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

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~$h^{-1}$~Mpc~$<$ SGY~$<$ 16~$h^{-1}$ 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~$h^{-1}$~Mpc~$<$ SGY~$<$ 27~$h^{-1}$~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~$\approx$~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