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

A Novel Method of Sentence Ordering Based on Support Vector Machine

PACLIC 23 / City University of Hong Kong / 3-5 December 200

Improving Image Captioning via Predicting Structured Concepts

Having the difficulty of solving the semantic gap between images and texts for the image captioning task, conventional studies in this area paid some attention to treating semantic concepts as a bridge between the two modalities and improved captioning performance accordingly. Although promising results on concept prediction were obtained, the aforementioned studies normally ignore the relationship among concepts, which relies on not only objects in the image, but also word dependencies in the text, so that offers a considerable potential for improving the process of generating good descriptions. In this paper, we propose a structured concept predictor (SCP) to predict concepts and their structures, then we integrate them into captioning, so as to enhance the contribution of visual signals in this task via concepts and further use their relations to distinguish cross-modal semantics for better description generation. Particularly, we design weighted graph convolutional networks (W-GCN) to depict concept relations driven by word dependencies, and then learns differentiated contributions from these concepts for following decoding process. Therefore, our approach captures potential relations among concepts and discriminatively learns different concepts, so that effectively facilitates image captioning with inherited information across modalities. Extensive experiments and their results demonstrate the effectiveness of our approach as well as each proposed module in this work.Comment: Accepted by EMNLP 2023 (Main Conference, Oral

Single-cell RNA-seq reveals developmental deficiencies in both the placentation and the decidualization in women with late-onset preeclampsia

Preeclampsia (PE) is a leading cause of maternal and fetal morbidity and mortality. Although increasing lines of evidence suggest that both the placenta and the decidua likely play roles in the pathogenesis of PE, the molecular mechanism of PE remains elusive partly because of the heterogeneity nature of the maternal-fetal interface. In this study, we perform single-cell RNA-seq on the placenta and the decidual from patients with late-onset PE (LOPE) and women in normal pregnancy. Analyses of single-cell transcriptomes reveal that in LOPE, there are likely a global development deficiency of trophoblasts with impaired invasion of extravillous trophoblasts (EVT) and increased maternal immune rejection and inflammation in the placenta, while there are likely insufficient decidualization of decidual stromal cells (DSC), increased inflammation, and suppressed regulatory functions of decidual immune cells. These findings improve our understanding of the molecular mechanisms of PE

Water pollutant fingerprinting tracks recent industrial transfer from coastal to inland China: a case study

In recent years, China’s developed regions have transferred industries to undeveloped regions. Large numbers of unlicensed or unregistered enterprises are widespread in these undeveloped regions and they are subject to minimal regulation. Current methods for tracing industrial transfers in these areas, based on enterprise registration information or economic surveys, do not work. The authors have developed an analytical framework combining water fingerprinting and evolutionary analysis to trace the pollution transfer features between water sources. We collected samples in Eastern China (industrial export) and Central China (industrial acceptance) separately from two water systems. Based on the water pollutant fingerprints and evolutionary trees, we traced the pollution transfer associated with industrial transfer between the two areas. The results are consistent with four episodes of industrial transfers over the past decade. The results also show likely types of the transferred industries - electronics, plastics, and biomedicines - that contribute to the water pollution transfer

Analysis of corrections to the eikonal approximation

Various corrections to the eikonal approximations are studied for two- and three-body nuclear collisions with the goal to extend the range of validity of this approximation to beam energies of 10 MeV/nucleon. Wallace's correction does not improve much the elastic-scattering cross sections obtained at the usual eikonal approximation. On the contrary, a semiclassical approximation that substitutes the impact parameter by a complex distance of closest approach computed with the projectile-target optical potential efficiently corrects the eikonal approximation. This opens the possibility to analyze data measured down to 10 MeV/nucleon within eikonal-like reaction models.Comment: 10 pages, 8 figure

An en masse phenotype and function prediction system for Mus musculus

Background: Individual researchers are struggling to keep up with the accelerating emergence of high-throughput biological data, and to extract information that relates to their specific questions. Integration of accumulated evidence should permit researchers to form fewer - and more accurate - hypotheses for further study through experimentation. Results: Here a method previously used to predict Gene Ontology (GO) terms for Saccharomyces cerevisiae (Tian et al.: Combining guilt-by-association and guilt-by-profiling to predict Saccharomyces cerevisiae gene function. Genome Biol 2008, 9(Suppl 1):S7) is applied to predict GO terms and phenotypes for 21,603 Mus musculus genes, using a diverse collection of integrated data sources (including expression, interaction, and sequence-based data). This combined 'guilt-by-profiling' and 'guilt-by-association' approach optimizes the combination of two inference methodologies. Predictions at all levels of confidence are evaluated by examining genes not used in training, and top predictions are examined manually using available literature and knowledge base resources. Conclusion: We assigned a confidence score to each gene/term combination. The results provided high prediction performance, with nearly every GO term achieving greater than 40% precision at 1% recall. Among the 36 novel predictions for GO terms and 40 for phenotypes that were studied manually, &gt;80% and &gt;40%, respectively, were identified as accurate. We also illustrate that a combination of 'guilt-by-profiling' and 'guilt-by-association' outperforms either approach alone in their application to M. musculus.Molecular and Cellular Biolog