gebhart/patrepeval huggingface dataset:
A gene-type-specific enhancer regulates the carbamyl phosphate synthetase I promoter by cooperating with the proximal GAG activating element (1995)

The rat carbamyl phosphate synthetase I gene is expressed in two cell types: hepatocytes and epithelial cells of the intestinal mucosa. The proximal promoter contains a single activating element, GAG, two repressor elements (sites I and III) and an anti-repressor element (site II). Although these elements together exhibit the potential for complex regulation, they are unable to confer tissue-specific promoter activity. Here we have identified a cell-type-specific enhancer that lies 10 kilobases upstream of the promoter. Unexpectedly, the enhancer also functioned in a gene-type-specific manner. The enhancer stimulated promoter activity exclusively through the proximal GAG element. Abrogation of GAG, either directly by mutation of GAG or indirectly by sites I and III repressors, abolished enhancer activation. Conversely, activation of the heterologous thymidine kinase promoter by the enhancer required the introduction of GAG. The requirement for GAG, therefore, functions to constrain the enhancer to a specific target promoter.
The HPr Kinase from Bacillus subtilis Is a Homo-oligomeric Enzyme Which Exhibits Strong Positive Cooperativity for Nucleotide and Fructose 1,6-Bisphosphate Binding (2000)

de niveau recherche, publis ou non, manant des tablissements d'enseignement et de recherche franais ou trangers, des laboratoires publics ou privs.
Protective Effect of the 5-Lipoxygenase Inhibitor Ardisiaquinone A on Hepatic Ischemia-Reperfusion Injury in Rats (2005)

The protective effects of the 5-lipoxygenase inhibitor ardisiaquinone A, a compound isolated from Ardisia sieboldii, on hepatic ischemia-reperfusion (I/R) injury was studied in rats. Hepatic I/R injury was induced by occlusion of the portal vein and the hepatic artery for 60 min, followed by reperfusion for 24 h. The content of leukotriene B (4) (LTB (4)) in the liver increased during ischemia. Serum alanine aminotransferase (ALT) levels, a marker of hepatic parenchymal cell injury, and hepatic myeloperoxidase (MPO) activity, a marker of neutrophil accumulation, significantly increased 6 - 9 h after reperfusion. Treatment with ardisiaquinone A (0.1 - 2 mg/kg, i. p.) 30 min prior to ischemia dose-dependently prevented the increase in LTB (4) content during ischemia (ID (50) = 0.645 mg/kg) with a slightly higher potency than that of AA-861 (ID (50) = 0.728 mg/kg), a known reference 5-lipoxygenase inhibitor. Ardisiaquinone A also attenuated the increase in MPO activity and serum ALT levels at 6 h after reperfusion (ID (50) = 1.71 mg/kg and 4.28 mg/kg, respectively). These protective effects were more efficient than those of AA-861 (ID (50) = 1.86 mg/kg and no effect, respectively), LY255283 (ID (50) = 18.1 mg/kg and 11.5 mg/kg, respectively), and ONO-4057 (ID (50) = 8.38 mg/kg and 9.44 mg/kg, respectively), which are LTB (4) receptor antagonists. These results suggest that ardisiaquinone A may protect the liver against damage due to I/R in rats.
Microheterogeneous Cytosolic High-Mobility Group Proteins from Broccoli Co-Purify with and Are Phosphorylated by Casein Kinase II (1994)

A group of low molecular weight protein substrates was found to co-purify with casein kinase II from broccoli (Brassica oleracea var italica). These substrates showed very high affinity toward casein kinase II and were efficiently phosphorylated even in the presence of an excess of exogenous substrates. The broccoli substrates were purified from cytosolic extracts as a double band of related proteins migrating at 18.7 and 20 kD. Further microheterogeneity was revealed by anion-exchange high-performance liquid chromatography and mass spectroscopy. The actual molecular masses of the three major components identified by mass spectroscopy were determined to be 12,691, 13,256, and 14,128 D. The substrates showed characteristic amino acid composition with a high content of polar amino acids, including about 20% each of acidic and basic amino acids. They were soluble in 2% trichloroacetic acid. The substrates cross-reacted with an antibody against wheat high-mobility group protein d (HMGd) but not HMGa. The isolated broccoli HMGs showed general DNA-binding activity without preference for AT-rich DNA. The presence of these HMG proteins in the cytosolic fraction is similar to the distribution characteristics of the animal HMG-1 subgroup. On the basis of amino acid composition and DNA-binding specificity, the isolated broccoli HMGs resemble other plant HMGs homologous to the HMG-1 subgroup.
Vaccination against AGE-LDL significant attenuates atherosclerosis in diabetic apoE mice (2011)

Objective To investigate the effects of vaccination against AGE-LDL in atherosclerosis and involved mechanism. Methods Male apoE deficient mice were fed with high fat and induced to diabetes by injection of streptozotocin intraperitoneal 8-week-old diabetic apo-E -/- mice were randomised to receive PBS, Al(OH) 3 , or Al(OH) 3 +AGE-LDL injection subcutaneous every 2 weeks. After 11 weeks, all mice were sacrificed. The concentration of serum total cholesterol, LDL, HDL, and triglyceride concentrations were measured. Atherosclerotic lesions were analysed by oil red O, MOMA-2 antibody, Masson's trichrome, and -SMC antibody, and DAB detection kit were used. FACS was used to assess the percentages of Th1, Th2, Treg and T17 cells. Total IgG, IgM, specific IgG and IgM against AGE-LDL, and relative cytokines in serum or splenocytes supernatant were also analysed. Results Compared with Al(OH) 3 or PBS alone, combined immunisation could significantly decrease atherosclerosis, without effects on body weight, serum cholesterol, triglycerides, and composition of plaque, which could induce specific IgG and IgM against AGE-LDL, upregulate Treg percentage of and IL-10 level in splenocytes supernatant, without altering Th1, Th2 or Th17 percentages. Conclusion Immunisation with AGE-LDL+Al(OH) 3 subcutaneous could inhibit atherosclerosis in diabetic apo-E -/- mice, involving humoral and cellular reaction against AGE-LDL, which would be a novel therapy strategy against atherosclerosis.
[Adhesion of polysulfide rubber impression material to dental metals (author's transl)]. (1982)

In order to investigate the adhesiveness of polysulfide rubber impression material to dental metals, we performed the tension test on the sample specimens which had been prepared by injecting the impression material into the gap between opposite metal surfaces finished brightly, thereafter observed the fractured surfaces. Pure metals decreased their adhesive strength to the impression material in order of Au, Pd greater than Ag greater than Cu. Some noble metal alloys containing gold and palladium in a large amount showed the good adhesiveness. In clinical using of 14 carat gold and gold-palladium-silver alloys for core metal, it should be noticed that polysulfide rubber adheres tightly to these alloys. Adhesive strength of copper was not so great comparing with noble metals, therefore the surface of copper tray should be roughned by emery paper above #500, aiming the mechanical bonding forth to increase. The surface of many metals which had left in regulated atmosphere for many hours showed the tendency to decrease their adhesiveness to the impression material. This tendency was not recognized on the metals which had appeared the failure of adhesion bond on the bright finished surfaces.
Basfia succiniciproducens gen. nov., sp. nov., a new member of the family Pasteurellaceae isolated from bovine rumen (2009)

Gram-negative, coccoid, non-motile bacteria that are catalase-, urease- and indole-negative, facultatively anaerobic and oxidase-positive were isolated from the bovine rumen using an improved selective medium for members of the Pasteurellaceae. All strains produced significant amounts of succinic acid under anaerobic conditions with glucose as substrate. Phenotypic characterization and multilocus sequence analysis (MLSA) using 16S rRNA, rpoB, infB and recN genes were performed on seven independent isolates. All four genes showed high sequence similarity to their counterparts in the genome sequence of the patent strain MBEL55E, but less than 95 % 16S rRNA gene sequence similarity to any other species of the Pasteurellaceae. Genetically these strains form a very homogeneous group in individual as well as combined phylogenetic trees, clearly separated from other genera of the family from which they can also be separated based on phenotypic markers. Genome relatedness as deduced from the recN gene showed high interspecies similarities, but again low similarity to any of the established genera of the family. No toxicity towards bovine, human or fish cells was observed and no RTX toxin genes were detected in members of the new taxon. Based on phylogenetic clustering in the MLSA analysis, the low genetic similarity to other genera and the phenotypic distinction, we suggest to classify these bovine rumen isolates as Basfia succiniciproducens gen. nov., sp. nov. The type strain is JF4016(T) (=DSM 22022(T) =CCUG 57335(T)).
Aging enhances vascular dysfunction induced by the Alzheimer's peptide β-amyloid (2004)

Aging is a major risk factor for Alzheimer's disease and the evidence suggests a role for cerebrovascular pathology in cognitive dysfunction. The hypothesis in this study is that aging is a significant risk factor in the effect of the Alzheimer peptide beta-amyloid on endothelium-dependent function of cerebral and peripheral vessels. The diameter response to acetylcholine, an endothelium-dependent vasodilator, was recorded in pressurized segments of rat posterior cerebral vessels from mature (3 months) and aged (20 months) rats. The threshold concentration of beta-amyloid for a significant decrease in the response to acetylcholine was lower in vessels from aged rats (10(-9) M) than in vessels from mature rats (10(-8) M). The threshold concentration of beta-amyloid for a significant decrease in the sensitivity to acetylcholine was lower for ring segments of aorta from aged rats (10(-10) M) than for aorta from mature rats (10(-8) M). Structural changes of the endothelium were first observed in electron micrographs of aorta from aged rats when the concentration of beta-amyloid was 10(-8) M, whereas structural changes in aorta from mature rats did not occur until the concentration of beta-amyloid was increased to 10(-7) M. The results suggest that aging increases the susceptibility of cerebral and peripheral blood vessels to beta-amyloid related dysfunction and that functional change precedes structural change.
Type- and Subcomplex-Specific Neutralizing Antibodies against Domain III of Dengue Virus Type 2 Envelope Protein Recognize Adjacent Epitopes (2007)

Neutralization of flaviviruses in vivo correlates with the development of an antibody response against the viral envelope (E) protein. Previous studies demonstrated that monoclonal antibodies (MAbs) against an epitope on the lateral ridge of domain III (DIII) of the West Nile virus (WNV) E protein strongly protect against infection in animals. Based on X-ray crystallography and sequence analysis, an analogous type-specific neutralizing epitope for individual serotypes of the related flavivirus dengue virus (DENV) was hypothesized. Using yeast surface display of DIII variants, we defined contact residues of a panel of type-specific, subcomplex-specific, and cross-reactive MAbs that recognize DIII of DENV type 2 (DENV-2) and have different neutralizing potentials. Type-specific MAbs with neutralizing activity against DENV-2 localized to a sequence-unique epitope on the lateral ridge of DIII, centered at the FG loop near residues E383 and P384, analogous in position to that observed with WNV-specific strongly neutralizing MAbs. Subcomplex-specific MAbs that bound some but not all DENV serotypes and neutralized DENV-2 infection recognized an adjacent epitope centered on the connecting A strand of DIII at residues K305, K307, and K310. In contrast, several MAbs that had poor neutralizing activity against DENV-2 and cross-reacted with all DENV serotypes and other flaviviruses recognized an epitope with residues in the AB loop of DIII, a conserved region that is predicted to have limited accessibility on the mature virion. Overall, our experiments define adjacent and structurally distinct epitopes on DIII of DENV-2 which elicit type-specific, subcomplex-specific, and cross-reactive antibodies with different neutralizing potentials.
A Review of Obinutuzumab (GA101), a Novel Type II Anti-CD20 Monoclonal Antibody, for the Treatment of Patients with B-Cell Malignancies (2016)

Obinutuzumab (GA101) is a novel, type II, glycoengineered, humanized anti-CD20 monoclonal antibody that has been developed to address the need for new therapeutics with improved efficacy in patients with lymphocytic leukemia and lymphoma of B-cell origin. Obinutuzumab has a distinct mode of action relative to type I anti-CD20 antibodies, such as rituximab, working primarily by inducing direct cell death and antibody-dependent cell-mediated cytotoxicity. Obinutuzumab is under investigation in a wide-ranging program of clinical trials in patients with B-cell malignancies. Efficacy as monotherapy has been reported in patients with relapsed/refractory indolent and aggressive non-Hodgkin lymphoma (NHL) and in chronic lymphocytic leukemia (CLL) of B-cell origin. Improved outcomes have also been noted when obinutuzumab is added to chemotherapy in patients with B-cell NHL, and superiority over rituximab has been reported with combination therapy in patients with CLL. Ongoing research is focusing on developing options for chemotherapy-free treatment and on new combinations of obinutuzumab with novel targeted agents.
Induction of Immune Tolerance in Mice with A Novel Mucosal Nanoemulsion Adjuvant and Self-Antigen (2012)

This study indicates that a low dose of mTg in NE can significantly enhance antigen uptake and Tregs, resulting in inhibition of experimental autoimmune thyroiditis development.
Herding Dynamic Weights for Partially Observed Random Field Models (2012)

Learning the parameters of a (potentially partially observable) random field model is intractable in general. Instead of focussing on a single optimal parameter value we propose to treat parameters as dynamical quantities. We introduce an algorithm to generate complex dynamics for parameters and (both visible and hidden) state vectors. We show that under certain conditions averages computed over trajectories of the proposed dynamical system converge to averages computed over the data. Our "herding dynamics" does not require expensive operations such as exponentiation and is fully deterministic.
Mitochondrial Dysfunction in Diabetes: From Molecular Mechanisms to Functional Significance and Therapeutic Opportunities (2009)

Given their essential function in aerobic metabolism, mitochondria are intuitively of interest in regard to the pathophysiology of diabetes. Qualitative, quantitative, and functional perturbations in mitochondria have been identified and affect the cause and complications of diabetes. Moreover, as a consequence of fuel oxidation, mitochondria generate considerable reactive oxygen species (ROS). Evidence is accumulating that these radicals per se are important in the pathophysiology of diabetes and its complications. In this review, we first present basic concepts underlying mitochondrial physiology. We then address mitochondrial function and ROS as related to diabetes. We consider different forms of diabetes and address both insulin secretion and insulin sensitivity. We also address the role of mitochondrial uncoupling and coenzyme Q. Finally, we address the potential for targeting mitochondria in the therapy of diabetes.
Current-Driven Resonant Excitation of Magnetic Vortices (2006)

A magnetic vortex core in a ferromagnetic circular nanodot has a resonance frequency originating from the confinement of the vortex core. By the micromagnetic simulation including the spin-transfer torque, we show that the vortex core can be resonantly excited by an ac (spin-polarized) current through the dot and that the resonance frequency can be tuned by the dot shape. The resistance measurement under the ac current successfully detects the resonance at the frequency consistent with the simulation.
Dispersion of carbon nanotubes in organic solvents initiated by hydrogen bonding interactions (2011)

Abstract Phase transfer of multiwalled carbon nanotubes (MWNTs) from an aqueous phase into an organic phase is achieved. The transfer uses the hydrogen‐bonding interactions between the disaccharide group of a sugar‐based amphiphile and oxygenated functional groups on the surface of MWNTs. The dispersion of carbon nanotubes in a wide range of organic solvents is enabled, which represents the first example of solubilization of carbon nanotubes in organic solvents via hydrogen bonding interactions. © 2012 American Institute of Chemical Engineers AIChE J, 58: 2997–3002, 2012
Communication on the Grassmann manifold: a geometric approach to the noncoherent multiple-antenna channel (2002)

We study the capacity of multiple-antenna fading channels. We focus on the scenario where the fading coefficients vary quickly; thus an accurate estimation of the coefficients is generally not available to either the transmitter or the receiver. We use a noncoherent block fading model proposed by Marzetta and Hochwald (see ibid. vol.45, p.139-57, 1999). The model does not assume any channel side information at the receiver or at the transmitter, but assumes that the coefficients remain constant for a coherence interval of length T symbol periods. We compute the asymptotic capacity of this channel at high signal-to-noise ratio (SNR) in terms of the coherence time T, the number of transmit antennas M, and the number of receive antennas N. While the capacity gain of the coherent multiple antenna channel is min{M, N} bits per second per Hertz for every 3-dB increase in SNR, the corresponding gain for the noncoherent channel turns out to be M* (1 - M*/T) bits per second per Hertz, where M*=min{M, N, [T/2]}. The capacity expression has a geometric interpretation as sphere packing in the Grassmann manifold.
The influence of the kappa agonist-spiradoline (U62066E) on the analgesic activity of some opioids at the spinal level. (1994)

Male Wistar rats were treated with morphine (MP) or pentazocine (PT) subcutaneously (sc) and then intrathecally (it) with a specific kappa receptor agonist spiradoline (U62066E). In another series of experiments methionine-(MENK) or leucine-enkephalin (LENK) were injected it with U62066E simultaneously. Then antinociceptive effect on thermal stimulus was measured 1 h using the tail immersion test. MP or LENK induced analgesia was enhanced by U62066E during the first 30 min of observation. MENK analgesic activity was potentiated by kappa receptor agonist only up to 5 min. U62066E acted biphasically on PT antinociceptive effect. These results suggest that kappa opioid receptors may participate in antinociceptive action of MP and LENK and in small degree for analgesic effect of PT and MENK at the spinal level.
Programmable Peptide-Cross-Linked Nucleic Acid Nanocapsules as a Modular Platform for Enzyme Specific Cargo Release (2017)

Herein we describe a modular assembly strategy for photo-cross-linking peptides into nucleic acid functionalized nanocapsules. The peptides embedded within the nanocapsules form discrete nanoscale populations capable of gating the release of molecular and nanoscale cargo using enzyme-substrate recognition as a triggered release mechanism. Using photocatalyzed thiol-yne chemistry, different peptide cross-linkers were effectively incorporated into the nanocapsules and screened against different proteases to test for degradation specificity both in vitro and in cell culture. By using a combination of fluorescence assays, confocal and TEM microscopy, the particles were shown to be highly specific for their enzyme targets, even between enzymes of similar protease classes. The rapid and modular nature of the assembly strategy has the potential to be applied to both intracellular and extracellular biosensing and drug delivery applications.
Full-diversity, high-rate space-time block codes from division algebras (2003)

We present some general techniques for constructing full-rank, minimal-delay, rate at least one space-time block codes (STBCs) over a variety of signal sets for arbitrary number of transmit antennas using commutative division algebras (field extensions) as well as using noncommutative division algebras of the rational field /spl Qopf/ embedded in matrix rings. The first half of the paper deals with constructions using field extensions of /spl Qopf/. Working with cyclotomic field extensions, we construct several families of STBCs over a wide range of signal sets that are of full rank, minimal delay, and rate at least one appropriate for any number of transmit antennas. We study the coding gain and capacity of these codes. Using transcendental extensions we construct arbitrary rate codes that are full rank for arbitrary number of antennas. We also present a method of constructing STBCs using noncyclotomic field extensions. In the later half of the paper, we discuss two ways of embedding noncommutative division algebras into matrices: left regular representation, and representation over maximal cyclic subfields. The 4/spl times/4 real orthogonal design is obtained by the left regular representation of quaternions. Alamouti's (1998) code is just a special case of the construction using representation over maximal cyclic subfields and we observe certain algebraic uniqueness characteristics of it. Also, we discuss a general principle for constructing cyclic division algebras using the nth root of a transcendental element and study the capacity of the STBCs obtained from this construction. Another family of cyclic division algebras discovered by Brauer (1933) is discussed and several examples of STBCs derived from each of these constructions are presented.
Transgene-mediated enkephalin release enhances the effect of morphine and evades tolerance to produce a sustained antiallodynic effect in neuropathic pain (2003)

We examined the pharmacologic characteristics of herpes simplex virus (HSV) vector-mediated expression of proenkephalin in the dorsal root ganglion in a rodent model of neuropathic pain. We found that: (i). vector-mediated enkephalin produced an antiallodynic effect that was reversed by naloxone; (ii). vector-mediated enkephalin production in animals with spinal nerve ligation prevented the induction of c-fos expression in second order sensory neurons in the dorsal horn of spinal cord; (iii). the effect of vector-mediated enkephalin enhanced the effect of morphine, reducing the ED(50) of morphine 10-fold; (iv). animals did not develop tolerance to the continued production of vector-mediated enkephalin over a period of several weeks; and, (v). vector transduction continued to provide an analgesic effect despite the induction of tolerance to morphine. This is the first demonstration of gene transfer to provide an analgesic effect in neuropathic pain. The pharmacologic analysis demonstrates that transgene-mediated expression and local release of opioid peptides produce some effects that are distinct from peptide analogues delivered pharmacologically.