gebhart/patrepeval huggingface dataset:
The Encapsulation of Squid Diisopropylphosphorofluoridate-Hydrolyzing Enzyme within Mouse Erythrocytes (1993)

Journal Article The Encapsulation of Squid Diisopropylphosphorofluoridate-Hydrolyzing Enzyme within Mouse Erythrocytes Get access W. DAVID MCGUINN, W. DAVID MCGUINN Department of Medical Pharmacology and Toxicology, Texas A&M University, College of MedicineCollege Station, Texas 77843-1114 Search for other works by this author on: Oxford Academic PubMed Google Scholar ELIZABETH P. CANNON, ELIZABETH P. CANNON Department of Medical Pharmacology and Toxicology, Texas A&M University, College of MedicineCollege Station, Texas 77843-1114 Search for other works by this author on: Oxford Academic PubMed Google Scholar CARIE T. CHUI, CARIE T. CHUI Department of Medical Pharmacology and Toxicology, Texas A&M University, College of MedicineCollege Station, Texas 77843-1114 Search for other works by this author on: Oxford Academic PubMed Google Scholar LUQI PEI, LUQI PEI Department of Medical Pharmacology and Toxicology, Texas A&M University, College of MedicineCollege Station, Texas 77843-1114 Search for other works by this author on: Oxford Academic PubMed Google Scholar ILONA PETRIKOVICS, ILONA PETRIKOVICS Department of Medical Pharmacology and Toxicology, Texas A&M University, College of MedicineCollege Station, Texas 77843-1114 Search for other works by this author on: Oxford Academic PubMed Google Scholar JAMES L. WAY JAMES L. WAY Department of Medical Pharmacology and Toxicology, Texas A&M University, College of MedicineCollege Station, Texas 77843-1114 Search for other works by this author on: Oxford Academic PubMed Google Scholar Toxicological Sciences, Volume 21, Issue 1, July 1993, Pages 38–43, https://doi.org/10.1093/toxsci/21.1.38 Published: 01 July 1993 Article history Received: 30 November 1992 Accepted: 08 March 1993 Published: 01 July 1993
Ballistic 2-D Imaging Through Scattering Walls Using an Ultrafast Optical Kerr Gate (1991)

An ultrafast optical shutter was used to image ultrasmall objects hidden behind scattering walls by a procedure that selects in time the ballistic component and rejects the scattered diffusive light. Scattering walls used in this experiment included human breast tissue, chicken breast tissue, and a water suspension of polystyrene particles with scattering coefficients up to 21.7. Submillimeter resolution was achieved for two-dimensional ballistic images of a single point, a double-point fluorescence source, and a bar test chart in or behind these different turbid media.
Identification of GTPase genes in the protozoa parasites Trypanosoma cruzi and Leishmania amazonensis. (1993)

A PCR based assay was designed in order to amplify putative ras gene sequences of the GTPase superfamily eventually present in Leishmania amazonensis and Trypanosoma cruzi. A set of primers corresponding to the conserved motifs G1 and G3 of the GTP binding proteins was synthesized. Sequencing of six PCR products (three from Leishmania and three from Trypanosoma) identified, however, two other different GTPases. The 270 bp L. amazonensis clone, pLef-11, shared an amino acid identity of around 80% with an eukaryotic elongation factor 1a of protein synthesis. On the other hand, the 168 bp T. cruzi clone, pTCr1, demonstrated over 60% amino acid identity to ras-related proteins of the rab-YPT-SEC4 family involved in control of vesicular traffic. To our knowledge, this is the first report of GTP binding protein genes in trypanosomatids.
Discovery of Novel Small Molecule Orally Bioavailable C−X−C Chemokine Receptor 4 Antagonists That Are Potent Inhibitors of T-Tropic (X4) HIV-1 Replication (2010)

The redesign of azamacrocyclic CXCR4 chemokine receptor antagonists resulted in the discovery of novel, small molecule, orally bioavailable compounds that retained T-tropic (CXCR4 using, X4) anti-HIV-1 activity. A structure-activity relationship (SAR) was determined on the basis of the inhibition of replication of X4 HIV-1 NL4.3 in MT-4 cells. As a result of lead optimization, we identified (S)-N'-((1H-benzo[d]imidazol-2-yl)methyl)-N'-(5,6,7,8-tetrahydroquinolin-8-yl)butane-1,4-diamine (AMD070) 2 as a potent and selective antagonist of CXCR4 with an IC(50) value of 13 nM in a CXCR4 125I-SDF inhibition binding assay. Compound 2 inhibited the replication of T-tropic HIV-1 (NL4.3 strain) in MT-4 cells and PBMCs with an IC(50) of 2 and 26 nM, respectively, while remaining noncytotoxic to cells at concentrations exceeding 23 microM. The pharmacokinetics of 2 was evaluated in rat and dog, and good oral bioavailability was observed in both species. This compound represents the first small molecule orally bioavailable CXCR4 antagonist that was developed for the treatment of HIV-1 infection.
Chemical, Physical, and Mechanical Characterization of Isocyanate Cross-linked Amine-Modified Silica Aerogels (2005)

We describe a new mechanically strong lightweight porous composite material obtained by encapsulating the skeletal framework of amine-modified silica aerogels with polyurea. The conformal polymer coating preserves the mesoporous structure of the underlying silica framework and the thermal conductivity remains low at 0.041 ± 0.001 W m-1 K-1. The potential of the new cross-linked silica aerogels for load-carrying applications was determined through characterization of their mechanical behavior under compression, three-point bending, and dynamic mechanical analysis (DMA). A primary glass transition temperature of 130 °C was identified through DMA. At room temperature, results indicate a hyperfoam behavior where in compression cross-linked aerogels are linearly elastic under small strains (<4%) and then exhibit yield behavior (until 40% strain), followed by densification and inelastic hardening. At room temperature the compressive Young's modulus and the Poisson's ratio were determined to be 129 ± 8 MPa and 0.18, respectively, while the strain at ultimate failure is 77% and the average specific compressive stress at ultimate failure is 3.89 × 105 N m kg-1. The specific flexural strength is 2.16 × 104 N m kg-1. Effects on the compressive behavior of strain rate and low temperature were also evaluated.
Hippocampal Neurons Become More Vulnerable to Glutamate after Subcritical Hypoxia: An in vitro Study (1990)

The neurotoxicity of glutamate and hypoxia was investigated in vitro on hippocampal neurons, which were obtained from 18-day-old rat fetuses and were maintained for 3 days in culture. Chemically defined medium without glutamate was used and the plating density was low enough that the effect of exogenously added glutamate could be directly evaluated. In the normal culture condition 1 mM glutamate was necessary to cause significant neuronal loss in the following 24 h. In marked contrast, when glutamate was added after subcritical hypoxic stress, a dose of glutamate as low as 10 microM could exhibit neurotoxicity. Administration of MK-801, a selective noncompetitive antagonist of the N-methyl-D-aspartate (NMDA) receptor, could in part reverse this increased susceptibility to low-dose glutamate after hypoxia, although MK-801 could not protect hippocampal neurons from high-dose glutamate. Therefore, both the NMDA receptor and other subclasses of the glutamate receptor may be involved in this neurotoxicity of glutamate. Different mechanisms of glutamate neurotoxicity with high and low doses are discussed. Our results showed that hippocampal neurons exposed to subcritical hypoxia become more vulnerable to glutamate than those without hypoxia. This increased susceptibility is of great interest to understanding the mechanism of slowly ongoing neuronal loss caused by ischemia or epilepsy.
Elliptic curves in Huff 's model. (2010)

The general Huff curves which contains Huff’s model as a special case is introduced in this paper. It is shown that every elliptic curve with three points of order 2 is isomorphic to a general Huff curve. Some fast explicit formulae for general Huff curves in projective coordinates are presented. These explicit formulae for addition and doubling are almost as fast as they are for the Huff curves in [9]. Finally, the number of isomorphism classes of general Huff curves defined over a finite field is enumerated.
The protein interaction map of bacteriophage lambda (2011)

Phage lambda serves as a benchmark for future studies of protein interactions among phage, viruses in general, or large protein assemblies. We conclude that we could not find all the known interactions because they require chaperones, post-translational modifications, or multiple proteins for their interactions. The lambda protein network connects 12 proteins of unknown function with well characterized proteins, which should shed light on the functional associations of these uncharacterized proteins.
Simple Mail Transfer Protocol (2008)

This document is a self-contained specification of the basic protocol for the Internet electronic mail transport. It consolidates, updates and clarifies, but doesn't add new or change existing functionality of the following:
Regulated degradation of ornithine decarboxylase requires interaction with the polyamine-inducible protein antizyme. (1992)

Intracellular degradation of vertebrate ornithine decarboxylase (ODC) is accelerated by polyamines, the products of the pathway controlled by ODC. Antizyme, a reversible, tightly binding protein inhibitor of ODC activity, is believed to be involved in this process. Mouse and Trypanosoma brucei ODCs are structurally similar, but the trypanosome enzyme, unlike that of the mouse, is not regulated by intracellular polyamines when expressed in hamster cells (L. Ghoda, D. Sidney, M. Macrae, and P. Coffino, Mol. Cell. Biol. 12:2178-2185, 1992). We found that mouse ODC interacts with antizyme in vitro but trypanosome ODC does not. To localize the region necessary for binding, we made a series of enzymatically active chimeric mouse-trypanosome ODCs and tested them for antizyme interaction. Replacing residues 117 to 140 within the 461-amino-acid mouse ODC sequence with the equivalent region of trypanosome ODC disrupted both antizyme binding and in vivo regulation. Formation of an antizyme-ODC complex is therefore required for regulated degradation.
An in vivo quantitative angiogenesis model using tumor cells entrapped in alginate. (1990)

A new in vivo system of monitoring tumor cell induced blood vessel growth using a sodium alginate entrapment process was developed. The alginate polymer of guluronic and mannuronic acids surrounds and sequesters cells from direct contact with their immediate environment, but permits diffusible angiogenic factors to pass through to induce neovascularization in the host. The alginate beads containing tumor cells were injected subcutaneously into animals and coalesced as a point source. The tumor cells are protected from direct contact with the host's immune system, so that various tumor types may be evaluated for their angiogenic potential across histocompatibility or species barriers. C57BI/6, BALB/c and nude mice as well as squirrel monkeys were used as host animals. This provided tumor cell testing in a syngeneic, allogeneic, or xenogeneic system. We found that alginate-Lewis lung carcinoma cells were potent inducers of blood vessel growth. As few as 100 alginate-Lewis lung carcinoma cells were needed to induce macroscopically visible blood vessels by 3 days. Dose-response experiments with alginate-Lewis lung carcinoma cells showed a greater level of blood vessel induction as cell numbers increased. Neovascularization was monitored qualitatively by macroscopic photography and microscopic histologic evaluation. Also, neovascularization was monitored quantitatively by measuring the level of hemoglobin at the injection site of alginate or by measuring the amount of radioactive red blood cells pooled at the injection site of the alginate beads. Both the measured levels of hemoglobin and radiolabeled red blood cells increased at the alginate site with each log increase of tumor cells delivered, which paralleled our findings at the macroscopic and microscopic level. This in vivo angiogenesis model was relatively simple and the procedures technically easy to perform. Most importantly, this model allowed both a qualitative and quantitative assessment of tumor-induced blood vessel growth.
Demonstration of Seven Epitopes on the Rh Antigen D Using Human Monoclonal Anti‐D Antibodies and Red Cells from D Categories (1989)

The agglutination patterns have been established for the reaction between 29 monoclonal antibodies with specificity for the Rh antigen D and red cells of D categories IIIa, IIIc, IVa, IVb, Va, Vc, VI and VII, which are known to lack certain epitopes on the D polypeptide. Six different agglutination patterns were recognized and interpreted to indicate the recognition of seven different epitopes. These epitopes are termed epD1 through to epD7. The separate existence of epD6 and epD7 is deduced from previous observations in inhibition studies using purified 125I-labelled antibodies; they cannot yet be distinguished in agglutination tests. The number of epitopes lacking from cells of each category varied between two and five. As all the antibodies agglutinated cells of categories IIIa, IIIc and VII and cells of categories II, IIIb and Vb were not available, it is probable that there are epitopes other than the seven presently recognized. Eighteen out of the 29 antibodies which were examined recognized epitopes epD6/7 and it is suggested either that antibodies recognizing these epitopes predominate in polyclonal anti-D sera, or that the lymphocytes producing these antibodies are preferentially selected during establishment of cell lines.
Solution structure of crotamine, a Na+ channel affecting toxin from Crotalus durissus terrificus venom (2003)

Crotamine is a component of the venom of the snake Crotalus durissus terrificus and it belongs to the myotoxin protein family. It is a 42 amino acid toxin cross-linked by three disulfide bridges and characterized by a mild toxicity (LD50 = 820 micro g per 25 g body weight, i.p. injection) when compared to other members of the same family. Nonetheless, it possesses a wide spectrum of biological functions. In fact, besides being able to specifically modify voltage-sensitive Na+ channel, it has been suggested to exhibit analgesic activity and to be myonecrotic. Here we report its solution structure determined by proton NMR spectroscopy. The secondary structure comprises a short N-terminal alpha-helix and a small antiparallel triple-stranded beta-sheet arranged in an alphabeta1beta2beta3 topology never found among toxins active on ion channels. Interestingly, some scorpion toxins characterized by a biological activity on Na+ channels similar to the one reported for crotamine, exhibit an alpha/beta fold, though with a beta1alphabeta2beta3 topology. In addition, as the antibacterial beta-defensins, crotamine interacts with lipid membranes. A comparison of crotamine with human beta-defensins shows a similar fold and a comparable net positive potential surface. To the best of our knowledge, this is the first report on the structure of a toxin from snake venom active on Na+ channel.
Gene therapy for the hemoglobin disorders: Past, present, and future (2000)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
The use of green fluorescent protein as a marker for Brucella vaccines (2010)

Brucellosis is an important malady of productive and wildlife animals and a worldwide zoonosis. The use of effective vaccines and the corresponding diagnostic tests that allow differentiating infected from vaccinated animals are essential tools to control the disease. For this, a prototype of Brucella abortus S19 vaccine expressing green fluorescent protein (S19-GFP) was constructed. The S19-GFP was readily identified under ultraviolet light by macroscopic and microscopic examination and maintained all the biochemical characteristics of the parental S19 vaccine. S19-GFP replicated ex vivo and in vivo, and protected mice against challenge with virulent B. abortus to the same extent as the isogenic S19. An immunoenzymatic assay designed to measure anti-GFP antibodies allowed the discrimination between mice vaccinated with S19-GFP and those immunized with S19. Both vaccines raised antibodies against lipopolysaccharide molecule to similar levels. This experimental model constitutes a "proof of concept" for the use of Brucella-GFP vaccines and associated diagnostic tests to distinguish vaccinated from naturally Brucella infected animals.
<title>The interface between probe and skin in noninvasive glucose sensing</title> (2003)

Non-invasive blood glucose sensing often employs contact measurement, that is, the optical probe directly contacts the skin to reduce specular reflection. The contact pressure and the variation of skin temperature therefore contribute much to interference incurred by the internal structure and composition change of the detecting part. In this paper, we are going to discuss the influence of contact pressure between fiberoptic probe and skin as well as heat transfer on spectral measurement. A through investigation is made on approaches to eliminate these factors for both contact and non-contact measurement.
Cytosolic phospholipase A2 activation is essential for beta 1 and beta 2 integrin-dependent adhesion of human eosinophils. (1999)

We examined the role of cytosolic phospholipase A2 (cPLA2) during human eosinophil adherence to ICAM-1- or VCAM-1-coated plates. IL-5-stimulated eosinophils adhered to ICAM-1 through the beta 2 integrin CD11b/CD18, while nonstimulated eosinophils did not. By contrast, nonstimulated eosinophils adhered to VCAM-1 through the beta 1-integrin VLA-4/CD29. Both IL-5-induced adhesion to ICAM-1 and spontaneous adhesion to VCAM-1 corresponded temporally to cPLA2 phosphorylation, which accompanied enhanced catalytic activity of cPLA2. The structurally unrelated cPLA2 inhibitors, arachidonyl trifluoromethylketone and surfactin, significantly inhibited eosinophil adhesion to ICAM-1 and VCAM-1 in a concentration-dependent manner. Inhibition of secretory PLA2, 5-lipoxygenase, or cyclooxygenase did not affect eosinophil adhesion. Addition of arachidonic acid to eosinophils after cPLA2 inhibition with arachidonyl trifluoromethylketone or surfactin did not reverse the blockade of adhesion to ICAM-1 or VCAM-1. However, CV-6209, a receptor-specific antagonist of platelet-activating factor, inhibited all integrin-mediated adhesion. The activated conformation of CD11b as identified by the mAb, CBRM1/5, as well as quantitative surface CD11b expression were up-regulated after IL-5 stimulation. However, cPLA2 inhibition neither prevented CBRM1/5 expression nor blocked surface Mac-1 up-regulation caused by IL-5. Our data suggest that cPLA2 activation and its catalytic product platelet-activating factor play an essential role in regulating beta 1 and beta 2 integrin-dependent adhesion of eosinophils. This blockade occurs even in the presence of up-regulated eosinophil surface integrin.
The Heparan Sulfate Motif (GlcNS6S-IdoA2S)3, Common in Heparin, Has a Strict Topography and Is Involved in Cell Behavior and Disease (2010)

Heparan sulfate (HS) is a structurally complex polysaccharide that interacts with a broad spectrum of extracellular effector ligands and thereby is thought to regulate a diverse array of biologic processes. The specificity of HS-ligand interactions is determined by the arrangement of sulfate groups on HS, which creates distinct binding motifs. Biologically important HS motifs are expected to exhibit regulated expression, yet there is a profound lack of tools to identify such motifs; consequently, little is known of their structures and functions. We have identified a novel phage display-derived antibody (NS4F5) that recognizes a highly regulated HS motif (HS(NS4F5)), which we have rigorously identified as (GlcNS6S-IdoA2S)(3). HS(NS4F5) exhibits a restricted expression in healthy adult tissues. Blocking HS(NS4F5) on cells in culture resulted in reduced proliferation and enhanced sensitivity to apoptosis. HS(NS4F5) is up-regulated in tumor endothelial cells, consistent with a role in endothelial cell activation. Indeed, TNF-α stimulated endothelial expression of HS(NS4F5), which contributed to leukocyte adhesion. In a mouse model of severe systemic amyloid protein A amyloidosis, HS(NS4F5) was expressed within amyloid deposits, which were successfully detected by microSPECT imaging using NS4F5 as a molecularly targeted probe. Combined, our results demonstrate that NS4F5 is a powerful tool for elucidating the biological function of HS(NS4F5) and can be exploited as a probe to detect novel polysaccharide biomarkers of disease processes.
Intrinsic molecular activities of the interferon-induced 2-5A-dependent RNase. (1994)

2-5A-dependent RNase (RNase L), a unique endoribonuclease that requires 5'-phosphorylated 2',5'-linked oligoadenylates (2-5A), functions in the molecular mechanism of interferon action. Because this enzyme is present at very low levels in nature, characterization and analysis have been limited. The molecular cloning of human, 2-5A-dependent RNase cDNA has facilitated its expression to high levels in insect cells by infecting with recombinant baculovirus. To determine the properties of the enzyme in the absence of other proteins, the recombinant 2-5A-dependent RNase was purified to homogeneity. The purified enzyme migrated as a monomer upon gel filtration in the absence of activator and showed highly specific, 2-5A-dependent RNase activity. The precise activator requirements were determined by stimulating the purified enzyme with a variety of 2',5'-linked oligonucleotides. The activated enzyme was capable of cleaving poly(rU) and, to a lesser extent, poly(rA), to sets of discrete products ranging from between 4 and 22 nucleotides in length. Reduced rates of 2-5A-dependent RNA cleavage were observed even after removal of ATP and chelation of divalent cations. However, optimal RNA cleavage rates required the presence of either manganese or magnesium and ATP.
Improved Synthesis of the Two-Photon Caging Group 3-Nitro-2-Ethyldibenzofuran and Its Application to a Caged Thymidine Phosphoramidite (2010)

A new and efficient route to the recently reported 3-nitro-2-ethyldibenzofuran caging group was developed. Furthermore, its installation on a thymidine phosphoramidite is described. This caging group is efficiently removed through light-irradiation at 365 nm.
A novel deep red/low infrared fluorescent flow cytometric probe, DRAQ5NO, for the discrimination of intact nucleated cells in apoptotic cell populations (2000)

The spectral properties of DRAQ5NO allow for the use of visible range fluorochromes and differential excitation in multilaser systems for tracking apoptotic populations with implications for the measurement of bioreductive potential in complex tumour populations simultaneously undergoing physiologically or drug-induced apoptosis.