gebhart/patrepeval huggingface dataset:
Covalent Organic Frameworks as Exceptional Hydrogen Storage Materials (2008)

We report the H2 uptake properties of six covalent organic frameworks (COFs) from first-principles-based grand canonical Monte-Carlo simulations. The predicted H2 adsorption isotherm is in excellent agreement with the only available experimental result (3.3 vs 3.4 wt % at 50 bar and 77 K for COF-5), also reported here, validating the predictions. We predict that COF-105 and COF-108 lead to a reversible excess H2 uptake of 10.0 wt % at 77 K, making them the best known storage materials for molecular hydrogen at 77 K. We predict that the total H2 uptake for COF-108 is 18.9 wt % at 77 K. COF-102 shows the best volumetric performance, storing 40.4 g/L of H2 at 77 K. These results indicate that the COF systems are most promising candidates for practical hydrogen storage.
Supramolecular organization of immature and mature murine leukemia virus revealed by electron cryo-microscopy: Implications for retroviral assembly mechanisms (1998)

We have used electron cryo-microscopy and image analysis to examine the native structure of immature, protease-deficient (PR-) and mature, wild-type (WT) Moloney murine leukemia virus (MuLV). Maturational cleavage of the Gag polyprotein by the viral protease is associated with striking morphological changes. The PR- MuLV particles exhibit a rounded central core, which has a characteristic track-like shell on its surface, whereas the WT MuLV cores display a polygonal surface with loss of the track-like feature. The pleomorphic shape and inability to refine unique orientation angles suggest that neither the PR- nor the WT MuLV adheres to strict icosahedral symmetry. Nevertheless, the PR- MuLV particles do exhibit paracrystalline order with a spacing between Gag molecules of approximately 45 A and a length of approximately 200 A. Because of the pleomorphic shape and paracrystalline packing of the Gag-RNA complexes, we raise the possibility that assembly of MuLV is driven by protein-RNA, as well as protein-protein, interactions. The maturation process involves a dramatic reorganization of the packing arrangements within the ribonucleoprotein core with disordering and loosening of the individual protein components.
Sensitivity and Specificity of a Universal Primer Set for the Rapid Diagnosis of Dengue Virus Infections by Polymerase Chain Reaction and Nucleic Acid Hybridization (1991)

A set of sense and anti-sense oligomeric DNA primers, degenerate in the third "wobble" base position of codons so as to match all known dengue virus sequences, was evaluated as universal primers in a polymerase chain reaction (PCR) assay for the rapid diagnosis of dengue virus infections. Virus-specific complementary DNA (cDNA) was prepared by reverse transcription (RT) of total RNA extracted from serum. Amplified cDNA was identified by nucleic acid hybridization with four serotype-specific, oligomeric DNA probes. Using sera from patients admitted with dengue fever, RT/PCR followed by nucleic acid hybridization using radiolabeled probes was 68% sensitive (50/74; 95% confidence interval [CI] = 57-78%) and 100% specific. Chemiluminescent detection of hybridized products was 62% sensitive (26/42; 95% CI = 46-75%). Using specimens from which a virus isolate had been obtained, RT/PCR followed by nucleic acid hybridization with radiolabeled probes was 80% sensitive (40/50; 95% CI = 69-91%) and 100% specific. The results suggest that RT/PCR using degenerate primers is a sensitive and specific method for the detection of dengue viruses in clinical specimens.
Influence of Na on the electro-optical properties of Cu(In,Ga)Se/sub 2/ (2002)

Polycrystalline Cu(In,Ga)Se/sub 2/ (CIGS) thin films, grown by coevaporation of the constituent elements with different amounts of sodium (Na), were investigated. In some devices, an increased Na content was achieved through the incorporation of a thin layer of NaF deposited on the substrate prior to the growth of CIGS. The effect of Na on the electro-optical properties was addressed through characterization of the finished devices using photoluminescence (PL) and capacitance techniques. Results indicate the beneficial effect of Na as evidenced by increases in the device efficiency, open-circuit voltage, and PL intensity. Furthermore, these measurements provide evidence that Na (1) increases the net carrier concentration, and (2) reduces the number of gap states including those that act as minority-carrier traps.
Synthetic peptide vaccine design: synthesis and properties of a high-density multiple antigenic peptide system. (1988)

A convenient and versatile approach to the direct synthesis of a peptide-antigen matrix by the solid-phase method is described. The approach is called the multiple antigen peptide system (MAP) and it utilizes a simple scaffolding of a low number of sequential levels (n) of a trifunctional amino acid as the core matrix and 2n peptide antigens to form a macromolecule with a high density of peptide antigens of final Mr 10,000. The MAP model chosen for study was an octa-branching MAP consisting of a core matrix made up of three levels of lysine and eight amino terminals for anchoring peptide antigens. The MAP, containing both the core matrix and peptides of 9-16 amino acids, was prepared in a single synthesis by the solid-phase method. Six different MAPs elicited specific antibodies in rabbits and mice, of which five produced antibodies that reacted with their corresponding native proteins. In rabbits, the sera had a considerably higher titer of antibodies than sera prepared from the same peptides anchored covalently to keyhole limpet hemocyanin as carrier. Thus, the MAP provided a general, but chemically unambiguous, approach for the preparation of carrier-bound antigens of predetermined and reproducible structure and might be suitable for generating vaccines.
The precursor form of IL-1α is an intracrine proinflammatory activator of transcription (2004)

Although most cytokines are studied for biological effects after engagement of their specific cell surface membrane receptors, increasing evidence suggests that some function in the nucleus. In the present study, the precursor form of IL-1alpha was overexpressed in various cells and assessed for activity in the presence of saturating concentrations of IL-1 receptor antagonist to prevent receptor signaling. Initially diffusely present in the cytoplasm of resting cells, IL-1alpha translocated to the to nucleus after activation by endotoxin, a Toll-like receptor ligand. The IL-1alpha precursor, but not the C-terminal mature form, activated the transcriptional machinery in the GAL4 system by 90-fold; a 50-fold increase was observed using only the IL-1alpha propiece, suggesting that transcriptional activation was localized to the N terminus where the nuclear localization sequence resides. Under conditions of IL-1 receptor blockade, intracellular overexpression of the precursor and propiece forms of IL-1alpha were sufficient to activate NF-kappaB and AP-1. Stable transfectants overproducing precursor IL-1alpha released the cytokines IL-8 and IL-6 but also exhibited a significantly lower threshold of activation to subpicomolar concentrations of tumor necrosis factor alpha or IFN-gamma. Thus, intracellular functions of IL-1alpha might play an unforeseen role in the genesis of inflammation. During disease-driven events, the cytosolic precursor moves to the nucleus, where it augments transcription of proinflammatory genes. Because this mechanism of action is not affected by extracellular inhibitors, reducing intracellular functions of IL-1alpha might prove beneficial in some inflammatory conditions.
Rituximab chimeric anti-CD20 monoclonal antibody therapy for relapsed indolent lymphoma: half of patients respond to a four-dose treatment program. (1998)

The response rate of 48% with IDEC-C2B8 is comparable to results with single-agent cytotoxic chemotherapy. Toxicity was mild. Attention needs to be paid to the rate of antibody infusion, with titration according to toxicity. Further investigation of this agent is warranted, including its use in conjunction with standard chemotherapy.
Proteolytic cleavage of the A subunit is essential for maximal cytotoxicity of Escherichia coli 0157:H7 Shiga-like toxin-1 (1999)

Members of the bacterial Shiga toxin family consist of a single A subunit that is non-covalently associated with a pentamer of B subunits. These toxins bind to receptors on susceptible mammalian cells and enter the cells by endocytic uptake. During cell entry, the 32 kDa A subunit is cleaved by the membrane-anchored protease furin to generate a catalytically active, 27.5 kDa A1 fragment and a 4.5 kDa A2 fragment. Previous studies have shown that mutating the furin site to prevent cleavage did not significantly affect toxin potency, suggesting that cleavage is not required for toxin activity. Here it is confirmed that preventing cleavage at the usual processing site does not prevent proteolytic processing of the Escherichia coli Shiga-like toxin-1 A subunit. However, simultaneous mutation of both the primary furin-recognition site and a nearby putative furin cleavage site did prevent intracellular processing of the A subunit. Comparison of the cytotoxicities of purified recombinant toxins to cultured mammalian cells demonstrated that even on prolonged incubation with toxin, the unprocessed mutant was 60-fold less toxic than the wild-type protein or other mutants still capable of being proteolytically processed during cell entry.
ChemInform Abstract: PHOSPHORAMIDES. V. SYNTHESIS OF 4,6‐BIS(DIMETHYLAMINO)THIENO(2,3‐B)PYRIDINES BY AN HMPT INDUCED RING CLOSURE REACTION (1977)

Abstract Die 2‐Amidothiophene (I) cyclisieren bei N235°C in Gegenwart von Hexamethylphosphorsäuretriamid (HMPT) zu den Thienopyridinen (II); neben (IIe) bildet sich auch das Dithienodiazocin (III) (9% Ausbeute).
Emerging Molecular Approaches to Pain Therapy (1999)

ADVERTISEMENT RETURN TO ISSUEPerspectiveNEXTEmerging Molecular Approaches to Pain TherapyMichael Williams, Elizabeth A. Kowaluk, and Stephen P. ArnericView Author Information Pharmaceutical Products Division, Abbott Laboratories, and CNS Diseases Research, DuPont Pharmaceuticals Cite this: J. Med. Chem. 1999, 42, 9, 1481–1500Publication Date (Web):April 21, 1999Publication History Received31 August 1998Published online21 April 1999Published inissue 1 May 1999https://doi.org/10.1021/jm9805034Copyright © 1999 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views2642Altmetric-Citations138LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit Read OnlinePDF (931 KB) Get e-AlertsSUBJECTS:Agonists,Antagonists,Neurophysiology,Peptides and proteins,Receptors Get e-Alerts
The Spinning of Silk-like Proteins Into Fibers (1997)

It is remarkable that so many different silk fibroin compositions are found in nature that are converted to high performance fibers by their respective organisms. In contrast, we note that there are a relatively small number of synthetic polymers that have led to commercial man-made fibers. In fact, the development of man-made fibers in the late nineteenth century was motivated by the desire to mimic silk, the only natural, continuous filament then available.KeywordsSilk FibroinFiber FormationVegetable ProteinSilk FiberProtein FiberThese keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.
Fas- or Ceramide-induced Apoptosis Is Mediated by a Rac1-regulated Activation of Jun N-terminal Kinase/p38 Kinases and GADD153 (1997)

In the present study, we show that Fas receptor ligation or cellular treatment with synthetic C6-ceramide results in activation or phosphorylation, respectively, of the small G-protein Rac1, Jun N-terminal kinase (JNK)/p38 kinases (p38-K), and the transcription factor GADD153. A signaling cascade from the Fas receptor via ceramide, Ras, Rac1, and JNK/p38-K to GADD153 is demonstrated employing transfection of transdominant inhibitory N17Ras, N17Rac1, c-Jun, or treatment with a specific p38-K inhibitor. The critical function of this signaling cascade is indicated by prevention of Fas- or C6-ceramide-induced apoptosis after inhibition of Ras, Rac1, or JNK/p38-K.
Free Sulfhydryl in Recombinant Monoclonal Antibodies (2002)

Monoclonal antibody (mAb) therapy applications have been growing rapidly in recent years. Like other recombinant protein drugs, therapeutic mAb's need to be well characterized to ensure their structural and functional integrity. IgG mAb's are composed of two heavy and two light chains covalently linked by interchain disulfide bonds. Each domain of the heavy or light chain contains one additional disulfide bond. Native IgG mAb's, with completely formed disulfide bonds, should not bear any free sulfhydryl. This report describes detection and quantification of free sulfhydryl in recombinant mAb's produced in Chinese hamster ovary (CHO) cells using a fluorescent technique. The method utilizes the fluorescent probe N-(1-pyrenyl)maleimide (NPM). The purified mAb's appear to be homogeneous under native conditions with approximately 0.02 mol of free sulfhydryl per mole of protein. Upon denaturation, minor species related to the mAb's are observed on sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), and the free sulfhydryl level is determined to be approximately 0.1 mol/mol of protein. These results suggest that a small portion of these recombinant mAb's lack in intermolecular disulfide bonds but remain noncovalently associated under native conditions. The formation of the free sulfhydryl containing mAb species is likely to occur during the culture process and/or protein folding process in the endoplasmic reticulum (ER).
gamma-Hydroxybutyrate conversion into GABA induces displacement of GABAB binding that is blocked by valproate and ethosuximide. (1997)

gamma-Hydroxybutyrate (GHB) has been reported to be a ligand for GABAB receptor(s), although with low or very low affinity (IC50 = 150-796 microM). In addition, several reports argue for a role of GHB via GABAB receptors in both in vivo and in vitro electro-physiological experiments. In the present study, we demonstrate that the inhibition of GHB's conversion into GABA by rat brain membranes blocks the ability of GHB to interfere with GABAB binding. In particular, the inhibition of GHB dehydrogenase by valproate or ethosuximide and the blockade of GABA-T by aminooxyacetic acid induce the disappearance of the GABA-like effect of GHB at GABAB, but also at GABAA, receptors. This finding could explain the misinterpretation of in vitro or in vivo experiments where GHB possesses a GABA-like effect. But in addition, it is postulated that the normal metabolism of GHB in brain induces GABAB mechanisms that could be blocked by the administration of valproate or ethosuximide.
Functional characterization of a signal transducing motif present in the T cell antigen receptor zeta chain. (1993)

A conserved sequence motif has been identified in a number of signaling subunits associated with hematopoietic cell antigen receptors. Here, we characterize signaling by a 17 amino acid motif that is triplicated in the T cell antigen receptor zeta chain. Analysis of zeta truncations and constructs containing the isolated motif demonstrates that this motif is sufficient for the induction of both proximal and distal events associated with T cell activation. Stimulation of truncations that contain either one, two, or three copies of the motif results in induction of an identical pattern of tyrosine phosphoproteins. Moreover, triplication of the NH2-terminal zeta motif results in enhanced signaling, suggesting a redundant role in signal amplification for the three motifs in zeta. Finally, we demonstrate the association of a recently identified protein tyrosine kinase ZAP-70 with this motif, and provide evidence for its involvement in zeta function.
Stearidonic Acid Increases the Red Blood Cell and Heart Eicosapentaenoic Acid Content in Dogs (2007)

Plant sources of omega-3 fatty acids (FA) are needed that can materially raise tissue levels of long-chain omega-3 FA [i.e., eicosapentaenoic acid (EPA; 20:5n-3) and docosahexaenoic acid (DHA; 20:6n-3)]. Stearidonic acid (SDA; 18:4n-3) is the delta-6 desaturase product of alpha-linolenic acid (ALA; 18:3n-3), and when fed to humans, increases red blood cell (RBC) content of EPA to a greater extent than does ALA. This study was undertaken to determine the dose-dependence and time course of the increase in the EPA and DHA content of the heart and RBC in dogs. Adult male Beagles were fed 21, 64, or 193 mg/kg of SDA in in their food daily for up to 12 weeks. Positive and negative controls were given EPA (43 mg/kg) or high oleic acid sunflower oil, respectively. The baseline EPA content of RBC was 0.38 +/- 0.03% which increased (P<0.01) in a dose-dependent manner, with the high dose of SDA and EPA achieving levels of 1.33 +/- 0.26 and 1.55. +/- 0.28%, respectively. In the heart, the content of EPA rose from 0.06 +/- 0.01 to 1.24 +/- 0.22% in the EPA group and to 0.81 +/- 0.32% in the high SDA group (both P<0.01). In both tissues, DHA did not change. Compared to dietary EPA, SDA was 20-23% as efficient in raising tissue EPA levels. In conclusion, SDA supplementation increased the EPA content of RBC and heart and may have utility as a plant-based source of omega-3 FA.
Large‐Scale In Vivo Synthesis of the Carbohydrate Moieties of Gangliosides GM1 and GM2 by Metabolically Engineered Escherichia coli (2003)

Two metabolically engineered Escherichia coli strains have been constructed to produce the carbohydrate moieties of gangliosides GM2 (GalNAcbeta-4(NeuAcalpha-3)Galbeta-4Glc; Gal = galactose, Glc = glucose, Ac = acetyl) and GM1 (Galbeta-3GalNAcbeta-4(NeuAcalpha-3)Galbeta-4Glc. The GM2 oligosaccharide-producing strain TA02 was devoid of both beta-galactosidase and sialic acid aldolase activities and overexpressed the genes for CMP-NeuAc synthase (CMP = cytidine monophosphate), alpha-2,3-sialyltransferase, UDP-GlcNAc (UDP = uridine diphosphate) C4 epimerase, and beta-1,4-GalNAc transferase. When this strain was cultivated on glycerol, exogenously added lactose and sialic acid were shown to be actively internalized into the cytoplasm and converted into GM2 oligosaccharide. The in vivo synthesis of GM1 oligosaccharide was achieved by taking a similar approach but using strain TA05, which additionally overexpressed the gene for beta-1,3-galactosyltransferase. In high-cell-density cultures, the production yields for the GM2 and GM1 oligosaccharides were 1.25 g L(-1) and 0.89 g L(-1), respectively.
In vitro electrophysiology of rat subicular bursting neurons (1997)

Intracellular recordings were used to study the electrophysiological properties of rat subicular neurons in a brain slice preparation in vitro. Cells were classified as bursting neurons (n = 102) based on the firing pattern induced by depolarizing current pulses. The bursting response recorded at resting membrane potential (−66.1 ± 6.2 mV, mean ± SD n = 94) was made up of a cluster of fast action potentials riding on a slow depolarization and was followed by an afterhyperpolarization. Tonic firing occurred at a membrane potential of approximately −55 mV. A burst also occurred upon termination of a hyperpolarizing current pulse. Tetrodotoxin (TTX, 1 μM) blocked the burst and decreased or abolished the underlying slow depolarization. These effects were not induced by the concomitant application of the Ca2+ channel blockers Co2+ (2 mM) and Cd2+ (1 mM). Subicular bursting neurons displayed voltage- and time-dependent inward rectifications of the membrane during depolarizing and hyperpolarizing current pulses. The inward rectification in the depolarizing direction was abolished by TTX, while that in the hyperpolarizing direction was blocked by extracellular Cs+ (3 mM), but not modified by Ba2+ (0.5–1 mM), TTX, or Co2+ and Cd2+. Tetraethylammonium (10 mM)-sensitive, outward rectification became apparent in the presence of TTX. These results suggest that neurons in the rat subiculum can display voltage-dependent bursts of action potentials as well as membrane rectification in the depolarizing and hyperpolarizing directions. These results also indicate that activation of a voltage-gated Na+ conductance may be instrumental in the initiation of bursting activity. Hippocampus 7:48–57, 1997. © 1997 Wiley-Liss, Inc.
Inducible isoforms of cyclooxygenase and nitric-oxide synthase in inflammation. (1994)

Cyclooxygenase (COX) converts arachidonic acid to prostaglandin H2, which is further metabolized to prostanoids. Two isoforms of COX exist: a constitutive (COX-1) and an inducible (COX-2) enzyme. Nitric oxide is derived from L-arginine by isoforms of nitric-oxide synthase (NOS; EC 1.14.13.39): constitutive (cNOS; calcium-dependent) and inducible (iNOS; calcium-independent). Here we have investigated inducible isoforms of COX and NOS in the acute, chronic, and resolving stages of a murine air pouch model of granulomatous inflammation. COX and NOS activities were measured in skin samples in the acute phase, up to 24 h. Activities in granulomatous tissue were measured at 3, 5, 7, 14, and 21 days for the chronic and resolving stages of inflammation. COX-1 and COX-2 proteins were assessed by Western blot. COX activity in the skin increased over the first 24 h and continued to rise up to day 14. COX-2 protein rose progressively, also peaking at day 14. COX-1 protein remained unaltered throughout. The iNOS activity increased over the first 24 h in the skin, with a further major increase in the granulomatous tissue between days 3 and 7, followed by a decrease at day 14 and a further increase at day 21. The rise in COX and NOS activities in the skin during the acute phase reinforces the proinflammatory role for prostanoids and suggests one also for nitric oxide. However, in the chronic and resolving stages, a dissociation of COX and NOS activity occurred. Thus, there may be differential regulation of these enzymes, perhaps due to the changing pattern of cytokines during the inflammatory response.
Experimental gas-fired pulse-combustion studies (1982)

Experimental studies conducted at Argonne National Laboratory on a gas-fired, water-cooled, Helmholtz-type pulse combustion burner are discussed. In addition to the experimental work, information is presented on the evolution of pulse combustion, the types of pulse combustion burners and their applications, and the types of fuels used. Also included is a survey of other pertinent studies of gas-fired pulse combustion. The burner used in the Argonne research effort was equipped with adjustable air and gas flapper valves and was operated stably over a heat-input range of 30,000 to 200,000 Btu/h. The burner's overall heat transfer in the pulsating mode was 22 to 31% higher than when the unit was operated in the steady mode. Important phenomena discussed include (1) effects on performance produced by inserting a corebustor to change tailpipe diameter, (2) effects observed following addition of an air-inlet decoupling chamber to the unit, and (3) occurrence of carbon monoxide in the exhaust gas.