Recently, automatically extracting biomedical relations has been a significant subject in biomedical research due to the rapid growth of biomedical literature. Since the adaptation to the biomedical ...domain, the transformer-based BERT models have produced leading results on many biomedical natural language processing tasks. In this work, we will explore the approaches to improve the BERT model for relation extraction tasks in both the pre-training and fine-tuning stages of its applications. In the pre-training stage, we add another level of BERT adaptation on sub-domain data to bridge the gap between domain knowledge and task-specific knowledge. Also, we propose methods to incorporate the ignored knowledge in the last layer of BERT to improve its fine-tuning.
The experiment results demonstrate that our approaches for pre-training and fine-tuning can improve the BERT model performance. After combining the two proposed techniques, our approach outperforms the original BERT models with averaged F1 score improvement of 2.1% on relation extraction tasks. Moreover, our approach achieves state-of-the-art performance on three relation extraction benchmark datasets.
The extra pre-training step on sub-domain data can help the BERT model generalization on specific tasks, and our proposed fine-tuning mechanism could utilize the knowledge in the last layer of BERT to boost the model performance. Furthermore, the combination of these two approaches further improves the performance of BERT model on the relation extraction tasks.
From celestial objects to every feature on Earth, geodesy provides a reference frame and is the foundation for surveying, mapping, and other geoscience activities. In Nepal, geodesy was officially ...introduced after 1924 to prepare the topographic map series. Although the previous geodetic project occurred with foreign assistance, Nepal is using national resources to conduct milestone projects such as the re-measurement of Mount Everest height in 2020 and the ongoing LiDAR survey of western Terai. Taking the 2015 Gorkha earthquake as a reference, this paper reviews the past and present geodetic activities in Nepal. It presents the history of conventional Nepal datum as a horizontal datum and Indian mean sea level-based vertical datum, and modern satellite geodesy works on the Himalayas. Considering recent earthquakes, continuous crustal motion, international and global compliance, and increasing demand for precise positional accuracy from the users and stakeholders, this paper discusses future directions to build, establish, maintain, and operate modern terrestrial, height, and gravity reference systems and frames. This paper consolidates many reports and experiences from Nepal and will serve as useful documentation for newcomers whose interests align in geodesy and Nepal.
Chinese hamster ovary (CHO) cells are widely used for mass production of therapeutic proteins in the pharmaceutical industry. With the growing need in optimizing the performance of producer CHO cell ...lines, research on CHO cell line development and bioprocess continues to increase in recent decades. Bibliographic mapping and classification of relevant research studies will be essential for identifying research gaps and trends in literature. To qualitatively and quantitatively understand the CHO literature, we have conducted topic modeling using a CHO bioprocess bibliome manually compiled in 2016, and compared the topics uncovered by the Latent Dirichlet Allocation (LDA) models with the human labels of the CHO bibliome. The results show a significant overlap between the manually selected categories and computationally generated topics, and reveal the machine-generated topic-specific characteristics. To identify relevant CHO bioprocessing papers from new scientific literature, we have developed supervized models using Logistic Regression to identify specific article topics and evaluated the results using three CHO bibliome datasets, Bioprocessing set, Glycosylation set, and Phenotype set. The use of top terms as features supports the explainability of document classification results to yield insights on new CHO bioprocessing papers.
Significant progress has been made in applying deep learning on natural language processing tasks recently. However, deep learning models typically require a large amount of annotated training data ...while often only small labeled datasets are available for many natural language processing tasks in biomedical literature. Building large-size datasets for deep learning is expensive since it involves considerable human effort and usually requires domain expertise in specialized fields. In this work, we consider augmenting manually annotated data with large amounts of data using distant supervision. However, data obtained by distant supervision is often noisy, we first apply some heuristics to remove some of the incorrect annotations. Then using methods inspired from transfer learning, we show that the resulting models outperform models trained on the original manually annotated sets.
Driven by the rapid growth of wireless devices and their need for innovative technologies to facilitate a Gigabit-per-second (Gbps) connectivity, visible light communication (VLC) has arisen as a ...candidate solution. However, the rapid growth of wireless devices necessitates the use of multiple access (MA) techniques to support multi-user Gbps connectivity. In this work, we consider non-orthogonal multiple access (NOMA) as a candidate MA technique for the downlink VLC systems and focus on grouping multiple users so that they can share the same resources. For the same, we propose two multi-user grouping schemes, which exploit the principles of power domain NOMA by maximizing the channel gain differences across the users in a group. The analytical and empirical results corroborate that the proposed schemes can be utilized to group multiple users and improve the overall achievable sum rate.
Abstract
Protein post-translational modifications (PTMs) play a pivotal role in numerous biological processes by modulating regulation of protein function. We have developed iPTMnet ...(http://proteininformationresource.org/iPTMnet) for PTM knowledge discovery, employing an integrative bioinformatics approach-combining text mining, data mining, and ontological representation to capture rich PTM information, including PTM enzyme-substrate-site relationships, PTM-specific protein-protein interactions (PPIs) and PTM conservation across species. iPTMnet encompasses data from (i) our PTM-focused text mining tools, RLIMS-P and eFIP, which extract phosphorylation information from full-scale mining of PubMed abstracts and full-length articles; (ii) a set of curated databases with experimentally observed PTMs; and iii) Protein Ontology that organizes proteins and PTM proteoforms, enabling their representation, annotation and comparison within and across species. Presently covering eight major PTM types (phosphorylation, ubiquitination, acetylation, methylation, glycosylation, S-nitrosylation, sumoylation and myristoylation), iPTMnet knowledgebase contains more than 654 500 unique PTM sites in over 62 100 proteins, along with more than 1200 PTM enzymes and over 24 300 PTM enzyme-substrate-site relations. The website supports online search, browsing, retrieval and visual analysis for scientific queries. Several examples, including functional interpretation of phosphoproteomic data, demonstrate iPTMnet as a gateway for visual exploration and systematic analysis of PTM networks and conservation, thereby enabling PTM discovery and hypothesis generation.
The conventional gold standard diagnostic method for canine demodicosis, the deep skin scrapings (DSS), is traumatic to the animal and appears aggressive in the eyes of the owner. A less invasive, ...sensitive, easy-to-perform and field-oriented diagnostic method for the rapid diagnosis of canine demodicosis is warranted. The present study aimed to develop a rapid less invasive diagnostic method using superglue (cyanoacrylate adhesive) slide impression (SSI). Ninety-seven client-owned dogs presented with clinical symptoms and signs suggestive of demodicosis were examined using SSI for detection of
Demodex
mites. A clean microscope slide was taken and a drop of superglue was placed on the slide. Immediately, the superglue-bearing slide surface was applied to the previously squeezed selected skin lesion with gentle pressure for 30 s. The slide was removed from the skin lesion and a drop of immersion oil was placed over the SSI. Another clean cover slide was applied and examined under the microscope at low-power magnification (× 10 lens). Of the 97 dogs, 90 dogs (92.8%) were detected positive for demodectic mites using the SSI method, whereas 86 (88.7%) dogs were found positive using the DSS technique. The SSI method was found to be equally sensitive to the DSS method. In summary, the SSI method is a new quick, sensitive, easy-to-perform, owner- and animal-friendly, less traumatic and field-oriented diagnostic application for demodicosis in dogs. It can be used for harvesting the live demodectic mites and monitoring miticidal therapies.
Aim
The aim of this study was to identify and characterize promising endophytes capable of enhancing the content of root alkaloids ajmalicine and serpentine in low alkaloid yielding genotype of ...Catharanthus roseus cultivar Prabal and the possible mechanisms involved.
Method and Result
Of the four strains isolated from alkaloid‐rich genotype of C. roseus cultivar Dhawal, endophytic strains CATDLF5 (Curvularia sp.) and CATDLF6 (Choanephora infundibulifera) enhanced serpentine content by 211·7–337·6%, while CATDRF2 (Aspergillus japonicus) and CATDS5 (Pseudomonas sp.) increased the content of ajmalicine by 123·4–203·8% in cultivar Prabal. Upregulated expression of key genes, geraniol 10‐hydroxylase, tryptophan decarboxylase and strictosidine synthase involved in terpenoid indole alkaloid (TIA) biosynthetic pathway was observed in endophyte inoculated plants. Upregulated Octadecanoid‐derivative Responsive Catharanthus AP2/ERF domain transcription activators like ORCA3 while, and downregulation of transcriptional repressor, ZCTs (Cys2/His2‐type zinc finger protein family) enhanced the expression of genes for secondary metabolite production in endophyte‐inoculated plants.
Conclusion
The present work concluded that the selected endophytes of C. roseus can enhance the ajmalicine and serpentine contents by modulating the expression of structural and regulatory genes of TIA biosynthetic pathway in root.
Significance and Impact of the Study
Endophytes can play an important role to enhance in planta content of pharmaceutically important alkaloids in C. roseus and can therefore be useful in reducing the cost of production of important alkaloids.
Due to its wide industrial use, chromium is considered a serious environmental pollutant. Contamination of soil and water by chromium (Cr) is of recent concern. Toxicity of Cr to plants depends on ...its valence state: Cr(VI) is highly toxic and mobile whereas Cr(III) is less toxic. Since plants lack a specific transport system for Cr, it is taken up by carriers of essential ions such as sulfate or iron. Toxic effects of Cr on plant growth and development include alterations in the germination process as well as in the growth of roots, stems and leaves, which may affect total dry matter production and yield. Cr also causes deleterious effects on plant physiological processes such as photosynthesis, water relations and mineral nutrition. Metabolic alterations by Cr exposure have also been described in plants either by a direct effect on enzymes or other metabolites or by its ability to generate reactive oxygen species which may cause oxidative stress. The potential of plants with the capacity to accumulate or to stabilize Cr compounds for bioremediation of Cr contamination has gained interest in recent years.
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