gebhart/patrepeval huggingface dataset:
IgG binding kinetics to oligo B protein A domains on lipid layers immobilized on a 27 MHz quartz‐crystal microbalance (2007)

Although molecular recognitions between membrane receptors and their soluble ligands have been analyzed using their soluble proteins in bulk solutions, molecular recognitions of membrane receptors should be studied on lipid membranes considering their orientation and dynamics on membrane surfaces. We employed Staphylococcal Protein A (SpA) oligo B domains with long trialkyl-tags from E. coli (LppBx, x = 1, 2, and 5) and immobilized LppBx on lipid layers using hydrophobic interactions from the trialkyl-tag, while maintaining the orientation of B domain-chains on a 27 MHz quartz-crystal microbalance (QCM; AT-cut shear mode). The binding of IgG Fc regions to LppBx on lipid layers was detected by frequency decreases (mass increases) on the QCM. The maximum amount bound (Delta m(max)), association constants (K(a)), association and dissociation rate constants (k(1) and k(-1), respectively) were obtained. Binding kinetics of IgG to LppB2 and LppB5 were quite similar, showing a simple 1:1 binding of the IgG Fc region to the B domain, when the surface coverage of LppB2 and LppB5 on the lipid surface is low (1.4%). When LppB5 was immobilized at the high surface coverage of 3.5%, the complex bindings of IgG such as one IgG bound to one or two LppB5 on the membrane could be observed. IgG-LppB1 binding was largely restricted because of steric hindrance on lipid surfaces. This gives a suggestion why Protein A has five IgG binding domains.
ChemInform Abstract: Synthetic Studies Toward Complex Polyether Macrolides of Marine Origin (1997)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Millimeter-Wave Spatial Multiplexing in an Indoor Environment (2009)

A unique feature of communication at millimeter (mm) wave carrier frequencies is that spatial multiplexing is available for multiple-input multiple-output (MIMO) links with moderate antenna spacing even without a rich scattering environment. In this paper, we investigate the potential for exploiting this observation for increasing the spectral efficiency of indoor 60 GHz links. We begin by establishing limits on the spatial degrees of freedom available for linear antenna arrays of constrained length. A system architecture designed to exploit the available degrees of freedom, including beamforming as well as spatial multiplexing, is proposed. We evaluate the link capacity achievable by the proposed architecture when operating in a simple indoor environment. The results illustrate the relationship between between the channel quality and the relative positions of the transmit and receive nodes.
Monocyte Derivatives Promote Angiogenesis and Myocyte Survival in a Model of Myocardial Infarction (2010)

In this study, we have investigated the hypothesis that previously reported beneficial effect of peripheral blood mononuclear cells cultured under angiogenic conditions on cardiovascular function following ischemia is not limited to EPCs but also to monocytes contained therein. We first purified and analyzed the phenotype and secretome of human and murine blood monocytes cultured under angiogenic conditions (named MDs for monocyte derivatives) and tested their effect in a mouse model of myocardial infarction (MI). FACS analysis of MDs shows that these cells express mature endothelial cell markers and that their proliferative capacity is virtually absent, consistent with their end-differentiated monocytic ontogeny. MDs secreted significant levels of HGF, IGF-1, MCP-1, and sTNFR-1 relative to their monocyte precursors. MDs were unable to form vascular networks in vitro when cultured on matrix coated flasks. Treatment of murine HL-1 cardiomyocyte cell line with MD-conditioned medium reduced their death induced by TNF-alpha, staurosporine, and oxidative stress, and this effect was dependent upon MD-derived sTNFR-1, HGF, and IGF-1. We further demonstrate that MD secretome promoted endothelial cell proliferation and capacity to form vessels in vitro and this was dependent upon MD-derived MCP-1, HGF, and IGF-1. Echocardiography analysis showed that MD myocardial implantation improved left ventricle fractional shortening of mouse hearts following MI and was associated with reduced myocardial fibrosis and enhancement of angiogenesis. Transplanted MDs and their secretome participate in preserving functional myocardium after ischemic insult and attenuate pathological remodeling.
<i>Mycobacterium tuberculosis</i> Eis protein initiates suppression of host immune responses by acetylation of DUSP16/MKP-7 (2012)

The intracellular pathogen Mycobacterium tuberculosis (Mtb) causes tuberculosis. Enhanced intracellular survival (Eis) protein, secreted by Mtb, enhances survival of Mycobacterium smegmatis (Msm) in macrophages. Mtb Eis was shown to suppress host immune defenses by negatively modulating autophagy, inflammation, and cell death through JNK-dependent inhibition of reactive oxygen species (ROS) generation. Mtb Eis was recently demonstrated to contribute to drug resistance by acetylating multiple amines of aminoglycosides. However, the mechanism of enhanced intracellular survival by Mtb Eis remains unanswered. Therefore, we have characterized both Mtb and Msm Eis proteins biochemically and structurally. We have discovered that Mtb Eis is an efficient N(ε)-acetyltransferase, rapidly acetylating Lys55 of dual-specificity protein phosphatase 16 (DUSP16)/mitogen-activated protein kinase phosphatase-7 (MKP-7), a JNK-specific phosphatase. In contrast, Msm Eis is more efficient as an N(α)-acetyltransferase. We also show that Msm Eis acetylates aminoglycosides as readily as Mtb Eis. Furthermore, Mtb Eis, but not Msm Eis, inhibits LPS-induced JNK phosphorylation. This functional difference against DUSP16/MKP-7 can be understood by comparing the structures of two Eis proteins. The active site of Mtb Eis with a narrow channel seems more suitable for sequence-specific recognition of the protein substrate than the pocket-shaped active site of Msm Eis. We propose that Mtb Eis initiates the inhibition of JNK-dependent autophagy, phagosome maturation, and ROS generation by acetylating DUSP16/MKP-7. Our work thus provides insight into the mechanism of suppressing host immune responses and enhancing mycobacterial survival within macrophages by Mtb Eis.
Influence of the ionization rate of a plasma discharge applied to the modification of a supersonic low Reynolds number flow field around a cylinder (2014)

International audience
Diet and Colon Cancer: Assessment of Risk by Fiber Type and Food Source (1988)

How fiber in the diet is related to the development of colon cancer was assessed in a population-based study conducted on 231 cases and 391 controls in Utah between 1979 and 1983. Crude fiber consistently decreased risk associated with colon cancer in both males [odds ratio (OR) = 0.4] and females (OR = 0.5). Dietary fiber, as analyzed by the method of A. S. Bitner, and neutral detergent fiber were not consistently related to colon cancer risk. Of the noncellulose polysaccharides examined, mannose and galactose were protective against cancers in the ascending colon in males (ORs = 0.5 and 0.3, respectively), whereas galactose and uronic acid were protective against cancers in the ascending colon in females (ORs = 0.5). Highest quartiles of intake of fruits and vegetables were also associated with a decreased risk of colon cancer in males (ORs = 0.3 and 0.6, respectively) and in females (ORs = 0.6 and 0.3, respectively) compared with lowest quartile of intake, whereas high intake of grains was not protective.
Surface-micromachined 2-D optical scanners with high-performance single-crystalline silicon micromirrors (2001)

We have developed a novel batch-fabrication single-crystalline silicon micromirror bonding process to fabricate optically flat micromirrors on polysilicon surface-micromachined two-dimensional (2-D) scanners. The electrostatically actuated 2-D scanner has a mirror area of 460 μm×460 μm and an optical scan angle of /spl plusmn/7.5/spl deg/. Compared with micromirror made by standard polysilicon surface-micromachining process, the radius of curvature of the micromirror has been improved by 150 times from 1.8 to 265 cm, with surface roughness <10 nm.
Photocatalytic Activity of Monodispersed Spherical TiO <sub>2</sub> Particles with Different Crystallization Routes (2003)

Monodispersed spherical TiO 2 particles were prepared by hydrothermal crystallization and/or calcination of spherical amorphous particles, synthesized by thermal hydrolysis of TiCl 4 . The crystallized spherical particles were secondary agglomerates of primary nanocrystallites. Different crystallization routes and conditions provided the spherical TiO 2 particles with wide particle characteristics, such as the fraction of crystallization, the size and shape of the primary nanocrystallites, and the specific surface area. The photocatalytic activity showed complex dependence on the crystallization routes and conditions. The complex dependence behavior could be explained by combining the effects of the fraction of crystallization, the specific surface area, and the adsorption ability for hydroxyl ions. Especially, in the present study, the hydrothermally crystallized TiO 2 particles with large primary nanocrystallites showed the highest photocatalytic activity. The high photocatalytic activity mainly resulted from the high surface adsorption ability for hydroxyl ions, which was closely related to the well‐developed (flat and faceted) morphology of primary nanocrystallite.
Scaleable purification process for gene therapy retroviral vectors (2007)

The combination of membrane separation and AEXc processes results in a feasible and scaleable purification strategy for MLV-derived vectors, allowing the removal of inhibitory contaminants thus yielding pure vectors with increased transduction efficiencies.
Human plasma lipoprotein [a]. Structural properties. (1983)

When lipoprotein [a] was isolated in the presence of the proteolytic inhibitor Trasylol, its apoprotein exhibited one dominant band corresponding to a molecular weight of about 1.2 million when analyzed by electrophoresis on 3.25% sodium dodecyl sulfate-polyacrylamide gels. After chemical reduction, this band was missing but was replaced by two bands, one corresponding to a molecular weight of about 490,000 and the other to a molecular weight of about 645,000. Before treatment with reducing agents, the apolipoprotein [a] and apolipoprotein B immunoreactivities were detectable in the same electrophoretic band, but after reduction the apolipoprotein [a] was demonstrated to be separate from the apolipoprotein B. These results suggest that the apoprotein of lipoprotein [a] is composed of two subunits which are similar in molecular weight and are held together by one or more disulfide bonds. One subunit possesses apolipoprotein [a] and the other apolipoprotein B immunoreactivity. The secondary structure of the apoprotein components within lipoprotein [a] has been studied by circular dichroism and found to differ significantly from the secondary structure of the apoproteins in low density lipoproteins and high density lipoproteins. About 30% alpha-helical structure was measured in lipoprotein [a] compared to 48% in low density lipoproteins and 70% in high density lipoproteins. Lipoprotein [a] exhibited a much higher percentage of disordered structure than either of the other two lipoproteins.
OFM: Optimized Flow Migration for NFV Elasticity Control (2018)

Network Function Virtualization (NFV) together with Software Defined Networking (SDN) offers the potential for enhancing service delivery flexibility and reducing overall costs. Based on the capability of dynamic creation and destruction of network function (NF) instances, NFV provides great elasticity in NF control, such as NF scaling out, scaling in, load balancing, etc. To realize NFV elasticity control, network traffic flows need to be redistributed across NF instances. However, deciding which flows are suitable for migration is a critical problem for efficient NFV elasticity control. In this paper, we propose to build an innovative flow migration controller, OFM Controller, to achieve optimized flow migration for NFV elasticity control. We identify the trigger conditions and control goals for different situations, and carefully design models and algorithms to address three major challenges including buffer overflow avoidance, migration cost calculation, and effective flow selection for migration. We implement the OFM Controller on top of NFV and SDN environments. Our evaluation results show that OFM Controller is efficient to support optimized flow migration in NFV elasticity control.
Pressure Affects the Structure and the Dynamics of the<scp>d</scp>-Galactose/<scp>d</scp>-Glucose-Binding Protein from<i>Escherichia coli</i>by Perturbing the C-Terminal Domain of the Protein (2006)

The effect of the pressure on the structure and stability of the D-galactose/D-glucose binding protein from Escherichia coli in the absence (GGBP) and in the presence (GGBP/Glc) of glucose was studied by Fourier transform infrared (FT-IR) spectroscopy and molecular dynamic (MD) simulations. FT-IR spectroscopy experiments showed that the protein beta-structures are more resistant than alpha-helices structures to pressure value increases. In addition, the infrared data indicated that the binding of glucose stabilizes the protein structure against high pressure values, and the protein structure does not completely unfold up to pressure values close to 9000 bar. MD simulations allow a prediction of the most probable configuration of the protein, consistent with the increasing pressures on the two systems. The detailed analysis of the structures at molecular level confirms that, among secondary structures, alpha-helices are more sensitive than beta-structures to the destabilizing effect of high pressure and that glucose is able to preserve the structure of the protein in the complex. Moreover, the evidence of the different resistance of the two domains of this protein to high pressure is investigated and explained at a molecular level, indicating the importance of aromatic amino acid in protein stabilization.
Demonstration of Species‐Specific Sensitization to Major Allergens of <i>Dermatophagoides</i> Species by Solid‐Phase Absorption of Human IgE Antibodies (1987)

Twenty-five mite-allergic patients in the Brussels area were tested with the skin-prick test (1, 5 and 10 histamine equivalents by prick test (HEP] and RAST with standardized extracts of Dermatophagoides pteronyssinus (Dp) and D. microceras (Dm). Highly significant correlations (0.69 less than rS less than 0.96) between the two species coincided with marginal, but highly significant (P less than 0.01), greater reactions to Dp in all comparisons. Species-specific IgE antibodies to antigen Dp-42 (= P1) and Dp-X were readily detected by solid-phase serum absorption with heterologous antigen and subsequent crossed radioimmunoelectrophoresis (CRIE). An absorption single radial immunodiffusion (SRID) technique, involving major allergens Dp-42, Dm-6 and Df-6 of Dp, Dm and D. farinae (Df), demonstrated the presence of IgE antibodies reacting with epitopes common to all species, epitopes common to two species, absent on the third, and epitopes strictly specific for Dp. The majority of patients with a strong IgE binding reacted to both common and strictly species-specific epitopes. The serological findings were in good agreement with the exposure situation in the area: by species-specific ELISA for dust allergen content, Dp occurred as the dominating species, 20 out of 24 homes having dust levels of Dp-42 above 30 ng/g. Five and four homes had detectable levels of Dm-6 and Df-6, respectively, in dust.
Viscoelastic Properties of Elastomers and Tire Wet Skid Resistance (1997)

Abstract Many studies concerning tire wet skid resistance have been published in the past, but they have in general involved the use of only a few grades of SBR and BR. We have evaluated the British Portable Skid Tester (BPST) wet skid resistance of eighteen sulfur curable polymers which might be used for automobile tires. These results have been analyzed in relation to the viscoelastic properties of the polymer systems. Analysis of wet skid resistance in terms of the peak value of tan δ over a prescribed temperature range, designated as T α , and abrasion loss—derived from the theory of rubber friction—was concluded to give a better general relationship for a wide range of polymers.
Spatial hole burning in Nd3+-fiber lasers suppressed by push-pull phase modulation (1991)

Spatial hole burning causes rapid mode jumping and spectral broadening in free-running long linear Nd3+-fiber lasers. Phase modulators at either end of the resonator, operating in antiphase, provide active spatial averaging and permit stable single-mode operation with a short-term linewidth of ≊5 kHz at 1088 nm wavelength.
Cervical cone margins as a predictor for residual dysplasia in post-cone hysterectomy specimens. (1994)

The presence of dysplasia at the cervical cone margin relates significantly with the presence of residual dysplasia in the post-cone hysterectomy specimen. The grade of residual dysplasia in the post-cone hysterectomy specimen increased as the grade of dysplasia in the conization specimen increased. Free margins on a cone biopsy specimen with dysplasia offer reassurance that invasive cancer is not present in the remaining uterus.
Risk assessment in cancer patients with fever and neutropenia: a prospective, two-center validation of a prediction rule. (1992)

This risk assessment model accurately stratified the medical risk of these patients using only clinical information available on the first day of their course. Low-risk patients are an appropriate population in which to study less intensive treatment strategies.
Rhizobacteria-Induced Priming in<i>Arabidopsis</i>Is Dependent on Ethylene, Jasmonic Acid, and<i>NPR1</i> (2007)

A nonpathogenic rhizobacterium, Pseudomonas putida LSW17S, elicited systemic protection against Fusarium wilt and pith necrosis caused by Fusarium oxysporum f. sp. lycopersici and P. corrugata in tomato (Lycopersicon esculentum L.). LSW17S also confers disease resistance against P. syringae pv. tomato DC3000 (DC3000) on Arabidopsis ecotype Col-0. To investigate mechanisms underlying disease protection, expression patterns of defense-related genes PR1, PR2, PR5, and PDF1.2 and cellular defense responses such as hydrogen peroxide accumulation and callose deposition were investigated. LSW17S treatment exhibited the typical phenomena of priming. Strong and faster transcription of defense-related genes was induced and hydrogen peroxide or callose were accumulated in Arabidopsis treated with LSW17S and infected with DC3000. In contrast, individual actions of LSW17S and DC3000 did not elicit rapid molecular and cellular defense responses. Priming by LSW17S was translocated systemically and retained for more than 10 days. Treatment with LSW17S reduced pathogen proliferation in Arabidopsis ecotype Col-0 expressing bacterial NahG; however, npr1, etr1, and jar1 mutations impaired inhibition of pathogen growth. Cellular and molecular priming responses support these results. In sum, LSW17S primes Arabidopsis for NPR1-, ethylene-, and jasmonic acid-dependent disease resistance, and efficient molecular and cellular defense responses.
Mitochondrial DNA Damage and Repair in RPE Associated with Aging and Age-Related Macular Degeneration (2011)

These data show macula-specific increases in mtDNA damage, heteroplasmic mutations, and diminished repair that are associated with aging and AMD severity.
Lnk inhibits erythropoiesis and Epo-dependent JAK2 activation and downstream signaling pathways (2005)

Erythropoietin (Epo), along with its receptor EpoR, is the principal regulator of red cell development. Upon Epo addition, the EpoR signaling through the Janus kinase 2 (JAK2) activates multiple pathways including Stat5, phosphoinositide-3 kinase (PI-3K)/Akt, and p42/44 mitogen-activated protein kinase (MAPK). The adaptor protein Lnk is implicated in cytokine receptor signaling. Here, we showed that Lnk-deficient mice have elevated numbers of erythroid progenitors, and that splenic erythroid colony-forming unit (CFU-e) progenitors are hypersensitive to Epo. Lnk(-/-) mice also exhibit superior recovery after erythropoietic stress. In addition, Lnk deficiency resulted in enhanced Epo-induced signaling pathways in splenic erythroid progenitors. Conversely, Lnk overexpression inhibits Epo-induced cell growth in 32D/EpoR cells. In primary culture of fetal liver cells, Lnk overexpression inhibits Epo-dependent erythroblast differentiation and induces apoptosis. Lnk blocks 3 major signaling pathways, Stat5, Akt, and MAPK, induced by Epo in primary erythroblasts. In addition, the Lnk Src homology 2 (SH2) domain is essential for its inhibitory function, whereas the conserved tyrosine near the C-terminus and the pleckstrin homology (PH) domain of Lnk are not critical. Furthermore, wild-type Lnk, but not the Lnk SH2 mutant, becomes tyrosine-phosphorylated following Epo administration and inhibits EpoR phosphorylation and JAK2 activation. Hence, Lnk, through its SH2 domain, negatively modulates EpoR signaling by attenuating JAK2 activation, and regulates Epo-mediated erythropoiesis.
Optical Reflection Measurement System Using A Swept Modulation Frequency Technique (1989)

A measurement system has been developed capable of mea-suring reflected optical power as low as 0.0025% with a spot size diam-eter of 24 Am. One application for this system is the characterization of small-area photodetectors. The operation of the measurement system is simple, allowing the operator to quickly make multiple reflection measurements, and it does not require a darkroom. The measurement system merges a microscope, for visual alignment and focusing of the laser beam, with a lightwave component analyzer using modulation vec-tor error correction. A measurement comparison between the analyzer-based system and a power-meter-based system showed that each sys-tem can measure reflections as low as 0.0025%. However, the analyzer-based system offers the advantage of identifying the location and magnitude of system reflections. The system operates at a wavelength of 1310 nm.
Mode switching control design with initial value compensation and its application to head positioning control on magnetic disk drives (1996)

To meet an increasing demand for high performance and large-capacity in magnetic hard disk drives, both fast response and precise positioning are strongly required for the head positioning control. A mode switching control (MSC) system, which includes a track seeking controller, a track following controller, and a switching function, is widely used to meet this requirement. The issue for MSC is to confirm a design method of servo mode switching. This paper proposes the initial value compensation method (IVC). The IVC inputs certain initial values in the controller state variables at mode switching in order to improve the transient response after switching. There are two approaches to determine the values: (1) minimizing a linear-quadratic function of the plant state variables; and (2) cancelling the unfavorable poles of the transfer function between initial values and head position by relocating zeros. Some experimental results are shown to be effective.