Epigenetic features are significantly associated with alternative splicing

<p>Abstract</p> <p>Background</p> <p>While alternative splicing (AS) contributes greatly to protein diversities, the relationship between various types of AS and epigenetic factors remains largely unknown.</p> <p>Results</p> <p>In this study, we discover that a number of epigenetic features, including DNA methylation, nucleosome occupancy, specific histone modifications and protein features, are strongly associated with AS. To further enhance our understanding of the association between these features and AS, we cluster our investigated features based on their association patterns with each AS type into four groups, with H3K36me3, EGR1, GABP, SRF, SIN3A and RNA Pol II grouped together and showing strongest association with AS. In addition, we find that the AS types can be classified into two general classes, namely the exon skipping related process (ESRP), and the alternative splice site selection process (ASSP), based on their association levels with the epigenetic features.</p> <p>Conclusion</p> <p>Our analysis thus suggests that epigenetic features are likely to play important roles in regulating AS.</p

Recurrent Temporal Revision Graph Networks

Temporal graphs offer more accurate modeling of many real-world scenarios than static graphs. However, neighbor aggregation, a critical building block of graph networks, for temporal graphs, is currently straightforwardly extended from that of static graphs. It can be computationally expensive when involving all historical neighbors during such aggregation. In practice, typically only a subset of the most recent neighbors are involved. However, such subsampling leads to incomplete and biased neighbor information. To address this limitation, we propose a novel framework for temporal neighbor aggregation that uses the recurrent neural network with node-wise hidden states to integrate information from all historical neighbors for each node to acquire the complete neighbor information. We demonstrate the superior theoretical expressiveness of the proposed framework as well as its state-of-the-art performance in real-world applications. Notably, it achieves a significant +9.6% improvement on averaged precision in a real-world Ecommerce dataset over existing methods on 2-layer models

Spectroscopic super-resolution fluorescence cell imaging using ultra-small Ge quantum dots

QMUL/CSC scholarship (2011611045); BBSRC grant (BB/J001473/1)

An expanded evaluation of protein function prediction methods shows an improvement in accuracy

Background: A major bottleneck in our understanding of the molecular underpinnings of life is the assignment of function to proteins. While molecular experiments provide the most reliable annotation of proteins, their relatively low throughput and restricted purview have led to an increasing role for computational function prediction. However, assessing methods for protein function prediction and tracking progress in the field remain challenging. Results: We conducted the second critical assessment of functional annotation (CAFA), a timed challenge to assess computational methods that automatically assign protein function. We evaluated 126 methods from 56 research groups for their ability to predict biological functions using Gene Ontology and gene-disease associations using Human Phenotype Ontology on a set of 3681 proteins from 18 species. CAFA2 featured expanded analysis compared with CAFA1, with regards to data set size, variety, and assessment metrics. To review progress in the field, the analysis compared the best methods from CAFA1 to those of CAFA2. Conclusions: The top-performing methods in CAFA2 outperformed those from CAFA1. This increased accuracy can be attributed to a combination of the growing number of experimental annotations and improved methods for function prediction. The assessment also revealed that the definition of top-performing algorithms is ontology specific, that different performance metrics can be used to probe the nature of accurate predictions, and the relative diversity of predictions in the biological process and human phenotype ontologies. While there was methodological improvement between CAFA1 and CAFA2, the interpretation of results and usefulness of individual methods remain context-dependent. Keywords: Protein function prediction, Disease gene prioritizationpublishedVersio

An Expanded Evaluation of Protein Function Prediction Methods Shows an Improvement In Accuracy

Background: A major bottleneck in our understanding of the molecular underpinnings of life is the assignment of function to proteins. While molecular experiments provide the most reliable annotation of proteins, their relatively low throughput and restricted purview have led to an increasing role for computational function prediction. However, assessing methods for protein function prediction and tracking progress in the field remain challenging. Results: We conducted the second critical assessment of functional annotation (CAFA), a timed challenge to assess computational methods that automatically assign protein function. We evaluated 126 methods from 56 research groups for their ability to predict biological functions using Gene Ontology and gene-disease associations using Human Phenotype Ontology on a set of 3681 proteins from 18 species. CAFA2 featured expanded analysis compared with CAFA1, with regards to data set size, variety, and assessment metrics. To review progress in the field, the analysis compared the best methods from CAFA1 to those of CAFA2. Conclusions: The top-performing methods in CAFA2 outperformed those from CAFA1. This increased accuracy can be attributed to a combination of the growing number of experimental annotations and improved methods for function prediction. The assessment also revealed that the definition of top-performing algorithms is ontology specific, that different performance metrics can be used to probe the nature of accurate predictions, and the relative diversity of predictions in the biological process and human phenotype ontologies. While there was methodological improvement between CAFA1 and CAFA2, the interpretation of results and usefulness of individual methods remain context-dependent

Aging Behavior of High-Viscosity Modified Asphalt Binder Based on Infrared Spectrum Test

In the rapid development of sponge city construction in China, porous asphalt pavement has been widely used. The high-viscosity modified asphalt used for porous asphalt pavements is utilised in a complex aging environment. In this study, infrared spectroscopy was used to test the changes in the functional groups of high-viscosity modified asphalt under the influence of ultraviolet radiation intensity, high temperature, and water corrosion conditions. The research results showed that under the influence of several environmental factors, the high-viscosity modified asphalt has no chemical reaction but does undergo physical changes. From the perspective of the functional group index, the carbonyl index is more suitable for evaluating the degree of ultraviolet aging, and the sulfoxide group index is more suitable for evaluating the effect of temperature on aging. The high-viscosity modified asphalt aging kinetic models, established with different functional group indexes as indicators, have different activation energies. The aging kinetic model established with the carbonyl index is more suitable for simulating traditional thermal-oxidative aging. This study provides a better plan to reveal the influence of different environmental factors on the aging performance of high-viscosity modified asphalt under complex environmental conditions

Multispectral Remote Sensing Image Change Detection Based on Twin Neural Networks

Remote sensing image change detection can effectively show the change information of land surface features such as roads and buildings at different times, which plays an indispensable role in application fields such as updating building information and analyzing urban evolution. At present, multispectral remote sensing images contain more and more information, which brings new development opportunities to remote sensing image change detection. However, this information is difficult to use effectively in change detection. Therefore, a change-detection method of multispectral remote sensing images based on a Siamese neural network is proposed. The features of dual-temporal remote sensing images were extracted based on the ResNet-18 network. In order to capture the semantic information of different scales and improve the information perception and expression ability of the algorithm for the input image features, an attention module network structure is designed to further enhance the extracted feature maps. Facing the problem of false alarms in change detection, an adaptive threshold comparison loss function is designed to make the threshold more sensitive to the remote sensing images in the data set and improve the robustness of the algorithm model. Moreover, the threshold segmentation method of the measurement module is used to determine the change area to obtain a better change-detection map domain. Finally, our experimental tests show that the proposed method achieves excellent performance on the multispectral OSCD detection data sets

Relation Learning Using Temporal Episodes for Motor Imagery Brain-Computer Interfaces

For practical motor imagery (MI) brain-computer interface (BCI) applications, generating a reliable model for a target subject with few MI trials is important since the data collection process is labour-intensive and expensive. In this paper, we address this issue by proposing a few-shot learning method called temporal episode relation learning (TERL). TERL models MI with only limited trials from the target subject by the ability to compare MI trials through episode-based training. It can be directly applied to a new user without being re-trained, which is vital to improve user experience and realize real-world MIBCI applications. We develop a new and effective approach where, unlike the original episode learning, the temporal pattern between trials in each episode is encoded during the learning to boost the classification performance. We also perform an online evaluation simulation, in addition to the offline analysis that the previous studies only conduct, to better understand the performance of different approaches in real-world scenario. Extensive experiments are completed on four publicly available MIBCI datasets to evaluate the proposed TERL. Results show that TERL outperforms baseline and recent state-of-the-art methods, demonstrating competitive performance for subject-specific MIBCI where few trials are available from a target subject and a considerable number of trials from other source subjects