Construction of Shoot Apical Meristem cDNA Yeast Library of <i>Brassica napus</i> L. and Screening of Proteins That Interact with the Inflorescence Regulatory Factors BnTFL1s by Lingxiong Zan, Haidong Liu, Xutao Zhao, Dezhi Du, Kaixiang Li

“…<i>BnTFL1s</i> (<i>BnaA10.TFL1</i> and <i>BnaC09.TFL1</i>), which encode the transcription factor <i>TERMINAL FLOWER 1 (TFL1),</i> have previously been identified as candidate genes controlling this trait through map-based cloning. …”
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TransformerPayne: Enhancing Spectral Emulation Accuracy and Data Efficiency by Capturing Long-range Correlations by Tomasz Różański, Yuan-Sen Ting, Maja Jabłońska

“…Analysis of TransformerPayne's attention maps revealed that they encode interpretable features common across many spectral lines of chosen elements. …”
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Synaptic enrichment and dynamic regulation of the two opposing dopamine receptors within the same neurons by Shun Hiramatsu, Kokoro Saito, Shu Kondo, Hidetaka Katow, Nobuhiro Yamagata, Chun-Fang Wu, Hiromu Tanimoto

“…In the fruit fly Drosophila melanogaster, Dop1R1 and Dop2R encode the D1- and D2-like receptors, respectively, and are reported to oppositely regulate intracellular cAMP levels. …”
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Avirulence depletion assay: Combining R gene-mediated selection with bulk sequencing for rapid avirulence gene identification in wheat powdery mildew. by Lukas Kunz, Jigisha Jigisha, Fabrizio Menardo, Alexandros G Sotiropoulos, Helen Zbinden, Shenghao Zou, Dingzhong Tang, Ralph Hückelhoven, Beat Keller, Marion C Müller

“…Wheat resistance breeding frequently relies on the use of resistance (R) genes that encode diverse immune receptors which detect specific avirulence (AVR) effectors and subsequently induce an immune response. …”
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Using informative priors to account for identifiability issues in occupancy models with identification errors by Monchy, Célian, Etienne, Marie-Pierre, Gimenez, Olivier

“…Through simulations, we compare different prior choices that encode varying levels of information, ranging from cases where no prior knowledge is available, to instances with accurate metrics on the performance of the identification, and scenarios based on generally accepted assumptions. …”
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Lake salinization on the Qinghai–Tibetan Plateau alters viral community composition and lifestyles by Yuan-Guo Xie, Yan-Ling Qi, Zhen-Hao Luo, Yan-Ni Qu, Jian Yang, Shi-Qiang Liu, Hai-long Yang, Dan-Wei Xie, Zimeng Wang, Hong-Chen Jiang, Zheng-Shuang Hua

“…These shifts are mirrored in the prokaryotic communities, with Alphaproteobacteria and their infecting temperate viruses, notably Casadabanvirus, becoming more prevalent in higher salinity zones. Viral genomes encode genes associated with osmotic stress adaptation, DNA recombination, and nutrient transport, which may facilitate host adaptation to saline stress. …”
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Candidate genes for productivity identified by genome-wide association study with indicators of class in the Russian meat merino sheep breed by A. Y. Krivoruchko, O. A. Yatsyk, E. Y. Safaryan

“…Determining the location of the analyzed SNPs relative to the latest annotation Oar_rambouillet_v1.0 allowed to identify 11 candidate genes presumably associated with the formation of a complex of phenotypic traits of animals in the exhibition group: RXFP2, ALOX5AP, MEDAG, OPN5, PRDM5, PTPRT, TRNAS-GGA, EEF1A1, FRY, ZBTB21-like, and B3GLCT-like. The listed genes encode proteins involved in the control of the cell cycle and DNA replication, regulation of cell proliferation and apoptosis, lipid and carbohydrate metabolism, the development of the inflammatory process and the work of circadian rhythms. …”
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Generative design of crystal structures by point cloud representations and diffusion model by Zhelin Li, Rami Mrad, Runxian Jiao, Guan Huang, Jun Shan, Shibing Chu, Yuanping Chen

“…To facilitate the discovery of stable materials, we present a framework for the generation of synthesizable materials leveraging a point cloud representation to encode intricate structural information. At the heart of this framework lies the introduction of a diffusion model as its foundational pillar. …”
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Epigene functional diversity: isoform usage, disordered domain content, and variable binding partners by Leroy Bondhus, Aileen A. Nava, Isabelle S. Liu, Valerie A. Arboleda

“…Conclusions Here we identify significant differences in isoform usage, disordered domain content, and variable binding partners between human epigenes and non-epigenes using various functional genomics datasets from Ensembl, ENCODE, GTEx, HPO, LINCS L1000, and BrainSpan. Our results contribute new knowledge to the growing field focused on developing targeted therapies for diseases caused by epigene mutations, such as chromatinopathies and cancers.…”
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Ethnicity-specific distribution of <em>TRPM8</em> gene variants in Eurasian populations: signs of selection by T. A. Potapova, A. G. Romashchenko, N. S. Yudin, M. I. Voevoda

“…The TRPM8 gene encodes the ion channel, which is a cold receptor in afferent neurons of the mammalian somatosensory system. …”
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Unified Visual-Aware Representations for Data Analytics by Ladislav Peska, Ivana Sixtova, David Hoksza, David Bernhauer, Jakub Lokoc, Tomas Skopal

“…The desired property of the visualizations is the ability to visually encode the semantic features of the original data. …”
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Decreased SynMuv B gene activity in response to viral infection leads to activation of the antiviral RNAi pathway in C. elegans. by Ashwin Seetharaman, Himani Galagali, Elizabeth Linarte, Mona H X Liu, Jennifer D Cohen, Kashish Chetal, Ruslan Sadreyev, Alex J Tate, Taiowa A Montgomery, Gary Ruvkun

“…About one-third of the score of mutants that enhance RNAi are in synMuv B genes, identified 30 years ago in unrelated screens for increased growth factor signaling. Many synMuv B genes encode dREAM complex chromatin-regulatory proteins found in nearly all animals and plants. …”
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Detector development for spin-echo SANS techniques using ZnS:Ag/6LiF and 6Li glass scintillators by Giacomo Mauri, G. Jeff Sykora, Gregory N. Smith, Steven R. Parnell, Robert M. Dalgliesh, Dirk Honecker, Sarah E. Mann, Erik M. Schooneveld, Nigel J. Rhodes

“…Abstract Neutron spin-echo techniques exploit Larmor precession of the neutron spin to encode either the scattering angle or energy. These are powerful means to extend the measurable momentum transfer (Q) and energy (E) range in neutron scattering measurements. …”
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The Central Roles of Noncoding RNA in Estrogen-Dependent Female Reproductive System Tumors by Jiajie Tu, Huan Yang, Lei Jiang, Yu Chen, Yu Chen, Zhe Li, Lei Li, Yuanyuan Zhang, Xiaochun Chen, He Chen, Zhiying Yu

“…Noncoding RNAs (ncRNAs) are defined as RNAs that do not encode proteins, including microRNAs (miRNAs) and long noncoding RNAs (lncRNAs), both of which have been reported in estrogen-dependent female reproductive system tumors. …”
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Auditory attention decoding based on neural-network for binaural beamforming applications by Roy Gueta, Elana Zion-Golumbic, Jacob Goldberger, Sharon Gannot

“…Several studies showed the ability to encode essential features of the attended speech from the cortex neural response, as recorded by the electroencephalography (EEG) signals. …”
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Complete Genome Sequence and Comparative Genome Analysis of Variovorax sp. Strains PAMC28711, PAMC26660, and PAMC28562 and Trehalose Metabolic Pathways in Antarctica Isolates by Prasansah Shrestha, Jayram Karmacharya, So-Ra Han, Jun Hyuck Lee, Hyun Park, Tae-Jin Oh

“…The genomic information was collected from the NCBI database and the CAZyme database, and Prokka annotation was used to find the genes that encode for the trehalose metabolic pathway. Likewise, CAZyme annotation (dbCAN2 Meta server) was performed to predict the CAZyme family responsible for trehalose biosynthesis and degradation enzymes. …”
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Molecular Characteristics, Synthase, and Food Application of Cereal β-Glucan by Lijing Sun, Mengyun Hu, Jie Zhao, Liangjie Lv, Yelun Zhang, Qian Liu, Li Zhang, Cuihong Yu, Peinan Wang, Qianying Li, Hui Li, Yingjun Zhang

“…It is well documented that cellulose synthase-like CslF/H/J genes encode synthases responsible for β-glucan biosynthesis in cereal grains. …”
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Comprehensive phenotypic analysis of multiple gene deletions of α-glucan synthase and Crh-transglycosylase gene families in Aspergillus niger highlighting the versatility of the fu... by Katharina J. Ost, Mark Arentshorst, Bruno M. Moerschbacher, Mareike E. Dirks-Hofmeister, Arthur F.J. Ram

“…The genome of A. niger contains five genes encoding putative α-1,3-glucan synthases (AgsA-E) and seven genes encoding putative glucan-chitin crosslinking enzymes (CrhA-G). …”
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Disease-associated genetic variants in the regulatory regions of human genes: mechanisms of action on transcription and genomic resources for dissecting these mechanisms by E. V. Ignatieva, E. A. Matrosova

“…Most of the variants identified by the GWAS technique are located in the noncoding regions of the human genome. According to the ENCODE project, the fraction of regions in the human genome potentially involved in transcriptional control is many times greater than the fraction of coding regions. …”
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SGCL-LncLoc: An Interpretable Deep Learning Model for Improving lncRNA Subcellular Localization Prediction with Supervised Graph Contrastive Learning by Min Li, Baoying Zhao, Yiming Li, Pingjian Ding, Rui Yin, Shichao Kan, Min Zeng

“…While previous computational methods have made progress in predicting lncRNA subcellular localization, most of them ignore the sequence order information by relying on k-mer frequency features to encode lncRNA sequences. In the study, we develope SGCL-LncLoc, a novel interpretable deep learning model based on supervised graph contrastive learning. …”
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