gebhart/patrepeval huggingface dataset:
Systemic and Site-Specific Effects of A-425619, a Selective TRPV1 Receptor Antagonist, on Wide Dynamic Range Neurons in CFA-Treated and Uninjured Rats (2005)

Systemic administration of A-425619, a potent and selective TRPV1 receptor antagonist that does not readily enter the CNS, produces antinociception in several rat models of pathological nociception, including complete Freund's adjuvant (CFA)-induced thermal hyperalgesia. To further understand the peripheral mechanisms of TRPV1-related antinociception, we examined the effects of systemic and site-specific injections of A-425619 on evoked and spontaneous firing of spinal wide dynamic range (WDR) neurons in uninjured rats and rats with peripheral inflammation (CFA; 48 h). In uninjured rats, capsaicin-evoked (1 microg) WDR activity was completely blocked by intraplantar administration of A-425619 (3-100 nmol). Systemic injection of A-425619 (3-30 micromol/kg, iv) reduced WDR responses to thermal stimulation in both CFA-inflamed (47 degrees C) and uninjured (52 degrees C) rats. However, the efficacy of A-425619 to attenuate thermal-evoked WDR activity was significantly greater (P < 0.01) in CFA-treated rats. Both intradorsal root ganglion (DRG; L5; 20 nmol) and intraplantar (30-300 nmol) injection of A-425619 reduced WDR responses to thermal stimulation. While the effectiveness of A-425619 was similar between CFA-inflamed and uninjured rats after intraplantar injection, the effects of A-425619 after intra-DRG injection were enhanced in the inflamed rats (compared with the uninjured rats). Spontaneous WDR discharges were unaltered by systemic or site-specific injections of A-425619. Thus noxious thermal stimulation triggers the transmission of TRPV1-related signals to spinal WDR neurons in both inflamed and uninjured animals. The apparent increase in TRPV1 signaling to WDR neurons after injury may be the result of changes to the distribution/sensitization of peripheral TRPV1 receptors.
Detection of Nonpolar Molecules by Means of Carrier Scattering in Random Networks of Carbon Nanotubes: Toward Diagnosis of Diseases via Breath Samples (2009)

Field effect transistors (FETs) based on random networks (RNs) of single-wall carbon nanotubes (CNTs) have several technological advantages. However, the low sensitivity (or no sensitivity) of RN-CNT sensors to nonpolar molecules is a problematic, negative feature that limits their applications in the detection of a wide variety of diseases via breath samples. In this paper, we show experimental evidence for the detection of both individual nonpolar molecules and patterns of nonpolar molecules, even in the presence of polar molecules in the same environment. We do so by preparing RN-CNT FETs and functionalizing them with organic films that exhibit distinctive electrical and physical (or mechanical) characteristics. Exposing the functionalized RN-CNTs to representative nonpolar breath biomarkers, and, for comparison, to polar molecules in the gas phase, and monitoring the changes in conductance, work function, and organic film thickness show sensitivity toward nonpolar molecules. We explain this observation by carrier scattering as a result of swelling of the organic film upon exposure to (nonpolar) chemical agents. Hence, the sensitivity towards nonpolar molecules can be tailored, even in the presence of polar molecules, by controlling the scattering of charge carrier through deliberate functionalization of CNTs. As examples for the technological impact of our findings, we describe ways to detect lung cancer and kidney disease using specially designed RN-CNT sensor arrays.
Synthesis, antimicrobial and insecticidal activity of some 4 H -1,2,4 triazole derivatives (2010)

1-(Substituted benzylidene) semicarbazide has been used as a precursor to synthesize some important biologically active 3-substituted phenyl, 4H-1,2,4 triazole derivatives. Reaction of ethanolic solution of schiff's base of substituted aromatic aldehyde 1 with ethanolic solution of FeCl 3 .6H 2 O (1 mole FeCl 3 .6H 2 O in 10 mL ethanol) yields the 4H-1,2,4 triazole-3-derivative 2. Several derivatives have been synthesized and screened for their antibacterial efficacy against Bacillus subtilis, Escherichia coli, Staphyllococcus aureus and Klebsiella pneumoniae, Antifungal activity against Aspergillus flavus, Fusarium oxysporum, Aspergillus niger and Trichoderma viridae and insecticidal activity against Periplaneta americana.
A Recombinant Human Glucagon-Like Peptide (GLP)-1–Albumin Protein (Albugon) Mimics Peptidergic Activation of GLP-1 Receptor–Dependent Pathways Coupled With Satiety, Gastrointestinal Motility, and Glucose Homeostasis (2004)

Peptide hormones exert unique actions via specific G protein-coupled receptors; however, the therapeutic potential of regulatory peptides is frequently compromised by rapid enzymatic inactivation and clearance from the circulation. In contrast, recombinant or covalent coupling of smaller peptides to serum albumin represents an emerging strategy for extending the circulating t(1/2) of the target peptide. However, whether larger peptide-albumin derivatives will exhibit the full spectrum of biological activities encompassed by the native peptide remains to be demonstrated. We report that Albugon, a human glucagon-like peptide (GLP)-1-albumin recombinant protein, activates GLP-1 receptor (GLP-1R)-dependent cAMP formation in BHK-GLP-1R cells, albeit with a reduced half-maximal concentration (EC(50)) (0.2 vs. 20 nmol/l) relative to the GLP-1R agonist exendin-4. Albugon decreased glycemic excursion and stimulated insulin secretion in wild-type but not GLP-1R(-/-) mice and reduced food intake after both intracerebroventricular and intraperitoneal administration. Moreover, intraperitoneal injection of Albugon inhibited gastric emptying and activated c-FOS expression in the area postrema, the nucleus of the solitary tract, the central nucleus of the amygdala, the parabrachial, and the paraventricular nuclei. These findings illustrate that peripheral administration of a larger peptide-albumin recombinant protein mimics GLP-1R-dependent activation of central and peripheral pathways regulating energy intake and glucose homeostasis in vivo.
On the Origin and Evolutionary Relationships of the Reverse Transcriptases Associated With Type III CRISPR-Cas Systems (2018)

Reverse transcriptases (RTs) closely related to those encoded by group II introns but lacking the intron RNA structure have been found associated with type III clustered regularly interspaced short palindromic repeats (CRISPR)-Cas systems, a prokaryotic immune system against invading viruses and foreign genetic elements. Two models have been proposed to explain the origin and evolutionary relationships of these RTs: (i) the "single point of origin" model, according to which these RTs originated from a single acquisition event in bacterial, with the various protein domains (RT, RT-Cas1, and Cas6-RT-Cas1 fusions) corresponding to single points in evolution; and (ii) the "various origins" model, according to which, independent acquisition events in different evolutionary episodes led to these fusions. We tested these alternative hypotheses, by analyzing and integrating published datasets of RT sequences associated with CRISPR-Cas systems and inferring phylogenetic trees by maximum likelihood (ML) methods. The RTs studied could be grouped into 13 clades, mostly in bacteria, in which they probably evolved. The various clades appear to form three independent lineages in bacteria and a recent lineage in archaea. Our data show that the Cas6 domain was acquired twice, independently, through RT-Cas1 fusion, in the bacterial lineages. Taken together, there more evidence to support the "various origins" hypothesis.
Phenotypic Stability of Articular Chondrocytes In Vitro: The Effects of Culture Models, Bone Morphogenetic Protein 2, and Serum Supplementation (2000)

Numerous in vitro culture models have been developed for the investigation of chondrocyte and cartilage biology. In this study, we investigated the stability of the chondrocytic phenotype in monolayer, aggregate, pellet, and explant culture models and assessed the effects of recombinant human bone morphogenetic protein 2 (rhBMP-2) and serum supplementation on the phenotype in each model. Phenotypic effects were assessed by analyses of procollagen type II, aggrecan, (V + C)- fibronectin, and procollagen type I messenger RNA expression. In monolayer cultures, we noted a characteristic loss of procollagen type II and induction of procollagen type I expression. The aggregate and pellet culture models supported matrix protein gene expression profiles more reflective of in vivo levels. In explant cultures, expression of matrix protein genes was consistently depressed. Treatment with rhBMP-2 significantly increased the expression of procollagen type II and aggrecan in monolayer cultures; however, other models showed comparatively little response. Similarly, serum supplementation significantly down-regulated procollagen type II and aggrecan expression in monolayer cultures but had less effect on gene expression in the other models. Serum supplementation increased procollagen type I expression in monolayer and aggregate cultures. These results suggest that the influence of exogenous BMP-2 and serum on expression of chondrocyte-specific matrix protein genes is influenced by aspects of substrate attachments, cellular morphology, and/or cytoskeletal organization. Finally, the analyses of fibronectin expression suggest that V and C region alternative splicing in chondrocytes is linked to the establishment of a three-dimensional multicellular complex.
Learning feed-forward one-shot learners (2016)

One-shot learning is usually tackled by using generative models or discriminative embeddings. Discriminative methods based on deep learning, which are very effective in other learning scenarios, are ill-suited for one-shot learning as they need large amounts of training data. In this paper, we propose a method to learn the parameters of a deep model in one shot. We construct the learner as a second deep network, called a learnet, which predicts the parameters of a pupil network from a single exemplar. In this manner we obtain an efficient feed-forward one-shot learner, trained end-to-end by minimizing a one-shot classification objective in a learning to learn formulation. In order to make the construction feasible, we propose a number of factorizations of the parameters of the pupil network. We demonstrate encouraging results by learning characters from single exemplars in Omniglot, and by tracking visual objects from a single initial exemplar in the Visual Object Tracking benchmark.
Multiple operating systems on one processor complex (1989)

As large computing systems continue to grow in capacity and to offer improved price/performance, there is an increasing requirement to consolidate systems onto one processor complex. This paper describes the reasons why users need to run multiple operating systems today, provides a brief history of IBM's partitioning products, and introduces the Processor Resource/Systems Manager™, a machine feature on the IBM 3090 Model E and ES/3090™ Model S processors that provides users with a flexible and efficient capability to run multiple operating systems on a single processor complex.
Structure and Mechanism of F 0 F 1 ‐Type ATP Synthases and ATPases (1991)

This chapter contains sections titled: Introduction Properties of the Enzyme Models for the Mechanism of Action of the Enzyme Uni-site Catalysis by Beef Heart Mitochondrial ATPase The High-Affinity Catalytic Site Is a Normal Catalytic Site on the Enzyme Uni-site Catalysis in Other F0F1-Type ATPases
Understanding the High Solubility of CO2 in an Ionic Liquid with the Tetracyanoborate Anion (2011)

The ionic liquid 1-ethyl-3-methylimidazolium tetracyanoborate, [emim][B(CN)(4)], shows greater CO(2) solubility than several popular ionic liquids (ILs) of different anions including [emim]bis(trifluoromethylsulfonyl)imide [emim][Tf(2)N]. Herein, both classical molecular dynamics simulation and quantum mechanical calculations were used to understand the high solubility of CO(2) in the [emim][B(CN)(4)] IL. We found that the solubility is dictated by the cation-anion interaction, while the CO(2)-anion interaction plays a secondary role. The atom-atom radial distribution functions (RDFs) between cation and anion show weaker interaction in [emim][B(CN)(4)] than in [emim][Tf(2)N]. A good correlation is observed between gas-phase cation-anion interaction energy with CO(2) solubility at 1 bar and 298 K, suggesting that weaker cation-anion interaction leads to higher CO(2) solubility. MD simulation of CO(2) in the ILs showed that CO(2) is closer to the anion than to the cation and that it interacts more strongly with [B(CN)(4)] than with [Tf(2)N]. Moreover, a higher volume expansion is observed in [emim][B(CN)(4)] than in [emim][Tf(2)N] at different mole fractions of CO(2). These results indicate that [B(CN)(4)] as a small and highly symmetric anion is unique in giving a high CO(2) solubility by interacting weakly with the cation and thus allowing easy creation of cavity for close contact with CO(2).
Kant and the Problem of Human Nature (2003)

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Positive Regulation of psbA Gene Expression by cis-Encoded Antisense RNAs in Synechocystis sp. PCC 6803 (2012)

The D1 protein of photosystem II in the thylakoid membrane of photosynthetic organisms is encoded by psbA genes, which in cyanobacteria occur in the form of a small gene family. Light-dependent up-regulation of psbA gene expression is crucial to ensure the proper replacement of the D1 protein. To gain a high level of gene expression, psbA transcription can be enhanced by several orders of magnitude. Recent transcriptome analyses demonstrated a high number of cis-encoded antisense RNAs (asRNAs) in bacteria, but very little is known about their possible functions. Here, we show the presence of two cis-encoded asRNAs (PsbA2R and PsbA3R) of psbA2 and psbA3 from Synechocystis sp. PCC 6803. These asRNAs are located in the 5' untranslated region of psbA2 and psbA3 genes. Their expression becomes up-regulated by light and down-regulated by darkness, similar to their target mRNAs. In the PsbA2R-suppressing strain [PsbA2R(-)], the amount of psbA2 mRNA was only about 50% compared with the control strain. Likewise, we identified a 15% lowered activity of photosystem II and a reduced amount of the D1 protein in PsbA2R(-) compared with the control strain. The function of PsbA2R in the stabilization of psbA2 mRNA was shown from in vitro RNase E assay when the AU box and the ribosome-binding site in the 5' untranslated region of psbA2 mRNA were both covered by PsbA2R. These results add another layer of complexity to the mechanisms that contribute to psbA gene expression and show PsbA2R as a positively acting factor to achieve a maximum level of D1 synthesis.
Mixed Stimuli-Responsive Magnetic and Gold Nanoparticle System for Rapid Purification, Enrichment, and Detection of Biomarkers (2010)

A new diagnostic system for the enrichment and detection of protein biomarkers from human plasma is presented. Gold nanoparticles (AuNPs) were surface-modified with a diblock copolymer synthesized using reversible addition-fragmentation chain transfer (RAFT) polymerization. The diblock copolymer contained a thermally responsive poly(N-isopropylacrylamide) (pNIPAAm) block, a cationic amine-containing block, and a semi-telechelic PEG₂-biotin end group. When a mixed suspension of 23 nm pNIPAAm-modified AuNPs was heated with pNIPAAm-coated 10 nm iron oxide magnetic nanoparticles (mNPs) in human plasma, the thermally responsive pNIPAAm directed the formation of mixed AuNP/mNP aggregates that could be separated efficiently with a magnet. Model studies showed that this mixed nanoparticle system could efficiently purify and strongly enrich the model biomarker protein streptavidin in spiked human plasma. A 10 ng/mL streptavidin sample was mixed with the biotinylated pNIPAAm-modified AuNPs and magnetically separated in the mixed nanoparticle system with pNIPAAm mNPs. The aggregates were concentrated into a 50-fold smaller fluid volume at room temperature where the gold nanoparticle reagent redissolved with the streptavidin target still bound. The concentrated gold-labeled streptavidin could be subsequently analyzed directly using lateral flow immunochromatography. This rapid capture and enrichment module thus utilizes the mixed stimuli-responsive nanoparticle system to achieve concentration of a gold-labeled biomarker that can be directly analyzed using lateral flow or other rapid diagnostic strategies.
Antithyroid Drugs (1984)

Over the past four decades, a great deal has been learned about the pharmacology and mechanisms of action of antithyroid drugs. Their ability to inhibit hormone biosynthesis involves complex interactions with thyroid peroxidase and thyroglobulin, many of which are still poorly understood. Their spectrum of activity is much wider than previously thought, and a number of clinically important extrathyroidal actions have been identified. Despite a greater appreciation for the intricacies of antithyroid-drug pharmacology, controversies still surround the use of these agents in the treatment of thyrotoxicosis. These controversies are apt to continue until the pathophysiology of Graves' disease is fully elucidated.
(S)-13-[(Dimethylamino)methyl]-10,11,14,15-tetrahydro-4,9:16,21-dimetheno- 1H,13H-dibenzo[e,k]pyrrolo[3,4-h][1,4,13]oxadiazacyclohexadecene-1,3(2H)-dione (LY333531) and Related Analogues:  Isozyme Selective Inhibitors of Protein Kinase Cβ (1996)

Protein kinase C (PKC) is a family of closely related serine and threonine kinases. Overactivation of some PKC isozymes has been postulated to occur in several diseases states, including diabetic complications. Selective inhibition of overactivated PKC isozymes may offer a unique therapeutic approach to disease states such as diabetic retinopathy. A novel series of 14-membered macrocycles containing a N-N'-bridged bisindolylmaleimide moiety is described. A panel of eight cloned human PKC isozymes (alpha, beta I, beta II, gamma, delta, epsilon, sigma, eta) was used to identify the series and optimize the structure and associated activity relationship. The dimethylamine analogue LY333531 (1), (S)-13-[(dimethylamino)methyl]-10,11,14,15-tetrahydro-4,9:16, 21-dimetheno-1H, 13H-dibenzo[e,k]pyrrolo[3,4-h][1,4,13]oxadiazacyclohexadecene++ +-1,3(2H)-dione, inhibits the PKC beta I (IC50 = 4.7 nM) and PKC beta II (IC50 = 5.9 nM) isozymes and was 76- and 61-fold selective for inhibition of PKC beta I and PKC beta II in comparison to PKC alpha, respectively. The additional analogues described in the series are also selective inhibitors of PKC beta. LY333531 (1) exhibits ATP dependent competitive inhibition of PKC beta I and is selective for PKC in comparison to other ATP dependent kinases (protein kinase A, calcium calmodulin, caesin kinase, src tyrosine kinase). The cellular activity of the series was assessed using bovine retinal capillary endothelial cells. Retinal endothelial cell dysfunction has been implicated in the development of diabetic retinopathy. Plasminogen activator activity stimulated by a phorbol ester (4 beta-phorbol 12,13-dibutyrate) in endothelial cells was inhibited by the compounds in the series with ED50 values ranging from 7.5 to 0.21 microM. A comparison of the PKC isozyme and related ATP dependent kinase inhibition profiles is provided for the series and compared to the profile for staurosporine, a nonselective PKC inhibitor. The cellular activity of the series is compared with that of the kinase inhibitor staurosporine.
Flavopiridol: a cytotoxic flavone that induces cell death in noncycling A549 human lung carcinoma cells. (1996)

Flavopiridol (NSC 649890, L86-8275), a potent inhibitor of cyclin-dependent kinase 1/p34cdc2 phosphorylation and kinase activity, is currently undergoing Phase I clinical testing as a potential antineoplastic agent. Previous studies have suggested that flavopiridol is cytostatic but not cytotoxic when applied to exponentially growing cells. In the present study, various human tumor cell lines were assayed for trypan blue exclusion and ability to form colonies after exposure to flavopiridol under a variety of growth conditions. When log phase A549 non-small cell lung cancer cells were examined 72 h after the start of a 24-h flavopiridol exposure, as many as 90% of the cells accumulated trypan blue. A 24-h exposure to 250-300 nM resulted in trypan blue uptake in 50% of A549 cells at 72 h and a 50% reduction in colony formation. Similar results were observed in HCT8 ileocecal adenocarcinoma, T98G glioblastoma, MCF-7 breast adenocarcinoma, and HL-60 leukemia cells. With A549 cells, identical results were obtained in actively growing logarithmic phase cells and growth-arrested confluent cells. Treatment with the DNA synthesis inhibitor aphidicolin only minimally affected the cytotoxicity of flavopiridol. In contrast, the RNA synthesis inhibitor 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole or the protein synthesis inhibitor cycloheximide reduced the cytotoxicity of flavopiridol. These results suggest that: (a) flavopiridol is not only cytostatic, but also cytotoxic to a variety of human tumor cell lines; (b) flavopiridol is equally active against cycling and noncycling A549 cells; and (c) RNA and protein synthesis appear to play a role in flavopiridol-induced cytotoxicity.
Blocking expression of inhibitory receptor NKG2A overcomes tumor resistance to NK cells (2019)

A key mechanism of tumor resistance to immune cells is mediated by expression of peptide-loaded HLA-E in tumor cells, which suppresses natural killer (NK) cell activity via ligation of the NK inhibitory receptor CD94/NKG2A. Gene expression data from approximately 10,000 tumor samples showed widespread HLAE expression, with levels correlating with those of KLRC1 (NKG2A) and KLRD1 (CD94). To bypass HLA-E inhibition, we developed a way to generate highly functional NK cells lacking NKG2A. Constructs containing a single-chain variable fragment derived from an anti-NKG2A antibody were linked to endoplasmic reticulum-retention domains. After retroviral transduction in human peripheral blood NK cells, these NKG2A Protein Expression Blockers (PEBLs) abrogated NKG2A expression. The resulting NKG2Anull NK cells had higher cytotoxicity against HLA-E-expressing tumor cells. Transduction of anti-NKG2A PEBL produced more potent cytotoxicity than interference with an anti-NKG2A antibody and prevented de novo NKG2A expression, without affecting NK cell proliferation. In immunodeficient mice, NKG2Anull NK cells were significantly more powerful than NKG2A+ NK cells against HLA-E-expressing tumors. Thus, NKG2A downregulation evades the HLA-E cancer immune-checkpoint, and increases the anti-tumor activity of NK cell infusions. Because this strategy is easily adaptable to current protocols for clinical-grade immune cell processing, its clinical testing is feasible and warranted.
Inverted and multiple nematic emulsions (1998)

We investigate experimentally the structures that form when small colloidal particles are suspended in a nematic solvent. These structures are anisotropic, and their formation is driven by interactions arising from the orientational elasticity of the nematic solvent. By using inverted and multiple nematic emulsions composed of water droplets dispersed in a thermotropic liquid crystal, we identify the nature of these interactions, and demonstrate that they can be controlled by the anchoring of the liquid crystal molecules at the surfaces of the droplets. When the anchoring is normal, the droplets form linear chains, suggesting a long-range dipole-dipole attraction between the particles. By contrast, the interactions are repulsive at short range, and prevent contact of the droplets, thereby stabilizing them against coalescence. When the anchoring is planar, the droplets generate distortions that have a quadrupolar character. The resultant elastic interactions lead to more compact, but still anisotropic, clusters.