bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cosmic ray simulator: A versatile apparatus for quantitative studies on the interaction of cosmic rays with frozen solids by on line and in situ quadrupole mass spectrometry and Fourier transform infrared spectroscopy
Authors: Kaiser R. I. , Gabrysch A. , Roessler K. 
Published: July 2002

The cosmic ray simulator consists of a 50 ℓ cylindrical stainless steel chamber. A rotable cold finger milled of a silver (111) monocrystal optimizes heat conductivity and is connected to a programmable, closed cycle helium refrigerator allowing temperature control of an attached silver wafer between 10 and 340 K (±0.5 K). Oil-free ultrahigh vacuum (UHV) conditions of ≊10−10 mbar are provided by a membrane, drag, and cryopump, hence guaranteeing a vacuum system free of any contamination. Ice layers of defined crystal structures and reproducible thickness of (5±1) μm are achieved by depositing gases, e.g., CH4, CD4, CD4/O2, and CH4/O2, with a computer-assisted thermovalve on the cooled wafer. These frosts are irradiated at 10 and 50 K with 7.3 MeV protons and 9 MeV α particles of the compact cyclotron CV28 in Forschungszentrum Jülich up to doses of 150 eV per molecule, i.e., simulating the distribution maximum of galactic cosmic ray particles interacting with primordial matter in space during 0.7×109 yr. During the experiments, gas phase and solid state are monitored for the first time quantitatively on line and in situ by a quadrupole mass spectrometer (QMS) via matrix interval arithmetic and a Fourier transform infrared spectrometer (FTIR) in an absorption-reflection mode at 62.5°.
For the first time, a cosmic ray simulator allows detailed and reproducible mechanistic studies on the interaction of cosmic ray particles with frozen gases in space based on pressure conditions (hydrocarbon free UHV conditions, the limitation of condensations of residual gases during an experiment to less than one monolayer), temperature regime (the use of silver monocrystals, FTIR in reflection, optimized ion currents, and target thicknesses &lt;5 μm restrict temperature increasing to 14 K), and defined target systems. In combination with two on line and in situ analyses techniques, i.e., FTIR and QMS, the machine yields unprecedented options such as computing the heating of the ice surfaces directly exposed to the ion beam by a calibrated QMS and a complete quantification of product distribution. Preliminary results indicate a strong temperature-dependent component of the reaction mechanisms in the frosts: surface layers are heated by impinging ions to (14±1) K and yield (70%–100%) of higher molecular weight species, such as C11D24, whereas 10 K regions produce majority of simpler hydrocarbons, e.g., C3D8. Second, O2 contaminations influence the experiments dramatically by trapping of diffusive H atoms as O2H and, thus, yield oxygen-containing yellow to brown residues after heating to 293 K. Irradiation of pure methane targets, however, produce no residues. But an increasing concentration of H atoms exceeding (6%±3%) leads to ejection of up to 90% of the frosts into vacuum.
A surface constrained all-atom solvent model for effective simulations of polar solutions
Authors: King Gregory , Warshel Arieh 
Published: July 2002

A consistent simulation of ionic or strongly polar solutes in polar solvents presents a major challenge from both fundamental and practical aspects. The frequently used method of periodic boundary conditions (PBC) does not correctly take into account the symmetry of the solute field. Instead of using PBC, it is natural to model this type of system as a sphere (with the solute at the origin), but the boundary conditions to be used in such a model are not obvious. Early calculations performed with our surface constrained soft sphere dipoles (SCSSD) model indicated that the dipoles near the surface of the sphere will show unusual orientational preferences (they will overpolarize) unless a corrective force is included in the model, and thus we implemented polarization constraints in this spherical model of polar solutions. More recent approaches that treated the surface with stochastic dynamics, but did not take into account the surface polarization effects, were also found to exhibit these nonphysical orientational preferences. The present work develops a surface constrained all-atom solvent (SCAAS) model in order to consistently treat the surface polarization effects in all-atom molecular dynamics simulations. The SCAAS model, which was presented in a preliminary way in previous works, introduces surface constraints as boundary conditions in order to make the necessarily finite system behave as if it was part of an infinite system. The performance of the model with regard to various properties of bulk water is examined by comparing its results to those obtained by PBC simulations. The results obtained from SCAAS models of different sizes are found to be similar to each other and to the corresponding PBC results. The performance of the model in simulations of solvated ions is emphasized and a comparison of the results obtained with spheres of different sizes demonstrates that the model does not possess significant size dependence. This indicates that the model can be used with a relatively small number of solvent molecules for convergent simulation of structure, energetics, and dynamics of polar solutions. The much simpler fixed
center Langevin dipoles (FCLD) model is also examined and found to provide a
powerful tool for estimating solvation free energies. Finally, a preliminary
study of the dielectric properties of the SCAAS model is reported and the potential of this model for exploring the correct implementation of the solvent reaction field is discussed.
Density-functional methods give accurate vibrational frequencies and spin densities for phenoxyl radical
Authors: Qin Yue , Wheeler Ralph A. 
Published: July 2002

The structure, electronic spin density ratios, harmonic vibrational frequencies, and deuterium isotopic vibrational frequency shifts for phenoxyl radical, C6H5Ȯ, were calculated by using spin unrestricted Hartree–Fock (UHF), second-order Mo/ller–Plesset perturbation (UMP2), and various density functional (DF) and hybrid Hartree–Fock/density functional (HF/DF) methods with a 6–31G(d) basis set. Computed results are compared with experiment and with recently published complete active space self-consistent field (CASSCF) and unrestricted natural orbital-complete active space (UNO-CAS) calculations to evaluate the accuracy of DF and HF/DF methods for the highly delocalized, strongly correlated phenoxyl radical. Bond lengths and angles calculated by using DF and HF/DF methods appear as accurate as those obtained by using the UMP2 method. The correlation functional of Vosko, Wilk, and Nusair combined with Slater’s exchange functional (SVWN) gives a structure closest to the best available CASSCF calculations, with the structures from three parameter hybrid HF/DF methods (B3P86 and B3LYP) nearly as good. Electronic spin density ratios computed by using DF methods are closest to experimentally derived spin density ratios, UHF spin densities are the worst, and the hybrid HF/DF methods give intermediate quality spin density ratios. Unscaled vibrational frequencies from the DF and HF/DF methods are closer to experimentally measured frequencies than uniformly scaled UHF or UMP2 frequencies.
Unscaled frequencies calculated by using the B3LYP method, for example, differ from the nine experimentally observed frequencies by an average of only 22 cm−1. The vibrational mode of phenoxyl radical observed experimentally at 1552 cm−1 is confirmed to correspond to a C=C stretching vibration and the band observed at 1505 cm−1 is primarily a C–O stretch. Vibrational modes of phenoxyl radical shift to lower frequencies upon deuteration and the larger shift of the C=C stretch, compared to the C–O stretch, confirms their assignment. Thus density functional methods give electronic spin density ratios, vibrational frequencies, mode assignments, and isotopic frequency shifts in good agreement with experiment and with more expensive UNO-CAS//CASSCF calculations for phenoxyl radical.
Hamilton’s principle in stochastic mechanics
Authors: Pavon Michele 
Published: July 2002

In this paper we establish three variational principles that provide new foundations for Nelson’s stochastic mechanics in the case of nonrelativistic particles without spin. The resulting variational picture is much richer and of a different nature with respect to the one previously considered in the literature. We first develop two stochastic variational principles whose Hamilton–Jacobi-like equations are precisely the two coupled partial differential equations that are obtained from the Schrödinger equation (Madelung equations). The two problems are zero-sum, noncooperative, stochastic differential games that are familiar in the control theory literature. They are solved here by means of a new, absolutely elementary method based on Lagrange functionals. For both games the saddle-point equilibrium solution is given by the Nelson’s process and the optimal controls for the two competing players are precisely Nelson’s current velocity v and osmotic velocity u, respectively. The first variational principle includes as special cases both the Guerra–Morato variational principle [Phys. Rev. D 27, 1774 (1983)] and Schrödinger original variational derivation of the time-independent equation.
It also reduces to the classical least action principle when the intensity of the underlying noise tends to zero. It appears as a saddle-point action principle. In the second variational principle the action is simply the difference between the initial and final configurational entropy. It is therefore a saddle-point entropy production principle. From the variational principles it follows, in particular, that both v(x,t) and u(x,t) are gradients of appropriate principal functions. In the variational principles, the role of the background noise has the intuitive meaning of attempting to contrast the more classical mechanical features of the system by trying to maximize the action in the first principle and by trying to increase the entropy in the second. Combining the two variational principles, we get the quantum Hamilton principle, i.e., a variational characterization of the logarithm of the wave function ψ. The Lagrangian is the Lagrangian of classical mechanics with the complex-valued velocity v−iu replacing the classical velocity. The dynamics is given by a stochastic differential equation for real-valued diffusions with complex-valued drift and driving noise processes. From the variational principle we derive a Newton-type law. We finally define the momentum process and show that its mean and variance coincide with those of the quantum momentum operator.
Thrombomucin, a Novel Cell Surface Protein that Defines Thrombocytes and Multipotent Hematopoietic Progenitors
Authors: McNagny Kelly M. , Pettersson Inger , Rossi Fabio , Flamme Ingo , Shevchenko Andrej , Mann Matthias , Graf Thomas 
Published: July 2002

MEP21 is an avian antigen specifically expressed on the surface of Myb-Ets–transformed multipotent hematopoietic precursors (MEPs) and of normal thrombocytes. Using nanoelectrospray tandem mass spectrometry, we have sequenced and subsequently cloned the MEP21 cDNA and named the gene thrombomucin as it encodes a 571–amino acid protein with an extracellular domain typical of the mucin family of proteoglycans. Thrombomucin is distantly related to CD34, the best characterized and most used human hematopoietic stem cell marker. It is also highly homologous in its transmembrane/intracellular domain to podocalyxinlike protein–1, a rabbit cell surface glycoprotein of kidney podocytes.
Single cell analysis of yolk sac cells from 3-d-old chick embryos revealed that thrombomucin is expressed on the surface of both lineage-restricted and multipotent progenitors. In the bone marrow, thrombomucin is also expressed on mono- and multipotent progenitors, showing an overlapping but distinct expression pattern from that of the receptor-type stem cell marker c-kit. These observations strengthen the notion that the Myb-Ets oncoprotein can induce the proliferation of thrombomucin-positive hematopoietic progenitors that have retained the capacity to differentiate along multiple lineages. They also suggest that thrombomucin and CD34 form a family of stem cell–specific proteins with possibly overlapping functions in early hematopoietic progenitors.
Ip-10 Inhibits Epidermal Growth Factor–Induced Motility by Decreasing Epidermal Growth Factor Receptor–Mediated Calpain Activity
Authors: Shiraha Hidenori , Glading Angela , Gupta Kiran , Wells Alan 
Published: July 2002

During wound healing, fibroblasts are recruited from the surrounding tissue to accomplish repair. The requisite migration and proliferation of the fibroblasts is promoted by growth factors including those that activate the epidermal growth factor receptor (EGFR). Counterstimulatory factors in wound fluid are postulated to limit this response; among these factors is the ELR-negative CXC chemokine, interferon inducible protein-10 (IP-10). We report here that IP-10 inhibited EGF- and heparin-binding EGF-like growth factor–induced Hs68 human dermal fibroblast motility in a dose-dependent manner (to 52% and 44%, respectively, at 50 ng/ml IP-10), whereas IP-10 had no effect on either basal or EGFR-mediated mitogenesis (96 ± 15% at 50 ng/ml). These data demonstrate for the first time a counterstimulatory effect of IP-10 on a specific induced fibroblast response, EGFR-mediated motility.To define the molecular basis of this negative transmodulation of EGFR signaling, we found that IP-10 did not adversely impact receptor or immediate postreceptor signaling as determined by tyrosyl phosphorylation of EGFR and two major downstream effectors phospholipase C-γ and erk mitogen-activated protein kinases. Morphological studies suggested which biophysical steps may be affected by demonstrating that IP-10 treatment resulted in an elongated cell morphology reminiscent of failure to detach the uropod; in support of this, IP-10 pretreatment inhibited EGF-induced cell detachment. These data suggested that calpain activity may be involved. The cell permeant agent, calpain inhibitor I, limited EGF-induced motility and de-adhesion similarly to IP-10. IP-10 also prevented EGF- induced calpain activation (reduced by 71 ± 7%). That this inhibition of EGF-induced calpain activity was secondary to IP-10 initiating a cAMP-protein kinase A-calpain cascade is supported by the following evidence: (a) the cell permeant analogue 8-(4-chlorophenylthio)-cAMP (CPT-cAMP) prevented EGF-induced calpain activity and motility; (b) other ELR-negative CXC chemokines, monokine induced by IFN-γ and platelet factor 4 that also generate cAMP, inhibited EGF-induced cell migration and calpain activation; and (c) the protein kinase A inhibitor Rp-8-Br-cAMPS abrogated IP-10 inhibition of cell migration, cell detachment, and calpain activation. Our findings provide a model by which IP-10 suppresses EGF-induced cell motility by inhibiting EGF-induced detachment of the trailing edges of motile cells.
Mutational analysis of the interaction between albumin‐binding domain from streptococcal protein G and human serum albumin
Authors: Linhult Martin , Binz Hans Kaspar , Uhlén Mathias , Hober Sophia 
Published: July 2002

AbstractStreptococcal protein G (SpG) is a bacterial cell surface receptor exhibiting affinity to both human immunoglobulin (IgG) and human serum albumin (HSA). Interestingly, the serum albumin and immunoglobulin‐binding activities have been shown to reside at functionally and structurally separated receptor domains. The binding domain of the HSA‐binding part has been shown to be a 46‐residue triple α‐helical structure, but the binding site to HSA has not yet been determined. Here, we have investigated the precise binding region of this bacterial receptor by protein engineering applying an alanine‐scanning procedure followed by binding studies by surface plasmon resonance (SPR). The secondary structure as well as the HSA binding of the resulting albumin‐binding domain (ABD) variants were analyzed using circular dichroism (CD) and affinity blotting. The analysis shows that the HSA binding involves residues mainly in the second α‐helix.
High‐Throughput, Living Single‐Cell, Multiple Secreted Biomarker Profiling Using Microfluidic Chip and Machine Learning for Tumor Cell Classification
Authors: Wang Chao , Wang Chunhua , Wu Yu , Gao Jianwei , Han Yingkuan , Chu Yujin , Qiang Le , Qiu Jiaoyan , Gao Yakun , Wang Yanhao , Song Fangteng , Wang Yihe , Shao Xiaowei , Zhang Yu , Han Lin 
Published: April 2022

AbstractSecreted proteins provide abundant functional information on living cells and can be used as important tumor diagnostic markers, of which profiling at the single‐cell level is helpful for accurate tumor cell classification. Currently, achieving living single‐cell multi‐index, high‐sensitivity, and quantitative secretion biomarker profiling remains a great challenge. Here, a high‐throughput living single‐cell multi‐index secreted biomarker profiling platform is proposed, combined with machine learning, to achieve accurate tumor cell classification. A single‐cell culture microfluidic chip with self‐assembled graphene oxide quantum dots (GOQDs) enables high‐activity single‐cell culture, ensuring normal secretion of biomarkers and high‐throughput single‐cell separation, providing sufficient statistical data for machine learning. At the same time, the antibody barcode chip with self‐assembled GOQDs performs multi‐index, highly sensitive, and quantitative detection of secreted biomarkers, in which each cell culture chamber covers a whole barcode array. Importantly, by combining the K‐means strategy with machine learning, thousands of single tumor cell secretion data are analyzed, enabling tumor cell classification with a recognition accuracy of 95.0%. In addition, further profiling of the grouping results reveals the unique secretion characteristics of subgroups. This work provides an intelligent platform for high‐throughput living single‐cell multiple secretion biomarker profiling, which has broad implications for cancer investigation and biomedical research.
Giant Spin Hall Effect and Spin–Orbit Torques in 5d Transition Metal–Aluminum Alloys from Extrinsic Scattering
Authors: Wang Peng , Migliorini Andrea , Yang See‐Hun , Jeon Jae‐Chun , Kostanovskiy Ilya , Meyerheim Holger , Han Hyeon , Deniz Hakan , Parkin Stuart S. P. 
Published: April 2022

AbstractThe generation of spin currents from charge currents via the spin Hall effect (SHE) is of fundamental and technological interest. Here, some of the largest SHEs yet observed via extrinsic scattering are found in a large class of binary compounds formed from a 5d element and aluminum, with a giant spin Hall angle (SHA) of ≈1 in the compound Os22Al78. A critical composition of the 5d element is found at which there is a structural phase boundary between poorly and highly textured crystalline material, where the SHA exhibits its largest value. Furthermore, a systematic increase is found in the spin Hall conductivity (SHC) and SHA at this critical composition as the atomic number of the 5d element is systematically increased. This clearly shows that the SHE and SHC are derived from extrinsic scattering mechanisms related to the potential mismatch between the 5d element and Al. These studies show the importance of extrinsic mechanisms derived from potential mismatch as a route to obtaining large spin Hall angles with high technological impact. Indeed, it is demonstrated that a state‐of‐the‐art racetrack device has a several‐fold increased current‐induced domain wall efficiency using these materials as compared to prior‐art materials.
Structured bubbling in layered gas‐fluidized beds subject to vibration: A CFD‐DEM study
Authors: Guo Qiang , Boyce Christopher M. 
Published: April 2022

AbstractBubble dynamics in gas fluidized beds are mathematically chaotic and difficult to predict. Various ways have been proposed in the past to alter the overall bubble dynamics to improve particular processes. In particular, it has been shown that pulsed gas flow and vibration can be used to transform the chaotic motion of gas bubbles into a dynamically structured pattern. The structured bubbling pattern does not change with the system width, opening opportunities to address key issues in scaling up gas‐solids bubbling fluidized beds. However, the pattern can only maintain for a limited particle height, well below the height of most industrial fluidized beds. Herein, we proposed to use a layered configuration with multiple stages of gas distributors to maintain the ordered bubbling structure to a higher particle height. Computational fluid dynamics‐discrete element method (CFD‐DEM) simulations performed here demonstrate the effectiveness and key parameters for maintaining structure in the proposed design, providing potential for industrial use.
Genetic analysis using targeted exome sequencing of 53 Vietnamese children with developmental and epileptic encephalopathies
Authors: Hieu Nguyen Le Trung , Thu Nguyen Thuy Minh , Ngan Le Tran Anh , Van Le Thi Khanh , Huy Do Phuoc , Linh Pham Thi Truc , Mai Nguyen Thi Quynh , Hien Huynh Thi Dieu , Hang Do Thi Thu 
Published: April 2022

AbstractDevelopmental and epileptic encephalopathies (DEE) refers to a group of rare and severe neurodevelopmental disorders where genetic etiologies can play a major role. This study aimed to elucidate the genetic etiologies of a cohort of 53 Vietnamese patients with DEE. All patients were classified into known electroclinical syndromes where possible. Exome sequencing (ES) followed by a targeted analysis on 294 DEE‐related genes was then performed. Patients with identified causative variants were followed for 6 months to determine the impact of genetic testing on their treatment. The diagnostic yield was 38.0% (20/53), which was significantly higher in the earlier onset group (<12 months) than in the later onset group (≥12 months). The 19 identified variants belonged to 11 genes with various cellular functions. Genes encoding ion channels especially sodium voltage‐gated channel were the most frequently involved. Most variants were missense variants and located in key protein functional domains. Four variants were novel and four had been reported previously but in different phenotypes. Within 6 months of further follow‐up, treatment changes were applied for six patients based on the identified disease‐causing variants, with five patients showing a positive impact. This is the first study in Vietnam to analyze the genetics of DEE. This study confirms the strong involvement of genetic etiologies in DEE, especially early onset DEE. The study also contributes to clarify the genotype–phenotype correlations of DEE and highlights the efficacy of targeted ES in the diagnosis and treatment of DEE.