Abstract
Motivation
Related to many important biological functions, intrinsically disordered regions (IDRs) are widely distributed in proteins. Accurate prediction of IDRs is critical for the protein ...structure and function analysis. However, the existing computational methods construct the predictive models solely in the sequence space, failing to convert the sequence space into the ‘semantic space’ to reflect the structure characteristics of proteins. Furthermore, although the length-dependent predictors showed promising results, new fusion strategies should be explored to improve their predictive performance and the generalization.
Results
In this study, we applied the Sequence to Sequence Learning (Seq2Seq) derived from natural language processing (NLP) to map protein sequences to ‘semantic space’ to reflect the structure patterns with the help of predicted residue–residue contacts (CCMs) and other sequence-based features. Furthermore, the Attention mechanism was used to capture the global associations between all residue pairs in the proteins. Three length-dependent predictors were constructed: IDP-Seq2Seq-L for long disordered region prediction, IDP-Seq2Seq-S for short disordered region prediction and IDP-Seq2Seq-G for both long and short disordered region predictions. Finally, these three predictors were fused into one predictor called IDP-Seq2Seq to improve the discriminative power and generalization. Experimental results on four independent test datasets and the CASP test dataset showed that IDP-Seq2Seq is insensitive with the ratios of long and short disordered regions and outperforms other competing methods.
Availability and implementation
For the convenience of most experimental scientists, a user-friendly and publicly accessible web-server for the powerful new predictor has been established at http://bliulab.net/IDP-Seq2Seq/. It is anticipated that IDP-Seq2Seq will become a very useful tool for identification of IDRs.
Supplementary information
Supplementary data are available at Bioinformatics online.
Abstract
In order to uncover the meanings of ‘book of life’, 155 different biological language models (BLMs) for DNA, RNA and protein sequence analysis are discussed in this study, which are able to ...extract the linguistic properties of ‘book of life’. We also extend the BLMs into a system called BioSeq-BLM for automatically representing and analyzing the sequence data. Experimental results show that the predictors generated by BioSeq-BLM achieve comparable or even obviously better performance than the exiting state-of-the-art predictors published in literatures, indicating that BioSeq-BLM will provide new approaches for biological sequence analysis based on natural language processing technologies, and contribute to the development of this very important field. In order to help the readers to use BioSeq-BLM for their own experiments, the corresponding web server and stand-alone package are established and released, which can be freely accessed at http://bliulab.net/BioSeq-BLM/.
Considering that the human brain uses ≈1015 synapses to operate, the development of effective artificial synapses is essential to build brain‐inspired computing systems. In biological synapses, the ...voltage‐gated ion channels are very important for regulating the action‐potential firing. Here, an electrolyte‐gated transistor using WO3 with a unique tunnel structure, which can emulate the ionic modulation process of biological synapses, is proposed. The transistor successfully realizes synaptic functions of both short‐term and long‐term plasticity. Short‐term plasticity is mimicked with the help of electrolyte ion dynamics under low electrical bias, whereas the long‐term plasticity is realized using proton insertion in WO3 under high electrical bias. This is a new working approach to control the transition from short‐term memory to long‐term memory using different gate voltage amplitude for artificial synapses. Other essential synaptic behaviors, such as paired pulse facilitation, the depression and potentiation of synaptic weight, as well as spike‐timing‐dependent plasticity are also implemented in this artificial synapse. These results provide a new recipe for designing synaptic electrolyte‐gated transistors through the electrostatic and electrochemical effects.
An electrolyte‐gated transistor using WO3 with a unique tunnel structure to successfully emulate the synaptic functions of both short‐term and long‐term plasticity is proposed. Short‐term plasticity is mimicked with the help of electrolyte ion dynamics under low gate bias, and the long‐term plasticity is realized via proton insertion in WO3 under high gate bias.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
Our study aimed to determine how lncRNA DANCR, miR-320a, and CTNNB1 interact with each other and regulate osteogenic differentiation in osteoporosis. qRT-PCR and western blotting were performed to ...determine the expression of DANCR, miR-320a, CTNNB1, and the osteoporosis- or Wnt/β-catenin pathway-related markers T-cell factor 1 (TCF-1), runt-related transcription factor 2 (RUNX2), alkaline phosphatase (ALP), osteocalcin (OCN), and osteopontin (OPN). Interactions between CTNNB1, DANCR, and miR-320a were predicted by bioinformatics approaches and validated using a luciferase assay. Osteoblastic phenotypes were evaluated by ALP staining, ALP activity assay and Alizarin Red staining. The bilateral ovariectomy method was used to establish an in vivo osteoporosis model. Bone morphological changes were examined using hematoxylin and eosin (H&E) and Alcian Blue staining. The expression levels of DANCR and miR-320a in BMSCs derived from osteoporosis patients were upregulated, whereas CTNNB1 expression was downregulated compared with that in healthy controls. Importantly, we demonstrated that miR-320a and DANCR acted independently from each other and both inhibited CTNNB1 expression, whereas the inhibitory effect was additive when miR-320a and DANCR were cooverexpressed. Moreover, we found that DANCR overexpression largely abrogated the effect of the miR-320a inhibitor on CTNNB1 expression and the Wnt/β-catenin signaling pathway in BMSCs during osteogenic differentiation. We further confirmed the results above in BMSCs derived from an osteoporosis animal model. Taken together, our findings revealed that DANCR and miR-320a regulated the Wnt/β-catenin signaling pathway during osteogenic differentiation in osteoporosis through CTNNB1 inhibition. Our results highlight the potential value of DANCR and miR-320a as promising therapeutic targets for osteoporosis treatment.
for the current development of our country, the development of industry is going hand in hand with the economic development of our country, with the development of industry, the overall maturity of ...machinery manufacturing industry is gradually increasing. In the mechanical manufacturing industry, connecting rod parts are one of the important components of piston engine and compressor, so for these two kinds of machinery, the importance of connecting rod parts is self-evident. This paper will take the machining technology of connecting rod and the corresponding furniture design in the processing process as the starting point to analyze the problems that need attention in the design and processing process.
Artificial synaptic devices are the essential hardware of neuromorphic computing systems, which can simultaneously perform signal processing and information storage between two neighboring artificial ...neurons. Emerging electrolyte‐gated transistors have attracted much attention for efficient synaptic emulation by using an addition gate terminal. Here, an electrolyte‐gated synaptic device based on the SrCoOx (SCO) films is proposed. It is demonstrated that the reversible modulation of SCO phase transforms the brownmillerite SrCoO2.5 and perovskite SrCoO3−δ
, through controlling the insertion and extraction of oxygen ions with electrolyte gating. Nonvolatile multilevel conduction states can be realized in the SCO films following this route. The synaptic functions such as the long‐term potentiation and depression of synaptic weight, spike‐timing‐dependent plasticity, as well as spiking logic operations in the device are successfully mimicked. These results provide an alternative avenue for future neuromorphic devices via electrolyte‐gated transistors with oxygen ions.
An electrolyte‐gated synaptic transistor with oxygen ions is presented. Nonvolatile multilevel conduction states can be realized in the SrCoOx
epitaxial films, through controlling the insertion and extraction of oxygen ions with electrolyte gating. Important synaptic functions such as the long‐term potentiation and depression of synaptic weight, spike‐timing‐dependent plasticity, as well as spiking logic operations are successfully emulated.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
Studies have shown that HSP20 (heat-shock protein 20) genes play important roles in regulating plant growth, development, and stress response. However, the grape HSP20 gene family has not been well ...studied.
A total of 48 VvHSP20 genes were identified from the grape genome, which were divided into 11 subfamilies (CI, CII, CIII, CV, CVI, CVII, MI, MII, ER, CP and PX/Po) based on a phylogenetic analysis and subcellular localization. Further structural analysis showed that most of the VvHSP20 genes (93.8%) had no intron or only one intron, while genes that clustered together based on a phylogenetic tree had similar motifs and evolutionarily conserved structures. The HSP20s share a conservedα-crystalline domain (ACD) and the different components of the ACD domain suggest the functional diversity of VvHSP20s. In addition, the 48 VvHSP20 genes were distributed on 12 grape chromosomes and the majority of VvHSP20 genes were located at the proximal or distal ends of chromosomes. Chromosome mapping indicated that four groups of VvHSP20 genes were identified as tandem duplication genes. Phytohormone responsive, abiotic and biotic stress-responsive, and plant development-related cis-elements were identified from the cis-regulatory elements analysis of VvHSP20s. The expression profiles of VvHSP20s genes (VvHSP20-1, 11, 14, 17, 18, 19, 20, 24, 25, 28, 31, 39, 42, and 43) were largely similar between RNA-Seq and qRT-PCR analysis after hydrogen peroxide (H
O
) treatment. The results showed that most VvHSP20s were down-regulated by H
O
treatment during fruit development. VvHSP20s genes were indeed found to be involved in the grape berry development and differences in their transcriptional levels may be the result of functional differentiation during evolution.
Our results provide valuable information on the evolutionary relationship of genes in the VvHSP20 family, which is useful for future studies on the functional characteristics of VvHSP20 genes in grape.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Soybean is grown worldwide for its high protein and oil content. Weeds compete fiercely for resources, which affects soybean yields. Because of the progressive enhancement of weed resistance to ...herbicides and the quickly increasing cost of manual weeding, mechanical weed control is becoming the preferred method of weed control. Mechanical weed control finds it difficult to remove intra-row weeds due to the lack of rapid and precise weed/soybean detection and location technology. Rhodamine B (Rh-B) is a systemic crop compound that can be absorbed by soybeans which fluoresces under a specific excitation light. The purpose of this study is to combine systemic crop compounds and computer vision technology for the identification and localization of soybeans in the field. The fluorescence distribution properties of systemic crop compounds in soybeans and their effects on plant growth were explored. The fluorescence was mainly concentrated in soybean cotyledons treated with Rh-B. After a comparison of soybean seedlings treated with nine groups of rhodamine B solutions at different concentrations ranging from 0 to 1440 ppm, the soybeans treated with 180 ppm Rh-B for 24 h received the recommended dosage, resulting in significant fluorescence that did not affect crop growth. Increasing the Rh-B solutions reduced crop biomass, while prolonged treatment times reduced seed germination. The fluorescence produced lasted for 20 days, ensuring a stable signal in the early stages of growth. Additionally, a precise inter-row soybean plant location system based on a fluorescence imaging system with a 96.7% identification accuracy, determined on 300 datasets, was proposed. This article further confirms the potential of crop signaling technology to assist machines in achieving crop identification and localization in the field.
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
Abstract
Motivation
Intrinsically disordered regions (IDRs) are widely distributed in proteins. Accurate prediction of IDRs is critical for the protein structure and function analysis. The IDRs are ...divided into long disordered regions (LDRs) and short disordered regions (SDRs) according to their lengths. Previous studies have shown that LDRs and SDRs have different proprieties. However, the existing computational methods fail to extract different features for LDRs and SDRs separately. As a result, they achieve unstable performance on datasets with different ratios of LDRs and SDRs.
Results
In this study, a two-layer predictor was proposed called DeepIDP-2L. In the first layer, two kinds of attention-based models are used to extract different features for LDRs and SDRs, respectively. The hierarchical attention network is used to capture the distribution pattern features of LDRs, and convolutional attention network is used to capture the local correlation features of SDRs. The second layer of DeepIDP-2L maps the feature extracted in the first layer into a new feature space. Convolutional network and bidirectional long short term memory are used to capture the local and long-range information for predicting both SDRs and LDRs. Experimental results show that DeepIDP-2L can achieve more stable performance than other exiting predictors on independent test sets with different ratios of SDRs and LDRs.
Availability and implementation
For the convenience of most experimental scientists, a user-friendly and publicly accessible web-server for the new predictor has been established at http://bliulab.net/DeepIDP-2L/. It is anticipated that DeepIDP-2L will become a very useful tool for identification of intrinsically disordered regions.
Supplementary information
Supplementary data are available at Bioinformatics online.
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