylation factor 1 (ARF1). The ARF1 SBS contains a conserved 19-bp stem that, together with its 100-nt apex, is critical for STAU1 binding. Besides the SBSs that are formed by intramolecular base-pairing, a group of SBSs are formed by intermolecular base-pairing between the 3'UTR Alu element of an SMD target and the Alu element within a long noncoding RNA (lncRNA), which we have called a ½- sbsRNA. One SMD target can be targeted by multiple ½-sbsRNAs, and a single ½- sbsRNA can target multiple SMD targets. Data suggest that intermolecular SBSs can also be formed by base-pairing of the 3'UTR Alu elements of different SMD targets (i.e. mRNA‒mRNA duplex). This finding expands the complicated mRNA regulatory network and enriches the function of mRNAs beyond encoding protein

mRNA-mRNA duplexes that autoelicit Staufen1-mediated mRNA decay

deca