gebhart/patrepeval huggingface dataset:
Characterization of the Shigella flexneri ipgD and ipgF genes, which are located in the proximal part of the mxi locus (1993)

The Shigella flexneri invasion process requires the synthesis of the Ipa proteins and their secretion by specific factors encoded by the mxi and spa genes, which are clustered upstream from the ipa operon. We report here the characterization of the ipgD, ipgE, and ipgF genes, which are located in the 5' end of the mxi locus. Analysis of IpgF-PhoA fusions endowed with high levels of alkaline phosphatase activity confirmed the functionality of a classical signal sequence detected in the sequence of IpgF. The ipgD and ipgF genes were each inactivated on the large virulence plasmid by insertion of a nonpolar cassette; each of the ipgD and ipgF mutants thus constructed showed the same invasive phenotype as the wild-type strain and was able to provoke keratoconjunctivitis in guinea pigs. It thus appears that two genes located at the ipa-proximal part of the mxi locus are not directly involved in invasion. Analysis of concentrated culture supernatants of the wild-type and ipgD strains indicated that secretion of one polypeptide, whose size was consistent with that predicted for the IpgD protein (60 kDa), was abolished in the ipgD mutant.
Detection of respiratory syncytial virus in nasopharyngeal secretions by shell vial technique (1991)

A shell vial technique was used to recover respiratory syncytial virus (RSV) from frozen nasopharyngeal specimens previously tested by rapid diagnostic methods. With specimens determined to be positive by direct fluorescence assay (DFA), the shell vial technique was at least as sensitive as conventional tissue culture (92 versus 90%). The majority of RSV isolates were detected within 16 h postinoculation, versus an average of 4.5 days by conventional techniques. Also, the shell vial method recovered RSV from 16 of 17 specimens (94%) which had previously tested positive by enzyme immunoassay (EIA). In addition, the shell vial method detected RSV in 4 and 11% of specimens previously determined to be negative by DFA and EIA, respectively. Therefore, we recommend the use of the shell vial technique for specimens testing negative by the rapid methods of DFA or EIA.
The Stewart Platform of General Geometry Has 40 Configurations (1993)

The Stewart platform is a six-degree-of-freedom, in-parallel linkage. It is used in automotive and flight simulators, positioning tables for assembly and robotic applications, and various other applications requiring linkages with high structural stiffness. It consists of a base link, a coupler link, and six adjustable-length legs supporting the coupler link. Each leg consists of a prismatic joint with ball-joint connections to the base and coupler, respectively. The forward kinematics problem for the Stewart platform may be stated as follows: given the values of the six prismatic joint displacement inputs to the linkage, compute the position and orientation of the coupler link. This problem may be set up as a system of nonlinear multivariate polynomial equations. We solve this problem using a numerical technique known as polynomial continuation. We show that for Stewart platforms of general geometry (i.e., platforms in which the linkage parameters are arbitrary complex numbers) this problem has 40 distinct solutions.
Micromachining of photonic devices by femtosecond laser pulses (2008)

In this paper we review the micromachining of photonic devices in several materials by means of ultrashort laser pulses. The physical mechanisms underlying the refractive index modification and the different laser systems used to induce such modification are discussed. A thorough review of the photonic devices demonstrated with the femtosecond laser microfabrication technique is presented. In particular, this paper is focused on photonic devices based on optical waveguides. The devices are organized into two categories: passive and active devices. In the former category power splitters, directional couplers, interferometers and Bragg gratings are reviewed, while in the latter amplifiers and lasers are discussed. Finally, conclusions and future perspectives of femtosecond laser micromachining in photonics are provided.
Multifunctional Nano-Architecture for Biomedical Applications (2006)

A multifunctional architecture for biomedical applications has been developed by deliberately combining the useful functions of superparamagnetism, luminescence, and surface functionality into one material. Good control of the core−shell architecture has been achieved by employing a sol−gel synthesis. Superparamagnetic iron oxide nanoparticles are first coated with silica to isolate the magnetic core from the surrounding. Subsequently, the dye molecules are doped inside a second silica shell to improve photostability and allow for versatile surface functionalities. The architecture has been characterized by transmission electron microscopy, UV−vis absorption and emission spectroscopy, energy-dispersive X-ray spectroscopy, X-ray diffraction, and magnetometry. The hybrid nanoparticles exhibit improved superparamagnetic behavior over the as-received nanoparticles with a significant decrease in the blocking temperature. The architecture shows emission properties similar to those of the free dye molecules, suggesting that the first silica shell successfully prevents luminescence quenching by minimizing dye−magnetic core interactions.
Aminoguanidine inhibits reactive oxygen species formation, lipid peroxidation, and oxidant-induced apoptosis. (1998)

Aminoguanidine (AG) treatment, like nerve growth factor (NGF) treatment, prevents diabetes-induced apoptosis of retinal Müller cells in the rat eye, but the mechanism involved is unknown. In this study, the effects of preincubation with AG on oxidant-induced apoptosis, oxidant-induced intracellular reactive oxygen species (ROS) production, and lipid peroxidation were determined in rat retinal Müller cells and compared with the effects of NGF, a protein that protects neuronal cells from oxidative stress. The effect of AG on rabbit vitreous lipid peroxide levels was also determined. After exposure to increasing concentrations of H2O2, there was a corresponding increase in the percentage of apoptotic Müller cells. Preincubation with AG for 48 h completely inhibited oxidant-induced apoptosis in response to 10 micromol/l H2O2 (+AG 0 vs. 10 micromol/l, NS), and reduced the percentage of apoptotic cells in response to 50 micromol/l H2O2 by 50% (+AG vs. -AG, P < 0.01). Longer preincubation did not increase the antiapoptotic effect of AG. The effect of AG was dose-dependent. Similar results were obtained after preincubation with NGF. Both AG and NGF preincubation prevented the twofold increase in oxidant-induced lipid peroxides. The fivefold increase in oxidant-induced ROS production was decreased 100% by NGF, but only 61% by AG preincubation. The twofold increase in vitreous lipid peroxide level in diabetic rabbits was completely prevented by AG treatment. AG reduced H2O2-induced benzoate hydroxylation in a dose-dependent manner. Intracellular glutathione content was unchanged. These data demonstrate that AG can act as an antioxidant in vivo, quenching hydroxyl radicals and lipid peroxidation in cells and tissues and preventing oxidant-induced apoptosis.
Preoperative Plasma Endoglin Levels Predict Biochemical Progression After Radical Prostatectomy (2008)

Preoperative plasma endoglin levels are associated with established features of advanced prostate cancer. More importantly, higher preoperative plasma endoglin levels are independent predictors of an increased risk of biochemical progression in patients treated with radical prostatectomy and bilateral pelvic lymphadenectomy.
The relevance and potential roles of microphysiological systems in biology and medicine (2014)

Microphysiological systems (MPS), consisting of interacting organs-on-chips or tissue-engineered, 3D organ constructs that use human cells, present an opportunity to bring new tools to biology, medicine, pharmacology, physiology, and toxicology. This issue of Experimental Biology and Medicine describes the ongoing development of MPS that can serve as in-vitro models for bone and cartilage, brain, gastrointestinal tract, lung, liver, microvasculature, reproductive tract, skeletal muscle, and skin. Related topics addressed here are the interconnection of organs-on-chips to support physiologically based pharmacokinetics and drug discovery and screening, and the microscale technologies that regulate stem cell differentiation. The initial motivation for creating MPS was to increase the speed, efficiency, and safety of pharmaceutical development and testing, paying particular regard to the fact that neither monolayer monocultures of immortal or primary cell lines nor animal studies can adequately recapitulate the dynamics of drug-organ, drug-drug, and drug-organ-organ interactions in humans. Other applications include studies of the effect of environmental toxins on humans, identification, characterization, and neutralization of chemical and biological weapons, controlled studies of the microbiome and infectious disease that cannot be conducted in humans, controlled differentiation of induced pluripotent stem cells into specific adult cellular phenotypes, and studies of the dynamics of metabolism and signaling within and between human organs. The technical challenges are being addressed by many investigators, and in the process, it seems highly likely that significant progress will be made toward providing more physiologically realistic alternatives to monolayer monocultures or whole animal studies. The effectiveness of this effort will be determined in part by how easy the constructs are to use, how well they function, how accurately they recapitulate and report human pharmacology and toxicology, whether they can be generated in large numbers to enable parallel studies, and if their use can be standardized consistent with the practices of regulatory science.
Engagement of FcεRI on Human Monocytes Induces the Production of IL-10 and Prevents Their Differentiation in Dendritic Cells (2001)

The local cytokine environment and the presence of stimulatory signals determine whether circulating monocytes will finally acquire characteristics of dendritic cells (DCs) or macrophages. Because FcepsilonRI expressed on professional APCs, e.g., monocytes and DCs, has been suggested to play a key role in the pathophysiology of atopic diseases, we evaluated the effect of receptor ligation on the generation of monocyte-derived DCs (MoDCs). Aggregation of FcepsilonRI at the initiation of the IL-4-GM-CSF-driven differentiation resulted in the emergence of macrophage-like cells with a strong expression of the mannose receptor and a low level of CD1a and the DC-specific markers CD83 and the actin-bundling protein (p55). These cells sustained the ability to take up FITC-labeled Escherichia coli by phagocytosis and were significantly less efficient in stimulating purified allogeneic T cells. In addition, receptor ligation of FcepsilonRI at the beginning of the culture prevented the generation of MoDCs, mainly due to a dramatic increase in the IL-10 production. These results suggest that FcepsilonRI aggregation prevents the generation of CD1a(+) MoDCs and imply a novel pivotal function of this receptor in modulating the differentiation of monocytes.
Sensibilité du modèle de la p-médiane au comportement spatial de l'usager (1995)

Sensitivity of the p-median model to the customer's spatial behaviour. — The assumption underlying the p- median model, that the customer moves to the nearest facility available, is undoubtedly unrealistic when dealing with a service supplying free and attractive usage. The object of this paper is to examine the sensitivity of the allocation obtained using the p- median to the allocation determined using a spatial interaction model. The result shows that the attractiveness of facilities and friction of distance exert comparatively little influence on allocation. This influence is an implicit function of the location of facilities and of the spatial distribution of customers.
Oxidative Stress in the Dahl Hypertensive Rat (1997)

Enhanced production of oxygen free radicals may play a role in hypertension by affecting vascular smooth muscle contraction, resistance to blood flow, and organ damage. The aim of this study was to determine whether oxygen free radicals are involved in the development of salt-induced hypertension. Dahl salt-sensitive (Dahl-S) and salt-resistant (Dahl-R) rats were fed either a high salt (6.0% NaCl) or low salt (0.3% NaCl) diet for 4 weeks. The high salt diet caused the development of severe hypertension in Dahl-S animals and had no effect on blood pressure in Dahl-R animals. A tetranitroblue tetrazolium dye was used to detect superoxide radicals in microvessels of the mesentery. Light absorption measurements revealed enhanced staining along the endothelium of arterioles and venules in hypertensive Dahl-S animals, with significantly lower values in normotensive animals. In addition, a Clark electrochemical electrode was used to measure hydrogen peroxide levels in fresh plasma. Hypertensive Dahl-S animals had a higher plasma hydrogen peroxide concentration compared with their normotensive counterparts (2.81+/-0.43 versus 2.10+/-0.41 micromol/L), while no difference was detected between high- and low salt-treated Dahl-R animals (1.70+/-0.35 versus 1.56+/-0.51 micromol/L). The plasma hydrogen peroxide levels of all groups correlated with mean arterial pressure (r=.77). These findings demonstrate an enhanced production of oxygen free radicals in the microvasculature of hypertensive Dahl-S rats.
SaFe: a general framework for integrated spatial and feature image search (2002)

We present a system for querying for images by the spatial and feature attributes of regions. The system enables the user to find the images that contain an arrangement of regions similar to that diagrammed in a query image. We propose a general framework which allows for different types of features (e.g., color, texture, shape, motion) to be integrated with spatial information in the query process. We demonstrate that integrated spatial and feature querying improves image search capabilities over previous content-based image retrieval methods.
Rescue of ΔF508-CFTR trafficking and gating in human cystic fibrosis airway primary cultures by small molecules (2006)

Cystic fibrosis (CF) is a fatal genetic disease caused by mutations in cftr, a gene encoding a PKA-regulated Cl(-) channel. The most common mutation results in a deletion of phenylalanine at position 508 (DeltaF508-CFTR) that impairs protein folding, trafficking, and channel gating in epithelial cells. In the airway, these defects alter salt and fluid transport, leading to chronic infection, inflammation, and loss of lung function. There are no drugs that specifically target mutant CFTR, and optimal treatment of CF may require repair of both the folding and gating defects. Here, we describe two classes of novel, potent small molecules identified from screening compound libraries that restore the function of DeltaF508-CFTR in both recombinant cells and cultures of human bronchial epithelia isolated from CF patients. The first class partially corrects the trafficking defect by facilitating exit from the endoplasmic reticulum and restores DeltaF508-CFTR-mediated Cl(-) transport to more than 10% of that observed in non-CF human bronchial epithelial cultures, a level expected to result in a clinical benefit in CF patients. The second class of compounds potentiates cAMP-mediated gating of DeltaF508-CFTR and achieves single-channel activity similar to wild-type CFTR. The CFTR-activating effects of the two mechanisms are additive and support the rationale of a drug discovery strategy based on rescue of the basic genetic defect responsible for CF.
Kinetics of the Gelation of Colloidal Silica at Geothermal Conditions, and Implications for Reservoir Modification and Management (2013)

Abstract not provided
Characterization of the Monomeric and Dimeric Forms of Latent and Active Matrix Metalloproteinase-9 (2000)

Matrix metalloproteinase-9 (MMP-9) is a member of the MMP family that has been associated with degradation of the extracellular matrix in normal and pathological conditions. A unique characteristic of MMP-9 is its ability to exist in a monomeric and a disulfide-bonded dimeric form. However, there exists a paucity of information on the properties of the latent (pro-MMP-9) and active MMP-9 dimer. Here we report the purification to homogeneity of the monomer and dimer forms of pro-MMP-9 and the characterization of their biochemical properties and interactions with tissue inhibitor of metalloproteinase (TIMP)-1 and TIMP-2. Gel filtration and surface plasmon resonance analyses demonstrated that the pro-MMP-9 monomeric and dimeric forms bind TIMP-1 with similar affinities. In contrast, TIMP-2 binds only to the active forms. After activation, the two enzyme forms exhibited equal catalytic competence in the turnover of a synthetic peptide substrate with comparable kinetic parameters for the onset of inhibition with TIMPs and for dissociation of the inhibited complexes. Kinetic analyses of the activation of monomeric and dimeric pro-MMP-9 by stromelysin 1 revealed K(m) values in the nanomolar range and relative low k(cat) values (1.9 x 10(-3) and 4.1 x 10(-4) s(-1), for the monomer and dimer, respectively) consistent with a faster rate (1 order of magnitude) of activation of the monomeric form by stromelysin 1. This suggests that the rate-limiting event in the activation of pro-MMP-9 may be a requisite slow unfolding of pro-MMP-9 near the site of the hydrolytic cleavage by stromelysin 1.
A Versatile Route to syn‐ and anti‐α‐Amino β‐Hydroxy Esters from β‐Keto Esters by Dynamic Kinetic Resolution with Ru‐SYNPHOS® Catalyst (2004)

Abstract A general and practical synthesis of both syn ‐ and anti ‐α‐amino β‐hydroxy esters with high levels of selectivity by the use of Ru‐SYNPHOS ® catalysts is reported. The key transformations include asymmetric hydrogenations of α‐ N ‐substituted β‐keto esters protected as α‐amido or α‐amino hydrochloride derivatives, respectively. The Ru II ‐catalyzed hydrogenation of α‐amino β‐keto ester hydrochlorides affords the corresponding anti ‐α‐amino β‐hydroxy esters with high diastereoselectivities (up to 99%) and enantioselectivities (up to 97%) through dynamic kinetic resolution (DKR). (© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2004)
Cell-surface-associated nucleic acid in tumorigenic cells made visible with platinum-pyrimidine complexes by electron microscopy. (1975)

Platinum-pyrimidine complexes have been used as the sole electron-dense stains for electron microscopy on 18 types of mammalian cells. These recently discovered complexes react avidly with nucleic acids in vitro, are antitumor agents, and are highly soluble in water. In cells, they are selective for regions rich in nucleic acid and make visible the cellular chromatin, nucleolus, and ribosomes. In addition, cells that are tumorigenic exhibit electron-dense patches at the plasma membrane; normal cells do not. The results of treatment of ascites sarcoma-180 cells with concanavalin A, nucleases, glycosidases, or a protease suggest that the electron-dense patches are DNA, with neuroaminic acid involved in the surface binding.
Identification of a factor VIII peptide, residues 2315–2330, which neutralizes human factor VIII C2 inhibitor alloantibodies: requirement of Cys2326 and Glu2327 for maximum effect (1999)

Factor VIII (FVIII) inhibitor alloantibodies react with combinations of the A2, C2 and A3-C1 domains of the FVIII molecule. Some inhibitors block binding of FVIII to both von Willebrand factor (VWF) and phospholipid, and recognize a C2 domain epitope which overlaps both binding sites. In order to determine the essential binding regions for alloantibodies inhibitory for FVIII activity, we have performed inhibitor neutralization assays and competitive inhibition assays using 10 overlapping synthetic peptides spanning the carboxy-terminal region of the C2 domain (residues 2288-2332). We found one peptide (2315-2330, L9) which neutralized the anti-FVIII activity of four out of five different C2 alloantibodies by 50%, 39%, 47% and 57%, respectively. Neutralization of these alloantibodies by recombinant C2 domain (residues 2173-2332) was 68%, 50%, 59%, 86% and >95%, respectively. The inhibitor which was not neutralized by L9 peptide and reacted by immunoblotting with peptide 2218-2307, did not prevent binding of FVIII to VWF and only partially inhibited binding of FVIII to phosphatidylserine. Mutants of the L9 peptide were prepared in which each residue from 2315-2330 was sequentially substituted by glycine. Inhibitor neutralization experiments using these peptides demonstrated that Arg2320 and Cys2326 or Glu2327 are important for the effect of L9 peptide, since their substitution by glycine reduced its neutralizing effect by 60% to >90%, suggesting that they are crucial for formation of the one of the C2 inhibitor epitopes.
Authentic HIV-1 Integrase Inhibitors (2010)

HIV-1 integrase (IN) is indispensable for HIV-1 replication and has become a validated target for developing anti-AIDS agents. In two decades of development of IN inhibition-based anti-HIV therapeutics, a significant number of compounds were identified as IN inhibitors, but only some of them showed antiviral activity. This article reviews a number of patented HIV-1 IN inhibitors, especially those that possess high selectivity for the strand transfer reaction. These compounds generally have a polar coplanar moiety, which is assumed to chelate two magnesium ions in the binding site. Resistance to those compounds, when given to patients, can develop as a result of IN mutations. We refer to those compounds as authentic IN inhibitors. Continued drug development has so far delivered one authentic IN inhibitor to the market (raltegravir in 2007). Current and future attention will be focused on the development of novel authentic IN inhibitors with the goal of overcoming viral resistance.
From neuroprosthetics to implanted FES control architecture (2008)

In this paper, we deal with complementary aspects of an implanted functional electrical stimulation control architecture: distributed stimulation units, deterministic implanted network, architecture implantation (electronic devices) and control over this network. We argue from analogy with embedded control architecture, of robots for example, from distributed control, closed-loop control, supervisory control and fieldbus considerations. The global embedded FES architecture on which can rely a functional rehabilitation is presented. We give some details on the distributed entities of this architecture as they constitute the interface between the artificial and living ldquoworldsrdquo, and we expose their interconnection through an intrabody network which is similar to an implanted fieldbus.