1,104 research outputs found
Mass Spectra Prediction with Structural Motif-based Graph Neural Networks
Mass spectra, which are agglomerations of ionized fragments from targeted
molecules, play a crucial role across various fields for the identification of
molecular structures. A prevalent analysis method involves spectral library
searches,where unknown spectra are cross-referenced with a database. The
effectiveness of such search-based approaches, however, is restricted by the
scope of the existing mass spectra database, underscoring the need to expand
the database via mass spectra prediction. In this research, we propose the
Motif-based Mass Spectrum Prediction Network (MoMS-Net), a system that predicts
mass spectra using the information derived from structural motifs and the
implementation of Graph Neural Networks (GNNs). We have tested our model across
diverse mass spectra and have observed its superiority over other existing
models. MoMS-Net considers substructure at the graph level, which facilitates
the incorporation of long-range dependencies while using less memory compared
to the graph transformer model.Comment: 19 pages, 3figure
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Systemic control of immune cell development by integrated carbon dioxide and hypoxia chemosensation in Drosophila.
Drosophila hemocytes are akin to mammalian myeloid blood cells that function in stress and innate immune-related responses. A multi-potent progenitor population responds to local signals and to systemic stress by expanding the number of functional blood cells. Here we show mechanisms that demonstrate an integration of environmental carbon dioxide (CO2) and oxygen (O2) inputs that initiate a cascade of signaling events, involving multiple organs, as a stress response when the levels of these two important respiratory gases fall below a threshold. The CO2 and hypoxia-sensing neurons interact at the synaptic level in the brain sending a systemic signal via the fat body to modulate differentiation of a specific class of immune cells. Our findings establish a link between environmental gas sensation and myeloid cell development in Drosophila. A similar relationship exists in humans, but the underlying mechanisms remain to be established
Ginseng and Its Active Components Ginsenosides Inhibit Adipogenesis in 3T3-L1 Cells by Regulating MMP-2 and MMP-9
The growth and development of adipose tissue are believed to require adipogenesis, angiogenesis, and extracellular matrix remodeling. As our previous study revealed that ginseng reduces adipose tissue mass in part by decreasing matrix metalloproteinase (MMP) activity in obese mice, we hypothesized that adipogenesis can be inhibited by ginseng and its active components ginsenosides (GSs). Treatment of 3T3-L1 adipocytes with Korean red ginseng extract (GE) inhibited lipid accumulation and the expression of adipocyte-specific genes (PPARγ, C/EBPα, aP2, and leptin). GE decreased both the mRNA levels and activity of MMP-2 and MMP-9 in 3T3-L1 cells. These effects were further inhibited by total GSs (TGSs) and individual GSs. TGSs and individual GSs also significantly decreased MMP-2 and MMP-9 reporter gene activities in the presence of phorbol 12-myristate 13-acetate (PMA), the MMP inducer. Among the GSs, Rb1 most effectively inhibited MMP activity. In addition, PMA treatment attenuated the inhibitory actions of GE and GSs on adipogenesis. Moreover, GE and GSs reduced the expression of NF-κB and AP-1, the transcription factors of MMP-2 and MMP-9. These results demonstrate that ginseng, in particular GSs, effectively inhibits adipogenesis and that this process may be mediated in part through the suppression of MMP-2 and MMP-9. Thus, ginseng and GSs likely have therapeutic potential for controlling adipogenesis
Colloidal dynamics and elasticity of dense wax particle suspensions over a wide range of volume fractions when tuning the softness by temperature
We report on the colloidal dynamics and rheology of liquid droplet emulsions and solid particle suspensions over a wide range of volume fractions. Diffusing wave spectroscopy and rheometry were utilized to study the micro/macroscale properties of 1-eicosene wax particles dispersed in water. By changing the temperature, the wax droplets change their properties from soft to hard or vice versa, which, depending on the density, may affect the system properties in a different way. Our measurements in the high volume fraction regime focus on the elasticity index and the plateau storage modulus, G'p. The results show a more pronounced increase of the modulus for the wax particle suspensions around the random close packing volume fraction compared to the emulsion
Large-scale filamentary structures around the Virgo cluster revisited
We revisit the filamentary structures of galaxies around the Virgo cluster,
exploiting a larger dataset based on the HyperLeda database than previous
studies. In particular, this includes a large number of low-luminosity
galaxies, resulting in better sampled individual structures. We confirm seven
known structures in the distance range 4~~Mpc~ SGY~ 16~
Mpc, now identified as filaments, where SGY is the axis of the supergalactic
coordinate system roughly along the line of sight. The Hubble diagram of the
filament galaxies suggests they are infalling toward the main-body of the Virgo
cluster. We propose that the collinear distribution of giant elliptical
galaxies along the fundamental axis of the Virgo cluster is smoothly connected
to two of these filaments (Leo~II~A and B). Behind the Virgo cluster
(16~~Mpc~ SGY~ 27~~Mpc), we also identify a new filament
elongated toward the NGC 5353/4 group ("NGC 5353/4 filament") and confirm a
sheet that includes galaxies from the W and M clouds of the Virgo cluster ("W-M
sheet"). In the Hubble diagram, the NGC 5353/4 filament galaxies show infall
toward the NGC 5353/4 group, whereas the W-M sheet galaxies do not show hints
of gravitational influence from the Virgo cluster. The filamentary structures
identified can now be used to better understand the generic role of filaments
in the build-up of galaxy clusters at z~~0.Comment: 8 pages, 4 figures, accepted for publication in Ap
Brownian dynamics of colloidal microspheres with tunable elastic properties from soft to hard
We study the Brownian thermal motion of a colloidal model system made by emulsifying hot liquid α-eicosene wax into an aqueous surfactant solution of sodium dodecyl sulfate (SDS). When this waxy oil-in-water emulsion is cooled below α- eicosene's melting point of Tc ≃ 25 °C, the microscale emulsion droplets solidify, effectively yielding a dispersed particulate system. So, the interiors of these wax droplets can be tuned from a viscous liquid to an elastic solid through very modest changes in absolute temperature. Using the multiple light scattering technique of diffusing wave spectroscopy (DWS), which is very sensitive to small-scale motion and shape fluctuations of dispersed colloidal objects, we show that the thermal fluctuations of the interfaces of these liquid droplets at higher temperature, seen in the DWS intensity–intensity correlation function at early times, effectively disappear when these droplets solidify at lower temperature. Thus, we show that the early-time behavior of this DWS correlation function can be used to probe mechanical properties of viscoelastic soft materials dispersed as droplets
Rapid Dye Regeneration Mechanism of Dye-Sensitized Solar Cells
During the light-harvesting process of dye-sensitized solar cells (DSSCs), the hole localized on the dye after the charge separation yields an oxidized dye, D^+. The fast regeneration of D^+ using the redox pair (typically the I^–/I_(3)^– couple) is critical for the efficient DSSCs. However, the kinetic processes of dye regeneration remain uncertain, still promoting vigorous debates. Here, we use molecular dynamics simulations to determine that the inner-sphere electron-transfer pathway provides a rapid dye regeneration route of ∼4 ps, where penetration of I^− next to D^+ enables an immediate electron transfer, forming a kinetic barrier. This explains the recently reported ultrafast dye regeneration rate of a few picoseconds determined experimentally. We expect that our MD based comprehensive understanding of the dye regeneration mechanism will provide a helpful guideline in designing TiO_2−dye−electrolyte interfacial systems for better performing DSSCs
Effect of heavy metals on phenylpropanoid biosynthesis in Euonymus alatus
The productivity of the phenylpropanoid biosynthesis pathway in plants varies depending on the type of stress. In this work, we looked into how different phenylpropanoid chemicals accumulated in Euonymus alatus following exposure to different concentrations of CuCl2 (0.1, 0.5, and 1 mM), HgCl2 (0.1, 0.5, and 1 mM), and NiSO4 (10, 50, and 100 mM). We analyzed some of the individual phenolic chemicals by high-performance liquid chromatography (HPLC). In nearly all cases, rutin showed the largest concentration among the phenylpropanoid chemicals, followed by epicatechin, sinapic acid, p-coumaric acid, trans-cinnamic acid, ferulic acid, and caffeic acid. However, due to the change in the concentration of the heavy metals, the amount of phenylpropanoid changed. The highest accumulation of phenylpropanoid was documented in 0.1 mM CuCl2, whereas it was reduced in 1 mM HgCl2 exposed plants. These findings unequivocally demonstrate that the phenylpropanoid metabolic pathway took part in the heavy metal tolerance process, which shielded E. alatus from the oxidative damage brought on by heavy metals. Thus, under a variety of environmental stress situations, this species with a high tolerance to heavy metals may survive
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