gebhart/patrepeval huggingface dataset:
Numerical Investigation of Transition Mechanisms Influencing the Development of Turbulent Wall Jets (2006)

The transitional region downstream of the nozzle exit in wall jets over plane and curved surfaces at high Reynolds numbers (Rej=10,000) is investigated using three-dimensional Navier{Stokes simulations. The transition process is crucial for the development of the turbulent wall jet since it leaves a strong signature farther downstream. During transition, energetic vortical structures (spanwise, streamwise) develop from hydrodynamic instabilities and propagate into the turbulent o w, while strongly inuencing the meano w characteristics, e.g., the spreading rate, the skin-friction, and ultimately the separation location. Smaller-sized Navier{Stokes simulations are employed for investigating the inuence of various o w parameters, such as the shape of the jet prole at the nozzle exit, the disturbance level, and also the eect of wall curvature on the overall development of the vortical structures and the mean o w. For some o w congurations, the transition mechanisms are investigated in greater detail using Direct Numerical Simulations with a grid-resolution that is ne enough for capturing the transition mechanisms during the later stages of the breakdown. The simulations show that the development of spanwise vortices during wall-jet transition leads to the formation of braid vortices that loop around the spanwise vortices and appear as streamwise vortices in the time-averaged o w. In the presence of wall curvature (Coanda wall jet), the strength of the spanwise vortices is
Antagonism of neutrophil adherence in the deteriorating stroke model in rabbits (1995)

✓ Adhesion of leukocytes to the endothelium can occur in a few hours after the onset of ischemia, and the actions of leukocytes have been suggested to aggravate reperfusion injury. Adhesion is a prerequisite for the harmful leukocyte actions. Rapid mediation of leukocyte adhesion and aggravation of reperfusion injury can occur through production of platelet-activating factor (PAF). The authors hypothesized that prevention of leukocyte adhesion during ischemia reperfusion would have beneficial effects and that these effects might be enhanced by a PAF antagonist. To test this hypothesis, rabbits were anesthetized with pentobarbital and subjected to severe spinal cord ischemia (25 minutes) followed by 30 minutes of reperfusion, at which time either vehicle, antibody against the CD11/CD18 (anti-CD) leukocyte adhesion molecule (1 mg/kg), or the anti-CD and PAF antagonist, WEB 2086 (3 mg/kg), was administered intravenously and the animals were monitored for 6.5 hours. Using a score from 0 to 5, recovery of motor function was improved at 5.5 hours by the CD antibody (2.0 ± 0.5 versus 0.4 ± 0.2 in the six animals in the vehicle group, p &lt; 0.05). No further improvement was induced by WEB 2086 in the six anti-CD treated animals (1.6 ± 0.7). Spinal cord blood flow (laser Doppler flowmetry) at 6 hours was at the preischemic level in the control animals (−7% ± 20%), but clearly increased in the anti-CD group (+73% ± 29%, p &lt; 0.5). The severity of blood-brain barrier damage in the spinal cord gray matter was decreased by the treatments. Extravasation of intravenously injected Evans blue albumin (EBA), measured by detection of EBA fluorescence, was reduced by approximately 50% in both treated groups (p &lt; 0.05). The number of morphologically normal motor neurons in the lumbar anterior horns of the infarcted spinal cord showed protection in the seven animals in the anti-CD treated group at 6.5 hours: 12.7 ± 1.7 versus 5.3 ±1.6 (vehicle), p &lt; 0.05 without an additional effect by PAF antagonist 12.2 ± 2.6 (anti-CD + WEB 2086). Our results suggest that ultraacute treatment of reperfusion injury based on special inhibition of leukocyte effects may be beneficial. Platelet-activating factor antagonism failed to enhance this therapeutic effect, which may suggest dependency on a common mechanism.
ImageRover: a content-based image browser for the World Wide Web (1997)

ImageRover is a search by image content navigation tool for the world wide web. To gather images expediently, the image collection subsystem utilizes a distributed fleet of WWW robots running on different computers. The image robots gather information about the images they find, computing the appropriate image decompositions and indices, and store this extracted information in vector form for searches based on image content. At search time, users can iteratively guide the search through the selection of relevant examples. Search performance is made efficient through the use of an approximate, optimized k-d tree algorithm. The system employs a novel relevance feedback algorithm that selects the distance metrics appropriate for a particular query.
Sulfated Polysaccharides Prevent Human Leukocyte Elastase-induced Acute Lung Injury and Emphysema in Hamsters (1990)

Studies were designed to explore the possibility that sulfated polysaccharides had the potential to prevent human leukocyte elastase (HLE)-induced lung injury. Arteparon (GAGPS), heparin, heparan sulfate, chondroitin sulfate, and dextran sulfate, but not dextran, inhibited HLE-mediated hydrolysis of succinyl-ala2-val-pNA. GAGPS, used as a paradigmatic sulfated polysaccharide, was a potent inhibitor of elastolysis in vitro. GAGPS given intratracheally prevented acute injury and emphysema in hamsters when administered up to 8 h before HLE insufflation. The results suggest that sulfated polysaccharides may be potent inhibitors of HLE-mediated lung injury.
Transparent photoacid generator (ALS) for ArF excimer laser lithography and chemically amplified resist (1994)

A novel photoacid generator, ALS (alkylsulfonium salt; cyclohexylmethyl(2-oxocyclohexyl)sulfonium trifluoromethane- sulfonate) for ArF excimer laser ((lambda) equals193 nm) lithography and a single-layer resist have been developed. ALS shows high transparency at 193 nm and photoacid generating capability on irradiation by ArF excimer laser. A novel methacrylate terpolymer, poly(tricyclo[5.2.1.0<SUP>2,6</SUP>]decanylmethacrylate-co-2- tetrahydropyranylmethacrylate-co-methacrylic acid), is synthesized as a base resin. The resist, consisting of ALS and the polymer, shows chemical amplification and good resolution. A 0.2-micrometers line and space negative-tone image is observed at 15 mJ/cm<SUP>2</SUP> dose using an ArF excimer laser.
Molecular Characterization of Off-Target Activities of Telithromycin: a Potential Role for Nicotinic Acetylcholine Receptors (2010)

Adverse effects have limited the clinical use of telithromycin. Preferential inhibition of the nicotinic acetylcholine receptors (nAChR) at the neuromuscular junction (α3β2 and NMJ), the ciliary ganglion of the eye (α3β4 and α7), and the vagus nerve innervating the liver (α7) could account for the exacerbation of myasthenia gravis, the visual disturbance, and the liver failure seen with telithromycin use. The studies presented here enable the prediction of expected side effects of macrolides in development, such as solithromycin (CEM-101).
Isolation and Characterization of Insulin-Like Growth Factor I (Somatomedin-C) from Cultures of Fetal Rat Calvariae* (1988)

Cultured bones have been shown to secrete local regulators of bone remodeling, such as beta 2-microglobulin, transforming growth factor-beta, and insulin-like growth factor (IGF), but the IGF secreted has not been characterized. In the present study, IGF from medium conditioned by 21-day-old fetal rat calvariae was isolated and characterized. IGF was purified using dialysis, gel filtration, and reverse phase HPLC. Amino acid composition was compatible with that of IGF I (somatomedin-C), and amino-terminal sequence analysis revealed homology with IGF-I. The concentration of IGF-I in the calvarial culture medium was 1 nM and was suppressed by cycloheximide. Calvaria-derived rat IGF I at 20 nM stimulated DNA and collagen synthesis by 42% and 26%, respectively, in monolayer cultures of osteoblast-rich rat parietal bone cells. This study indicates that locally produced IGF-I regulates bone formation in cultures of 21-day-old fetal rat calvariae.
Genuine Monovalent Ligands of TrkA Nerve Growth Factor Receptors Reveal a Novel Pharmacological Mechanism of Action (2000)

Developing small molecule agonistic ligands for tyrosine kinase receptors has been difficult, and it is generally thought that such ligands require bivalency. Moreover, multisubunit receptors are difficult to target, because each subunit contributes to ligand affinity, and each subunit may have distinct and sometimes opposing functions. Here, the nerve growth factor receptor subunits p75 and the tyrosine kinase TrkA were studied using artificial ligands that bind specifically to their extracellular domain. Bivalent TrkA ligands afford robust signals. However, genuine monomeric and monovalent TrkA ligands afford partial agonism, activate the tyrosine kinase activity, cause receptor internalization, and induce survival and differentiation in cell lines and primary neurons. Monomeric and monovalent TrkA ligands can synergize with ligands that bind the p75 subunit. However, the p75 ligands used in this study must be bivalent, and monovalent p75 ligands have no effect. These findings will be useful in designing and developing screens of small molecules selective for tyrosine kinase receptors and indicate that strategies for designing agonists of multisubunit receptors require consideration of the role of each subunit. Last, the strategy of using anti-receptor mAbs and small molecule hormone mimics as receptor ligands could be applied to the study of many other heteromeric cell surface receptors.
High-power supercontinuum generation in highly nonlinear, dispersion-shifted fibers by use of a continuous-wave Raman fiber laser (2004)

High-power supercontinua are demonstrated in highly nonlinear, dispersion-shifted fibers with a continuous-wave Raman fiber laser. Supercontinuum growth is experimentally studied under different combinations of fiber length and launch power to show output powers as high as 3.2 W and bandwidths greater than 544 nm. Modulation instability (MI) is observed to seed spectral broadening at low launch powers, and the interplay between MI and stimulated Raman scattering plays an important role in the growth of the continuum at high launch powers. The effect on continuum generation of parametric four-wave mixing coupled with the higher-order dispersion properties of the fiber is investigated.
SiO2 in Si Microdevices (2003)

1. Introduction.- 2. Outline of Silicon Processes.- 3. Basic Characteristics of SiO2.- 4. Oxide Defect Locating Method.- 5. Correlation between p-Si and n-Si Minority-Carrier Recombination Lifetimes.- 6. Wafer Transient Deformation Obseration.- 7. SiO2 Weak Spots Originating in Si Wafers.- 8. Wafer Cleaning Process Affecting SiO2 Dielectric Strength.- 9. Selective Oxidation Process Inducing SiO2 Weak-Spots.- 10. Thermal Oxidation Causing SiO2 Instability.- 11. Polysilicon Gate Formation Process Affecting SiO2 Quality.- 12. Metal Interconnect Formation Process Causing SiO2 Deterioration.- 13. Si-SiO2 Weak-Spots System Repaired from Plasma Damage Through Water Pouring.- 14. Local Weak-Spots Found in Poly-Oxides and Buried Oxides.- 15. Oxides Reliability.
High Resolution Image Reconstruction: High Resolution Image Reconstruction from a Sequence of Rotated and Translated Frames. (1996)

Abstract : Some imaging sytems employ detector arrays which are not dense enough to meet the Nyquist criteria during image acquisition. This is particularly true for many staring infrared imagers. Thus, the full resolution afforded by the optics is not being realized in such a system. This paper presents a technique for estimating a high resolution image, with reduced aliasing, from a sequence of undersampled rotated and translationally shifted frames. Such an image sequence can can be obtained if an imager is mounted on a moving platform, such as an aircraft. Several approaches to this problem have been proposed in the literature. Here we extend some of this previous work. In particular, we define an observation model which incorporates accurate knowledge of the optical system. The high resolution image estimate is formed by minimizing a regularized cost function which is based on the observation model. We consider both gradient descent and conjugate gradient optimization procedures to minimize the cost function. We show that the conjugate gradient optimization provides rapid convergence. Detailed experimental results are provided to illustrate the performance of the proposed algorithm using both visible and infrared images.
An Agarose Gel Electrophoretic Method for Analysis of Hyaluronan Molecular Weight Distribution (1994)

An electrophoretic method is described for determining the molecular weight distribution of hyaluronan (HA). The method involves separation of HA by electrophoresis on a 0.5% agarose gel, followed by detection of HA using the cationic dye Stains-All (3,3'-dimethyl-9-methyl-4,5,4'5'-dibenzothiacarbocyanine). The recommended sample load is 7 micrograms. Calibration of the method with HA standards of known molecular weight has established a linear relationship between electrophoretic mobility and the logarithm of the weight-average molecular weight over the range of approximately 0.2-6 x 10(6). The separated HA pattern may also be visualized after electrotransfer of HA from the agarose gel to a nylon membrane. The membrane may be stained with the dye alcian blue. Alternatively, specific detection of HA from impure samples can be achieved by probing the nylon membrane with biotin-labeled HA-binding protein and subsequent interaction with a streptavidin-linked gold reagent and silver staining for amplification. The electrophoretic method was used to analyze HA in two different liquid connective tissues. Normal human knee joint synovial fluid showed a narrow HA molecular weight distribution, with a peak at 6-7 x 10(6). Owl monkey vitreous HA also showed a narrow molecular weight distribution, with a peak at 5-6 x 10(6). These results agree well with available published data and indicate the applicability of the method to the analysis of impure HA samples which may be available in limited amounts.
Antibody humanization by molecular dynamics simulations—in‐silico guided selection of critical backmutations (2016)

Monoclonal antibodies represent the fastest growing class of biotherapeutic proteins. However, as they are often initially derived from rodent organisms, there is a severe risk of immunogenic reactions, hampering their applicability. The humanization of these antibodies remains a challenging task in the context of rational drug design. "Superhumanization" describes the direct transfer of the complementarity determining regions to a human germline framework, but this humanization approach often results in loss of binding affinity. In this study, we present a new approach for predicting promising backmutation sites using molecular dynamics simulations of the model antibody Ab2/3H6. The simulation method was developed in close conjunction with novel specificity experiments. Binding properties of mAb variants were evaluated directly from crude supernatants and confirmed using established binding affinity assays for purified antibodies. Our approach provides access to the dynamical features of the actual binding sites of an antibody, based solely on the antibody sequence. Thus we do not need structural data on the antibody-antigen complex and circumvent cumbersome methods to assess binding affinities. © 2016 The Authors Journal of Molecular Recognition Published by John Wiley & Sons Ltd.
Tumorigenic activity of the BCR-ABL oncogenes is mediated by BCL2. (1995)

BCR-ABL is a chimeric oncogene generated by translocation of sequences from the c-abl protein-tyrosine kinase gene on chromosome 9 into the BCR gene on chromosome 22. Alternative chimeric proteins, p210BCR-ABL and p190BCR-ABL, are produced that are characteristic of chronic myelogenous leukemia and acute lymphoblastic leukemia, respectively. Their role in the etiology of human leukemia remains to be defined. Transformed murine hematopoietic cells can be used as a model of BCR-ABL function since these cells can be made growth factor independent and tumorigenic by the action of the BCR-ABL oncogene. We show that the BCR-ABL oncogenes prevent apoptotic death in these cells by inducing a Bcl-2 expression pathway. Furthermore, BCR-ABL-expressing cells revert to factor dependence and nontumorigenicity after Bcl-2 expression is suppressed. These results help to explain the ability of BCR-ABL oncogenes to synergize with c-myc in cell transformation.
Structure of the Mycobacterium tuberculosis antigen 88, a protein related to the Escherichia coli PstA periplasmic phosphate permease subunit (1994)

We report the cloning and sequencing of the gene coding for antigen 88 from Mycobacterium tuberculosis by using monoclonal antibodies to screen an expression library in lambda gt11. The gene encodes a 403-amino-acid-residue protein with a calculated molecular mass of 43,790 Da which contains seven putative transmembrane alpha-helical domains and presents a significant homology to the PstA protein of Escherichia coli. In its N-terminal region, it contains a 61-amino-acid region highly homologous to the fifth transmembrane helix of E. coli PstC. PstA and PstC are the two hydrophobic subunits of an E. coli periplasmic phosphate permease. Since the phosphate-binding subunit of this putative permease in M. tuberculosis has previously been characterized, i.e., the 38-kDa mycobacterial protein (also called protein antigen b, Ag 5, and Ag 78) homologous to PstS of E. coli, it seems likely that functional permeases analogous to the periplasmic permeases of gram-negative bacteria also exist in mycobacteria.
Low On-Voltage Operation AlGaN/GaN Schottky Barrier Diode with a Dual Schottky Structure (2005)

We propose a novel Schottky barrier diode with a dual Schodky structure combined with an AlGaN/GaN heterostructure. The purpose of this diode was to lower the on-state voltage and to maintain the high reverse breakdown voltage. An AlGaN/GaN heterostructure was grown using a metalorganic chemical vapor deposition (MOCVD). The Schottky barrier diode with a dual Schottky structure was fabricated on the AlGaN/GaN heterostructure. As a result, the on-voltage of the diode was below 0.1 V and the reverse breakdown voltage was over 350 V.
Aggressive peripheral T-cell lymphomas containing Epstein-Barr viral DNA: a clinicopathologic and molecular analysis (1991)

The Epstein-Barr virus (EBV) has been shown to be associated with posttransplant lymphoma, Hodgkin's disease, and T-cell lymphoma, in addition to African Burkitt's lymphoma. In a retrospective study of 56 consecutive cases of T-cell lymphoma, EBV DNA was found by Southern blot and in situ DNA hybridization in 10 (20%) of 50 peripheral T-cell lymphomas, but in none of six cases of T-lymphoblastic lymphoma. Peripheral T-cell lymphomas containing EBV DNA could be subclassified into three categories according to histology and immunophenotypic studies: (1) T-cell lymphoma of the helper phenotype, five cases. Two cases had histologic features resembling angioimmunoblastic lymphadenopathy (AILD). (2) T-cell lymphoma of the cytotoxic/suppressor phenotype, four cases. AILD-like features could also be recognized in two cases. Reed-Sternberg-like giant cells were identified in three cases designated Hodgkin-like T-cell lymphoma. (3) Angiocentric T-cell lymphoma or lymphomatoid granulomatosis in one case, initially affecting the skin and nose; no T-cell subset could be defined. Six of the eight EBV DNA-positive patients tested for serum EBV antibodies had elevated titers of IgG antiviral capsid antigen (greater than 640) and/or early antigen (greater than 10). From combined studies of Southern blot hybridization by using EBV termini fragment probe and in situ DNA hybridization, the EBV genomes appeared to be clonotypically proliferated in the neoplastic T cells. The patients in all three groups usually had prolonged fever preceding the diagnosis, hepatosplenomegaly, an aggressive clinical course, and poor response to chemotherapy; nine died with a median survival of only 8 months. We propose that these EBV-associated aggressive T-cell lymphomas, like human T-cell leukemia/lymphoma virus-positive T-cell lymphoma, have characteristic clinicopathologic features and should be treated as a separate disease entity.
GRANULOCYTE-MACROPHAGE-COLONY-STIMULATING FACTOR-DEPENDENT PERITONEAL MACROPHAGE RESPONSES DETERMINE SURVIVAL IN EXPERIMENTALLY INDUCED PERITONITIS AND SEPSIS IN MICE (2008)

Granulocyte-macrophage-colony-stimulating factor (GM-CSF) plays a critical role in innate immunity by stimulating the differentiation of tissue macrophages via the transcription factor PU.1. Previous studies showed that GMCSF-deficient(GM-CSF-/-) mice had susceptibility to and impaired clearance of group B streptococcal bacteria by macrophages. For these studies, we hypothesized that GM-CSF-/- mice have increased susceptibility to peritonitis caused by immune dysfunction of peritoneal macrophages. We examined the role of peritoneal macrophages in pathogen clearance, cytokine responses, and survival in a murine cecal ligation and puncture (CLP) model of peritonitis/sepsis. Surprisingly, CLP minimally affected survival in GM-CSF-/- mice while markedly reducing survival in wild-type mice. This was not explained by differences in the composition of microbial flora, rates of bacterial peritonitis, or sepsis, all of which were similar in GM-CSF-/- and wild-type mice. However, survival correlated with peritoneal and serum TNF-alpha and IL-6 levels that were significantly lower in GM-CSF-/- than in control mice. After peritoneal LPS instillation, GM-CSF-/- mice also had improved survival and reduced TNF-alpha and IL-6 responses. In vitro studies demonstrated reduced secretion of TNF-alpha and IL-6 by peritoneal macrophages isolated from sham GM-CSF-/- mice as compared with macrophages from sham control mice. Peritoneal instillation of GM-CSF-/-/PU.1+ macrophages, but not GM-CSF-/-/PU.1+ macrophages into GM-CSF-/- mice conferred susceptibility to death after CLP or peritoneal LPS exposure. These results demonstrate that GM-CSFY/PU.1-dependent peritoneal macrophage responses are a critical determinant of survival after experimentally induced peritonitis/sepsis or exposure to LPS and have implications for therapies to treat such infections.
Optoelectronic properties of semiconductor lasers butt-coupled to optical fibers (1988)

The authors have theoretically and experimentally examined the electrical noise properties of a semiconductor laser coupled to a single-mode fiber with a plane endface. It is found that the performance of semiconductor lasers butt-coupled to optical fibers critically depends on the axial position of the fiber. Measurements show that the influence of the fiber may change the output power as much as +or-40% and the modulation bandwidth, determined by the relaxation frequency by as much as +or-35% (for a bias 15% above the solitary threshold). Moreover, the pulse response and the longitudinal mode spectrum deteriorate if the laser-to-fiber distance departs from its optimal value. The authors propose a nonoptical scheme for maintaining the optimal laser-to-fiber distance so as to avoid these degrading effects.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>