gebhart/patrepeval huggingface dataset:
From Rhesus macaque to human: structural evolutionary pathways for immunoglobulin G subclasses (2019)

The Old World monkey, Rhesus macaque (Macaca mulatta, Mm), is frequently used as a primate model organism in the study of human disease and to test new vaccines/antibody treatments despite diverging before chimpanzees and orangutans. Mm and humans share 93% genome identity with substantial differences in the genes of the adaptive immune system that lead to different functional IgG subclass characteristics, Fcγ receptors expressed on innate immune cells, and biological interactions. These differences put limitations on Mm use as a primary animal model in the study of human disease and to test new vaccines/antibody treatments. Here, we comprehensively analyzed molecular properties of the Fc domain of the four IgG subclasses of Rhesus macaque to describe potential mechanisms for their interactions with effector cell Fc receptors. Our studies revealed less diversity in the overall structure among the Mm IgG Fc, with MmIgG1 Fc being the most structurally like human IgG3, although its CH2 loops and N297 glycan mobility are comparable to human IgG1. Furthermore, the Fcs of Mm IgG3 and 4 lack the structural properties typical for their human orthologues that determine IgG3’s reduced interaction with the neonatal receptor and IgG4’s ability for Fab-arm exchange and its weaker Fcγ receptor interactions. Taken together, our data indicate that MmIgG1-4 are less structurally divergent than the human IgGs, with only MmIgG1 matching the molecular properties of human IgG1 and 3, the most active IgGs in terms of Fcγ receptor binding and Fc-mediated functions. PDB accession numbers for deposited structures are 6D4E, 6D4I, 6D4M, and 6D4N for MmIgG1 Fc, MmIgG2 Fc, MmIgG3 Fc, and MmIgG4 Fc, respectively.
Role of hydrogen surface coverage during anodic plasma deposition of hydrogenated nanocrystalline germanium (1998)

Nanocrystalline Ge:H films were deposited on the anode of a conventional plasma-enhanced chemical vapor deposition system using highly H2-diluted GeH4 as source gas. The structural changes with substrate temperature, hydrogen dilution, and rf power were investigated by x-ray diffraction and Raman scattering. The hydrogen content and H bonding configuration were determined by infrared absorption spectroscopy. It was found that increased rf power mainly favors nucleation of grains while increased H2 dilution mainly favors the subsequent growth of grains. Transitions from an amorphous to a crystalline and then back to an amorphous phase are observed as the substrate temperature is increased. The amorphous phase at high temperatures and variations in the preferred crystallite orientations are explained by changes in the diffusion length of adsorbed precursors due to changing hydrogen coverage on the growing surface.
Publisher Correction: Nonlinear mechanics of human mitotic chromosomes (2022)

In the version of this article initially published, Extended Data Fig. 5 was a duplicate of Extended Data Fig. 6. The correct image is now in place in the HTML and PDF versions of the article.
Synergistic Inhibition Effect of Rare Earth in the Corrosion of the AA2024-T3 and CFRP in Galvanic Couple (2017)

Inhibition effect of LaN3O9.6H2O, 3-amino-1,2,4-triazole (ATA) and 5-chlorobenzotriazole (5-Cl-BTA) at various concentrations (0.5, 2, 4 and 6) was analyzed to observe the corrosion behavior of the AA2024 in galvanic couple with CFRP using zero resistance ammeter and electrochemical impedance spectroscopy (EIS). A solution of 0.05 M NaCl was used as electrolyte. Results have shown that the addition of LaN3O9.6H2O at different concentration decreased the current density up to 21 h of exposition at the aggressive media, with a trend of decrease trough the time. Moreover, modulus of impedance showed that the electron flow decreased in the presence of La3+, rising its maximum efficiency at 6mM with a value of 92%. Furthermore, 5-Cl-BTA presented its highest efficiency at 6mM with a value of 72%.
Real-time observation of non-equilibrium liquid condensate confined at tensile crack tips in oxide glasses (2005)

Since crack propagation in oxide materials at low crack velocities is partly determined by chemical corrosion, proper knowledge of the crack tip chemistry is crucial for understanding fracture in these materials. Such knowledge can be obtained only from in situ studies because the processes that occur in the highly confined environment of the crack tip are very different from those that take place at free surfaces, or that can be traced post mortem. We report the occurrence of hydrous liquid condensate between the two fracture surfaces in the vicinity of the tip of tensile cracks in silica. Observations are performed in real-time by means of atomic force microscopy (AFM) at continuously controlled crack velocities in the regime of stress corrosion. Condensate formation and changes in extent and shape are demonstrated for a wide range of macroscopic humidity at different crack speeds. Its liquid character is confirmed by the study of AFM phase-contrast data. It is believed that this evidence of a nanoscale liquid hydrous phase at the crack tip will enable novel insights in the chemistry of failure of oxide materials.
New strategies in ion channel screening for drug discovery: are there ways to improve its productivity? (2014)

In the imminent future, we will see a paradigm shift in ion channel drug screening toward using APC-based platforms for primary drug library screens. This way, the redundancy of the drug discovery process and the risk of false-negatives could be drastically reduced. Furthermore, cardiac safety can be addressed early, avoiding late-phase withdrawals with promising drug candidates. It is our firm belief that APC-based ion channel HTS will facilitate the discovery of candidates, which otherwise would have not been found, and shorten the drug development cycle, saving time and cost.
Optical properties of GaN grown on ZnO by reactive molecular beam epitaxy (1997)

High quality wurtzite GaN epilayers have been grown on ZnO(0001) substrates by reactive molecular beam epitaxy. Photoluminescence and reflectivity measurements point to high quality presumably due to the near match of both the crystal lattice parameter and the stacking order between GaN and ZnO. In addition, the good films lack the characteristic yellow photoluminescence band. Any misorientation of the GaN epilayer planes with respect to the ZnO substrate is not detectable with polarized reflectivity. The x-ray double crystal diffraction measurements indicate this misorientation is much smaller than those for GaN epilayers on SiC and Al2O3 .
TLR2 signalling orchestrates neutrophil activation in acute coronary syndrome with intact fibrous cap – results from the OPTICO-ACS study (2020)

Abstract Background Neutrophil granulocytes are key players of the innate immunity, participating in the initiation and progression of atherosclerosis. However, the exact mechanisms of neutrophil activation after acute coronary syndrome (ACS) are poorly understood, especially in the context of the two predominant ACS-causing pathophysiologies - ACS with intact fibrous cap (IFC-ACS) and ACS with ruptured fibrous cap (RFC-ACS). Therefore, the current study focuses on immunophenotyping and ex-vivo functional characterization of neutrophils with regard to the molecular differences between IFC-ACS and RFC-ACS. Methods Using high-resolution optical coherence tomography (OCT) of the ACS-causing culprit lesion and re-evaluation by a second OCT-core lab, thirty-two IFC-ACS-patients were matched to thirty-two RFC-ACS-patients by gender, age and diabetes. Local and systemic blood samples were obtained from the site of the ACS-causing culprit lesion (LOC) and from the arterial sheath (SYS), respectively. Neutrophil abundance and surface marker expression were quantified by flow cytometry. Fresh neutrophils were isolated for functional analysis and ex-vivo assessment of cell-toxicity in a co-culture with human aortic endothelial cells (HAECs). Neutrophil secretion of active MMP9 was evaluated by fluorescence-based zymography in supernatants of isolated neutrophils and in patients' plasma samples. Results Neutrophils of patients with IFC-ACS show significantly higher expression of the toll-like receptor 2 (TLR2) in comparison to RFC-ACS-derived neutrophils (LOC: 1991±492.8 vs. 1615±440.2; p=0.01; SYS: 2062±464.4 vs. 1670±525.1; p=0.0056). Ex-vivo TLR2-stimulation of local neutrophils in patients with IFC-ACS led to increased toxicity of their secretome and aggravated endothelial cell death in co-culture, as compared to neutrophils from RFC-ACS patients (+59% dead HAECs, IFC-LOC vs. RFC-LOC; p=0.0078). Furthermore, TLR2-stimulation using Pam3CSK4 triggered higher activity rates of MMP9 exclusively in local neutrophils of IFC-ACS-patients (+38.9%±6.1% in IFC-LOC vs. RFC-LOC; p=0.0154). This effect was reversed in IFC-ACS-derived neutrophils being pre-treated with an anti-TLR2 neutralizing antibody (−58.4% ±5.2%, IFC-LOC-anti-TLR2 vs. IFC-LOC-vehicle; p=0.0069). Additionally, MMP9 activity was higher in plasma obtained from the culprit site of IFC-ACS patients (74.1 U/ml ±4.1 vs. 70.0 U/ml ±5.1, IFC-LOC vs. RFC-LOC; p=0.01). Conclusion The current study demonstrates novel TLR2-dependant neutrophil activation patterns at the coronary culprit lesion of IFC-ACS, leading to higher endothelial cell toxicity and MMP9 activity. Further studies need to assess whether a temporary blockade of TLR2 activation could be a possible therapeutic target in the era of personalized medicine. Funding Acknowledgement Type of funding source: Public Institution(s). Main funding source(s): Berlin Institute of Health (BIH), German Center for Cardiovascular Research
Acquisition of a classification model for a risk search system from unbalanced textual examples (2009)

This paper proposes a method that acquires a more appropriate classification model for a risk search system analysing corporate reputation information included in bulletin board sites. The method inductively acquires the model from textual examples composed of many negative examples and a few positive examples. It selects two kinds of important negative examples by referring to expressions related to a specific label. Here, the label represents the contents of the papers. Finally, the method uses the selected negative examples and all the positive examples to acquire the model. The paper verifies the effectiveness of the method through comparative experiments.
Stress-dependent elasticity and wave propagation — New insights and connections (2021)

ABSTRACT To establish a consistent framework for seismic wave propagation that accommodates the effects of stress changes, it is critical to take into account the different definitions of stress and their corresponding effects on seismic quantities (e.g., wave speeds) as dictated by continuum mechanics. Revisiting this fundamental theoretical foundation, we first emphasize the role of stress within various forms of the wave equation resulting from different choices of stress definitions. Subsequently, using this basis, we investigate connections among existing theories that describe the variation of elastic moduli as a function of changes in stress. We find that there is a direct connection between predicting stress-induced elastic changes with the well-known third-order elasticity tensor and the recently proposed adiabatic pressure derivatives of elastic moduli. However, each of these approaches has different merits and drawbacks in terms of experimental validation as well as in their use. In addition, we investigate the connection with another general approach that relies on micromechanical structures (e.g., cracks and pores). Although this can be done algebraically, it remains unclear as to which definition of stress and which corresponding constitutive relationship should be considered in practical scenarios. We support our analysis with validations using previously published benchmark experimental data.
Au(I)‐Catalyzed Cyclization of Enynes Bearing an Olefinic Cycle. (2007)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Structure of Lamellar Polysiloxane Induced by Interaction between Carboxylate (Alkanoate and Alkylsuccinate) and Aminosilane (Aminopropyl- and Aminoethylaminopropylsilanes) (2009)

Abstract We demonstrate that the dehydration condensation of 3-aminopropylsilane (APTES) and 3-(2-aminoethyl)aminopropylsilane (AeAPTES) in the presence of alkylsuccinate and alkanoic acid provide layered polysiloxanes where the interlayer is filled with self-assembled carboxylate. Their structure was investigated by XRD, IR, and 29Si NMR. Lamellar solids were successfully obtained by the combination of monocarboxylate–APTES and dicarboxylate–AeAPTES, while the addition of alkanol and TEOS was necessary for the synthesis by cross combinations, dicarboxylate–APTES and monocarboxylate–AeAPTES. The series of lamellar solids with different interlayer distance are formed with alkylsuccinate and AeAPTES. The d-spacing is increased linearly with the number of carbons in the alkyl chain of surfactant. Only T3 species is detected in the 29Si NMR spectrum of hexadecylsuccinic acid–AeAPTES, implying that the structure of polysiloxane is a thin layer with complete condensation of silane molecules. This structural uniqueness is also supported by the IR bands due to Si–O–Si asymmetric vibration at 1132–1140 cm−1, suggesting a large Si–O–Si angle. This is because an angle near 180° is necessary for the structure of a R–SiO1.5 layer solid that has organic groups equally populated on both sides. The amount of Fe3+ sorbed in diaminoalkylpolysiloxanes was smaller than in monoaminoalkylpolysiloxane.
Neural Network Based Model Predictive Control (1999)

Model Predictive Control (MPC), a control algorithm which uses an optimizer to solve for the optimal control moves over a future time horizon based upon a model of the process, has become a standard control technique in the process industries over the past two decades. In most industrial applications, a linear dynamic model developed using empirical data is used even though the process itself is often nonlinear. Linear models have been used because of the difficulty in developing a generic nonlinear model from empirical data and the computational expense often involved in using nonlinear models. In this paper, we present a generic neural network based technique for developing nonlinear dynamic models from empirical data and show that these models can be efficiently used in a model predictive control framework. This nonlinear MPC based approach has been successfully implemented in a number of industrial applications in the refining, petrochemical, paper and food industries. Performance of the controller on a nonlinear industrial process, a polyethylene reactor, is presented.
Targeting Ras with Macromolecules (2017)

Activating Ras mutations are associated with 30% of all human cancers and the four Ras isoforms are highly attractive targets for anticancer drug discovery. However, Ras proteins are challenging targets for conventional drug discovery because they function through intracellular protein -protein interactions and their surfaces lack major pockets for small molecules to bind. Over the past few years, researchers have explored a variety of approaches and modalities, with the aim of specifically targeting oncogenic Ras mutants for anticancer treatment. This perspective will provide an overview of the efforts on developing "macromolecular" inhibitors against Ras proteins, including peptides, macrocycles, antibodies, nonimmunoglobulin proteins, and nucleic acids.
Impact of errors in recorded compressed breast thickness measurements on volumetric density classification using <scp>volpara</scp> v1.5.0 software (2016)

The current QC standard of ±5 mm error in recorded CBT creates the potential for error in mammographic density measurement. This may lead to inaccurate classification of mammographic density. The current QC standard for assessing mammographic density should be reconsidered.
Cell blotting and isoelectric focusing of neuroblastoma‐derived heparin‐binding neurotrophic activities: Detection of basic fibroblast growth factor protein and mRNA (1993)

Neuroblastoma cells have been shown to contain growth factors, which may be involved in the regulation of cell proliferation and/or differentiation. We have examined whether human IMR-32 neuroblastoma cells store factors with a capacity to promote neuron survival and differentiation. Heparin affinity chromatography, cell blotting, and isoelectric focusing of IMR-32 cell extracts revealed multiple neurotrophic activities at molecular weights of 16.8, 24.1, 39.0, 45.3, 52.3 and isoelectric points of 4.0, 5.0, 8.3, 9.0. Immunocytochemistry, immunoblotting, and radio-immunoassay with specific antibodies suggests that one neurotrophic activity is immunologically identical with basic fibroblast growth factor (bFGF). This assumption is supported by Northern blot analysis, which shows a 6.0 kb bFGF transcript.
Location of histones on simian virus 40 DNA. (1975)

The physical location of histone molecules in a simian virus 40 DNA-histone complex isolated from purified virions was examined using site-specific restriction endonucleases. The complex contains four host histone species but lacks histone F1. Histones prevent complete cleavage of SV40 DNA by two restriction enzymes, HindIII and EcoRI. From the pattern of DNA fragments resulting from cleavage of the histone-DNA complex by the HindIII endonuclease, which makes six breaks on purified SV 40 DNA, we have concluded that histones are randomly arranged on SV40 DNA relative to restriction enzyme cleavage sites. The EcoRI endonuclease, which makes one break in SV40 NDA, was used to determine the degree of physical coverage of the SV 40 DNA molecule by histones. We observed that 80% of the EcoRI sites in the complex are accessible to the enzyme while 20% are "closed." This degree of coverage is consistent with the mass ratio of DNA:histone in the complex as revealed by the buoyant density of the formaldehyde-fixed complex. We conclude that the histones in the complex are located randomly on the SV 40 genome and cover approximatley 20% of the DNA. These results suggest that the histone species F2b, F2al, F2a2, and F3 are bound without regard to nucleotide sequence of SV 40 DNA.
Spectroscopy by Inverse Raman Scattering (1978)

Spectroscopy by inverse Raman scattering (SIRS) is one of many new techniques in molecular spectroscopy made possible by the development of high power lasers. Although SIRS was first demonstrated experimentally by Jones and Stoicheff in 1964 (1), its growth was somewhat limited by certain technical difficulties. However, some of the properties inherent to SIRS show good potential for applications in chemistry, ranging from high resolution spectroscopy to chemical analysis. Theoretical Considerations From a conceptual point of view, SIRS involves physical processes that may not be immediately obvious. The best way to appreciate the physical processes that lead to SIRS is to relate it to normal Raman scattering (RS). In Figure 1(a), we show the molecular transitions involved in RS, Molecules are excited by light at the frequency ωL to some intermediate state, which can be real or vitual, and arrive at the Raman-active level with the emission of a photon
1814 Simulation of Fire Spread and Evacuation Dynamics (2007)

Since Cellular Automata (CA) have been proposed by von Neumann in the late 1940s, CA have been applied in a variety of scientific researches on complex system, including traffic models and biological fields. It is an idealization of a physical system in which space and time are all discrete. In this study, we have simulated evacuation dynamics in fire by Real-coded Cellular Automata (RCA), which we proposed as a new approach for pedestrian flow. To consider the fire spread in discrete space in calculation code, percolation model has been used.
Spinal Somatostatin for Patients with Cancer (1994)

Professor of Anesthesiology, Vice Chair for Research, Department of Anesthesiology, Anesthesia Research Laboratory, 0818 University of California, San Diego 9500 Gilman Drive, La Jolla, California 92093-0818
Platelet-Activating Factor (PAF)-induced invasion involves a complex signaling cascade in vascular endothelial cells. (2004)

3594 Platelet-activating factor (PAF), a potent phospholipid second messenger, promotes in vivo angiogenesis by stimulation of vascular endothelial cell migration and invasion, thus acting as a mediator of vascularization for tumor growth and metastasis. We have elucidated a complex signaling cascade upon stimulation of the G-protein-coupled, seven transmembrane PAF receptor in human umbilical vein endothelial cells (HUVEC). Activation of the PAF receptor induces specific, receptor-associated pertussis toxin-insensitive Gα q protein stimulation of adenylate cyclase, increased levels of cAMP, and induction of PKA in HUVEC, all of which requires the activation of Gα q protein coupled to the PAF receptor. The use of PAF receptor antagonists, as well as either inhibition of Gα q protein or adenylate cyclase, attenuates phosphorylation of Src by PAF; indeed, there is an absolute requirement for PKA activation in the PAF-PAF receptor signaling to Src. We have previously demonstrated that both Src and JAK-2 phosphorylate STAT-3 in HUVEC in a temporally regulated fashion. Our recent studies show that the initial signal to STAT-3 through the PAF-PAF receptor signaling mechanism involves the activation of Gα q protein, adenylate cyclase, and PKA, whereas the delayed and prolonged phosphorylation of STAT-3 by PAF is independent of these signaling intermediates. Activation of the Gα q protein-coupled PAF receptor by PAF also stimulates the early phosphorylation of PLCβ3 and does not involve Src, while there is no requirement of G-proteins for the activation of PLCγ1 by the PAF-PAF receptor mechanism. The Src inhibitor PP1 attenuates the delayed activation of PLCγ1 by PAF, suggesting the importance of Src in the PAF-mediated activation of PLCγ1. The Gα q protein-coupled PAF-PAF receptor-signaling cascade also phosphorylates FAK in a time dependent manner, and its activation is independent of the adenylate cyclase/PKA axis in HUVEC. Stimulation of the tyrosine phosphorylation of FAK by PAF-PAF receptor signaling cascade induces the binding of Src, p130 Cas , SHC, and paxillin to FAK in HUVEC. The biological consequence of this signaling cascade is the upregulation of mRNA levels for the matrix metalloproteinase MT1-MMP and the regulatory protein TIMP-2 . The concomitant temporal increases in expression of MT1-MMP and TIMP-2 lead to conversion of latent proMMP2 to MMP2, resulting in increased capacity to degrade the extracellular matrix and migrate. Taken together, we demonstrate that PAF is an important intermediate in vascular remodeling during pathological angiogenesis.