gebhart/patrepeval huggingface dataset:
IL-18 Gene Transfer by Adenovirus Prevents the Development of and Reverses Established Allergen-Induced Airway Hyperreactivity (2001)

We examined the role of IL-18 in preventing the development of and in reversing established allergen-induced airway inflammation and airway hyperreactivity (AHR), the cardinal features of asthma. IL-18, which potently induces IFN-gamma, was administered into the respiratory tract as cDNA in a replication-deficient adenovirus (Adv). Treatment of OVA-sensitized mice with the IL-18-expressing Adv reduced allergen-specific IL-4 production, airway eosinophilia, and mucus production, increased IFN-gamma production, and prevented the development of AHR. The effects of the IL-18 Adv treatment were dependent on the presence of IFN-gamma and IL-12. Moreover, administration of the IL-18 Adv to mice with established AHR greatly reduced AHR and IL-4 production and increased IFN-gamma production. These results demonstrate that IL-18, when administered by Adv into the respiratory tract, effectively reduces AHR and replaces an established Th2-biased immune response with a Th1-biased response.
Demecolcine-Induced Oocyte Enucleation for Somatic Cell Cloning: Coordination Between Cell-Cycle Egress, Kinetics of Cortical Cytoskeletal Interactions, and Second Polar Body Extrusion1 (2003)

Studies were designed to further explore the use of pharmacological agents to produce developmentally competent enucleated mouse oocytes for animal cloning by somatic cell nuclear transfer. Metaphase II oocytes from CF-1 and B6D2F1 strains were activated with ethanol and subsequently exposed to demecolcine at various times postactivation. Chromosome segregation, spindle dynamics, and polar body (PB) extrusion were monitored by fluorescence microscopy using DNA-, microtubule-, and microfilament-selective probes. Exposure to demecolcine did not affect rates of oocyte activation induced by ethanol but did disrupt the coordination of cytokinesis and karyokinesis, suppressing the extent and completion of spindle rotation and second PB extrusion in a strain-dependent manner. Moreover, strain- and treatment-specific variations in the rate of oocyte enucleation were also detected. In particular, CF1 oocytes were more efficiently enucleated relative to B6D2F1 oocytes, and demecolcine treatments initiated early after activation resulted in higher enucleation rates than when treatment was delayed. The observed strain differences are possibly caused by a combination of factors, such as the time course of meiotic cell-cycle progression after ethanol activation, the degree of spindle rotation, and the extent of second PB extrusion. These results suggest that developmentally competent cytoplasts can be produced by timely exposure of activated oocytes to agents that disrupt spindle microtubules. However, the utility of the demecolcine-induced enucleation protocol will require further investigation into factors linking karyokinesis to cytokinesis at the levels of cell-cycle control and oocyte cytoskeletal remodeling following artificial or natural means of egg activation.
The effects of intrathecal hypotension on tissue perfusion and pathophysiological outcome after acute spinal cord injury (2008)

Cerebrospinal fluid drainage effectively lowers intrathecal pressure and decreases the amount of tissue damage in an animal model of spinal cord injury. Further studies are needed to determine whether different draining regimens can improve motor or electrophysiological outcomes.
Isolation in a single step of a highly enriched murine hematopoietic stem cell population with competitive long-term repopulating ability (1989)

A simple procedure is described for the quantitation and enrichment of murine hematopoietic cells with the capacity for long-term repopulation of lymphoid and myeloid tissues in lethally irradiated mice. To ensure detection of the most primitive marrow cells with this potential, we used a competitive assay in which female recipients were injected with male "test" cells and 1 to 2 x 10(5) "compromised" female marrow cells with normal short-term repopulating ability, but whose long-term repopulating ability had been reduced by serial transplantation. Primitive hematopoietic cells were purified by flow cytometry and sorting based on their forward and orthogonal light-scattering properties, and Thy-1 and H-2K antigen expression. Enrichment profiles for normal marrow, and marrow of mice injected with 5-fluorouracil (5-FU) four days previously, were established for each of these parameters using an in vitro assay for high proliferative potential, pluripotent colony-forming cells. When all four parameters were gated simultaneously, these clonogenic cells were enriched 100-fold. Both day 9 and day 12 CFU-S were copurified; however, the purity (23%) and enrichment (75-fold) of day 12 CFU-S in the sorted population was greater with 5-FU-treated cells. Five hundred of the sorted 5-FU marrow cells consistently repopulated recipient lymphoid and myeloid tissues (greater than 50% male, 1 to 3 months post-transplant) when co-injected with 1 to 2 x 10(5) compromised female marrow cells, and approximately 100 were sufficient to achieve the same result in 50% of recipients under the same conditions. This relatively simple purification and assay strategy should facilitate further analysis of the heterogeneity and regulation of stem cells that maintain hematopoiesis in vivo.
Object representation by means of nonminimal division quadtrees and octrees (1985)

Quadtree representation of two-dimensional objects is performed with a tree that describes the recursive subdivision of the more complex parts of a picture until the desired resolution is reached. At the end, all the leaves of the tree are square cells that lie completely inside or outside the object. There are two great disadvantages in the use of quadtrees as a representation scheme for objects in geometric modeling system: The amount of memory required for polygonal objects is too great, and it is difficult to recompute the boundary representation of the object after some Boolean operations have been performed. In the present paper a new class of quadtrees, in which nodes may contain zero or one edge, is introduced. By using these quadtrees, storage requirements are reduced and it is possible to obtain the exact backward conversion to boundary representation. Algorithms for the generation of the quadtree, Boolean operations, and recomputation of the boundary representation are presented, and their complexities in time and space are discussed. Three-dimensional algorithms working on octrees are also presented. Their use in the geometric modeling of three-dimensional polyhedral objects is discussed.
Summarizability in OLAP and statistical data bases (2002)

The summarizability of OLAP (online analytical processing) and statistical databases is an a extremely important property, because violating this condition can lead to erroneous conclusions and decisions. In this paper, we explore the conditions for summarizability. We introduce a framework for precisely specifying the context in which statistical objects are defined. We use a three-step process to define normalized statistical objects. Using this framework, we identify three necessary conditions for summarizability. We provide specific tests for each of the conditions that can be verified either from semantic knowledge or by checking the statistical database itself. We also provide the reasoning for our belief that these three summarizability conditions are sufficient as well.
Small applied electric fields guide migration of hippocampal neurons (2008)

Effectively directed neuron migration is critical for development and repair in the central nervous system (CNS). Endogenous electric fields (EFs) are widespread in developing and regenerating tissues and regulate a variety of cell behaviors including directed cell migration. Electrically-directed neuronal migration has not been tested previously and we show that an applied EF directs migration of hippocampal neurons toward the cathode at a field strength of 120 mV/mm, close to the physiological range. Reversal of the field polarity reversed the direction of neuron migration. Neuron migration from an explant also was directed by an applied EF. Mechanistically, EF-guided migration was transduced by activation of the second messenger molecules ROCK (Rho-associated protein kinase) and PI3 kinase (phosphoinositide-3 kinase) since their pharmacological inhibition decreased the directedness and speed of neuron migration. This work demonstrates that rat hippocampal neurons respond to applied EFs with directional migration and raises the possibility that EFs may be used as a cue to direct neuronal migration in novel strategies to repair the CNS.
Prevention of hepatitis C virus infection in chimpanzees after antibody-mediated in vitro neutralization. (1994)

Hepatitis C virus (HCV) is the most important etiologic agent of non-A, non-B hepatitis and is a major cause of chronic liver disease and hepatocellular carcinoma. Development of an effective vaccine would be the most practical method for prevention of the infection, but whether infection with HCV elicits protective immunity in the host is unclear. Neutralization of HCV in vitro was attempted with plasma of a chronically infected patient, and the residual infectivity was evaluated by inoculation of eight seronegative chimpanzees. The source of HCV was plasma obtained from a patient during the acute phase of posttransfusion non-A, non-B hepatitis, which had previously been titered for infectivity in chimpanzees. Neutralization was achieved with plasma obtained from the same patient 2 yr after the onset of primary infection but not with plasma obtained 11 yr later, although both plasmas contained antibodies against nonstructural and structural (including envelope) HCV proteins. Analysis of sequential viral isolates from the same patient revealed significant genetic divergence as early as 2 yr after infection. However, the HCV recovered from the patient 2 yr after the infection had a striking sequence similarity with the HCV recovered from one of the chimpanzees inoculated with the acute-phase virus, suggesting that the progenitor of the new strain was already present 2 yr earlier. This evidence, together with the different sequences of HCV recovered from the chimpanzees that received the same inoculum, confirms that HCV is present in vivo as a quasispecies. These results provide experimental evidence in vivo that HCV infection elicits a neutralizing antibody response in humans but suggest that such antibodies are isolate-specific. This result raises concerns for the development of a broadly reactive vaccine against HCV.
Ruthenium(II) Complexes of 6,7-Dicyanodipyridoquinoxaline:  Synthesis, Luminescence Studies, and DNA Interaction (2000)

The hexaflurophosphate and chloride salts of a series of ruthenium(II) complexes incorporating a new dipyridophenazine-based ligand, dicnq (6,7-dicyanodipyrido[2,2-d:2',3'-f]quinoxaline), are synthesized in good-to-moderate yields. These mono ([Ru(phen)2(dicnq)]2+; phen = 1,10-phenanthroline), bis ([Ru(phen)(dicnq)2]2+), and tris ([Ru(dicnq)3]2+) complexes are fully characterized by elemental analysis, infrared, FAB-MS, 1H NMR, and cyclic voltammetric methods. Results of absorption titration and thermal denaturation studies reveal that these complexes are moderately strong binders of calf-thymus (CT) DNA, with their binding constants spanning the range (1-3) x 10(4) M-1. On the other hand, under the identical set of experimental conditions of light and drug dose, the DNA (pBR 322)-photocleavage abilities of these ruthenium(II) complexes follow the order [Ru(phen)2(dicnq)]2+ > [Ru(phen)(dicnq)2]2+ >> [Ru(dicnq)3]2+, an order which is the same as that observed for their MLCT emission quantum yields. Steady-state emission studies carried out in nonaqueous solvents and in aqueous media with or without DNA reveal that while [Ru(dicnq)3]2+ is totally nonemissive under these solution conditions, both [Ru(phen)2(dicnq)]2+ and [Ru(phen)(dicnq)2]2+ are luminescent and function as "molecular light switches" for DNA. Successive addition of CT DNA to buffered aqueous solutions containing the latter two complexes results in an enhancement of the emission in each case, with the enhancement factors at saturation being approximately 16 and 8 for [Ru(phen)2(dicnq)]2+ and [Ru(phen)(dicnq)2]2+, respectively. These results are discussed in light of the relationship between the structure-specific deactivations of the MLCT excited states of these metallointercalators and the characteristic features of their DNA interactions, and attempts are made to compare and contrast their properties with those of analogous dipyridophenazine-based complexes, including the ones reported in the preceding paper.
HaloTag: a novel reporter gene for positron emission tomography. (2011)

Among the many molecular imaging techniques, reporter gene imaging has been a dynamic area of research. The HaloTag protein is a modified haloalkane dehalogenase which was designed to covalently bind to synthetic ligands (i.e. the HaloTag ligands [HTL]). Covalent bond formation between the HaloTag protein and the chloroal-kane within the HTL occurs rapidly under physiological conditions, which is highly specific and essentially irreversible. Over the years, HaloTag technology has been investigated for various applications such as in vitro/in vivo imaging, protein purification/trafficking, high-throughput assays, among others. The goal of this study is to explore the use of the HaloTag protein as a novel reporter gene for positron emission tomography (PET) imaging. By attaching a HaloTag -reactive chloroalkane to 1, 4, 7-triazacyclononane-N, N', N"-triacetic acid (NOTA) through hydrophilic linkers, the resulting NOTA-conjugated HTLs were labeled with (64)Cu and tested for PET imaging in living mice bearing 4T1-HaloTag-ECS tumors, which stably express the HaloTag protein on the cell surface. Significantly higher uptake of (64)Cu-NOTA-HTL-S (which contains a short hydrophilic linker) in the 4T1-HaloTag-ECS than the non-HaloTag-expressing 4T1 tumors was observed, which demonstrated the HaloTag specificity of (64)Cu-NOTA-HTL-S and warranted future investigation of the HaloTag protein as a PET reporter gene.
Discoordinate gene expression of gyrA and gyrB in response to DNA gyrase inhibition in Escherichia coli (1997)

The intracellular level of DNA supercoiling is regulated in Escherichia coli by a homeostatic control mechanism that includes DNA gyrase and topoisomerase I gene expression. Despite several biochemical and genetical evidence that supports the existence of a homeostatic regulation mechanism, there are only few studies focusing gyrA and gyrB gene expression in connection to the mechanism involved in the regulation of DNA supercoiling in vivo. To study DNA gyrase gene expression and to be able to isolate mutants with altered expression of DNA gyrase, we constructed a new chromosomal reporter system based on two translational fusions of gyrA and gyrB to lacZ Using this stable monitor system in a robust wild type, we simultaneously studied the influence of several inhibitors of DNA gyrase (quinolones and coumarins) on gyrA and gyrB gene expression as well as on the intracellular level of DNA supercoiling. Surprisingly, we found a delayed and differential response of gyrA and gyrB gene expression following inhibition of DNA gyrase by quinolones or coumarins. Whereas both groups of drugs were able to increase the expression of gyrA, the gyrB gene expression was only induced by the coumarins. Although the action of the quinolones was able to alter DNA supercoiling, we never observed any induction of gyrB from the chromosome. These results revealed that the gene expressio of gyrA appears to be more sensitive to alterations in DNA supercoiling than the gyrB gene expression and suggest that probably additional regulatory mechanisms on the post-translational level might be involved in the regulation of DNA supercoiling and DNA gyrase gene expression.
Coadministration of Glucagon-Like Peptide-1 During Glucagon Infusion in Humans Results in Increased Energy Expenditure and Amelioration of Hyperglycemia (2012)

Glucagon and glucagon-like peptide (GLP)-1 are the primary products of proglucagon processing from the pancreas and gut, respectively. Giving dual agonists with glucagon and GLP-1 activity to diabetic, obese mice causes enhanced weight loss and improves glucose tolerance by reduction of food intake and by increase in energy expenditure (EE). We aimed to observe the effect of a combination of glucagon and GLP-1 on resting EE and glycemia in healthy human volunteers. In a randomized, double-blinded crossover study, 10 overweight or obese volunteers without diabetes received placebo infusion, GLP-1 alone, glucagon alone, and GLP-1 plus glucagon simultaneously. Resting EE--measured using indirect calorimetry--was not affected by GLP-1 infusion but rose significantly with glucagon alone and to a similar degree with glucagon and GLP-1 together. Glucagon infusion was accompanied by a rise in plasma glucose levels, but addition of GLP-1 to glucagon rapidly reduced this excursion, due to a synergistic insulinotropic effect. The data indicate that drugs with glucagon and GLP-1 agonist activity may represent a useful treatment for type 2 diabetes and obesity. Long-term studies are required to demonstrate that this combination will reduce weight and improve glycemia in patients.
Clostridium botulinum C2 toxin is internalized by clathrin- and Rho-dependent mechanisms (2010)

Clostridium botulinum C2 toxin is an ADP-ribosyltransferase, causing depolymerization of the actin cytoskeleton in eukaryotic cells. The C2 toxin is a binary toxin consisting of the enzymatic subunit C2I and the binding subunit C2II. Proteolytical activation of the binding subunit triggers the formation of heptameric structures (C2IIa), which bind to cellular receptors. C2I is able to bind to C2IIa oligomers, and it has been suggested that the whole complex is internalized by a raft-dependent mechanism. Here we analysed by which mechanism C2 toxin is endocytosed. In HeLa cells expressing a dominant-negative dynamin mutant, cytotoxicity and C2 toxin uptake were blocked. Furthermore, siRNA-mediated knockdown of flotillins or inhibition of Arf6 function, proteins suggested to be involved in dynamin-independent endocytosis, did not affect C2 toxicity. Knockdown of caveolin did not inhibit endocytosis of C2 toxin, whereas inhibition of clathrin function reduced the uptake of C2 toxin and delayed the cytotoxic effect. Finally, we found evidence for a Rho-mediated uptake of C2 toxin. In conclusion, C2 toxin is endocytosed by dynamin-dependent mechanisms and we provide evidence for involvement of clathrin and Rho.
Short Tandem Repeat Typing Technologies used in Human Identity Testing (2007)

Short tandem repeat (STR) typing methods are widely used today for human identity testing applications including forensic DNA analysis. Following multiplex PCR amplification, DNA samples containing the length-variant STR alleles are typically separated by capillary electrophoresis and genotyped by comparison to an allelic ladder supplied with a commercial kit. This article offers a brief perspective on the technologies and issues involved in STR typing.
Direct Introduction of Single Protein Channels and Pores into Lipid Bilayers (2005)

We have developed a mechanical method for inserting single pores and channels into lipid bilayers. A hand-operated hydrogel probe, coated with a layer of proteins, is mechanically engaged with the lipid bilayer. The two major classes of membrane proteins (beta barrels and alpha-helix bundles) that can be inserted, thereby demonstrating the wide applicability of the approach. Recordings from the proteins show that they retain electrical properties that are the same as those of proteins inserted from solution. Protein-loaded probes can be used repeatedly, allowing individual pores to be rapidly screened one at a time. The method has implications for fundamental studies of cell membranes, array fabrication, and chemical screening.
Conserved HIV‐1 Epitopes Continuously Elicit Subdominant Cytotoxic T‐Lymphocyte Responses (2009)

Subdominant CTL recognition of conserved HIV-1 epitopes commonly occurs from the primary through chronic stages of HIV-1 infection. These findings underscore the challenge in designing T cell-based vaccines that can induce immunodominant CTL responses to conserved HIV-1 regions.
Lattice symmetry of the cholesteric blue phases (1983)

The cholesteric blue phases (BP I and BP II) can be modeled as cubic lattices of disclinations in a cholesteric matrix. In an earlier paper we presented results of free-energy calculations for three models with ${O}^{2}(P{4}_{2}32),{O}^{5}(I432)$, and ${O}^{8}(I{4}_{1}32)$ space-group symmetry. In the present paper calculations for a fourth model, also of ${O}^{8}$ symmetry, are presented (we differentiate these models as ${O}^{8(+)}$ and ${O}^{8(\ensuremath{-})}$, respectively). For a number of cholesterol derivatives we assign the ${O}^{8(\ensuremath{-})}$ structure to the BP I, and the ${O}^{2}$ structure to BP II, on the following evidence: For the case of equal elastic constants the calculations show a crossover of the free energy, the ${O}^{2}$ structure being lowest at the higher temperatures, and ${O}^{8(\ensuremath{-})}$ at lower temperatures. (However, the crossover may disappear for other values of the elastic constants.) The assignment is consistent with the observed BP I and BP II lattice constants in terms of cholesteric pitch. There is excellent agreement between calculated and observed intensities of the Bragg reflections. Some details of the observed Bragg-diffraction spectra are also discussed.
DNA bar coding and pyrosequencing to identify rare HIV drug resistance mutations (2007)

Treatment of HIV-infected individuals with antiretroviral agents selects for drug-resistant mutants, resulting in frequent treatment failures. Although the major antiretroviral resistance mutations are routinely characterized by DNA sequencing, treatment failures are still common, probably in part because undetected rare resistance mutations facilitate viral escape. Here we combined DNA bar coding and massively parallel pyrosequencing to quantify rare drug resistance mutations. Using DNA bar coding, we were able to analyze seven viral populations in parallel, overall characterizing 118 093 sequence reads of average length 103 bp. Analysis of a control HIV mixture showed that resistance mutations present as 5% of the population could be readily detected without false positive calls. In three samples of multidrug-resistant HIV populations from patients, all the drug-resistant mutations called by conventional analysis were identified, as well as four additional low abundance drug resistance mutations, some of which would be expected to influence the response to antiretroviral therapy. Methods for sensitive characterization of HIV resistance alleles have been reported, but only the pyrosequencing method allows all the positions at risk for drug resistance mutations to be interrogated deeply for many HIV populations in a single experiment.