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《Information processing & management》2023,60(5):103475
Effective passage retrieval is crucial for conversation question answering (QA) but challenging due to the ambiguity of questions. Current methods rely on the dual-encoder architecture to embed contextualized vectors of questions in conversations. However, this architecture is limited in the embedding bottleneck and the dot-product operation. To alleviate these limitations, we propose generative retrieval for conversational QA (GCoQA). GCoQA assigns distinctive identifiers for passages and retrieves passages by generating their identifiers token-by-token via the encoder–decoder architecture. In this generative way, GCoQA eliminates the need for a vector-style index and could attend to crucial tokens of the conversation context at every decoding step. We conduct experiments on three public datasets over a corpus containing about twenty million passages. The results show GCoQA achieves relative improvements of +13.6% in passage retrieval and +42.9% in document retrieval. GCoQA is also efficient in terms of memory usage and inference speed, which only consumes 1/10 of the memory and takes in less than 33% of the time. The code and data are released at https://github.com/liyongqi67/GCoQA. 相似文献
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《Information processing & management》2022,59(3):102891
Syntax parse trees are a method of representing sentence structure and are often used to provide models with syntax information and enhance downstream task performance. Because grammar and syntax are inherently linked, the incorporation of syntax parse trees in GEC is a natural solution. In this work, we present a method of incorporating syntax parse trees for Grammatical Error Correction (GEC). Building off a strong sequence-to-sequence Transformer baseline, we present a unified parse integration method for GEC that allows for the use of both dependency and constituency parse trees, as well as their combination - a syntactic graph. Specifically, on the sentence encoder, we propose a graph encoder that can encode dependency trees and constituent trees at the same time, yielding two representations for terminal nodes (i.e., the token of the sentence) and non-terminal nodes. We next use two cross-attentions (NT-Cross-Attention and T-Cross-Attention) to aggregate these source syntactic representations to the target side for final corrections prediction. In addition to evaluating our models on the popular CoNLL-2014 Shared Task and JFLEG GEC benchmarks, we affirm the effectiveness of our proposed method by testing both varying levels of parsing quality and exploring the use of both parsing formalisms. With further empirical exploration and analysis to identify the source of improvement, we found that rich syntax information provided clear clues for GEC; a syntactic graph composed of multiple syntactic parse trees can effectively compensate for the limited quality and insufficient error correction capability of a single syntactic parse tree. 相似文献
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《Information processing & management》2023,60(6):103479
In recent years, Zero-shot Node Classification (ZNC), an emerging and more difficult task is starting to attract attention, where the classes of testing nodes are unobserved in the training stage. Existing studies for ZNC mainly utilize Graph Neural Networks (GNNs) to construct the feature subspace to align with the classes’ semantic subspace, thus enabling knowledge transfer from seen classes to unseen classes. However, the modeling of the node feature is single-view and unilateral, e.g., the bag-of-words vector, which is not enough to fully describe the characteristics of the node itself. To address this dilemma, we propose to develop the Multi-View Enhanced zero-shot node classification paradigm (MVE) to promote the machine’s generality to approach the human-like thinking mode. Specifically, multi-view features are obtained from different aspects such as pre-trained model embeddings, knowledge graphs, statistic methods, and then fused by a contrastive learning module into the compositional node representation. Meanwhile, a developed Graph Convolutional Network (GCN) is used to make the nodes fully absorb the information of neighbors while the over-smooth issue is alleviated by multi-view features and the proposed contrastive learning mechanism. Experimental results conducted on three public datasets show an average 25% improvement compared to baseline methods, proving the superiority of our multi-view learning framework. The code and data can be found at https://github.com/guaiqihen/MVE. 相似文献
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Caffeic acid (CA; 3,4-dihydroxycinnamic acid) is an aromatic compound obtained by the phenylpropanoid pathway. This natural product has antioxidant, antitumor, antiviral, and anti-inflammatory activities. It is also a precursor of CA phenethyl ester (CAPE), a compound with potential as an antidiabetic and liver-protective agent. CA can be found at low concentrations in plant tissues, and hence, its purification is difficult and expensive. Knowledge regarding the pathways, enzymes, and genes involved in CA biosynthesis has paved the way for enabling the design and construction of microbial strains with the capacity of synthesizing this metabolite. In this review, metabolic engineering strategies for the generation of Escherichia coli strains for the biotechnological production of CA are presented and discussed.How to cite: Hernández-Chávez G, Martinez A, Gosset G. Metabolic engineering strategies for caffeic acid production in Escherichia coli. Electron J Biotechnol 2019;38. https://doi.org/10.1016/j.ejbt.2018.12.004. 相似文献
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BackgroundButyrate is a histone deacetylase inhibitor that induces apoptosis and inhibits cell proliferation of colorectal cancer cells. To improve its anticancer activity, butyrate has been evaluated mixed with drugs and different molecules. Plant antimicrobial peptides are attractive anticancer alternative molecules because they show selective cytotoxic activity against different cancer cell lines. In this work, we explore if the plant defensin γ-thionin (Capsicum chinense) can improve butyrate activity on Caco-2 cell line and we also determined the mechanism of death activated.ResultsThe combined treatment of γ-thionin (3.5 µM) and butyrate (50 mM) showed higher cytotoxicity on Caco-2 cells with respect to single treatments. Also, the combined treatment reduced cell proliferation and exhibited a higher rate of apoptosis than single treatments. Combined treatment induced caspases 8 and 9 activation to an extent comparable with that of butyrate while γ-thionin did not activate caspases. Additionally, reactive oxygen species generation preceded the onset of apoptosis, and superoxide anion production was higher in cells treated with the combined treatment.ConclusionsThe γ-thionin from Habanero chili pepper improved the butyrate cytotoxicity on Caco-2 cells. This effect occurred through apoptosis induction associated with reactive oxygen species production. Therefore, the combination of butyrate with cytotoxic antimicrobial peptides could be an attractive strategy for cancer therapy.How to cite: Velázquez-Hernández ME, Ochoa-Zarzosa A, López-Meza JE, Defensin γ-thionin from Capsicum chinense improves butyrate cytotoxicity on human colon adenocarcinoma cell line Caco-2. Electron J Biotechnol 2021;52. https://doi.org/10.1016/j.ejbt.2021.04.009 相似文献
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BackgroundSalep is obtained by grinding dried orchid tubers and used as a valuable ingredient in the food industry. Because of the glucomannan content of salep, it is thought to have prebiotic potential. However, there is little information in studies concerning the fermentation characteristics and potential prebiotic properties of salep. The objective of this study was to investigate the effect of salep on bifidobacterial growth by measuring the highest optical density (OD), calculating the specific growth rates, and determining the production of lactic acid and short-chain fatty acids (acetic, propionic, and butyric acid) as a result of bacterial fermentation.ResultThe OD and pH values obtained in this study showed that salep was utilized as a source of assimilable carbon and energy by the Bifidobacterium species (BS). All Bifidobacterium strains produced lactic, acetic, propionic, and butyric acid, indicating that salep is readily fermented by these bacteria. Salep at 1% (w/v) showed a similar effect on bifidobacterial growth as that promoted by 1% (w/v) glucose used as a traditional carbon source.ConclusionsBifidobacterium species can develop in media containing salep as well as in glucose and exhibit the potential to be used as new sources of prebiotics.How to cite: Usta-Gorgun B, Yilmaz-Ersan L. Short-chain fatty acid production by the Bifidobacterium species in the presence of salep. Electron J Biotechnol 2020;47. https://doi.org/10.1016/j.ejbt.2020.06.004. 相似文献
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BackgroundPyruvic acid (PA), a vital α-oxocarboxylic acid, plays an important role in energy and carbon metabolism. The oleaginous yeast Yarrowia lipolytica (Y. lipolytica) has considerable potential for the production of PA. An increased NaCl concentration reportedly increases the biomass and PA yield of Y. lipolytica.ResultsTo increase the yield of PA, the NaCl-tolerant Y. lipolytica A4 mutant was produced using the atmospheric and room temperature plasma method of mutation. The A4 mutant showed growth on medium containing 160 g/L NaCl. The PA yield of the A4 mutant reached 97.2 g/L at 120 h (0.795 g/g glycerol) in a 20-L fermenter with glycerol as the sole carbon source, which was 28.9% higher than that of the parental strain.ConclusionThe PA yield from Y. lipolytica can be improved by increasing its NaCl tolerance.How to cite: Yuan W, Lin X, Zhong S, et al. Enhanced pyruvic acid yield in an osmotic stress-resistant mutant of Yarrowia lipolytica. Electron J Biotechnol 2020;44. https://doi.org/10.1016/j.ejbt.2020.01.002. 相似文献
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BackgroundChia seeds are gaining increasing interest among food producers and consumers because of their prohealth properties.ResultsThe aim of this work was to evaluate the potential of chia seeds to act as acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) inhibitors. The highest inhibitory activity against AChE and BChE was observed for colored seed ethanol extracts. A positive correlation was found between the presence of quercetin and isoquercetin as well as protocatechuic, hydroxybenzoic, and coumaric acids and the activity of extracts as AChE and BChE inhibitors. It has also been shown that grain fragmentation affects the increase in the activity of seeds against cholinesterases (ChE). Furthermore, seeds have been shown to be a source of substances that inhibit microbial growth.ConclusionsIt was found that the chia seed extracts are rich in polyphenols and inhibit the activity of ChEs; therefore, their use can be considered in further research in the field of treatment and prevention of neurodegenerative diseases.How to cite: Kobus-Cisowska J, Szymanowska D, Maciejewska P, et al. In vitro screening for acetylcholinesterase and butyrylcholinoesterase inhibition and antimicrobial activity of chia seeds (Salvia hispanica). Electron J Biotechnol 2019;37. https://doi.org/10.1016/j.ejbt.2018.10.002 相似文献
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BackgroundCollagen is the most abundant protein in animals and can be obtained from residues of the food industry. Its hydrolysate has many desirable properties that make it suitable as an additive in foods and cosmetics, or as a component of scaffold materials to be used in biomedicine.ResultsWe report here the characterization of type I collagen from five different sources, namely bovine, porcine, chicken, trout and salmon, as well as their hydrolysates by means of bioinformatics tools. As expected, the results showed that bovine and porcine collagen, as well as trout and salmon collagen, can be used interchangeably due to their high identity. This result is consistent with the evolution of proteins with highly identical sequences between related species. Also, 156 sequences were found as potential bioactive peptides, 126 from propeptide region and 30 from the central domain, according to the comparison with reported active sequences.ConclusionsCollagen analysis from a bioinformatic approach allowed us to classify collagen from 5 different animal sources, to establish its interchangeability as potential additive in diverse fields and also to determine the content of bioactive peptides from its in silico hydrolysis.How to citeNuñez SM, Guzmán F, Valencia P, et al. Collagen as a source of bioactive peptides: a bioinformatics approach. Electron J Biotechnol 2020; 48. https://doi.org/10.1016/j.ejbt.2020.09.009. 相似文献
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Chloroplast biotechnology has emerged as a promissory platform for the development of modified plants to express products aimed mainly at the pharmaceutical, agricultural, and energy industries. This technology’s high value is due to its high capacity for the mass production of proteins. Moreover, the interest in chloroplasts has increased because of the possibility of expressing multiple genes in a single transformation event without the risk of epigenetic effects. Although this technology solves several problems caused by nuclear genetic engineering, such as turning plants into safe bio-factories, some issues must still be addressed in relation to the optimization of regulatory regions for efficient gene expression, cereal transformation, gene expression in non-green tissues, and low transformation efficiency. In this article, we provide information on the transformation of plastids and discuss the most recent achievements in chloroplast bioengineering and its impact on the biopharmaceutical and agricultural industries; we also discuss new tools that can be used to solve current challenges for their successful establishment in recalcitrant crops such as monocots.How to cite: Quintín Rascón-Cruz Q, González-Barriga CD, Iglesias-Figueroa BF, et al. Plastid transformation: Advances and challenges for its implementation in agricultural crops. Electron J Biotechnol 2021;51. https://doi.org/10.1016/j.ejbt.2021.03.005 相似文献
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Azotobacter vinelandii is a gram-negative soil bacterium that produces two biopolymers of biotechnological interest, alginate and poly(3-hydroxybutyrate), and it has been widely studied because of its capability to fix nitrogen even in the presence of oxygen. This bacterium is characterized by its high respiration rates, which are almost 10-fold higher than those of Escherichia coli and are a disadvantage for fermentation processes. On the other hand, several works have demonstrated that adequate control of the oxygen supply in A. vinelandii cultivations determines the yields and physicochemical characteristics of alginate and poly(3-hydroxybutyrate).Here, we summarize a review of the characteristics of A. vinelandii related to its respiration systems, as well as some of the most important findings on the oxygen consumption rates as a function of the cultivation parameters and biopolymer production.How to cite: Castillo T, García A, Padilla-Córdova C, et al. Respiration in Azotobacter vinelandii and its relationship with the synthesis of biopolymers. Electron J Biotechnol 2020;48. https://doi.org/10.1016/j.ejbt.2020.08.001 相似文献
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Since more than twenty years ago, some species of bacteria and fungi have been used to produce protein biomass or single-cell protein (SCP), with inexpensive feedstock and wastes being used as their sources of carbon and energy. The role of SCP as a safe food and feed is being highlighted more because of the worldwide protein scarcity. Even though SCP has been successfully commercialized in the UK for decades, study of optimal fermentation conditions, various potential substrates, and a broad range of microorganisms is still being pursued by many researchers. In this article, commonly used methods for the production of SCP and different fermentation systems are briefly reviewed, with submerged fermentation being highlighted as a more commonly used method. Emphasis is given to the effect of influencing factors on the biomass yield and productivity in an effort to provide a comprehensive review for researchers in related fields of interest.How to cite: Reihani SFS, Khosravi-Darani K. Influencing factors on single cell protein production by submerged fermentation: A review. Electron J Biotechnol 2019;37. https://doi.org/10.1016/j.ejbt.2018.11.005. 相似文献
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BackgroundBiologically active peptides produced from fish wastes are gaining attention because their health benefits. Proteases produced by halophilic microorganisms are considered as a source of active enzymes in high salt systems like fish residues. Hence, the aim of this study was the bioprospection of halophilic microorganisms for the production of proteases to prove their application for peptide production.ResultsHalophilic microorganisms were isolated from saline soils of Mexico and Bolivia. An enzymatic screening was carried out for the detection of lipases, esterases, pHB depolymerases, chitinases, and proteases. Most of the strains were able to produce lipases, esterases, and proteases, and larger hydrolysis halos were detected for protease activity. Halobacillus andaensis was selected to be studied for proteolytic activity production; the microorganism was able to grow on gelatin, yeast extract, skim milk, casein, peptone, fish muscle (Cyprinus carpio), and soy flour as protein sources, and among these sources, fish muscle protein was the best inducer of proteolytic activity, achieving a protease production of 571 U/mL. The extracellular protease was active at 50°C, pH 8, and 1.4 M NaCl and was inhibited by phenylmethylsulfonyl fluoride. The proteolytic activity of H. andaensis was used to hydrolyze fish muscle protein for peptide production. The peptides obtained showed a MW of 5.3 kDa and a radical scavenging ability of 10 to 30% on 2,2-diphenyl-1-picrylhydrazyl and 2,2-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) and a ferric reducing ability of plasma.ConclusionThe use of noncommercial extracellular protease produced by H. andaensis for biologically active peptide production using fish muscle as the protein source presents a great opportunity for high-value peptide production.How to cite: Delgado-García M, Flores-Gallegos AC, Kirchmayr M, et al. Bioprospection of proteases from Halobacillus andaensis for bioactive peptide production from fish muscle protein. Electron J Biotechnol 2019;39. https://doi.org/10.1016/j.ejbt.2019.03.001. 相似文献
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BackgroundMilk whey, a byproduct of the dairy industry has a negative environmental impact, can be used as a raw material for added-value compounds such as galactooligosaccharides (GOS) synthesis by β-galactosidases.ResultsB-gal42 from Pantoea anthophila strain isolated from tejuino belonging to the glycosyl hydrolase family GH42, was overexpressed in Escherichia coli and used for GOS synthesis from lactose or milk whey. Crude cell-free enzyme extracts exhibited high stability; they were employed for GOS synthesis reactions. In reactions with 400 g/L lactose, the maximum GOS yield was 40% (w/w) measured by HPAEC-PAD, corresponding to 86% of conversion. This enzyme had a strong predilection to form GOS with β(1 → 6) and β(1 → 3) galactosyl linkages. Comparing GOS synthesis between milk whey and pure lactose, both of them at 300 g/L, these two substrates gave rise to a yield of 38% (60% of lactose conversion) with the same product profile determined by HPAEC-PAD.ConclusionsB-gal42 can be used on whey (a cheap lactose source) to produce added value products such as galactooligosaccharides.How to cite: Yañez-Ñeco CV, Cervantes FV, Amaya-Delgado L, et al. Synthesis of β(1→3) and β(1→6) galactooligosaccharides from lactose and whey using a recombinant β-galactosidase from Pantoea anthophila. Electron J Biotechnol 2021;49. https://dx.doi.org/10.1016/j.ejbt.2020.10.004 相似文献
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Science has greatly contributed to the advancement of technology and to the innovation of production processes and their applications. Cleaning products have become indispensable in today’s world, as personal and environmental hygiene is important to all societies worldwide. Such products are used in the home, in most work environments and in the industrial sectors. Most of the detergents on the market are synthesised from petrochemical products. However, the interest in reducing the use of products harmful to human health and the environment has led to the search for detergents formulated with natural, biodegradable surfactant components of biological (plant or microbiological) origin or chemically synthesised from natural raw materials usually referred to as green surfactants. This review addresses the different types, properties, and uses of surfactants, with a focus on green surfactants, and describes the current scenario as well as the projections for the future market economy related to the production of the different types of green surfactants marketed in the world.How to cite: Farias CBB, Almeida FCG, Silva IA, et al. Production of green surfactants: Market prospects. Electron J Biotechnol 2021;51. https://doi.org/10.1016/j.ejbt.2021.02.002 相似文献
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BackgroundTraditionally, microbial genome sequencing has been restrained to the species grown in pure culture. The development of culture-independent techniques over the last decade allows scientists to sequence microbial communities directly from environmental samples. Metagenomics is the study of complex genome by the isolation of DNA of the whole community. Next generation sequencing (NGS) of metagenomic DNA gives information about the microbial and taxonomical characterization of a particular niche. The objective of the present research is to study the microbial and taxonomical characterization of the metagenomic DNA, isolated from the frozen soil sample of a glacier in the north western Himalayas through NGS.ResultsThe glacier community comprised of 16 phyla with the representation of members belonging to Proteobacteria and Acidobacteria. The number of genes annotated through the Kyoto Encyclopedia of Genes and Genomes (KEGG), GO, Pfam, Clusters of Orthologous Groups of proteins (COGs), and FIG databases were generated by COGNIZER. The annotation of genes assigned in each group from the metagenomics data through COG database and the number of genes annotated in different pathways through KEGG database were reported.ConclusionResults indicate that the glacier soil taken in the present study, harbors taxonomically and metabolically diverse communities. The major bacterial group present in the niche is Proteobacteria followed by Acidobacteria, and Actinobacteria, etc. Different genes were annotated through COG and KEGG databases that integrate genomic, chemical, and systemic functional information.How to cite: Gupta V, Singh I, Rasool S, et al. Next Generation sequencing and microbiome’s taxonomical characterization of frozen soil of North Western Himalayas of Jammu and Kashmir, India. Electron J Biotechnol 2020;45. https://doi.org/10.1016/j.ejbt.2020.03.003. 相似文献