| 1. |
- Ambikan, Anoop T., et al.
(författare)
-
Systems-level temporal immune-metabolic profile in Crimean-Congo hemorrhagic fever virus infection
- 2023
-
Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 120:37
-
Tidskriftsartikel (refereegranskat)abstract
- Crimean-Congo hemorrhagic fever (CCHF) caused by CCHF virus (CCHFV) is one of the epidemic-prone diseases prioritized by the World Health Organisation as public health emergency with an urgent need for accelerated research. The trajectory of host response against CCHFV is multifarious and remains unknown. Here, we reported the temporal spectrum of pathogenesis following the CCHFV infection using genome-wide blood transcriptomics analysis followed by advanced systems biology analysis, temporal immune-pathogenic alterations, and context-specific progressive and postinfection genome-scale metabolic models (GSMM) on samples collected during the acute (T0), early convalescent (T1), and convalescent-phase (T2). The interplay between the retinoic acid-inducible gene-I-like/nucleotide-binding oligomerization domain-like receptor and tumor necrosis factor signaling governed the trajectory of antiviral immune responses. The rearrangement of intracellular metabolic fluxes toward the amino acid metabolism and metabolic shift toward oxidative phosphorylation and fatty acid oxidation during acute CCHFV infection determine the pathogenicity. The upregulation of the tricarboxylic acid cycle during CCHFV infection, compared to the noninfected healthy control and between the severity groups, indicated an increased energy demand and cellular stress. The upregulation of glycolysis and pyruvate metabolism potentiated energy generation through alternative pathways associated with the severity of the infection. The downregulation of metabolic processes at the convalescent phase identified by blood cell transcriptomics and single-cell type proteomics of five immune cells (CD4+ and CD8+ T cells, CD14+ monocytes, B cells, and NK cells) potentially leads to metabolic rewiring through the recovery due to hyperactivity during the acute phase leading to post-viral fatigue syndrome.
|
|
| 2. |
- Argun, Aykut, et al.
(författare)
-
Non-Boltzmann stationary distributions and nonequilibrium relations in active baths
- 2016
-
Ingår i: Physical Review E - Statistical, Nonlinear, and Soft Matter Physics. - 1539-3755 .- 1550-2376. ; 94
-
Tidskriftsartikel (refereegranskat)abstract
- Most natural and engineered processes, such as biomolecular reactions, protein folding, and population dynamics, occur far from equilibrium and therefore cannot be treated within the framework of classical equilibrium thermodynamics. Here we experimentally study how some fundamental thermodynamic quantities and relations are affected by the presence of the nonequilibrium fluctuations associated with an active bath. We show in particular that, as the confinement of the particle increases, the stationary probability distribution of a Brownian particle confined within a harmonic potential becomes non-Boltzmann, featuring a transition from a Gaussian distribution to a heavy-tailed distribution. Because of this, nonequilibrium relations (e.g., the Jarzynski equality and Crooks fluctuation theorem) cannot be applied. We show that these relations can be restored by using the effective potential associated with the stationary probability distribution. We corroborate our experimental findings with theoretical arguments.
|
|
| 3. |
- Aydin, Alhun, et al.
(författare)
-
Discrete and Weyl density of states for photonic dispersion relation
- 2019
-
Ingår i: Physica Scripta. - : IOP Publishing. - 0031-8949 .- 1402-4896. ; 94:10
-
Tidskriftsartikel (refereegranskat)abstract
- The current density of states (DOS) calculations do not take into account the essential discretenessof the state space, since they rely on the unbounded continuum approximation. Recently, discrete DOS based on the quantum-mechanically allowable minimum energy interval has been introducedfor quadratic dispersion relation. In this work, we consider systems exhibiting photonic (photon-like) dispersion relation and calculate the related density and number of states (NOS). Also, a Weyl's conjecture-based DOS function is calculated for photons and acoustic phonons at low frequency limit,by considering the bounded continuum approach. We show that discrete DOS function reducesto expressions of bounded and unbounded continua in the appropriate limits. The uctuationsin discrete DOS completely disappear under accumulation operators. It's interesting that relativeerrors of NOS and DOS functions with respect to discrete ones have exactly the same character withthe ones of quadratic dispersion relation. Furthermore, the application of discrete and Weyl DOS for the calculation of internal energy of a photon gas is presented and importance of discrete DOSis discussed. It's shown that discrete DOS function given in this work needs to be used wheneverthe low energy levels of a physical system are heavily occupied.
|
|
