Learning "O" Helps for Learning More: Handling the Concealed Entity Problem for Class-incremental NER

As the categories of named entities rapidly increase in real-world applications, class-incremental learning for NER is in demand, which continually learns new entity classes while maintaining the old knowledge. Due to privacy concerns and storage constraints, the model is required to update without any annotations of the old entity classes. However, in each step on streaming data, the "O" class in each step might contain unlabeled entities from the old classes, or potential entities from the incoming classes. In this work, we first carry out an empirical study to investigate the concealed entity problem in class-incremental NER. We find that training with "O" leads to severe confusion of "O" and concealed entity classes, and harms the separability of potential classes. Based on this discovery, we design a rehearsal-based representation learning approach for appropriately learning the "O" class for both old and potential entity classes. Additionally, we provide a more realistic and challenging benchmark for class-incremental NER which introduces multiple categories in each step. Experimental results verify our findings and show the effectiveness of the proposed method on the new benchmark

Mudskipper genomes provide insights into the terrestrial adaptation of amphibious fishes

Mudskippers are amphibious fishes that have developed morphological and physiological adaptations to match their unique lifestyles. Here we perform whole-genome sequencing of four representative mudskippers to elucidate the molecular mechanisms underlying these adaptations. We discover an expansion of innate immune system genes in the mudskippers that may provide defence against terrestrial pathogens. Several genes of the ammonia excretion pathway in the gills have experienced positive selection, suggesting their important roles in mudskippers’ tolerance to environmental ammonia. Some vision-related genes are differentially lost or mutated, illustrating genomic changes associated with aerial vision. Transcriptomic analyses of mudskippers exposed to air highlight regulatory pathways that are up- or down-regulated in response to hypoxia. The present study provides a valuable resource for understanding the molecular mechanisms underlying water-to-land transition of vertebrates

The oyster genome reveals stress adaptation and complexity of shell formation

The Pacific oyster Crassostrea gigas belongs to one of the most species-rich but genomically poorly explored phyla, the Mollusca. Here we report the sequencing and assembly of the oyster genome using short reads and a fosmid-pooling strategy, along with transcriptomes of development and stress response and the proteome of the shell. The oyster genome is highly polymorphic and rich in repetitive sequences, with some transposable elements still actively shaping variation. Transcriptome studies reveal an extensive set of genes responding to environmental stress. The expansion of genes coding for heat shock protein 70 and inhibitors of apoptosis is probably central to the oyster's adaptation to sessile life in the highly stressful intertidal zone. Our analyses also show that shell formation in molluscs is more complex than currently understood and involves extensive participation of cells and their exosomes. The oyster genome sequence fills a void in our understanding of the Lophotrochozoa. © 2012 Macmillan Publishers Limited. All rights reserved

In Situ Fabrication of a Superhydrophobic ORMOSIL Coating on Wood by an Ammonia–HMDS Vapor Treatment

A superhydrophobic ORMOSIL (organically modified silicate) coating was in situ fabricated on a wood surface by ammonia–hexamethylisilazane (HMDS) vapor treatment. The wood was immerged in tetraethoxysilane (TEOS), and then the TEOS absorbed on the wood surface was hydrolyzed and condensed to hydrophobic SiO2 nanoparticles with ammonia and HDMS vapor treatment. The effect of the treatment temperature and time on the hydrophobicity of wood was investigated. At a treatment temperature of 50 °C, a superhydrophobic surface was achieved on the wood with a treatment time longer than 2 h. SEM images indicated that there were SiO2 nanoparticles fabricated on the wood surface, and FTIR revealed that the hydrophobic –Si(CH3)3 groups were incorporated on the wood surface. The ORMOSIL-modified wood possessed improved liquid repellency. The water absorption decreased significantly from 72.3% to 31.9% after modification

Vector Spatial Big Data Storage and Optimized Query Based on the Multi-Level Hilbert Grid Index in HBase

Faced with the rapid growth of vector data and the urgent requirement of low-latency query, it has become an important and timely challenge to effectively achieve the scalable storage and efficient access of vector big data. However, a systematic method is rarely seen for vector polygon data storage and query taking spatial locality into account in the storage schema, index construction and query optimization. In the paper, we focus on the storage and topological query of vector polygon geometry data in HBase, and the rowkey in the HBase table is the concatenation of the Hilbert value of the grid cell to which the center of the object entity’s MBR belongs, the layer identifier and the order code. Then, a new multi-level grid index structure, termed Q-HBML, that incorporates the grid-object spatial relationship and a new Hilbert hierarchical code into the multi-level grid, is proposed for improving the spatial query efficiency. Finally, based on the Q-HBML index, two query optimization strategies and an optimized topological query algorithm, ML-OTQ, are presented to optimize the topological query process and enhance the topological query efficiency. Through four groups of comparative experiments, it has been proven that our approach supports better performance

The Synaptic Vesicle Protein 2A Interacts With Key Pathogenic Factors in Alzheimer's Disease: Implications for Treatment

Alzheimer’s disease (AD), a serious neurodegenerative disease, is pathologically characterized by synaptic loss and dysfunction. Synaptic vesicle protein 2A (SV2A) is an indispensable vesicular protein specifically expressed in synapses and can be used as a biomarker for synaptic density. We found that the expression of SV2A was down-regulated in the hippocampus of AD patients, yet the relation of SV2A to other hallmarks of AD pathology such as amyloid precursor protein (APP), β-amyloid (Aβ), and Tau protein is not thoroughly clear. In addition, SV2A colocalized with APP and was down-regulated at Aβ deposition. Moreover, we found that SV2A deficiency leads to a simultaneous increase in Aβ and Tau hyperphosphorylation, while SV2A overexpression was associated with downregulation of β-site APP cleaving enzyme 1 and apolipoprotein E genes. In addition, evidence gained in the study points to the phosphatidylinositol 3-kinase signaling pathway as a possible mediator in SV2A regulation influencing the incidence and development of AD. With limited effective diagnostic methods for AD, a close interplay between SV2A and AD-related proteins demonstrated in our study may provide novel and innovative diagnostic and therapeutic opportunities.ISSN:2296-634

Data_Sheet_1_Phage-prokaryote coexistence strategy mediates microbial community diversity in the intestine and sediment microhabitats of shrimp culture pond ecosystem.docx

Emerging evidence supports that the phage-prokaryote interaction drives ecological processes in various environments with different phage life strategies. However, the knowledge of phage-prokaryote interaction in the shrimp culture pond ecosystem (SCPE) is still limited. Here, the viral and prokaryotic community profiles at four culture stages in the intestine of Litopenaeus vannamei and cultural sediment microhabitats of SCPE were explored to elucidate the contribution of phage-prokaryote interaction in modulating microbial communities. The results demonstrated that the most abundant viral families in the shrimp intestine and sediment were Microviridae, Circoviridae, Inoviridae, Siphoviridae, Podoviridae, Myoviridae, Parvoviridae, Herelleviridae, Mimiviridae, and Genomoviridae, while phages dominated the viral community. The dominant prokaryotic genera were Vibrio, Formosa, Aurantisolimonas, and Shewanella in the shrimp intestine, and Formosa, Aurantisolimonas, Algoriphagus, and Flavobacterium in the sediment. The viral and prokaryotic composition of the shrimp intestine and sediment were significantly different at four culture stages, and the phage communities were closely related to the prokaryotic communities. Moreover, the phage-prokaryote interactions can directly or indirectly modulate the microbial community composition and function, including auxiliary metabolic genes and closed toxin genes. The interactional analysis revealed that phages and prokaryotes had diverse coexistence strategies in the shrimp intestine and sediment microhabitats of SCPE. Collectively, our findings characterized the composition of viral communities in the shrimp intestine and cultural sediment and revealed the distinct pattern of phage-prokaryote interaction in modulating microbial community diversity, which expanded our cognization of the phage-prokaryote coexistence strategy in aquatic ecosystems from the microecological perspective and provided theoretical support for microecological prevention and control of shrimp culture health management.</p

Genome and Transcriptome Analysis of the Fungal Pathogen <i>Fusarium oxysporum</i> f. sp. <i>cubense</i> Causing Banana Vascular Wilt Disease

<div><p>Background</p><p>The asexual fungus <i>Fusarium oxysporum</i> f. sp. <i>cubense</i> (Foc) causing vascular wilt disease is one of the most devastating pathogens of banana (<i>Musa</i> spp.). To understand the molecular underpinning of pathogenicity in Foc, the genomes and transcriptomes of two Foc isolates were sequenced.</p><p>Methodology/Principal Findings</p><p>Genome analysis revealed that the genome structures of race 1 and race 4 isolates were highly syntenic with those of <i>F. oxysporum</i> f. sp. <i>lycopersici</i> strain Fol4287. A large number of putative virulence associated genes were identified in both Foc genomes, including genes putatively involved in root attachment, cell degradation, detoxification of toxin, transport, secondary metabolites biosynthesis and signal transductions. Importantly, relative to the Foc race 1 isolate (Foc1), the Foc race 4 isolate (Foc4) has evolved with some expanded gene families of transporters and transcription factors for transport of toxins and nutrients that may facilitate its ability to adapt to host environments and contribute to pathogenicity to banana. Transcriptome analysis disclosed a significant difference in transcriptional responses between Foc1 and Foc4 at 48 h post inoculation to the banana ‘Brazil’ in comparison with the vegetative growth stage. Of particular note, more virulence-associated genes were up regulated in Foc4 than in Foc1. Several signaling pathways like the mitogen-activated protein kinase Fmk1 mediated invasion growth pathway, the FGA1-mediated G protein signaling pathway and a pathogenicity associated two-component system were activated in Foc4 rather than in Foc1. Together, these differences in gene content and transcription response between Foc1 and Foc4 might account for variation in their virulence during infection of the banana variety ‘Brazil’.</p><p>Conclusions/Significance</p><p>Foc genome sequences will facilitate us to identify pathogenicity mechanism involved in the banana vascular wilt disease development. These will thus advance us develop effective methods for managing the banana vascular wilt disease, including improvement of disease resistance in banana.</p></div

Spider genomes provide insight into composition and evolution of venom and silk

Spiders are ecologically important predators with complex venom and extraordinarily tough silk that enables capture of large prey. Here we present the assembled genome of the social velvet spider and a draft assembly of the tarantula genome that represent two major taxonomic groups of spiders. The spider genomes are large with short exons and long introns, reminiscent of mammalian genomes. Phylogenetic analyses place spiders and ticks as sister groups supporting polyphyly of the Acari. Complex sets of venom and silk genes/proteins are identified. We find that venom genes evolved by sequential duplication, and that the toxic effect of venom is most likely activated by proteases present in the venom. The set of silk genes reveals a highly dynamic gene evolution, new types of silk genes and proteins, and a novel use of aciniform silk. These insights create new opportunities for pharmacological applications of venom and biomaterial applications of silk