Article
Biochemical Research Methods
Omer Ali, Amna Farooq, Mingyi Yang, Victor X. Jin, Magnar Bjoras, Junbai Wang
Summary: The abc4pwm tool efficiently clusters PWMs from multiple sources, generates representative motifs for each cluster, evaluates clustering quality automatically, and filters out incorrectly clustered PWMs. It can also automatically update the human DNA-Binding Domain (DBD) family database, classify known human TF PWMs to the respective DBD family, and conduct TF motif searching and motif discovery using a new ensemble learning approach.
BMC BIOINFORMATICS
(2022)
Article
Mathematics, Applied
Hussam Al Daas, Pierre Jolivet, Tyrone Rees
Summary: This paper presents a new spectral coarse space that can be constructed algebraically, and it is efficient for non-self-adjoint operators. Numerical experiments and comparisons show that the proposed method outperforms state-of-the-art preconditioners.
SIAM JOURNAL ON SCIENTIFIC COMPUTING
(2023)
Article
Engineering, Industrial
Juliana Bonomi Santos, Aline Rodrigues Fernandes, Pedro Tonhozi de Oliveira, Lais Moltene Maia, Raul Beal Partyka
Summary: This paper provides a theoretical framework for decoding the orchestration of Entrepreneurial Ecosystems (EEs). The framework analyzes the orchestration in terms of form and content, exploring cases with single or multiple orchestrators and emphasizing the roles and activities orchestrators should undertake. This work is important for driving EE development and enhancing ecosystem-level results.
Article
Fisheries
Yasmin M. M. Canalli, Bruno E. E. Soares, Cassia M. M. Sakuragui
Summary: This study investigated the effects of changes in water depth and transparency on the distribution of macrophyte communities in an Amazon rainforest wetland. The results showed that free-floating life forms and rooted-floating species both responded negatively to increases in water depth and transparency, while submerged species responded positively to increased transparency.
MARINE AND FRESHWATER RESEARCH
(2023)
Article
Fisheries
Xing Ren, Ming Zhu, Yubo Wu, Di Huang, Peng Li, Yan Wang
Summary: The study found that gamma-irradiated feather meal can more effectively replace fish meal in golden pompano diet compared to non-gamma-irradiated feather meal, and the dietary fish meal content can be reduced while maintaining growth and nutritional parameters for golden pompano.
AQUACULTURE RESEARCH
(2022)
Article
Multidisciplinary Sciences
Lijun Wang, Xiuling You, Dengfeng Ruan, Rui Shao, Hai-Qiang Dai, Weiliang Shen, Guo-Liang Xu, Wanlu Liu, Weiguo Zou
Summary: This study investigates the role of TET family of DNA demethylases in mammalian skeletal development. The findings show that loss of TETs leads to hypermethylation, decreasing chromatin accessibility of RUNX2 target genes, thus repressing osteoblast differentiation and resulting in skeletal defects in mice.
NATURE COMMUNICATIONS
(2022)
Article
Computer Science, Artificial Intelligence
Slah Drira, Sai G. S. Pai, Ian F. C. Smith
Summary: Information on occupants in buildings is valuable for security, energy management, and caregiving purposes. Typical methods for occupant localization using mobile devices and cameras compromise privacy. This paper introduces a model-based approach utilizing errordomain model falsification (EDMF) to improve the accuracy of occupant localization by incorporating physics-based models in the interpretation of vibration measurements.
ADVANCED ENGINEERING INFORMATICS
(2021)
Article
Food Science & Technology
Jin Li, Yaqiong Jian, Ruonan Liu, Xianfeng Zhao, Jiangyi Mao, Wei Wei, Chenyu Jiang, Lina Zhang, Yi Wang, Peng Zhou
Summary: This study found that combined intake of fish oil and choline can increase the uptake of DHA in the brain, as well as enhance the synthesis and release of acetylcholine, thereby improving learning and memory abilities in mice.
Article
Chemistry, Analytical
Nicholas D. Schmitt, Joshua M. Berger, Jeremy B. Conway, Jeffrey N. Agar
Summary: Intact protein fragmentation often lacks sequence coverage within proteins' interiors. Collisionally activated dissociation (CAD) produces internal fragmentation within proteins' interiors, filling existing gaps in sequence coverage. Challenges in identifying internal fragments, such as "frameshift ambiguity," can be overcome through optimizing methods and considering fragmentation propensities.
ANALYTICAL CHEMISTRY
(2021)
Article
Evolutionary Biology
Michelle M. Leger, Nuria Ros-Rocher, Sebastian R. Najle, Inaki Ruiz-Trillo
Summary: The Rel/NF-kappa B transcription factor family plays diverse roles in immunity, development, and differentiation in animals. New research suggests that these proteins originated earlier than previously thought, in the last common ancestor of animals and fungi. The proteins in the sister group to fungi also contain elements necessary for subcellular regulation of Rel/NF-kappa B, similar to those found in animals.
GENOME BIOLOGY AND EVOLUTION
(2022)
Article
Engineering, Multidisciplinary
Yuteng Zhang, Hongliang Zhang, Rui Wang, Bin Chen, Haiyang Pan
Summary: In this study, a multi-level weighted dynamic adversarial adaptation network (MWDAAN) is proposed for partial transfer diagnosis. A parallel sample filtering scheme is designed to enhance the effect of correcting noise weights and adequately evaluate the transferability of source samples. Experimental results demonstrate the effectiveness and superiority of the proposed method.
Article
Multidisciplinary Sciences
Huijing Yin, Jingshu Wang, Hui Li, Yinjue Yu, Xiaoling Wang, Lili Lu, Cuiting Lv, Bin Chang, Wei Jin, Wenwen Guo, Chunxia Ren, Gong Yang
Summary: The study demonstrates that the ECM1 isoform ECM1a promotes tumorigenesis and chemoresistance, while the isoform ECM1b acts as a tumor suppressor. This suggests that targeting ECM1a, integrin alpha X beta 2, hnRNPLL, and ABCG1 could be potential strategies for treating cancers associated with ECM1-activated signaling.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Erika Chacin, Karl-Uwe Reusswig, Jessica Furtmeier, Priyanka Bansal, Leonhard A. Karl, Boris Pfander, Tobias Straub, Philipp Korber, Christoph F. Kurat
Summary: Using genome-scale biochemical reconstitution, it was found that ORC establishes nucleosome depletion over replication origins by coordinating chromatin remodelers. The ORC's role in nucleosome organization is crucial for efficient chromosome replication.
Article
Immunology
Guillaume Voisinne, Marie Locard-Paulet, Carine Froment, Emilie Maturin, Marisa Goncalves Menoita, Laura Girard, Valentin Mellado, Odile Burlet-Schiltz, Bernard Malissen, Anne Gonzalez de Peredo, Romain Roncagalli
Summary: This study uses time-resolved high-throughput proteomic analyses to investigate the impact of ligand affinity on early T cell receptor signaling. By identifying and quantifying phosphorylation events and protein-protein interactions, the study reveals differences in signalosome formation between low and high-affinity ligands.
Article
Biochemistry & Molecular Biology
Chi-Chuan Lin, Kin Man Suen, Polly-Anne Jeffrey, Lukasz Wieteska, Jessica A. Lidster, Peng Bao, Alistair P. Curd, Amy Stainthorp, Caroline Seiler, Hans Koss, Eric Miska, Zamal Ahmed, Stephen D. Evans, Carmen Molina-Paris, John E. Ladbury
Summary: This study reveals a state of liquid-liquid phase separation that brings activated receptor tyrosine kinases (RTKs) to localized high concentrations of required proteins, overcoming the ambiguity of random diffusion. The study also discovers the formation process of phase-separated droplets comprising a ternary complex including RTK, phosphatase SHP2, and phospholipase PLC gamma 1, and identifies a previously undescribed interface. The complex combines kinase and phosphatase activities to control phosphorylation state and provides a scaffold for active PLC gamma 1 to facilitate access to its plasma membrane substrate. Thus, liquid-liquid phase separation modulates RTK signaling with potential consequences for therapeutic intervention.