gebhart/patrepeval huggingface dataset:
Autophosphorylation of the intracellular domain of the epidermal growth factor receptor results in different effects on its tyrosine kinase activity with various peptide substrates. Phosphorylation of peptides representing Tyr(P) sites of phospholipase C-gamma. (1991)

The effect of autophosphorylation on the tyrosine kinase activity of the epidermal growth factor receptor (EGFR) is not well understood. We previously demonstrated that phospholipase C-gamma physically associates with the EGF-activated EGFR, but not with a kinase-negative mutant of the EGFR, and, moreover, that only the tyrosine-phosphorylated EGFR is able to associate with phospholipase C-gamma. We have now investigated the effect of autophosphorylation on the tyrosine kinase activity of the EGFR by employing the purified kinase-active intracellular domain of the EGFR (EGFR-IC) produced by a baculovirus expression system. Synthetic peptides, including ones which contain the individual major tyrosine phosphorylation sites of phospholipase C-gamma, were used as substrates. We found that the extensively prephosphorylated EGFR-IC exhibited similar reaction kinetics to the unphosphorylated EGFR-IC when angiotensin II was used as a nonspecific substrate. In contrast there was a clear stimulation of kinase activity due to autophosphorylation of the EGFR-IC when peptides representing either the major autophosphorylation site of the EGFR or the EGFR phosphorylation sites of phospholipase C-gamma were used as substrates. However, the modes of stimulation for these peptides differed. The binding affinity (Km) for the unphosphorylated EGFR-IC for the peptide containing Tyr-771 of phospholipase C-gamma was relatively poor compared with other peptides, but improved 5-6-fold when the EGFR-IC was prephosphorylated. On the other hand, autophosphorylation improved the reaction velocity (Vm) of the phosphorylation of other peptides by 2-3-fold, with little or no increase in affinity. These results suggest that autophosphorylation of the EGFR may induce a conformational change of its kinase domain which enhances its kinase activity with exogenous substrates and may induce association with phospholipase C-gamma by increasing its affinity to a domain containing Tyr-771.
Stable Transfection of<i>Trypanosoma cruzi</i>Epimastigotes with the Trypomastigote-Specific Complement Regulatory Protein cDNA Confers Complement Resistance (1998)

Trypanosoma cruzi blood stage trypomastigotes are highly resistant to complement-mediated killing in normal serum. A previously described trypomastigote surface glycoprotein was shown to have binding affinity for human complement components C3b and C4b and restrict activation of the complement cascade, thus preventing lysis of the parasites. Insect stage epimastigotes do not produce detectable levels of this 160-kDa complement regulatory protein (CRP) and are highly sensitive to the lytic effects of complement. Epimastigotes were stably transfected with a T. cruzi expression vector carrying the trypomastigote CRP cDNA and produced fully functional recombinant CRP. The recombinant CRP had binding affinity for C3b, and the transfected epimastigotes were protected from complement-mediated lysis. These results demonstrate for the first time that a developmentally regulated gene of T. cruzi trypomastigotes can be expressed in noninfectious epimastigotes and that production of CRP by epimastigotes is sufficient to confer a virulence-associated trait. Furthermore, these studies demonstrate the critical role that trypomastigote CRP plays in the protection of parasites from the deleterious effects of complement, thus establishing the protein as a virulence factor of T. cruzi.
Intrinsic Defect in T Cell Production of Interleukin (IL)-13 in the Absence of Both IL-5 and Eotaxin Precludes the Development of Eosinophilia and Airways Hyperreactivity in Experimental Asthma (2002)

Interleukin (IL)-5 and IL-13 are thought to play key roles in the pathogenesis of asthma. Although both cytokines use eotaxin to regulate eosinophilia, IL-13 is thought to operate a separate pathway to IL-5 to induce airways hyperreactivity (AHR) in the allergic lung. However, identification of the key pathway(s) used by IL-5 and IL-13 in the disease process is confounded by the failure of anti-IL-5 or anti-IL-13 treatments to completely inhibit the accumulation of eosinophils in lung tissue. By using mice deficient in both IL-5 and eotaxin (IL-5/eotaxin(-/-)) we have abolished tissue eosinophilia and the induction of AHR in the allergic lung. Notably, in mice deficient in IL-5/eotaxin the ability of CD4(+) T helper cell (Th)2 lymphocytes to produce IL-13, a critical regulator of airways smooth muscle constriction and obstruction, was significantly impaired. Moreover, the transfer of eosinophils to IL-5/eotaxin(-/-) mice overcame the intrinsic defect in T cell IL-13 production. Thus, factors produced by eosinophils may either directly or indirectly modulate the production of IL-13 during Th2 cell development. Our data show that IL-5 and eotaxin intrinsically modulate IL-13 production from Th2 cells and that these signaling systems are not necessarily independent effector pathways and may also be integrated to regulate aspects of allergic disease.
Printing Equipment for Ansco Color Film (1950)

The Scenetester takes the place of a cinex machine in manufacturing Ansco Color prints. Its primary function is to make it possible for the timer to select for a given color original or dupe the proper color correction filters and printing density. The Scenetester must match the printer or printers it is teamed with for absolute light output, color balance, exposure time and light changes. This paper describes a Bell & Howell Model D printer modified for color printing and a Scenetester which was made for darkroom operation. The Scenetester prints 16 frames simultaneously through 16 different color correction filters and was designed to work with modified Bell & Howell Model D printers.
Speech/non-speech discrimination based on contextual information integrated bispectrum LRT (2006)

This letter shows an effective statistical voice activity detection algorithm based on the integrated bispectrum, which is defined as a cross spectrum between the signal and its square and inherits the ability of higher order statistics to detect signals in noise with many other additional advantages: 1) its computation as a cross spectrum leads to significant computational savings, and 2) the variance of the estimator is of the same order as that of the power spectrum estimator. The decision rule is formulated in terms of an average likelihood ratio test (LRT) involving successive integrated bispectrum speech features. With these and other innovations, the proposed method reports significant improvements in speech/pause discrimination as well as in speech recognition over standardized techniques such as ITU-T G.729, ETSI AMR, and AFE VADs, and over recently published VADs
Overcoming JVM HotSwap constraints via binary rewriting (2008)

Java HotSpot VM provides a facility for replacing classes at runtime called HotSwap. One design property of HotSwap is that the signature of a replaced class must remain the same between different versions, which significantly constrains the programmer modifying a class to be replaced. Specifically, the programmer is precluded from adding new methods, constructors, or fields, or even changing the signatures of existing methods or fields. This paper presents a novel approach that overcomes these constraints of HotSwap by using binary refactoring, a technique that rewrites the binary representation of a program without affecting its functionality. A series of micro and macro benchmarks we conducted demonstrate that the approach is extensible and efficient. In particular, the new binary refactoring technique, which enables the approach, produces highly-efficient refactored application versions, outperforming a widely-used prior technique by as much as an order of magnitude. These initial results indicate that by rewriting the bytecode of a swapped program, one can effectively overcome constraints of HotSwap with minimal performance overhead.
Monocular-vision based SLAM using Line Segments (2007)

This paper presents a method to incorporate 3D line segments in vision based SLAM. A landmark initialization method that relies on the Plucker coordinates to represent a 3D line is introduced: a Gaussian sum approximates the feature initial state and is updated as new observations are gathered by the camera. Once initialized, the landmarks state is estimated along an EKF-based SLAM approach: constraints associated with the Plucker representation are considered during the update step of the Kalman filter. The whole SLAM algorithm is validated in simulation runs and results obtained with real data are presented.
Multi-Branch Tomlinson-Harashima Precoding Design for MU-MIMO Systems: Theory and Algorithms (2014)

Tomlinson-Harashima precoding (THP) is a nonlinear processing technique employed at the transmit side which is a dual to the successive interference cancelation (SIC) detection at the receive side. Like SIC detection, the performance of THP strongly depends on the ordering of the precoded symbols. The optimal ordering algorithm, however, is impractical for multiuser MIMO (MU-MIMO) systems with multiple receive antennas due to the fact that the users are geographically distributed. In this paper, we propose a multi-branch THP (MB-THP) scheme and algorithms that employ multiple transmit processing and ordering strategies along with a selection scheme to mitigate interference in MU-MIMO systems. Two types of multi-branch THP (MB-THP) structures are proposed. The first one employs a decentralized strategy with diagonal weighted filters at the receivers of the users and the second uses a diagonal weighted filter at the transmitter. The MB-MMSE-THP algorithms are also derived based on an extended system model with the aid of an LQ decomposition, which is much simpler compared to the conventional MMSE-THP algorithms. Simulation results show that a better bit error rate (BER) performance can be achieved by the proposed MB-MMSE-THP precoder with a small computational complexity increase.
Regulation of the Src protein tyrosine kinase (1995)

Members of the Src family of protein tyrosine kinases are involved in a variety of cellular processes, including cell growth, cell differentiation and neuronal signalling. N-terminal to the catalytic domain, Src family members contain a Src homology 2 (SH2) domain, a Src homology 3 (SH3) domain, and a unique domain, all capable of protein-protein interactions. Negative regulation by phosphorylation of a conserved tyrosine residue at the C-terminal tail of the molecules is characteristic of this family of enzymes. Phosphorylation of this residue causes the intramolecular interactions of the SH2 domain with the tail, and of the SH3 domain with an as yet undefined region, probably within the catalytic domain. Enzymatically active Src family kinases, on the other hand, are phosphorylated at a tyrosine in the middle of the catalytic domain and phosphorylation of this residue is a prerequisite for high activity. Regulators of these enzymes may thus act by altering the phosphorylation state of the two key tyrosine residues or by interfering with the regulatory intramolecular interactions, either by direct binding or by modification of the interfaces involved.
Animating Infection: Simulated Movement and Digital Zombie Hordes (2022)

Zombie blockbuster films generate their iconic zombie hordes using the same crowd simulation software biologists use to model cellular infection. These hordes and the humans they chase stage the struggle between two forms of molecular movement: randomized collision versus direction-oriented movement. By thematizing the effects of nonhuman movement within extensive visual effects sequences, these films merge two drastically different scales of the body—interior multitudes and migratory populations—and challenge biopolitical theories that see health as largely regulated by nation-states through controlled transportation networks and policed borders.
Untargeted Plasma Metabolite Profiling Reveals the Broad Systemic Consequences of Xanthine Oxidoreductase Inactivation in Mice (2012)

A major challenge in systems biology is integration of molecular findings for individual enzyme activities into a cohesive high-level understanding of cellular metabolism and physiology/pathophysiology. However, meaningful prediction for how a perturbed enzyme activity will globally impact metabolism in a cell, tissue or intact organisms is precluded by multiple unknowns, including in vivo enzymatic rates, subcellular distribution and pathway interactions. To address this challenge, metabolomics offers the potential to simultaneously survey changes in thousands of structurally diverse metabolites within complex biological matrices. The present study assessed the capability of untargeted plasma metabolite profiling to discover systemic changes arising from inactivation of xanthine oxidoreductase (XOR), an enzyme that catalyzes the final steps in purine degradation. Using LC-MS coupled with a multivariate statistical data analysis platform, we confidently surveyed >3,700 plasma metabolites (50-1,000 Da) for differential expression in XOR wildtype vs. mice with inactivated XOR, arising from gene deletion or pharmacological inhibition. Results confirmed the predicted derangements in purine metabolism, but also revealed unanticipated perturbations in metabolism of pyrimidines, nicotinamides, tryptophan, phospholipids, Krebs and urea cycles, and revealed kidney dysfunction biomarkers. Histochemical studies confirmed and characterized kidney failure in xor-nullizygous mice. These findings provide new insight into XOR functions and demonstrate the power of untargeted metabolite profiling for systemic discovery of direct and indirect consequences of gene mutations and drug treatments.
Regulation of Th1 and Th17 Cell Differentiation and Amelioration of Experimental Autoimmune Encephalomyelitis by Natural Product Compound Berberine (2010)

Berberine (BBR), an isoquinoline alkaloid derived from plants, is widely used as an anti-inflammatory remedy in traditional Chinese medicine. In this study, we showed that BBR was efficacious in the amelioration of experimental autoimmune encephalomyelitis (EAE) through novel regulatory mechanisms involving pathogenic Th1 and Th17 cells. BBR inhibited differentiation of Th17 cells and, to a lesser degree, Th1 cells through direct actions on the JAK/STAT pathway, whereas it had no effect on the relative number of CD4(+)Foxp3(+) regulatory T cells. In addition, BBR indirectly influenced Th17 and Th1 cell functions through its effect on the expression and function of costimulatory molecules and the production of IL-6, which was attributable to the inhibition of NF-kappaB activity in CD11b(+) APCs. BBR treatment completely abolished the encephalitogenicity of MOG(35-55)-reactive Th17 cells in an adoptive transfer EAE model, and the same treatment significantly inhibited the ability of MOG(35-55)-reactive Th1 cells to induce EAE. This study provides new evidence that natural compounds, such as BBR, are of great value in the search for novel anti-inflammatory agents and therapeutic targets for autoimmune diseases.
<i>In Situ</i> Surface Passivation and CMOS-Compatible Palladium–Germanium Contacts for Surface-Channel Gallium Arsenide MOSFETs (2008)

In this letter, we report a novel n-channel GaAs MOSFET featuring TaN/HfAlO/GaAs gate stack with in situ surface passivation (vacuum anneal and silane treatment), alternative gold-free palladium-germanium (PdGe) source and drain (S/D) ohmic contacts, and silicon plus phosphorus coimplanted S/D regions. With the novel in situ surface passivation, excellent capacitance-voltage characteristics with low-frequency dispersion and small stretch-out can be achieved, indicating low interface state density. This surface-channel GaAs device exhibits excellent transistor output characteristics with a high drain current on/off ratio of 105 and a high peak electron mobility of 1230 cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> /V ldr s. In addition, gold contamination concerning CMOS technology can be alleviated with the successful integration of low-resistance PdGe ohmic contacts.
FIELD EVAPORATION AND FIELD ION MICROSCOPY STUDY OF THE MORPHOLOGY OF PHASES PRODUCED AS A RESULT OF LOW TEMPERATURE PHASE TRANSFORMATIONS IN THE IRON-CHROMIUM SYSTEM (1989)

The morphology of the iron-rich α and chromium-enriched α' phases produced in iron-chromium alloys upon aging within the low temperature miscibility gap has been characterized by field evaporation and field ion microscopy. The morphology of the phases was found to change with composition and aging temperature. At low chromium levels, the morphology of the phases consisted of isolated, roughly spherical islands of the α' phase embedded in an α matrix. As the chromium level increased, this morphology smoothly changed into an isotropic network where both the α and α' phases were highly interconnected networks.
Spectral and cyclic voltammetric characterization of self-assembled monolayers on gold of pyrene end-labeled oligonucleotide duplexes (1999)

Self-assembled monolayers of sulfur-terminated oligonucleotide duplexes were formed on flat gold surfaces, either by exposure of a self-assembled monolayer bearing one oligonucleotide strand to the complementary strand or by preformation of a oligonucleotide duplex that was then deposited on a fresh gold surface. Virtually identical spectral behavior was observed whether the duplex was produced before deposition or by in situ complementary association. With a duplex bearing an appropriate pyrene end-label, the resulting thin film was photoresponsive. Surface emission measurements show no evidence for pyrene aggregation on the modified surfaces. The polarity of the photocurrent, reflecting photoinduced electron transfer initiated by photoexcitation of pyrene, is opposite that expected from the oligonucleotide-mediated reduction of the appended pyrene excited state.Key words: oligonucleotide, self-assembled monolayer, duplex formation, photoelectrochemistry, surface emission.
GaAs interfacial self-cleaning by atomic layer deposition (2008)

The reduction and removal of surface oxides from GaAs substrates by atomic layer deposition (ALD) of Al2O3 and HfO2 are studied using in situ monochromatic x-ray photoelectron spectroscopy. Using the combination of in situ deposition and analysis techniques, the interfacial “self-cleaning” is shown to be oxidation state dependent as well as metal organic precursor dependent. Thermodynamics, charge balance, and oxygen coordination drive the removal of certain species of surface oxides while allowing others to remain. These factors suggest proper selection of surface treatments and ALD precursors can result in selective interfacial bonding arrangements.
Immunization of rabbits against <i>Pasteurella multocida</i> using a commercial swine vaccine (2000)

Elaboration of heat-labile toxin (PMT) is an important virulence factor in some isolates of Pasteurella multocida from rabbits. Previously, we reported that immunization with inactivated PMT (IPMT) stimulated protective immunity to challenges from PMT. To test the hypothesis that immunization with a commercial swine vaccine containing IPMT stimulates similar protective immunity, groups of five rabbits were inoculated twice intramuscularly (i.m.), 10 days apart, with 0.5 ml of sterile saline or a commercial swine P. multocida bacterin-toxoid (BT). In addition, a group was inoculated intranasally with 5 microg of IPMT. Serum and nasal lavage samples were taken on days 0, 7, 14 and 21 after initial immunization and assayed by ELISA for anti-PMT antibody. Serum IgG and nasal lavage IgA were detectable by day 14 in BT and IPMT-immunized rabbits, but not in the saline controls. Groups of similarly inoculated rabbits were then challenged intranasally with 28 microg of PMT 21 days after initial immunization, and necropsied 7 days later, along with control challenged and non-challenged rabbits. Histological lesion severity was graded on a numerical scale. Non-immunized and saline, challenged controls developed more severe pneumonia, pleuritis, nasal turbinate atrophy and testicular atrophy than IPMT and BT-immunized rabbits. The results confirm the hypothesis that immunization with a commercial swine P. multocida BT confers protective immunity in rabbits against challenges from PMT.
Novel immunosuppressive agent, FK506. In vitro effects on the cloned T cell activation. (1987)

The present study shows the in vitro effects of a novel immunosuppressive agent, FK506, in comparison with cyclosporin A (CsA). FK506 inhibited concanavalin A response and allo-mixed lymphocyte reaction of murine splenic lymphocytes in a dose-dependent manner, and at 40- to 200-fold lower concentrations than CsA. Allo-cytolytic T lymphocyte induction from murine thymocytes was also inhibited by FK506, whereas the ability of cytolytic T lymphocyte to lyse targets was not affected by the agent. Immunosuppressive effects of FK506 were further characterized by using antigen specific-proliferative T lymphocyte clones, BC.21 and KO.6. FK506 inhibited the proliferation of T cell clones stimulated with specific antigens in a dose-dependent manner, and at about 100-fold lower concentrations than CsA. However, cloned T cells, once activated, were scarcely affected by the agent; interleukin-2 (IL-2) driven proliferation of cloned T cells was not inhibited. On the other hand, it was found that FK506 inhibited both IL-2 secretion and IL-2 receptor expression of BC.21 after stimulation with the specific antigen. FK506 also inhibited the proliferation of BC.21 stimulated with phorbol 12-myristate 13-acetate plus calcium ionophore, indicating that it directly affected the signaling pathway downward from the perturbation of the Ti/T3 complex. Finally, it was suggested that FK506 and CsA synergistically inhibited the antigen-driven proliferation of cloned T cells. These results indicate that the novel immunosuppressive agent, FK506, affects T cell activation with mechanisms similar to those of CsA but at considerably lower concentrations.
Collapse and Conservation of Shark Populations in the Northwest Atlantic (2003)

Overexploitation threatens the future of many large vertebrates. In the ocean, tunas and sea turtles are current conservation concerns because of this intense pressure. The status of most shark species, in contrast, remains uncertain. Using the largest data set in the Northwest Atlantic, we show rapid large declines in large coastal and oceanic shark populations. Scalloped hammerhead, white, and thresher sharks are each estimated to have declined by over 75% in the past 15 years. Closed-area models highlight priority areas for shark conservation, and the need to consider effort reallocation and site selection if marine reserves are to benefit multiple threatened species.