21 papers · ranked by Valyu relevance
Robert M. Erdmann, Colette L. Picard
RNA-directed DNA methylation (RdDM) is a biological process in which [non-coding RNA]() molecules direct the addition of [DNA methylation]() to specific DNA sequences. The RdDM pathway is unique to [plants](), although other mechanisms of RNA-directed [chromatin]() modification have also been described in [fungi]() and…
Jianxu Wang, Qing Lyu, Ge Wang
Low-dose CT (LDCT) denoising remains an important yet challenging problem in medical imaging. Although recent learning-based methods have shown promising performance, those optimized using classical pixel-level objectives often produce over-smoothed reconstructions. Existing mainstream generative models, such as…
Fang-Fang Fu, R. Kelly Dawe, Jonathan I. Gent
Plants make use of three types of DNA methylation, each characterized by distinct DNA methyltransferases. One type, RNA-directed DNA methylation (RdDM), is guided by siRNAs to the edges of transposons that are close to genes, areas called mCHH islands in maize. Another type, chromomethylation, is guided by histone H3…
Debaditya Shome, Pritam Sarkar, Ali Etemad
The high prevalence of cardiovascular diseases (CVDs) calls for accessible and cost-effective continuous cardiac monitoring tools. Despite Electrocardiography (ECG) being the gold standard, continuous monitoring remains a challenge, leading to the exploration of Photoplethysmography (PPG), a promising but more basic…
Taku Sasaki, Zdravko J. Lorković, Shih-Chieh Liang, Antonius J. M. Matzke + 2 more
'Antonius J. M. Matzke' 'Marjori Matzke' 'Peter Meyer'] RDM1 (RNA-DIRECTED DNA METHYLATION1) is a small plant-specific protein required for RNA-directed DNA methylation (RdDM). RDM1 interacts with RNA polymerase II (Pol II), ARGONAUTE4 (AGO4), and the de novo DNA methyltransferase DOMAINS REARRANGED METHYLTRANSFERASE2…
Michael Wassenegger, Athanasios Dalakouras, Henryk Hanokh Czosnek, Kriton Kalantidis + 2 more
'Kriton Kalantidis' 'Ahmed Hadidi' 'Robert A. Owens'] Viroids are plant pathogenic, circular, non-coding, single-stranded RNAs (ssRNAs). Members of the Pospiviroidae family replicate in the nucleus of plant cells through double-stranded RNA (dsRNA) intermediates, thus triggering the host’s RNA interference (RNAi)…
Authors not listed
We present the RAW domain diffusion model (RDDM), an end-to-end diffusion model that restores photo-realistic images directly from the sensor RAW data. While recent sRGB-domain diffusion methods achieve impressive results, they are caught in a dilemma between high fidelity and realistic generation. As these models…
León-Ruiz Jesús, Espinal-Centeno Annie, Blilou Ikram, Scheres Ben + 2 more
Transposable elements and other repetitive elements are silenced by the RNA-directed DNA methylation pathway (RdDM). In RdDM, POLIV-derived transcripts are converted into double stranded RNA (dsRNA) by the activity of RDR2 and subsequently processed into 24 nucleotide short interfering RNAs (24 -nt siRNAs) by DCL3.…
Auwalu Abdu, Henrik Mihály Szaker, András Kis, Dávid Polgári + 4 more
Plant specific RNA-directed DNA methylation (RdDM) mediates the DNA methylation of specific DNA sequences directed by 24-nucleotide long (nt) small interfering (si)RNAs. In crop plants we have limited information about the biological roles of the RdDM pathway including barley (Hordeum vulgare L). Here, we show that…
Kaushik Panda, Lexiang Ji, Drexel A. Neumann, Josquin Daron + 2 more
'Robert J. Schmitz' 'R. Keith Slotkin'] Background Chromatin modifications such as DNA methylation are targeted to transposable elements by small RNAs in a process termed RNA-directed DNA methylation (RdDM). In plants, canonical RdDM functions through RNA polymerase IV to reinforce pre-existing transposable element…
Kelly J. Dew-Budd, Hiu Tung Chow, Timmy Kendall, Brandon C. David + 3 more
In plants, de novo DNA methylation is guided by 24-nt short interfering (si)RNAs in a process called RNA-directed DNA methylation (RdDM). Primarily targeted at transposons, RdDM causes transcriptional silencing and can indirectly influence expression of neighboring genes. During reproduction, a small number of siRNA…
Ruth Y. Akinmusola, Catherine-Axa Wilkins, James Doughty, Xuan Hieu Cao
'Xuan Hieu Cao'] Epigenetic modifications are indispensable for regulating gene bodies and TE silencing. DECREASE IN DNA METHYLATION 1 (DDM1) is a chromatin remodeller involved in histone modifications and DNA methylation. Apart from maintaining the epigenome, DDM1 also maintains key plant traits such as flowering time…
Yide Liu, Haijiang Sun, Xiaowen Zhang, Qiaoyuan Liu + 2 more
'Chongzhuo Xiao'] Abstract—Remote Sensing Image Super-Resolution (RSISR) aims to reconstruct high-resolution (HR) remote sensing (RS) images from low-resolution (LR) RS images inputs by overcoming the physical limitations of imaging systems. As a specialized task in the RS domain, RSISR provides critical support for…
Meredith J. Sigman, Kaushik Panda, Rachel Kirchner, Lauren L. McLain + 5 more
In mammals and plants, cytosine DNA methylation is essential for the epigenetic repression of transposable elements and foreign DNA. In plants, DNA methylation is guided by small interfering RNAs (siRNAs) in a self-reinforcing cycle termed RNA-directed DNA methylation (RdDM). RdDM requires the specialized RNA…
Authors not listed
Machine learning of the one-electron reduced density matrix (1-RDM) provides a computationally efficient surrogate to conventional electronic structure methods. In this work, we train models that map the electron–nuclear interaction potential to the 1-RDM with such an accuracy that predicted 1-RDMs deviate from fully…
Sanidhya Kashyap, Dai Qin, Steve Byan, Virendra J. Marathe + 1 more
'Sanketh Nalli'] Persistence of updates to remote byte-addressable persistent memory (PM), using RDMA operations (RDMA updates), is a poorly understood subject. Visibility of RDMA updates on the remote server is not the same as persistence of those updates. The remote server's configuration has significant implications…
Yuhong Wang, Sam Michael, Ruili Huang, Jinghua Zhao + 5 more
'Danielle Bougie' 'Qiang Shu' 'Paul Shinn' 'Hongmao Sun'] Abstract: To generate drug molecules of desired properties with computational methods is the holy grail in pharmaceutical research. Here we describe an AI strategy, retro drug design, or RDD, to generate novel small molecule drugs from scratch to meet predefined…
Andrew McNutt, Fatimah Bisiriyu, Sophia Song, Ananya Vyas + 2 more
Conformer generation, the assignment of realistic 3D coordinates to a small molecule, is fundamental to structure based drug design. Conformational ensembles are required for rigid-body matching algorithms, such as shape-based or pharmacophore approaches, and even methods that treat the ligand flexibly, such as…
Sen Wu, Ya-nan Hu, Jingxiang Wang, Dianming Sun + 3 more
Multiresonant thermally activated delayed fluorescence (MR-TADF) compounds are attractive for use in organic light-emitting diodes as they show narrowband emission, are bright, and can harvest both singlet and triplet excitons for the emission of light. Reflected in the paucity of examples of orange-to-red emitters…
Dimitar Georgiev, Simon Vilms Pedersen, Ruoxiao Xie, Álvaro Fernández-Galiana + 2 more
Raman spectroscopy is a non-destructive and label-free chemical analysis technique, which plays a key role in the analysis and discovery cycle of various branches of science. Nonetheless, progress in Raman spectroscopic analysis is still impeded by the lack of software, methodological and data standardisation, and the…
Authors not listed
Drug Discovery is a very lengthy and resource-consuming process. However, a variety of advanced Artificial Intelligence (AI) and Deep Learning (DL) techniques are being utilized to accelerate and advance DD, such as Large Language Models (LLMs). This survey is in aim of discovering and comparing the currently available…