gebhart/patrepeval huggingface dataset:
Comparison of the fibrin-binding activities in the N- and C-termini of fibronectin (1999)

Fibronectin (Fn) binds to fibrin in clots by covalent and non-covalent interactions. The N- and C-termini of Fn each contain one non-covalent fibrin-binding site, which are composed of type 1 (F1) structural repeats. We have previously localized the N-terminal site to the fourth and fifth F1 repeats (4F1.5F1). In the current studies, using proteolytic and recombinant proteins representing both the N- and C-terminal fibrin-binding regions, we localized and characterized the C-terminal fibrin-binding site, compared the relative fibrin-binding activities of both sites and determined the contribution of each site to the fibrin-binding activity of intact Fn. By fibrin-affinity chromatography, a protein composed of the 10F1 repeat through to the C-terminus of Fn (10F1–COOH), expressed in COS-1 cells, and 10F1–12F1, produced in Saccharomyces cerevisiae, displayed fibrin-binding activity. However, since 10F1 and 10F1.11F1 were not active, the presence of 12F1 is required for fibrin binding. A proteolytic fragment of 14.4 kDa, beginning 14 residues N-terminal to 10F1, was isolated from the fibrin-affinity matrix. Radio-iodinated 14.4 kDa fibrin-binding peptide/protein (FBP) demonstrated a dose-dependent and saturable binding to fibrin-coated wells that was both competitively inhibited and reversed by unlabelled 14.4 kDa FBP. Comparison of the fibrin-binding affinities of proteolytic FBPs from the N-terminus (25.9 kDa FBP), the C-terminus (14.4 kDa) and intact Fn by ELISA yielded estimated Kd values of 216, 18 and 2.1 nM, respectively. The higher fibrin-binding affinity of the N-terminus was substantiated by the ability of both a recombinant 4F1.5F1 and a monoclonal antibody (mAb) to this site to maximally inhibit biotinylated Fn binding to fibrin by 80%, and by blocking the 90% inhibitory activity of a polyclonal anti-Fn, by absorption with the 25.9 kDa FBP. We propose that whereas the N-terminal site appears to contribute to most of the binding activity of native Fn to fibrin, the specific binding of the C-terminal site may strengthen this interaction.
Invariant-based recognition of complex curved 3D objects from image contours (2002)

To recognize three-dimensional objects bounded by smooth curved surfaces from monocular image contours, viewpoint-dependent image features must be related to object geometry. Contour bitangents and inflections along with associated parallel tangents points are the projection of surface points that lie on the occluding contour for a five-parameter family of scaled orthographic projection viewpoints. An invariant representation can be computed from these image features and seen for modeling and recognizing objects. Modeling is achieved by moving an object in front of a camera to obtain a curve of possible invariants. The relative camera-object motion is not required, and 3D models are not utilized. At recognition time, invariants computed from a single image are used to index the model database. Using the matched features, independent qualitative and quantitative verification procedures eliminate potential false matches. Examples from an implementation are presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Catalysis of cis/trans isomerization in native HIV-1 capsid by human cyclophilin A (2002)

Packaging of cyclophilin A (CypA) into HIV-1 virions is essential for efficient replication; however, the reason for this is unknown. Incorporation is mediated through binding to the Gly-89-Pro-90 peptide bond of the N-terminal domain of HIV-1 capsid (CA(N)). Despite the fact that CypA is a peptidyl-prolyl cis/trans isomerase, catalytic activity on CA(N) has not been observed previously. We show here, using NMR exchange spectroscopy, that CypA does not only bind to CA(N) but also catalyzes efficiently the cis/trans isomerization of the Gly-89-Pro-90 peptide bond. In addition, conformational changes in CA(N) distal to the CypA binding loop are observed on CypA binding and catalysis. The results provide experimental evidence for efficient CypA catalysis on a natively folded and biologically relevant protein substrate.
Pathophysiological effects of albumin dialysis in acute-on-chronic liver failure: A randomized controlled study (2004)

The pathophysiological basis of acute-on-chronic liver failure (ACLF) is unclear but systemic inflammatory response is thought to be important. In patients with ACLF, the molecular adsorbents recirculating system (MARS) improves individual organ function, but the effect of MARS on the proposed mediators of systemic inflammatory response is unclear. The present study was designed to determine the effect of MARS on the cytokine profile, oxidative stress, nitric oxide, and ammonia. A total of 18 patients with alcohol-related ACLF due to inflammation-related precipitants were randomized to receive standard medical therapy (SMT) alone, or with MARS therapy over 7 days. Plasma cytokines, malondialdehyde (MDA), free radical production, nitrate / nitrite (NOx), and ammonia were measured. Encephalopathy improved significantly with MARS (P < .01), but not with SMT. Mean arterial pressure and renal function remained unchanged. No significant change of plasma cytokines and ammonia levels were observed in either group. Plasma MDA levels did not change either. There was a fall in NOx (P < .05) with MARS, but not with SMT. In conclusion, in inflammation-related ACLF patients, albumin dialysis using MARS results in improvement of encephalopathy, independent of changes of ammonia or cytokines, without improving blood pressure or renal function. These results should temper the liberal use of MARS until further data is available.
Some Problems of International Organization. Second Montague Burton Lecture on International Relations (1944)

Some Problems of International Organization. Second Montague Burton Lecture on International Relations Get access Some Problems of International Organization. Second Montague Burton Lecture on International Relations. By C. K. Webster Litt.D., F.B.A., Professor of International History at the University of London. 1944. (Leeds: University of Leedsv. 8½″ × 5½″. 18 pp. 6d.) J. V. Wilson J. V. Wilson Search for other works by this author on: Oxford Academic Google Scholar International Affairs, Volume 20, Issue 4, October 1944, Page 562, https://doi.org/10.2307/3017146 Published: 01 October 1944
Cellular and Molecular Changes Associated With Inhibitory Effect of Pioglitazone on Neointimal Growth in Patients With Type 2 Diabetes After Zotarolimus-Eluting Stent Implantation (2010)

Our data present early cellular and immunologic changes by pioglitazone that might have been associated with antirestenotic and antiatherogenic effects in diabetic patients. Inhibiting proinflammatory responses while promoting antiinflammatory circuits, together with an antiproliferative action, may, in part, account for the antirestenotic effect of pioglitazone by altering vascular remodeling processes in the early phase.
Imaging the Impact of Chemically Inducible Proteins on Cellular Dynamics In Vivo (2012)

The analysis of dynamic events in the tumor microenvironment during cancer progression is limited by the complexity of current in vivo imaging models. This is coupled with an inability to rapidly modulate and visualize protein activity in real time and to understand the consequence of these perturbations in vivo. We developed an intravital imaging approach that allows the rapid induction and subsequent depletion of target protein levels within human cancer xenografts while assessing the impact on cell behavior and morphology in real time. A conditionally stabilized fluorescent E-cadherin chimera was expressed in metastatic breast cancer cells, and the impact of E-cadherin induction and depletion was visualized using real-time confocal microscopy in a xenograft avian embryo model. We demonstrate the assessment of protein localization, cell morphology and migration in cells undergoing epithelial-mesenchymal and mesenchymal-epithelial transitions in breast tumors. This technique allows for precise control over protein activity in vivo while permitting the temporal analysis of dynamic biophysical parameters.
Use of Mecamylamine in the Management of Hypertension (1957)

MBuTsH cortisone was donated by the Medical Research Council. Since
Transverse mode dynamics of VCSELs through space-time domain simulation (1999)

An approximation to the Maxwell-Semiconductor Bloch equations is used to model transverse mode dynamics of vertical-cavity surface-emitting lasers (VCSELs). The time-evolution of the spatial profiles of the laser field and carrier density is solved by a finite-difference algorithm. The algorithm is fairly general; it can handle devices of any shape, which are either gain or index guided or both. Also there is no a priori assumption about the type or number of modes. The physical modeling includes the nonlinear carrier dependence of the optical gain and refractive index and dispersion effects on the gain and the refractive index are also included.
A simple, rapid method for isolating RNA from paraffin-embedded tissues for reverse transcription-polymerase chain reaction (RT-PCR). (1994)

Described here is a simple, rapid technique for isolating RNA from archived formalin-fixed, paraffin-embedded tissues (PETs). Using this modified acid guanidinium thiocyanate method, RNA sufficient as a template for the reverse transcription-polymerase chain reaction (RT-PCR) can be isolated in 2 hr from a single 20-microns-thick section of tissue. Spliced mRNA corresponding to portions of the estrogen receptor (ER) gene was successfully amplified from fixed, embedded human breast cancers containing increased amounts of ER protein. This method makes it feasible to safely and efficiently isolate RNA from large numbers of routinely processed paraffin blocks for retrospective studies of endogenous proteins such as hormone receptors, oncogenes, and viruses.
Spatially Coupled Split-Component Codes With Iterative Algebraic Decoding (2017)

We analyze a class of high performance, low decoding-data-flow error-correcting codes suitable for high bit-rate optical-fiber communication systems. A spatially coupled split-component ensemble is defined, generalizing from the most important codes of this class, staircase codes and braided block codes, and preserving a deterministic partitioning of component-code bits over code blocks. Our analysis focuses on low-complexity iterative algebraic decoding, which, for the binary erasure channel, is equivalent to a generalization of the peeling decoder. Using the differential equation method, we derive a vector recursion that tracks the expected residual graph evolution throughout the decoding process. The threshold of the recursion, for asymptotically long component codes, is found using potential function analysis. We generalize the analysis to mixture ensembles consisting of more than one type of component code. We give an example of a mixture ensemble consisting of two component codes, which has better performance than spatially-coupled split-component ensembles consisting of only one component code. The analysis extends to the binary symmetric channel by assuming miscorrection-free component-code decoding. Simple upper bounds on the number of errors correctable by the ensemble are derived. Finally, we analyze the threshold of spatially coupled split-component ensembles under beyond bounded-distance component decoding.
α4 integrin increases anoikis of human osteosarcoma cells (2003)

Cell motility, growth, and proliferation are regulated by adhesion to the extracellular matrix. Detachment of adherent cells from extracellular matrix results in induction of apoptosis ("anoikis"). Transformed cells often show an anchorage-independent growth that enables them to acquire a motile, invasive phenotype. This phenotype has been associated with the altered expression and function of the integrin family of transmembrane proteins that mediate cell adhesion to the extracellular matrix. Although alpha4 integrin is normally expressed on leukocyte subpopulations, a number of metastatic melanomas and sarcomas express it as well. In this study, we demonstrated the expression of alpha4 integrins on the human osteosarcoma cell line SAOS and on metastatic osteosarcoma lesions from the lung and pericardium. We further demonstrated that alpha4 integrin is coupled to the beta1 subunit by biochemical analysis and by using a mAb directed against a combinatorial epitope unique to the alpha4beta1 molecule. SAOS cells undergo anoikis when adherence is denied. Anoikis involved the activation of caspase 3 and the release of cytochrome c from mitochondria. Treatment of non-adherent SAOS with an anti-alpha4 mAb increased anoikis while anti-beta1 integrin mAbs did not alter anoikis, thus indicating a novel function for the alpha4 subunit in the control of cell death. Since integrins can control cell migration, proliferation, and apoptosis these results demonstrate a potential role for alpha4 integrin during multiple aspects of osteosarcoma metastasis.
Intranodal administration of mRNA encoding nucleoprotein provides cross-strain immunity against influenza in mice (2019)

Current human influenza vaccines lack the adaptability to match the mutational rate of the virus and therefore require annual revisions. Because of extensive manufacturing times and the possibility that antigenic alterations occur during viral vaccine strain production, an inherent risk exists for antigenic mismatch between the new influenza vaccine and circulating viruses. Targeting more conserved antigens such as nucleoprotein (NP) could provide a more sustainable vaccination strategy by inducing long term and heterosubtypic protection against influenza. We previously demonstrated that intranodal mRNA injection can induce potent antigen-specific T-cell responses. In this study, we investigated whether intranodal administration of mRNA encoding NP can induce T-cell responses capable of protecting against a heterologous influenza virus challenge. BALB/c mice were immunized in the inguinal lymph nodes with different vaccination regimens of mRNA encoding NP. Immune responses were compared with NP DNA vaccination via IFN-γ ELISPOT and in vivo cytotoxicity. For survival experiments, mice were prime-boost vaccinated with 17 µg NP mRNA and infected with 1LD50 of H1N1 influenza virus 8 weeks after boost. Weight was monitored and viral titers, cytokines and immune cell populations in the bronchoalveolar lavage, and IFN-γ responses in the spleen were analyzed. Our results demonstrate that NP mRNA induces superior systemic T-cell responses against NP compared to classical DNA vaccination. These responses were sustained for several weeks even at low vaccine doses. Upon challenge infection, vaccination with NP mRNA resulted in reduced lung viral titers and improved recovery from infection. Finally, we show that vaccination with NP mRNA affects the immune response in infected lungs by lowering immune cell infiltration while increasing the fraction of T cells, monocytes and MHC II+ alveolar macrophages within immune infiltrates. This change was associated with altered levels of both pro- and anti-inflammatory cytokines. These findings suggest that intranodal vaccination with NP mRNA induces cross-strain immunity against influenza, but also highlight a paradox of influenza immunity, whereby robust immune responses can provide protection, but can also transiently exacerbate symptoms during infection.
Applicability of Coomassie brilliant blue G-250 as the staining dye for paper and cellulose acetete electrophoretic analysis of serum proteins (1974)

The staining ability of 5 dyes was compared by staining a known amount of human serum albumin spotted on a sheet of Separax, eluting the protein-bound dye, and measuring absorbancy at respective peak wave lengths. The relative color intensity of G-250 was much higher than that of R-250, Ponceau 3R, Amidoblack 10B or Procion blue. The colorimetric value of G-250 binding to serum protein fractions considerably fluctuated because of an unavoidable inaccuracy of spotting of the protein solution onto Separax. However, the relative proportion of protein fractions (expressed in percentage) showed a reasonable variation, especially when serum was diluted 5-fold with saline. The similar tendency was obtained when the stained protein fractions were measured using densitometer. A few examples of the G-250 staining method applied to paper electrophoresis of cerebrospinal fluid and urinary proteins were presented.
Transition from the Tetragonal to Cubic Phase of Organohalide Perovskite: The Role of Chlorine in Crystal Formation of CH<sub>3</sub>NH<sub>3</sub>PbI<sub>3</sub> on TiO<sub>2</sub> Substrates (2015)

The role of chlorine in the superior electronic property and photovoltaic performance of CH3NH3PbI(3-x)Clx perovskite has attracted recent research attention. Here, we study the impact of chlorine in the perspective of the crystal structure of the perovskite layer, which can provide important understanding of its excellent charge mobility and extended lifetimes. In particular, we find that in the presence of chlorine (PbCl2 or CH3NH3Cl), when CH3NH3PbI3 films are deposited on a TiO2 mesoporous layer instead of a planar TiO2 substrate, a stable cubic phase rather than the commonly observed tetragonal phase is formed in CH3NH3PbI3 perovskite at room temperature. The relative peak intensity of two major facets of cubic CH3NH3PbI3 crystals, (100)C and (200)C facets, can also be easily tuned, depending on the film thickness. Furthermore, compared with pristine CH3NH3PbI3 perovskite films, in the presence of chlorine, CH3NH3PbI3 crystals grown on planar substrates exhibit strong preferred orientations on (110)T and (220)T facets.
Principles of antibody catalysis (1988)

Abstract Antibodies have now been shown to catalyze a variety of chemical transformations, including hydrolytic, concerted, and bimolecular reactions. The inherent chirality of the antibody binding pocket has been exploited to exert precise stereochemical control over their catalyzed reactions. The mechanisms by which antibodies catalyze reactions are not expected to differ in any general way from those of natural enzymes. Antibodies use their binding energy to stabilize species of higher free energy which appear along the reaction coordinate or effect general acid/base catalysis. The advent of catalytic antibodies promises new catalysts that extend the range of catalysis by proteins to chemical transformations that were not required during the evolution of enzymes.
Dual-Wavelength InAlGaAs–InP Laterally Coupled Distributed Feedback Laser (2006)

The design and operation of a novel dual-wavelength laterally coupled (LC) distributed feedback (DFB) semiconductor laser are reported. The laser has two different grating periods, one on each sidewall. Stable dual-mode emission, with low threshold currents and good extinction ratio approaching 30 dB, has been demonstrated. Generation of millimeter-wave signals by photomixing has been performed, and the linewidths of each of the individual modes and of the beat mode have been measured as a function of the injection current. It is observed that while the linewidth of the separate modes has a modest dependence on the injection level, the linewidth of the beat mode experiences a strong decrease as the injected current increases
Directional Epitaxial Crystallization and Tentative Crystal Structure of Poly(9,9‘-di-<i>n</i>-octyl-2,7-fluorene) (2007)

Directional epitaxial crystallization is used to prepare highly oriented films of poly(9,9‘-di-n-octyl-2,7-fluorene) (PFO). This orientation method implies the use of a crystallizable aromatic solvent (1,3,5-trichlorobenzene) playing successively the role of the solvent for PFO for T > 63 °C and the role of an orienting substrate below this temperature. Extended areas of the oriented PFO can be formed on a given substrate after simple evaporation of the crystallized solvent under vacuum. The effect of annealing on the thin film structure and morphology was followed by transmission electron microscopy (TEM) in bright field and dark field modes and atomic force microscopy. Upon annealing, oriented crystalline PFO lamellae and axialites are formed by coalescence of smaller nanocrystalline domains. As shown by electron diffraction, a single-crystal-like structure is formed after a short annealing of the as-oriented films at 210 °C and slow cooling (0.5 °C/min) to room temperature. The films consist of oriented lamellar crystals in edge-on orientation on the SiO2 substrate, and the PFO chains are oriented parallel to the TCB stacking direction (cTCB). The reflection rules deduced from various selected area electron diffraction (SAED) patterns obtained by rotation-tilt indicate that PFO crystallizes in an orthorhombic structure with Pnb21 space group. A tentative crystal structure was obtained from the simulations of the SAED patterns and molecular modeling. The epitaxial relationship at the PFO/TCB interface suggests that 1D epitaxy is involved: the PFO chains are oriented parallel to the stacking direction of TCB (c-axis); the 3.95 Å distance between TCB molecules matches closely the reticular distance of 4.1 Å corresponding to dense planes of n-octyl side groups of interdigitated PFO chains.
Large margin transductive transfer learning (2009)

Recently there has been increasing interest in the problem of transfer learning, in which the typical assumption that training and testing data are drawn from identical distributions is relaxed. We specifically address the problem of transductive transfer learning in which we have access to labeled training data and unlabeled testing data potentially drawn from different, yet related distributions, and the goal is to leverage the labeled training data to learn a classifier to correctly predict data from the testing distribution.
Distribution of Time-Bin Entangled Qubits over 50 km of Optical Fiber (2004)

We report experimental distribution of time-bin entangled qubits over 50 km of optical fibers. Using actively stabilized preparation and measurement devices we demonstrate violation of the Clauser-Horne-Shimony-Holt Bell inequality by more than 15 standard deviations without removing the detector noise. In addition we report a proof-of principle experiment of quantum key distribution over 50 km of optical fibers using entangled photon.