Results 131 to 140 of about 669,188 (305)

Structured Chemical Reaction Modeling with Multitask Graph Neural Networks

Abstract Modeling chemical reactions requires connecting fine-grained atom–bond edits with broader semantic categories. Yet, most machine learning approaches model these aspects in isolation: atom mapping, reaction center identification, and reaction classification are treated as separate problems.
Astero, Maryam, Li, Anchen, Casiraghi, Elena, Rousu, Juho   +3 more
openaire   +1 more source

Pore Network Modeling of Intraparticle Transport Phenomena Accompanied by Chemical Reactions

Industrial & Engineering Chemistry Research
In this work, a 3D pore network model (PNM) is introduced for modeling reaction-diffusion phenomena, with and without coupled heat transfer, in a spherical porous catalyst particle. The particle geometry is generated by packing thousands of microspheres inside a large sphere to represent the 3D geometry, porosity, and tortuosity of a spherical catalyst
A. Fathiganjehlou, E. A. J. F. Peters, K. A. Buist, J. A. M. Kuipers   +3 more
openaire   +2 more sources

Transcriptional network analysis of PTEN‐protein‐deficient prostate tumors reveals robust stromal reprogramming and signs of senescent paracrine communication

Molecular Oncology, EarlyView.
Combining PTEN protein assessment and transcriptomic profiling of prostate tumors, we uncovered a network enriched in senescence and extracellular matrix (ECM) programs associated with PTEN loss and conserved in a mouse model. We show that PTEN‐deficient cells trigger paracrine remodeling of the surrounding stroma and this information could help ...
Ivana Rondon‐Lorefice, Jose I. Lopez, Aitziber Ugalde‐Olano, Maite Zufiaurre, Ianire Astobiza, Natalia Martin‐Martin, Laura Bozal‐Basterra, Saioa Garcia‐Longarte, Amaia Zabala‐Letona, Sofia Rey, Aida Santos‐Martin, Miguel Unda, Ana Loizaga‐Iriarte, Mariona Graupera, Paolo Nuciforo, Arkaitz Carracedo, Isabel Mendizabal   +16 more
wiley   +1 more source

Diffusive network connected chemical reaction networks

Systems Science & Control Engineering
A novel type of networked Chemical Reaction Network (CRN) model is proposed in this paper where the CRN subsystem nodes are connected in a bi-directional state-difference-driven way, forming a diffusive network. The diffusive connecting elements can also
Katalin M. Hangos, Wijaya Kurniawan, Lőrinc Márton   +2 more
doaj   +1 more source

Markov chain aggregation and its application to rule-based modelling

, 2018
Rule-based modelling allows to represent molecular interactions in a compact and natural way. The underlying molecular dynamics, by the laws of stochastic chemical kinetics, behaves as a continuous-time Markov chain. However, this Markov chain enumerates
A Ganguly, AN Gorban, BB Aldridge, CV Rao, DF Anderson, DT Gillespie, DT Gillespie, EJ Deeds, H Conzelmann, HH McAdams, HW Kang, J Feret, J Feret, J Feret, J Fisher, ML Blinov, ML Blinov, NM Borisov, TG Kurtz, V Danos, V Danos, WS Hlavacek   +21 more
core   +1 more source

Potential therapeutic targeting of BKCa channels in glioblastoma treatment

Molecular Oncology, EarlyView.
This review summarizes current insights into the role of BKCa and mitoBKCa channels in glioblastoma biology, their potential classification as oncochannels, and the emerging pharmacological strategies targeting these channels, emphasizing the translational challenges in developing BKCa‐directed therapies for glioblastoma treatment.
Kamila Maliszewska‐Olejniczak, Karolina Pytlak, Sandra Jaworowska, Bogusz Kulawiak, Piotr Bednarczyk   +4 more
wiley   +1 more source

Type-dependent irreversible stochastic spin models for genetic regulatory networks at the level of promotion-inhibition circuitry

, 2015
We describe an approach to model genetic regulatory networks at the level of promotion-inhibition circuitry through a class of stochastic spin models that includes spatial and temporal density fluctuations in a natural way. The formalism can be viewed as
de Oliveira, Mário J., Mendonça, J. Ricardo G.   +1 more
core   +1 more source

LINC01116, a hypoxia‐lncRNA marker of pathological lymphangiogenesis and poor prognosis in lung adenocarcinoma

Molecular Oncology, EarlyView.
The LINC01116 long noncoding RNA is induced by hypoxia and associated with poor prognosis and high recurrence rates in two cohorts of lung adenocarcinoma patients. Here, we demonstrate that besides its expression in cancer cells, LINC01116 is markedly expressed in lymphatic endothelial cells of the tumor stroma in which it participates in hypoxia ...
Marine Gautier‐Isola, Rafael Lopes Goncalves, Marin Truchi, Caroline Lacoux, Célia Scribe, Hugo Cadis, Laetitia Guardini, Sophie Bekisz, Marius Ilié, Paul Hofman, Georges Vassaux, Bernard Mari, Roger Rezzonico   +12 more
wiley   +1 more source

Nanoscale chemical reaction exploration with a quantum magnifying glass

Nature Communications
Nanoscopic systems exhibit diverse molecular substructures by which they facilitate specific functions. Theoretical models of them, which aim at describing, understanding, and predicting these capabilities, are difficult to build.
Katja-Sophia Csizi, Miguel Steiner, Markus Reiher   +2 more
doaj   +1 more source

ATF4‐mediated stress response as a therapeutic vulnerability in chordoma

Molecular Oncology, EarlyView.
We screened 5 chordoma cell lines against 100+ inhibitors of epigenetic and metabolic pathways and kinases and identified halofuginone, a tRNA synthetase inhibitor. Mechanistically halofuginone induces an integrated stress response, with eIF2alpha phosphorylation, activation of ATF4 and its target genes CHOP, ASNS, INHBE leading to cell death ...
Lucia Cottone, James Dunford, Eleanor Calcutt, Vicki Gamble, Filiz Senbabaoglu Aksu, Lorena Ligammari, Georgina Wherry, Giorgia Gaeta, John C. Christianson, Adrienne M. Flanagan, Udo Oppermann, Adam P. Cribbs   +11 more
wiley   +1 more source