gebhart/patrepeval huggingface dataset:
Isomeric Complexes of Peptides with Class II Proteins of the Major Histocompatibility Complex (1996)

An important event in the generation of an immune response is the activation of T cells by peptides bound to the class II proteins of the major histocompatiblity complex (MHC). Binding of a peptide to an MHC protein is stabilized by multiple interactions between the protein, peptide side-chains, and peptide backbone. Unstable protein−peptide complexes that precede formation of long-lived complexes are presumably engaged in a smaller number of these binding interactions. To investigate the effect of peptide structure on the formation of unstable complexes, we have strategically modified a peptide that forms only long-lived complexes (dissociation rate constant koff = 2.5 × 10-6 s-1). Dissociation of the modified peptide from an MHC protein is biphasic with dissociation rate constants koff = 5.3 × 10-4 and 2.6 × 10-6 s-1. Thus, at least two detectable complexes are formed. These results demonstrate that changes in peptide structure alone are sufficient to result in the formation of isomeric structures of MHC protein−peptide complexes.
Oxygen-radical-mediated permeability edema and vasoconstriction in isolated perfused rabbit lungs. (1982)

Oxygen radicals have been implicated in the pathogenesis of permeability pulmonary edema. To determine directly if O2 radicals can cause increased alveolar-capillary membrane (ACM) permeability and low-pressure permeability edema, we chemically produced O2 radicals in the sale perfusates of isolated rabbit lungs. The O2 radicals generated by xanthine oxidase caused protein-rich edema and increases in lung perfusion pressures that were inhibitable by catalase (hydrogen peroxide scavenger) or dimethylthiourea (hydroxyl radical scavenger) but not by superoxide dismutase. To determine the effect of O2 radicals on ACM permeability without interference from increased perfusion pressures, we used papaverine to maintain baseline perfusion pressures during O2 radical exposure and then assessed ACM integrity by evaluating the response of isolated lungs to elevated outflow pressures (10 mmHg for 10 min). Under these conditions, increased ACM permeability manifested by weight gains and lavage albumin accumulations occurred in lungs treated with xanthine oxidase but not in control lungs. We conclude that O2 radicals can cause increased ACM permeability and vasoconstriction in isolated lungs.
Correlation Between Pair Interactions of Adsorbed Atoms and Adsorption Layer Superstructure Formation (1983)

When atoms adsorb on an atomically perfect surface, they often form a superstructured adsorption layer at sub-monolayer coverages. Although it is generally agreed that the lateral interactions between adatoms are responsible for the formation of adlayer superstructures, no direct experimental evidence exists. Using the field ion microscope, we have measured pair energies as function of distances for a few atomic pairs on the W (110) plane. In general, the interactions are non-monotonic in distance dependence, and are about 100 meV in strength. The Si-Si interaction is most interesting. Using this data the relative two dimensional binding energy per adatom in an adsorption layer can be calculated. We find the (2 √2/√3 × 4/√3) R35.26° superstructure, or in a conventional unit cell the p(2 × 1), has the lowest energy. We have searched and found this adlayer structure. Our Monte Carlo simulation, which generates an adlayer of minimum free energy and maximum entropy consistent with the measured pair energies, also shows the same superstructure. Thus the lateral interaction of adatoms is indeed responsible for the adlayer superstructure formation, and the pair potential between two adatoms can now be measured from the FIM experiment with sufficient accuracy to correlate well with the formation of adlayer superstructure. No covalent bonds are formed between Si adatoms.
Local mode predictions for excited stretching vibrational states of HCCD and H 12C 13CH (1983)

Calculation are performed for the stretching vibrational states of acetylene HCCD and H12C13H on the Oak Ridge computing systems. The results of these calculations agree with the recent observations by photo-acoustic spectroscopy. (AIP)
Electronic Structure and Bonding in Crystalline Y 10 [SiO 4 ] 6 N 2 (2003)

The electronic structure and bonding of the complex ceramic crystal Y 10 [SiO 4 ] 6 N 2 is studied by a first‐principles method. It is shown that this crystal is an insulator with a direct band gap of 1.3 eV. It has some unique properties related to the one‐dimensional chain structure in the c ‐direction and the planar N‐Y bonding in the x ‐ y plane.
Secret sharing schemes based on min-entropies (2014)

Fundamental results on secret sharing schemes (SSSs) are discussed in the setting where security and share size are measured by (conditional) min-entropies. We first formalize a unified framework of SSSs based on (conditional) Rέnyi entropies, which includes SSSs based on Shannon and min entropies etc. as special cases. By deriving the lower bound of share sizes in terms of Rέnyi entropies based on the technique introduced by Iwamoto-Shikata, we obtain the lower bounds of share sizes measured by min entropies as well as by Shannon entropies in a unified manner. As the main contributions of this paper, we show two existential results of non-perfect SSSs based on min-entropies under several important settings. We first show that there exists a nonperfect SSS for arbitrary binary secret information and arbitrary monotone access structure. In addition, for every integers k and n (k ≤ n), we prove that the ideal non-perfect (k, n)-threshold scheme exists even if the distribution of the secret is not uniformly distributed.
Benchmarking Molecular Dynamics Force Fields for All-Atom Simulations of Biological Condensates (2023)

Proteins containing intrinsically disordered regions are integral components of the cellular signaling pathways and common components of biological condensates. Point mutations in the protein sequence, genetic at birth or acquired through aging, can alter the properties of the condensates, marking the onset of neurodegenerative diseases such as ALS and dementia. While the all-atom molecular dynamics method can, in principle, elucidate the conformational changes that arise from point mutations, the applications of this method to protein condensate systems is conditioned upon the availability of molecular force fields that can accurately describe both structured and disordered regions of such proteins. Using the special-purpose Anton 2 supercomputer, we benchmarked the efficacy of nine presently available molecular force fields in describing the structure and dynamics of a Fused in sarcoma (FUS) protein. Five-microsecond simulations of the full-length FUS protein characterized the effect of the force field on the global conformation of the protein, self-interactions among its side chains, solvent accessible surface area and the diffusion constant. Using the results of dynamic light scattering as a benchmark for the FUS radius of gyration, we identified several force fields that produced FUS conformations within the experimental range. Next, we used these force fields to perform ten-microsecond simulations of two structured RNA binding domains of FUS bound to their respective RNA targets, finding the choice of the force field to affect stability of the RNA-FUS complex. Taken together, our data suggest that a combination of protein and RNA force fields sharing a common four-point water model provides an optimal description of proteins containing both disordered and structured regions and RNA-protein interactions. To make simulations of such systems available beyond the Anton 2 machines, we describe and validate implementation of the best performing force fields in a publicly available molecular dynamics program NAMD. Our NAMD implementation enables simulations of large (tens of millions of atoms) biological condensate systems and makes such simulations accessible to a broader scientific community.
Metal—Polymer Interfaces: Studies with X-Ray Photoemission (1981)

The interfaces formed by evaporating copper, nickel and chromium layers on polystyrene, polyvinyl alcohol, polyethylene oxide, polyvinyl methyl ether, polyvinyl acetate and polymethyl methacrylate have been studied with X-ray photoemission spectroscopy (XPS). At submonolayer coverages of the metals, the peak positions and widths of the metallic electron core levels vary significantly from one polymer substrate to another. Most of these variations can be accounted for in terms of changes in the atomic and extra-atomic relaxation energies during the photoemission process. Much of this change is brought about when the metal atom deposited on an oxygen containing polymer interacts with the substrate oxygen and forms a metal-oxygen-polymer complex. The presence of this complex is verified by changes in the photoemission lineshapes of the substrate carbon and oxygen atoms. The XPS signature of these various complexes are quite similar and suggest that they are chelate-like complexes.
Psychotropic drug use during pregnancy: weighing the risks. (1998)

Although psychotropic drugs have not been tested or approved by the Food and Drug Administration for use during pregnancy, some women continue to take these medications while they are pregnant, particularly since mood and anxiety disorders cluster in women during childbearing years. The relative risks and benefits of drug therapy for these women must be weighed with each patient and treatment limited to those situations in which risks to mother and fetus from the disorder are presumed to exceed the risk of drug treatment. Risks of psychotropic drug use during pregnancy include teratogenic effects, direct neonatal toxicity, and the potential for longer term neurobehavioral sequelae. Of growing concern is the risk of untreated psychiatric disorder as it may potentially affect fetoplacental integrity and fetal central nervous system development. Coordination of care with the patient, her husband or partner, and the obstetrician is essential, as is careful medical record documentation when treating pregnant patients with psychiatric disorders.
Maintenance of the plasma cell pool is independent of memory B cells (2008)

Humoral memory to an antigen (Ag) is maintained for several decades in the form of memory B cells and serum Ab. In fact, plasma cells (PCs) that secrete Ab are known to be long-lived and could be solely responsible for maintaining the long-lived Ab titers. Alternatively, it has been proposed that the PC compartment is maintained for long periods by the differentiation of memory cells into long-lived PCs as a result of nonspecific stimulation. This model predicts accelerated decay of PC numbers in the absence of memory cells for the same Ag. To address this prediction, we have developed a mouse model system that combined the ability to deplete B cells with the ability to detect Ag-specific memory and PCs. After establishing an immune response, we depleted Ag-specific memory B cells with an anti-hCD20 mAb and determined the effect on the PC compartment over 16 weeks. Using a combination of surface markers, we demonstrated that memory B cells remained depleted over the course of the experiment. However, despite this absence of memory cells for an extended duration, PC numbers in spleen and bone marrow did not decline, which indicates that the PC compartment does not require a significant contribution from memory B cells for its maintenance and instead that PCs are sufficiently long-lived to maintain Ab titers over a long period without renewal. This observation settles an important controversy in B cell biology and has implications for the design of vaccines and for B cell depletion therapy in patients.
Free cholesterol transfer to high-density lipoprotein (HDL) upon triglyceride lipolysis underlies the U-shape relationship between HDL-cholesterol and cardiovascular disease (2019)

Free cholesterol transfer to HDL upon TGRL lipolysis may underlie the U-shape relationship between HDL-C and cardiovascular disease, linking HDL-C to triglyceride metabolism and atherosclerosis.
LC–MS/MS Based Quantitation of ABC and SLC Transporter Proteins in Plasma Membranes of Cultured Primary Human Retinal Pigment Epithelium Cells and Immortalized ARPE19 Cell Line (2017)

The retinal pigment epithelium (RPE) forms the outer blood-retinal barrier between neural retina and choroid. The RPE has several important vision supporting functions, such as transport mechanisms that may also modify pharmacokinetics in the posterior eye segment. Expression of plasma membrane transporters in the RPE cells has not been quantitated. The aim of this study was to characterize and compare transporter protein expression in the ARPE19 cell line and hfRPE (human fetal RPE) cells by using quantitative targeted absolute proteomics (QTAP). Among 41 studied transporters, 16 proteins were expressed in hfRPE and 13 in ARPE19 cells. MRP1, MRP5, GLUT1, 4F2hc, TAUT, CAT1, LAT1, and MATE1 proteins were detected in both cell lines within 4-fold differences. MPR7, OAT2 and RFC1 were detected in the hfRPE cells, but their expression levels were below the limit of quantification in ARPE19 cells. PCFT was detected in both studied cell lines, but the expression was over 4-fold higher in hfRPE cells. MCT1, MCT4, MRP4, and Na<sup>+</sup>/K<sup>+</sup> ATPase were upregulated in the ARPE19 cell line showing over 4-fold differences in the quantitative expression values. Expression levels of 25 transporters were below the limit of quantification in both cell models. In conclusion, we present the first systematic and quantitative study on transporter protein expression in the plasma membranes of ARPE19 and hfRPE cells. Overall, transporter expression in the ARPE19 and hfRPE cells correlated well and the absolute expression levels were similar, but not identical. The presented quantitative expression levels could be a useful basis for further studies on drug permeation in the outer blood-retinal barrier.
Photoexcited carriers, phonons, and their scattering measured in semiconductor junctions by transient extreme ultraviolet spectroscopy (2017)

We use transient XUV spectroscopy to measure the carrier and phonon dynamics for each atomic-species in a semiconductor or semiconductor heterojunction, giving the technique potential for table-top photovoltaic device characterization. First, the electron populations, phonon populations, and their scattering pathways are measured in the A, L, and Γ valleys of Si(100) from femtoseconds to hundreds of picosecond. Second, the Si(100) is coated with TiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> and Ni to form a metal-insulator-semiconductor (MIS) junction. The Si L <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">23</sub> , Ni M <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">23</sub> , and Ti M <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">23</sub> edges are probed using XUV radiation from 20 eV to 150 eV, measuring the photoexcited charge-transfer, equilibration, and lattice dynamics for each component of the MIS junction.
Abstract IA24: Understanding and tackling differing vascular niches in glioma (2015)

Abstract Glioblastoma multiforme (GBM) is the most belligerent adult brain tumor, which is defined by its aggressive growth due to uncontrolled cellular proliferation, resistance to apoptosis, diffuse infiltration and invasion, propensity for necrosis and hypoxia, and vigorous angiogenesis. Recurrence of these invasive tumors is inevitable despite advanced multimodal therapy with surgery followed by radiation and temozolomide treatment resulting in a dismal median survival of beyond one year. A recent milestone in glioma research has been the revelation that therapies targeting other cell types besides tumor cells; i.e., the cell constituents of the vascular niche can convey substantial improvements in radiographic response, progression-free survival, and quality of life. The changing perspective on the environment as a functional contributor represents a profound shift in the approach to biology and therapeutic decisions in GBM. Here, we describe paracrine signaling pathways of the differing vascular niches that regulate angiogenesis or tumor invasiveness and present therapeutic modalities to target those to more efficiently block diffuse and angiogenic GBM growth. Citation Format: Gabriele Bergers. Understanding and tackling differing vascular niches in glioma. [abstract]. In: Proceedings of the AACR Special Conference: Advances in Brain Cancer Research; May 27-30, 2015; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2015;75(23 Suppl):Abstract nr IA24.
Green Production of Lead-free Bzt-bct Thin Films for Applications in Mems Devices (2021)

This paper reports the production of Lead-free (1-x)(BaZr0.2Ti0.8O3)-x(Ba0.7Ca0.3O3) ferro/piezoelectric thin films by means of repeated chemical solution deposition routes. Two different kinds of precursor solutions were compared: i) a literature standard precursor solution involving the use of 2-methoxyethanol (2-MOE) which is a toxic and carcinogenic solvent and ii) a “greener” precursor solution based on 1-methoxy-2-propanol (PGME), a non-toxic and non-carcinogenic solvent. Morphology, crystal structure and ferroelectric behavior of the films is also reported.
Domain structure control of (001)∕(100)-oriented epitaxial Pb(Zr,Ti)O3 films grown on (100)cSrRuO3∕(100)SrTiO3 substrates (2005)

The domain structure and electrical properties were systematically investigated in (001)∕(100)-oriented tetragonal epitaxial Pb(Zr0.35,Ti0.65)O3 thin films grown on (100)cSrRuO3∕(100)SrTiO3 substrates by metalorganic chemical vapor deposition. The wide range of domain structures with various volume fractions of c-domains from 0.05 to 1.0 was systematically controlled by changing the growth temperature from 380to540°C and the film thickness from 50to380nm, while keeping the other processing conditions the same. Reducing the deposition temperature and∕or increasing the film thickness reduced the population of c-domains. The relative dielectric constant (≈500) of the a-domain dominant films (volume fraction of c-axis-oriented domains, VC≈0.05) was larger than that (≈300) of the c-domain dominant ones (VC≈1.0). In the c-domain dominant region, the saturation and remanent polarization changed linearly with the volume fraction of c-domains. In the a-domain dominant region, they showed extraordinary large values, suggesting that a-domain switching makes a large contribution in this region.
Boosting the Capacitance of an Aqueous Zinc-Ion Hybrid Energy Storage Device by Using Poly(3,3′-dihydroxybenzidine)-Modified Nanoporous Carbon Cathode (2019)

Aqueous electrochemical energy storage devices are highly safe, low cost, and environmentally benign, yet suffer from low energy storage capacity. Here, we devise a novel cathode material for making aqueous Zn-ion hybrid energy storage devices with high areal capacitance. A pseudocapacitive polymer, poly(3,3′-dihydroxybenzidine, DHB), is electrodeposited onto the surfaces of porous active carbon (AC) granules to increase the capacitance. This composite coating has high mass loading, leading to high areal capacitance in F cm–2 scale. The flexible sandwich-structured cell made by combing the poly(3,3′-DHB)/AC cathode and the Zn foil anode shows stable electrochemical performance upon bending. The areal capacitance of this cell is up to 1.3 F cm–2, and the maximum energy and power densities are 0.18 mWh cm–2 and 4.01 mW cm–2, respectively. Moreover, a Zn-ion micro cell is fabricated by combing two sets of carbon-paper-based finger electrodes, one is plated with Zn and the other is coated with the poly(3,3′-DHB)/AC composite. The in-plane micro cell shows a high areal capacitance of 1.1 F cm–2 and a high areal energy density of 152 μWh cm–2. Our research suggests a new approach to make high-capacitance Zn-ion hybrid energy storage devices with different forms to meet various applications.
High-quality shape from multi-view stereo and shading under general illumination (2011)

Multi-view stereo methods reconstruct 3D geometry from images well for sufficiently textured scenes, but often fail to recover high-frequency surface detail, particularly for smoothly shaded surfaces. On the other hand, shape-from-shading methods can recover fine detail from shading variations. Unfortunately, it is non-trivial to apply shape-from-shading alone to multi-view data, and most shading-based estimation methods only succeed under very restricted or controlled illumination. We present a new algorithm that combines multi-view stereo and shading-based refinement for high-quality reconstruction of 3D geometry models from images taken under constant but otherwise arbitrary illumination. We have tested our algorithm on several scenes that were captured under several general and unknown lighting conditions, and we show that our final reconstructions rival laser range scans.
Detergent binding explains anomalous SDS-PAGE migration of membrane proteins (2009)

Migration on sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) that does not correlate with formula molecular weights, termed "gel shifting," appears to be common for membrane proteins but has yet to be conclusively explained. In the present work, we investigate the anomalous gel mobility of helical membrane proteins using a library of wild-type and mutant helix-loop-helix ("hairpin") sequences derived from transmembrane segments 3 and 4 of the human cystic fibrosis transmembrane conductance regulator (CFTR), including disease-phenotypic residue substitutions. We find that these hairpins migrate at rates of -10% to +30% vs. their actual formula weights on SDS-PAGE and load detergent at ratios ranging from 3.4-10 g SDS/g protein. We additionally demonstrate that mutant gel shifts strongly correlate with changes in hairpin SDS loading capacity (R(2) = 0.8), and with hairpin helicity (R(2) = 0.9), indicating that gel shift behavior originates in altered detergent binding. In some cases, this differential solvation by SDS may result from replacing protein-detergent contacts with protein-protein contacts, implying that detergent binding and folding are intimately linked. The CF-phenotypic V232D mutant included in our library may thus disrupt CFTR function via altered protein-lipid interactions. The observed interdependence between hairpin migration, SDS aggregation number, and conformation additionally suggests that detergent binding may provide a rapid and economical screen for identifying membrane proteins with robust tertiary and/or quaternary structures.