gebhart/patrepeval huggingface dataset:
Characterization of Human Tissue Factor (TF)–Specific Monoclonal Antibodies Prepared Using a Rapid Immunization Protocol (2005)

Tissue factor (TF) plays an important, physiological role in hemostasis. Recent studies have demonstrated the over-expression of TF in a number of solid tumor types and its pathological roles in angiogenesis and tumor metastasis. In this study, we report the development and characterization of a panel of murine MAbs that are specific for human TF, but do not inhibit TF-mediated blood coagulation. By using a modified repetitive immunizations at multiple sites (RIMMS) protocol in conjunction with an efficient hybridoma cloning procedure, anti-TF MAbs were generated within a relatively short time frame of 5-6 weeks. Following primary screening by ELISA, the binding of the MAbs to the native form of human TF was demonstrated in flow cytometry using a stable cell line expressing human TF. Several of these TF-specific MAbs did not inhibit blood coagulation in a blood coagulation assay and bound with high affinity (0.5-2 nM) to human TF in BIAcore analyses. Importantly, this study represents an independent evaluation of the RIMMS strategy for MAb generation and demonstrates that class-switched, high-affinity MAbs can be generated rapidly and reliably using RIMMS.
Studies on the Biosynthesis of Mannan in Micrococcus lysodeikticus (1969)

Abstract The carrier lipid involved in the enzymatic synthesis of mannosyl-1-phosphoryl-undecaprenol was isolated from the crude lipids of Micrococcus lysodeikticus and identified as undecaprenyl phosphate. In the presence of a particulate enzyme from M. lysodeikticus undecaprenyl phosphate serves as an acceptor of a mannosyl group from GDP-mannose, with concomitant production of GDP. Optimal rates of enzymatic synthesis of mannosyl-1-phosphoryl-undecaprenol require the presence of Mg++ ion, and a surfaceactive compound, such as phosphatidylglycerol. An isomer of undecaprenyl phosphate, ficaprenyl (11) phosphate, serves as a substrate for mannosyl-1-phosphoryl-undecaprenol synthetase.
Random mutagenesis of the thymidine kinase gene of varicella-zoster virus (1992)

To understand the relationship between the primary structure and function of varicella-zoster virus thymidine kinase (VZV TK; EC 2.7.1.21), we established rapid screening and phenotypic selection of mutant VZV TK genes in TK-deficient Escherichia coli C600 by using a constitutive pKK223-3 expression plasmid. In this screening system, mutant TK genes generated by random mutagenesis were identified by the sensitivity of E. coli-expressing VZV TKs to 5-bromo-2'-deoxyuridine and 1-beta-D-arabinofuranosyl-E-5-(2-bromovinyl) uracil. Twenty-four mutant clones with amino acid substitutions were isolated, and their nucleotide sequence and enzymatic activities were determined. Of the 24 clones, 20 had single amino acid substitutions, 2 clones had double amino acid substitutions, and 1 clone had triple amino acid substitutions. In 17 cases of single amino acid substitution, six mutations led to lost enzyme activity, and four of these six mutations centered in the ATP-binding site. The other 11 mutations resulted in reduction of both TK and thymidylate kinase activities or only thymidylate kinase activity and were located in scattered positions in the VZV TK gene, although 5 mutations showed a tendency to cluster in the region between positions 251 and 260.
Finite-Amplitude Motion of a Piston in a Shallow Cavity (1961)

Nonlinear effects in the resonance behavior of a driven piston in a short, fluid-filled cavity are analyzed. More specialized treatments of this problem have been given previously in studies of distortion in back-enclosed loudspeakers (see, for example, H. F. Olson, Preprint No. 143, 1960 Audio Engineering Society Convention). The present work deals with liquid-filled as well as gas-filled cavities; it is assumed only that the fluid's pressure-density relation may be expressed accurately by p − po = ρoco2[s + (B/2A)s2 + (C/3A)s2], where s is the condensation and the subscript o denotes a static value. Also, the effect of finite length of the cavity is taken into account. The equation of motion of the piston, a generalized Duffing's equation, is derived. The steady-state solution of this equation contains a modified form of the small-signal solution plus second-, third-, and higher-harmonic terms. The frequency response curve differs markedly from the one predicted by small-signal theory. The results show that measurements of the piston motion might be used to determine the coefficients B/A and C/A in the fluid's pressure-density relation. A push-pull piston-cavity arrangement is also described.
Effect of Thermal Expansion Mismatch and Fiber Coating on the Fiber/Matrix Interfacial Shear Stress in Ceramic Matrix Composites (1988)

A modified indentation technique has been used to measure the interfacial shear stress in a number of ceramic matrices containing silicon carbide fibers. It was shown that the frictional component of interfacial stress was essentially zero when matrix thermal expansion was lower than that of the fiber and increased linearly with thermal expansion mismatch when matrix thermal expansion was higher. The interfacial shear stress was lowered when the fibers were coated with BN. Lower matrix shear stresses resulted in a more extensive fiber pullout during the composite fracture.
Water and steam injectivity retention with calcium chloride pretreatments (1968)

Formation permeability damage by clays can cause severe decreases in water and steam injectivity. The principal damage mechanisms are clay expansion and dispersion which are affected by the type of cations adsorbed on clay surfaces and the total salinity of the flowing solution. Clay damage by fresh water may be held to a minimum by pretreating the rock with calcium chloride. A calcium chloride preflush improved steam injectivity in several Huntington Beach Field wells. Also, a preflush made it possible to steam stimulate the First Zone in Whittier Field where, without the preflush, it was not possible to inject adequate quantities of steam. These laboratory and field studies are briefly described.
Researchers Seek New Uses for Sildenafil (2003)

CHICAGO—Now that time and experience have established the role of sildenafil nitrate (Viagra) in the treatment of erectile dysfunction (ED), researchers are turning their attention to studying how the drug may improve outcomes for other problems, as well as its safety and efficacy when combined with other therapies. Studies presented here at the Annual Scientific Meeting of the American Urological Association in late April found researchers pondering the use of sildenafil in patients with rapid ejaculation, in men with ED and lower urinary tract symptoms, and those undergoing radical prostatectomies. “With the efficacy and safety issues of sildenafil for erectile dysfunction basically settled, from a scientific point of view, you need to explore new frontiers,” said Harin Padma-Nathan, MD, clinical professor at the Keck School of Medicine of the University of Southern California in Los Angeles. Those new frontiers center around sildenafil’s enhancement of nitric oxide, a signaling molecule that controls a diverse range of physiological processes in many tissues. Scientists believe that nitric oxide regulates vascular tone and promotes blood vessel relaxation, and plays roles in the immune system, nervous system, and in inflammation. When stimulated, nitric oxide activates the enzyme guanylate cyclase. This, in turn, increases levels of cyclic guanosine monophosphate (cGMP), which causes smooth muscle relaxation. In the penis, this allows an inflow of blood leading to erection. Another enzyme, phosphodiesterase type 5 (PDE5) degrades the effectiveness of cGMP and its ability to create smooth muscle relaxation (leading to ED). Sildenafil inhibits PDE5, allowing cGMP to function more effectively.
TLR4 Mediates Vaccine-Induced Protective Cellular Immunity to <i>Bordetella pertussis</i> : Role of IL-17-Producing T Cells (2006)

Whole cell pertussis vaccines (Pw) induce Th1 responses and protect against Bordetella pertussis infection, whereas pertussis acellular vaccines (Pa) induce Ab and Th2-biased responses and also protect against severe disease. In this study, we show that Pw failed to generate protective immunity in TLR4-defective C3H/HeJ mice. In contrast, protection induced with Pa was compromised, but not completely abrogated, in C3H/HeJ mice. Immunization with Pw, but not Pa, induced a population of IL-17-producing T cells (Th-17), as well as Th1 cells. Ag-specific IL-17 and IFN-gamma production was significantly lower in Pw-immunized TLR4-defective mice. Furthermore, treatment with neutralizing anti-IL-17 Ab immediately before and after B. pertussis challenge significantly reduced the protective efficacy of Pw. Stimulation of dendritic cells (DC) with Pw promoted IL-23, IL-12, IL-1beta, and TNF-alpha production, which was impaired in DC from TLR4-defective mice. B. pertussis LPS, which is present in high concentrations in Pw, induced IL-23 production by DC, which enhanced IL-17 secretion by T cells, but the induction of Th-17 cells was also dependent on IL-1. In addition, we identified a new effector function for IL-17, activating macrophage killing of B. pertussis, and this bactericidal activity was less efficient in macrophages from TLR4-defective mice. These data provide the first definitive evidence of a role for TLRs in protective immunity induced by a human vaccine. Our findings also demonstrate that activation of innate immune cells through TLR4 helps to direct the induction of Th1 and Th-17 cells, which mediate protective cellular immunity to B. pertussis.
The Binding of Murine IgM to Staphylococcal A Protein (1978)

The binding of Staph A protein to murine immunoglobulins has previously been thought to be restricted to the IgG2 and IgG3 classes. In this study five IgM proteins were assessed for binding, and of these one showed marked Staph A binding. Pepsin digestion of this IgM molecule produced several different sized fragments, and the binding studies with these fragments indicated that the binding site is in the CH2 domain.
Accurate method for determining adhesion of cantilever beams (1999)

Using surface micromachined samples, we demonstrate the accurate measurement of cantilever beam adhesion by using test structures which are adhered over long attachment lengths. We show that this configuration has a deep energy well, such that a fracture equilibrium is easily reached. When compared to the commonly used method of determining the shortest attached beam, the present method is much less sensitive to variations in surface topography or to details of capillary drying.
The High-Affinity <i>E. coli</i> Methionine ABC Transporter: Structure and Allosteric Regulation (2008)

The crystal structure of the high-affinity Escherichia coli MetNI methionine uptake transporter, a member of the adenosine triphosphate (ATP)-binding cassette (ABC) family, has been solved to 3.7 angstrom resolution. The overall architecture of MetNI reveals two copies of the adenosine triphosphatase (ATPase) MetN in complex with two copies of the transmembrane domain MetI, with the transporter adopting an inward-facing conformation exhibiting widely separated nucleotide binding domains. Each MetI subunit is organized around a core of five transmembrane helices that correspond to a subset of the helices observed in the larger membrane-spanning subunits of the molybdate (ModBC) and maltose (MalFGK) ABC transporters. In addition to the conserved nucleotide binding domain of the ABC family, MetN contains a carboxyl-terminal extension with a ferredoxin-like fold previously assigned to a conserved family of regulatory ligand-binding domains. These domains separate the nucleotide binding domains and would interfere with their association required for ATP binding and hydrolysis. Methionine binds to the dimerized carboxyl-terminal domain and is shown to inhibit ATPase activity. These observations are consistent with an allosteric regulatory mechanism operating at the level of transport activity, where increased intracellular levels of the transported ligand stabilize an inward-facing, ATPase-inactive state of MetNI to inhibit further ligand translocation into the cell.
Multiresolution analysis for surfaces of arbitrary topological type (1997)

Multiresolution analysis and wavelets provide useful and efficient tools for representing functions at multiple levels of detail. Wavelet representations have been used in a broad range of applications, including image compression, physical simulation, and numerical analysis. In this article, we present a new class of wavelets, based on subdivision surfaces, that radically extends the class of representable functions. Whereas previous two-dimensional methods were restricted to functions difined on R 2 , the subdivision wavelets developed here may be applied to functions defined on compact surfaces of arbitrary topological type. We envision many applications of this work, including continuous level-of-detail control for graphics rendering, compression of geometric models, and acceleration of global illumination algorithms. Level-of-detail control for spherical domains is illustrated using two examples: shape approximation of a polyhedral model, and color approximation of global terrain data.
Selection of Non-aggregating VH Binders from Synthetic VH Phage-Display Libraries (2008)

The particular interest in VH antibody fragments stems from the fact that they can rival their "naturally occurring" single-domain antibody (sdAb) counterparts (camelid VHHs and shark VNARs) with regard to such desirable characteristics as stability, solubility, expression, and ability to penetrate cryptic epitopes and outperform them in terms of less immunogenicity, a much valued property in human immunotherapy applications. However, human VHs are typically prone to aggregation. Various approaches for developing non-aggregating human VHs with binding specificities have relied on a combination of recombinant DNA technology and phage-display technology. VH gene libraries are constructed synthetically by randomizing the CDRs of a single VH scaffold fused to a gene encoding a phage coat protein. Recombinant phage expressing the resulting VH libraries in fusion with the pIII protein is propagated in Escherichia coli. Monoclonal phage displaying VHs with specificities for target antigens are isolated from the libraries by a process called panning. The exertion of stability pressure in addition to binding pressure during panning ensures that the isolated VH binders are also non-aggregating. The genes encoding the desired VHs selected from the libraries are packaged within the phage particles, linking genotype and phenotype, hence making possible the identification of the selected VHs through identifying its physically linked genotype. Here, we describe the application of recombinant DNA and phage-display technologies for the construction of a phage-displayed human VH library, the panning of the library against a protein, and the expression, purification, and characterization of non-aggregating VHs isolated by panning.
Tip-Enhanced Raman Spectroscopy with Picosecond Pulses (2013)

Tip-enhanced Raman spectroscopy (TERS) can probe chemistry occurring at surfaces with both nanometer spectroscopic and submolecular spatial resolution. Combining ultrafast spectroscopy with TERS allows for picosecond and, in principle, femtosecond temporal resolution. Here we couple an optical parametric oscillator (OPO) with a scanning tunneling microscopy (STM)-TERS microscope to excite the tip plasmon with a picosecond excitation source. The plasmonic tip was not damaged with OPO excitation, and TER spectra were observed for two resonant adsorbates. The TERS signal under ultrafast pulsed excitation decays on the time scale of 10 s of seconds; whereas with continuous-wave excitation no decay occurs. An analysis of possible decay mechanisms and their temporal characteristics is given.
Modeling of an IPMC Actuator-driven Zero-Net-Mass-Flux Pump for Flow Control (2006)

In this article, a systematic design method on an ionic polymer-metal composite (IPMC)-driven zero-net-mass-flux (ZNMF) pump is introduced for the flow control on a micro air vehicle ’s (MAV) wing. Since IPMC can generate a large deformation under a low input voltage along with its ability to operate in air, and its easier manufacture in a small size, it is considered to be an ideal material for the actuating diaphragm. Several parametric studies, using numerical methods, were performed to find an optimal shape of the diaphragm in order to maximize the stroke volume. Through these parametric studies, electrode shapes and pressure effects on the stroke volume were investigated. It was also found that the resonance of the normal mode analysis of the optimal circle-shaped diaphragm would not affect the stroke volume because the computed fundamental frequency is much higher than the considered driving frequency range (40 Hz). Based on the optimal circle-shaped diaphragm, a prototype ZNMF pump, with a slot, is designed for the flow control on an MAV wing. By using the flight speed of the MAV considered in this work and the flow velocity through the pump ’s slot, the calculated non-dimensional frequency and the momentum coefficient ensure the feasibility of the designed ZNMF pump as a flow control device.
Network traffic on-line classification using decision tree fast parallel processing strategy (2012)

At present, most of the current traffic classification technology is adopted by the means of offline classification, unable to realize real-time online classification. A novel approach for network traffic online classification is proposed in this paper. A strategy of converting the C4.5 decision tree data structure to parallel data structure called encoded data structure is proposed. The encoded data structure is very easy for hardware realization, based on FPGA parallel and pipeline technology. It only needs two clock cycles to complete C4.5 decision tree search process without extra write and read controls. Experimental results show that the throughput of the classification system can reach to 1 Gbit/s on the NetFPGA2.1.3 platform, and we expect that this design can be expanded to the NetFPGA-10G platform and the throughput can reach to 10 Gbit/s. The classification accuracy can reach to more than 97% if we choose the appropriate evaluation algorithm and search algorithm to obtain the effective features set.
Scattering Tomography and Its Application to Sooting Diffusion Flames (1994)

A new analytical tomographic reconstruction technique was developed for the determination of the extinction and scattering coefficient distributions in axisymmetric media. This method, called “scattering tomography,” was tested for several particle concentration profiles corresponding to those for diffusion flames. After that, a series of experiments were performed on sooting acetylene flames using an argon-ion laser nephelometer. The experimental results were reduced using both the transmission and scattering tomography techniques to obtain the extinction coefficient profiles. It was shown that in the center of the flame, the results from these two approaches were in good agreement. Scattering tomography can be used to determine both the absorption and scattering coefficient distributions in the medium. In addition to that, it is preferable over the transmission tomography if the medium is optically very thin and particles are predominantly scattering.
Influence of soil surface manipulation on soil temperature in relation to peanut production (2013)

Soil temperature is recognised as one of the most important factors in crop production. Some degree of manual control of soil temperature is possible through regulation of soil surface cover. The effect of eight mulch treatments ( rice husk, rice husk incorporated, paddy straw, saw dust, water mulch, transparent polyethylene, black polyethylene and bare) on the soil temperature during various growth phases of peanut crop (Arachis hypogaea L.) were investigated on a lateritic sandy loam soil (ultisols). These experiments were conducted for two consecutive seasons. Plastic mulches raised the temperature upto 5 0C generally during afternoon whereas vegetative mulches depressed the same. Between the plastic mulches, black polyethylene covered field recorded lower soil temperature (upto 20 C) than the transparent one. Water mulches due to their high specific heat capacity acted as a heat sink during the day and heat source at night. The vegetative mulches suppressed the soil temperature and did not allow the radiant energy to contact the soil directly and emitted back the energy to the atmosphere. Among the vegetative mulches, rice husk and saw dust proved better than paddy straw and rice husk incorporated. The type and amount of soil cover which modify micro-climate and soil edaphic environment, may help to plan the farming practice for better crop growth and production.
Inducible Nitric Oxide Synthase Inhibition of Weibel-Palade Body Release in Cardiac Transplant Rejection (2001)

Background Inducible nitric oxide synthase (iNOS, or NOS2) reduces the severity of accelerated graft arteriosclerosis (AGA) in transplanted organs, although the precise mechanism is unclear. Methods and Results We transplanted wild-type murine hearts into either wild-type or NOS2-null recipient mice; we then measured cardiac allograft survival and analyzed tissue sections by immunohistochemistry. We have confirmed that NOS2 increases cardiac allograft survival. We now show that there is less inflammation of cardiac allografts in wild-type hosts than in NOS2-null hosts. Furthermore, staining for von Willebrand factor reveals that the presence of NOS2 is correlated with the presence of Weibel-Palade bodies inside endothelial cells, whereas the absence of NOS2 is correlated with the release of Weibel-Palade bodies. Conclusions Weibel-Palade bodies contain mediators that promote thrombosis and inflammation. Therefore, nitric oxide (NO) may stabilize the vessel wall and prevent endothelial activation in part by inhibiting the release of the contents of Weibel-Palade bodies. Prevention of Weibel-Palade body release might be a mechanism by which NO protects the vessel wall from inflammatory disorders such as atherosclerosis or graft arteriosclerosis.
Peak power reduction scheme based on subcarrier scrambling for MC-CDMA systems (2004)

A new PAPR (peak-to-average power ratio) reduction scheme is proposed for MC-CDMA (multicarrier-CDMA) using subcarrier scrambling. Based on the fact that the PAPR of the MC-CDMA signal is highly dependent on the scrambling pattern of the subcarriers irrespective of users' data symbols, the optimum fixed scrambling patterns for each combination of user spreading codes are searched to achieve the minimum PAPR. This enables the system to dynamically allocate the optimum scrambling pattern during system operation. The proposed scheme achieves a significant reduction in PAPR compared to random scrambling, especially for a small number of users. A simple suboptimum scrambling scheme is also proposed where a common scrambling pattern is used irrespective of the code combinations.