Abstract Background In a previous paper, we classified populated HLA class I alleles into supertypes and subtypes based on the similarity of 3D landscape of peptide binding grooves, using newly defined structure distance metric and hierarchical clustering approach. Compared to other approaches, our method achieves higher correlation with peptide binding specificity, intra-cluster similarity (cohesion), and robustness. Here we introduce HLA-Clus, a Python package for clustering HLA Class I alleles using the method we developed recently and describe additional features including a new nearest neighbor clustering method that facilitates clustering based on user-defined criteria. Results The HLA-Clus pipeline includes three stages: First, HLA Class I structural models are coarse grained and transformed into clouds of labeled points. Second, similarities between alleles are determined using a newly defined structure distance metric that accounts for spatial and physicochemical similarities. Finally, alleles are clustered via hierarchical or nearest-neighbor approaches. We also interfaced HLA-Clus with the peptide:HLA affinity predictor MHCnuggets. By using the nearest neighbor clustering method to select optimal allele-specific deep learning models in MHCnuggets, the average accuracy of peptide binding prediction of rare alleles was improved. Conclusions The HLA-Clus package offers a solution for characterizing the peptide binding specificities of a large number of HLA alleles. This method can be applied in HLA functional studies, such as the development of peptide affinity predictors, disease association studies, and HLA matching for grafting. HLA-Clus is freely available at our GitHub repository (https://github.com/yshen25/HLA-Clus).
Endometrial extracellular vesicles (EVs) are emerging as important players in reproductive biology. However, how their proteome is regulated throughout the menstrual cycle is not known. Such information can provide novel insights into biological processes critical for embryo development, implantation, and successful pregnancy. Using mass spectrometry‐based quantitative proteomics, we show that small EVs (sEVs) isolated from uterine lavage of fertile women (UL‐sEV), compared to infertile women, are laden with proteins implicated in antioxidant activity (SOD1, GSTO1, MPO, CAT). Functionally, sEVs derived from endometrial cells enhance antioxidant function in trophectoderm cells. Moreover, there was striking enrichment of invasion‐related proteins (LGALS1/3, S100A4/11) in fertile UL‐sEVs in the secretory (estrogen plus progesterone‐driven, EP) versus proliferative (estrogen‐driven, E) phase, with several players downregulated in infertile UL‐sEVs. Consistent with this, sEVs from EP‐ versus E‐primed endometrial epithelial cells promote invasion of trophectoderm cells. Interestingly, UL‐sEVs from fertile versus infertile women carry known players/predictors of embryo implantation (PRDX2, IDHC), endometrial receptivity (S100A4, FGB, SERPING1, CLU, ANXA2), and implantation success (CAT, YWHAE, PPIA), highlighting their potential to inform regarding endometrial status/pregnancy outcomes. Thus, this study provides novel insights into proteome reprograming of sEVs and soluble secretome in uterine fluid, with potential to enhance embryo implantation and hence fertility.
In order to establish data to be used for comparison with future evolution related to climate change, physical, chemical and biological characteristics of dew and rainwater as collected during the 2005 dry season (plus a few data during the 2004 dry season) are reported. They have been collected in two characteristic tropical islands of French Polynesia, Tikehau (TKH), a low-lying coral atoll in the Tuamotu Archipelago, and the mountainous Tahiti island at the University of French Polynesia (TAH). Trade winds dominate the trajectory of air masses, ensuring constant temperature and humidity to the lower layers of the atmosphere where dew forms. In addition to the comparison of dew yields with a physical model using simple meteorological data (air and dew point temperatures, windspeed, cloud cover), the following parameters were studied: pH, electrical conductivity (EC), total dissolved solids (TDS), total hardness, suspended matter, ion concentration with major cations (Ca2+, K+, Na+, Mg2+, NH4+) and major anions (Cl−, SO42−, NO3−), reviviscible aerobe microorganisms and compared to two Polynesian spring waters (“Eau Royale” and “Vaimato”). Dew, with a chemical composition mainly consisting of Na+, Ca2+, Mg2+, Cl− and SO42−, exhibits much higher ion concentration than rain and compares well with the composition of local spring waters. The values of pH, EC and TDS are larger in dew than in rainwater. At TAH, the volume weighted mean (VWM) pH values of dew were 6.05 in 2004 and 5.23 in 2005, larger than the pH of rain (4.69). The VWM dew EC (at TAH, 203 μS·cm−1 in 2004 and 237 μS·cm−1 in 2005; 321 μS·cm−1 at TKH in 2005) and dew TDS (152 mg·L−1 at TAH and 225 mg·L−1 at TKH) were higher than the corresponding quantities in rain. Mean total hardness (TH) values of dew water are much higher than in rainwater (2.8 for dew versus 0.5 for rain at TAH and 5.7 for dew versus 0.5 for rain at TKH). Ions Na+, Mg2+ and Cl− are clearly of sea origin while the presence of Ca2+ is due to coral particles. From their chemical characteristics, dew and rainwater could be used as an alternative source of water in dry season but, due to the presence of reviviscible aerobe microorganisms at 22 °C and 36 °C (>300 CFU·mL−1), water must be disinfected to be potable.
The thermal electron emission rate constant for C$_{60}^-$ has been deduced over a range of 4 eV internal energy from storage ring measurements of the decays of ions reheated with single photons absorption. The thermal radiation from the ions is quantified with respect to continuous cooling and discrete photon quenching.
Within the framework of a Dirac bubble potential model for the C60 fullerene shell, we calculated the time delay in slow-electron elastic scattering by C60. It appeared that the time of transmission of an electron wave packet through the Dirac bubble potential sphere that simulates a real potential of the C60 cage exceeds by more than an order of magnitude the transmission time via a single atomic core. Resonances in the time delays are due to the temporary trapping of electron into quasi-bound states before it leaves the interaction region.
Melby Johny, Jolijn Onvlee, Thomas Kierspel
et al.
We demonstrate the spatial separation of pyrrole and pyrrole(H$_2$O) clusters from the other atomic and molecular species in a supersonically-expanded beam of pyrrole and traces of water seeded in high-pressure helium gas. The experimental results are quantitatively supported by simulations. The obtained pyrrole(H$_2$O) cluster beam has a purity of ~100 %. The extracted rotational temperature of pyrrole and pyrrole(H$_2$O) from the original supersonic expansion is $T_\text{rot}=0.8\pm0.2$ K, whereas the temperature of the deflected, pure-pyrrole(H$_2$O) part of the molecular beam corresponds to $T_\text{rot}\approx0.4$ K.
The mechanisms of phase change of argon during picosecond laser internal ablation are studied using molecular dynamics simulations. It is found that propagation of stress wave and fluctuation of temperature are periodical. The phase change process from solid to liquid to supercritical fluid then back to solid occurs as combined results of heating and the propagation of tensile stress wave induced by the laser pulse and the limited internal space.
We re-examine the series of resonances found earlier in atomic three-body systems by solving the Faddeev-Merkuriev integral equations. These resonances are rather broad and line-up at each threshold with gradually increasing gaps, the same way for all thresholds and irrespective of the spatial symmetry. We relate these resonances to the Gailitis mechanism, which is a consequence of the polarization potential.
Brian J. Harding, Jonathan J. Makela, John W. Meriwether
AbstractWe introduce a technique for estimating the regional thermospheric wind field from measurements made by a network of interferometers. Unlike previous work, this technique does not make assumptions about the functional form of the wind field and instead uses inverse theory to find the smoothest wind field that agrees with the measurements. This technique is general and applies to any network making radial velocity measurements. We show reconstructions of the thermospheric wind field over the eastern United States and over eastern Brazil, using data from two distinct networks of Fabry‐Perot interferometers measuring the Doppler shift of the 630.0 nm airglow emission. In Brazil, we find direct evidence of a convergent wind field during the period of rapid thermospheric temperature increase associated with the equatorial midnight temperature maximum.
Several versions of low‐ to middle‐latitude geomagnetic indices are examined throughout a 24 year interval and during storm time with respect to a normalized epoch timeline based on several key storm features. In particular, we conduct a quantitative comparison of the storm time superpositioning of the Dst, SYM‐H, and 1 min U.S. Geological Survey Dst indices using error analysis and employing descriptive statistics to assess the similarities and differences between them. The events are then categorized by storm intensity and examined as a function of the storm phase. While the indices are highly correlated with each other, dramatic deviation between the indices exists at certain storm epoch times. In particular, the error increases at storm peak and especially for more intense storms. The differences at storm peak are, on average, 20% of the peak value of the indices. These differences arise from the choice of magnetometer stations to include in each index and the various methodologies used to compile the individual perturbation measurements into a global value. The conclusions are that multiple indices should be considered when determining low‐ to middle‐latitude magnetic perturbations and that the difference between the indices should be considered as an error estimate on these values.
We study the elastic scattering of atomic argon by electron in the presence of a bichromatic laser field in the second Born approximation. The target atom is approximated by a simple screening potential and the continuum states of the impinging and emitting electrons are described as Volkov states. We evaluate the S-matrix elements numerically. The dependence of differential cross section on the relative phase between the two laser components is presented. The results obtained in the first and second Born approximation are compared and analysed.
In this study, we investigate the structure of the polar alkali-Strontium diatomic molecules as possible candidates for the realization of samples of new species of ultracold polar molecules. Using a quantum chemistry approach based on Effective Core Potentials and Core Polarization Potentials, we model these systems as effective three valence electron systems, allowing for calculation of electronic properties with Full Configuration Interaction. The potential curve and the permanent dipole moment of the $^2Σ^+$ ground state are determined as functions of the internuclear distances for LiSr, NaSr, KSr, RbSr, and CsSr molecules. These molecules are found to exhibit a significant permanent dipole moment, though smaller than those of the alkali-Rb molecules.
Sandip De, S. Alireza Ghasemi, Alexander Willand
et al.
We re-examine the question of whether the geometrical ground state of neutral and ionized clusters are identical. Using a well defined criterion for being "identical" together, the extensive sampling methods on a potential energy surface calculated by density functional theory, we show that the ground states are in general different. This behavior is to be expected whenever there are metastable configurations which are close in energy to the ground state, but it disagrees with previous studies.
Hui Li, Robert J. Le Roy, Pierre-Nicholas Roy
et al.
Clusters of para-hydrogen (pH2) have been predicted to exhibit superfluid behavior, but direct observation of this phenomenon has been elusive. Combining experiments and theoretical simulations, we have determined the size evolution of the superfluid response of pH2 clusters doped with carbon dioxide (CO2). Reduction of the effective inertia is observed when the dopant is surrounded by the pH2 solvent. This marks the onset of molecular superfluidity in pH2. The fractional occupation of solvation rings around CO2 correlates with enhanced superfluid response for certain cluster sizes.