gebhart/patrepeval huggingface dataset:
Asialoglycoprotein Receptor Deficiency in Mice Lacking the Major Receptor Subunit (2001)

The asialoglycoprotein receptor is an abundant hetero-oligomeric endocytic receptor that is predominantly expressed on the sinusoidal surface of the hepatocytes. A number of physiological and pathophysiological functions have been ascribed to this hepatic lectin (HL), the removal of desialylated serum glycoproteins and apoptotic cells, clearance of lipoproteins, and the sites of entry for hepatotropic viruses. The assembly of two homologous subunits, HL-1 and HL-2, is required to form functional, high affinity receptors on the cell surface. However, the importance of the individual subunits for receptor transport to the cell surface is controversial. We have previously generated HL-2-deficient mice and showed that the expression of HL-1 was significantly reduced, and the functional activity as the asialoglycoprotein receptor was virtually eliminated. However, we failed to detect phenotypic abnormalities. To explore the significance of the major HL-1 subunit for receptor expression and function in vivo, we have disrupted the HL-1 gene in mice. Homozygous HL-1-deficient animals are superficially normal. HL-2 expression in the liver is virtually abrogated, indicating that HL-1 is strictly required for the stable expression of HL-2. Although these mice are almost unable to clear asialo-orosomucoid, a high affinity ligand for asialoglycoprotein receptor, they do not accumulate desialylated glycoproteins or lipoproteins in the plasma.
Enzyme-catalyzed DNA unwinding. A DNA-dependent ATPase from E. coli. (1979)

We have isolated a new DNA-dependent ATPase from E. coli. The enzyme has been purified to greater than 90% purity. It appears to be composed of two identical polypeptide chains of molecular weight 20,000. The enzyme catalyzed the hydrolysis of ATP in the presence, but not in the absence, of single-stranded DNA. Double-stranded DNA is not a cofactor. The products of hydrolysis are ADP and Pi. The enzyme also catalyzed strand separation of duplex DNA in the presence of ATP and E. coli DNA binding protein. Two E. coli proteins capable of promoting strand separation have been reported previously and have been termed helicase I and II (Abdel-Monem, M., and Hoffmann-Berling, H. (1977) Eur. J. Biochem. 79, 33-38). Accordingly, this protein is named helicase III.
Direct Assessment of CXCR4 Mutant Conformations Reveals Complex Link between Receptor Structure and Gαi Activation (2006)

Ligand binding to G protein-coupled receptors (GPCRs) is thought to induce changes in receptor conformation that translate into activation of downstream effectors. The link between receptor conformation and activity is still insufficiently understood, as current models of GPCR activation fail to take an increasing amount of experimental data into account. To elucidate structure-function relationships in GPCR activation, we used bioluminescence resonance energy transfer to directly assess the conformation of mutants of the chemokine receptor CXCR4. We analyzed substitutions in the arginine cage DRY motif and in the conserved asparagine N(3.35)119, which are pivotal molecular switches for receptor conformation and activation. G(alpha)(i) activation of the mutants was either similar to wild-type CXCR4 (D133N, Y135A, and N119D) or resulted in loss of activity (R134A and N119K). Mutant N119S was constitutively active but further activated by agonist. Bioluminescence resonance energy transfer analysis suggested no simple correlation between conformational changes in response to ligand binding and activation of G(alpha)(i) by the mutants. Different conformations of active receptors were detected (for wild-type CXCR4, D133N, and N119S), suggesting that different receptor conformations are able to trigger G(alpha)(i) activity. Several conformations were also found for inactive mutants. These data provide biophysical evidence for different receptor conformations being active with respect to a single readout. They support models of GPCR structure-activity relationships that take this conformational flexibility of active receptors into account.
Controllable Synthesis of Organic–Inorganic Hybrid MoOx/Polyaniline Nanowires and Nanotubes (2011)

A novel chemical oxidative polymerization approach has been proposed for the controllable preparation of organic-inorganic hybrid MoO(x)/polyaniline (PANI) nanocomposites based on the nanowire precursor of Mo(3)O(10)(C(6)H(8)N)(2)·2H(2)O with sub-nanometer periodic structures. The nanotubes, nanowires, and rambutan-like nanoparticles of MoO(x)/PANI were successfully obtained through simply modulating the pH values to 2.5-3.5, ≈2.0 and ≈1.0, respectively. Through systematic physicochemical characterization, such as scanning electron microscopy, transmission electron microscopy, X-ray photoelectron spectroscopy, Raman spectroscopy, and so forth, the composition and structure of MoO(x)/PANI hybrid nanocomposites are well confirmed. It is found that the nanowire morphology of the precursor is the key to achieve the one-dimensional (1D) structures of final products. A new polymerization-dissolution mechanism is proposed to explain the formation of such products with different morphologies, in which the match between polymerization and dissolution processes of the precursor plays the important role. This approach will find a new way to controllably prepare various organic-inorganic hybrid 1D nanomaterials especially for polymer-hybrid nanostructures.
Transdermal Influenza Immunization with Vaccine-Coated Microneedle Arrays (2009)

The present results show that delivery of inactivated influenza virus through the skin using metal microneedle arrays induced strong humoral and cellular immune responses capable of conferring protection against virus challenge as efficiently as intramuscular immunization, which is the standard vaccination route. In view of the convenience of delivery and the potential for self-administration, vaccine-coated metal microneedles may provide a novel and highly effective immunization method.
The Inhibition of Potential Parallelism by Conditional Jumps (1972)

This note reports the results of an examination of seven programs originally written for execution on a conventional computer (CDC-3600). We postulate an infinite machine, one with an infinite memory and instruction stack, infinite registers and memory, and an infinite number of functional units. This machine wiU exectite a program in parallel at maximum speed by executing each instruction at the earliest possible moment.
DESIRE: Distant Future Prediction in Dynamic Scenes with Interacting Agents (2017)

We introduce a Deep Stochastic IOC RNN Encoder-decoder framework, DESIRE, for the task of future predictions of multiple interacting agents in dynamic scenes. DESIRE effectively predicts future locations of objects in multiple scenes by 1) accounting for the multi-modal nature of the future prediction (i.e., given the same context, future may vary), 2) foreseeing the potential future outcomes and make a strategic prediction based on that, and 3) reasoning not only from the past motion history, but also from the scene context as well as the interactions among the agents. DESIRE achieves these in a single end-to-end trainable neural network model, while being computationally efficient. The model first obtains a diverse set of hypothetical future prediction samples employing a conditional variational auto-encoder, which are ranked and refined by the following RNN scoring-regression module. Samples are scored by accounting for accumulated future rewards, which enables better long-term strategic decisions similar to IOC frameworks. An RNN scene context fusion module jointly captures past motion histories, the semantic scene context and interactions among multiple agents. A feedback mechanism iterates over the ranking and refinement to further boost the prediction accuracy. We evaluate our model on two publicly available datasets: KITTI and Stanford Drone Dataset. Our experiments show that the proposed model significantly improves the prediction accuracy compared to other baseline methods.
Mechanism of electrical enhancement of efficacy of antibiotics in killing biofilm bacteria (1994)

The bioelectric effect, in which electric fields are used to enhance the efficacy of biocides and antibiotics in killing biofilm bacteria, has been shown to reduce the very high concentrations of these antibacterial agents needed to kill biofilm bacteria to levels very close to those needed to kill planktonic (floating) bacteria of the same species. In this report, we show that biofilm bacteria are readily killed by an antibiotic on all areas of the active electrodes and on the surfaces of conductive elements that lie within the electric field but do not themselves function as electrodes. Considerations of electrode geometry indicate that very low (< 100 microA/cm2) current densities may be effective in this electrical enhancement of antibiotic efficacy against biofilm bacteria, and flow experiments indicate that this bioelectric effect does not appear to depend entirely on the possible local electrochemical generation of antibacterial molecules or ions. These data are expected to facilitate the use of the bioelectric effect in the prevention and treatment of device-related bacterial infections that are caused by bacteria that grow in biofilms and thereby frustrate antibiotic chemotherapy.
Optimization of computer-generated holograms by an artificial neural network (2002)

Several computer-generated hologram (CGH) methods, such as the direct binary search, simulated annealing and genetic algorithm, have been proposed or used in order to decrease the quantum noise and reconstruction noise or to optimize the CGH. Since these methods are iterative approaches, they require long computation time to generate a CGH. In this paper, we propose a new method based on an artificial neural network (ANN) to reduce the high computation cost. In this scheme, we first use a couple of known optimized CGHs, which may be obtained by the traditional optimization methods, as teaching signals to train the ANN. With the trained ANN, we can easily and quickly obtain an optimized CGH without the optimization process for other input images.
Blood-brain barrier and new approaches to brain drug delivery. (1992)

Morbidity caused by brain dysfunction affects more than 50 million persons in the United States. Although new neuropharmaceuticals have the potential for treating specific brain diseases, they may not effectively enter brain from blood. Safe strategies are needed for drug delivery through the brain capillary wall, which makes up the blood-brain barrier in vivo. Two of these strategies are reviewed, as are related new developments in the molecular and cell biology of the brain capillary endothelium. The production of chimeric peptides represents a physiologic-based strategy for drug delivery. It entails the covalent coupling of the neuropharmaceutical to a brain transport vector, allowing transportation through the blood-brain barrier. Another strategy is biochemical opening of the blood-brain barrier: intracarotid leukotriene infusion is a method for selectively increasing blood-brain barrier permeability in brain tumors without affecting barrier permeability in normal brain tissue.
A prokaryotic-like mode of cytoplasmic eukaryotic ribosome binding to the initiation codon during internal translation initation of hepatitis C and classical swine fever virus RNAs (1998)

Initiation of translation of hepatitis C virus and classical swine fever virus mRNAs results from internal ribosomal entry. We reconstituted internal ribosomal entry in vitro from purified translation components and monitored assembly of 48S ribosomal preinitiation complexes by toe-printing. Ribosomal subunits (40S) formed stable binary complexes on both mRNAs. The complex structure of these RNAs determined the correct positioning of the initiation codon in the ribosomal "P" site in binary complexes. Ribosomal binding and positioning on these mRNAs did not require the initiation factors eIF3, eIF4A, eIF4B, and eIF4F and translation of these mRNAs was not inhibited by a trans-dominant eIF4A mutant. Addition of Met-tRNAiMet, eIF2, and GTP to these binary ribosomal complexes resulted in formation of 48S preinitiation complexes. The striking similarities between this eukaryotic initiation mechanism and the mechanism of translation initiation in prokaryotes are discussed.
Mammalian DNA topoisomerase I mediates the enhancement of radiation cytotoxicity by camptothecin derivatives. (1997)

The role of DNA topoisomerase I as a biochemical mediator of radiosensitization in cultured mammalian cells by camptothecin derivatives was studied. We found that, in Chinese hamster DC3F cells, camptothecin enhanced the cytotoxicity of radiation in a schedule-dependent manner. At 4 microM, a sensitizer enhancement ratio of 1.45 was observed when radiation was used concurrently with or immediately after drug treatment. By comparison, no enhancement was obtained if radiation preceded camptothecin treatment. Consistently, in human breast cancer MCF-7 cells, sensitizer enhancement ratios of 1.43, 1.38, and 1.05 were observed when radiation was used concurrently with, immediately after, or prior to treatment with 20(S)-10,11-methylenedioxycamptothecin (MDCamp). Three studies indicated that an intact stereospecific interaction between camptothecin derivatives and DNA topoisomerase I is essential in the induction of radiosensitization: (a) higher concentrations of camptothecin were required to radiosensitize the camptothecin-resistant DC3F/C-10 cells; (b) a newly identified topoisomerase 1-targeting Hoechst 33342 also radiosensitized DC3F cells; and (c) 20(S)-methylenedioxycamptothecin, but not its noncytotoxic 20(R)-stereoisomer, radiosensitized MCF-7 cells by obliterating the "shoulder" of the radiation survival curve. The mechanism of radiosensitization was investigated in DC3F cells. We found that camptothecin only minimally enhanced the cytoxic effect of radiation in G1-phase cells obtained by a mitotic shake-off technique as well as in plateau-phase cells arrested by growing to confluency. Our data suggest a potential development of topoisomerase I drugs as radiosensitizers in treating human malignancies.
Chemical and Spectral Properties of Putidamonooxin, the Iron‐Containing and Acid‐Labile‐Sulfur‐Containing Monooxygenase of a 4‐Methoxybenzoate O‐Demethylase from Pseudomonas putida (1978)

Gel chromatography indicates that putidamonooxin has a molecular weight of about 126,000. On the other hand, the amino acid composition and the iron-to-protein ratio point to a minimal molecular weight of 33,000 and 31,000 respectively. On sodium dodecylsulfate/polyacrylamide gel electrophoresis the enzyme migrated as a homogeneous band corresponding to a molecular weight of about 40,000. The number of spots found in the tryptic peptide map of the carboxymethylated and digested enzyme indicates that putidamonooxin is composed of three or four identical subunits. After covalent cross-linking of the subunits with dimethyl suberimidate and subsequent dodecylsulfate electrophoresis the main bands were in the molecular weight range of 40,000, 87,000 and 124,000. These findings lead us to propose that putidamonooxin is either a trimer or tetramer. The amino acid composition of putidamonooxin and related data calculated from this are given. The isoelectric point was shown by isoelectric focusing to be a pH 4.7. Low-temperature optical spectra of the reduced and oxidized enzyme as well as of three different putidamonooxin.substrate complexes are given together with those recorded at 10 degrees C. Enzyme.substrate binding spectra are observed with the oxidized putidamonooxin but not with the reduced enzyme. For the oxidized putidamonooxin a molar absorption coefficient at 455nm of 14.7mM-1 cm-1 was determined. Ks values of putidamonooxin towards different substrates and substrate analogues (i.e. tight couplers, partial uncouplers and uncouplers) are presented and possible reasons for the difference between the Ks values here obtained and the previously reported Km values are discussed.
STUDIES ON PROTEINOGENOUS AMINES. I. THE SYNTHESIS OF β-IMIDAZOLYLETHYLAMINE (HISTAMINE). (1918)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSTUDIES ON PROTEINOGENOUS AMINES. I. THE SYNTHESIS OF β-IMIDAZOLYLETHYLAMINE (HISTAMINE).Karl K. Koessler and Milton Th. HankeCite this: J. Am. Chem. Soc. 1918, 40, 11, 1716–1726Publication Date (Print):November 1, 1918Publication History Published online1 May 2002Published inissue 1 November 1918https://pubs.acs.org/doi/10.1021/ja02244a012https://doi.org/10.1021/ja02244a012research-articleACS PublicationsRequest reuse permissionsArticle Views281Altmetric-Citations24LEARN 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 InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Cytokines expression in SLE nephritis. (2011)

Renal involvement is a common manifestation in course of systemic lupus erythematous (SLE) and may occur at any time. In SLE nephritis, the pattern of glomerular injury is primarily related to the formation of the immune deposits in situ, due major to antidouble-stranded DNA (anti-dsDNA) antibodies and anti- C1q. Immune complexes deposits can induce the inflammatory response by activation of adhesion molecules on endothelium, resulting in the recruitment of pro inflammatory leukocytes. Activated and damaged glomerular cells, infiltrating macrophages, B and T cells produced cytokines that play a pivotal role as inflammatory mediators to extend renal injury. In serum of SLE patients, the concentrations of IL-6, IL-17, IL-12, INF-gamma, IL-18, IL-10 and TNF-alpha are higher than healthy people and this increase correlate with disease activity. It is well established possible correlation between urinary cytokines levels (IL-6, IL-10, INF-gamma and TGF-beta) and disease activity. In fact, Systemic Lupus Erythematosus Disease Activity Index (SLEDAI) correlate with cytokines over-expression, in particular IL-17, IL-10, TNF-alpha and the axis INF-gamma/IL-12. Recent studies are promising about proteinuria reduction and improving renal function through cytokine blockade therapy.
The Unfolded Protein Response Pathway in (1996)

In eukaryotic cells, accumulation of unfolded proteins in the endoplasmic reticulum (ER) results in a transcriptional induction of a number of ER chaperone proteins. In Saccharomyces cerevisiae, the putative transmembrane receptor kinase, Ire1p (Ern1p), has been implicated as the sensor of unfolded proteins in the ER that initiates transmittance of the unfolded protein signal from the ER to the nucleus. We have shown that the cytoplasmic domain of Ire1p receptor indeed has intrinsic Ser/Thr kinase activity and contains Ser/Thr phosphorylation sites as well. The cytoplasmic domain is also shown to form oligomers in vivo and in vitro. The ability to form oligomers primarily resides within the last 130 amino acids of the cytoplasmic domain, a region that is dispensable for in vitro kinase activity of the receptor. Oligomerization of the cytoplasmic domains is required for receptor trans-phosphorylation and subsequent activation of the kinase function. The activated kinase may transmit the unfolded protein signal from the ER to the nucleus to activate the transcription of the chaperone genes in the nucleus.
Mapping of surface glycoproteins of Trypanosoma cruzi by two-dimensional electrophoresis. A correlation with the cell invasion capacity (1984)

The cell-surface iodinatable proteins of Trypanosoma cruzi have been analyzed by two-dimensional polyacrylamide gel electrophoresis under equilibrium conditions. Antigenic polypeptides were characterized after immunoprecipitation and glycoproteins were identified by means of lectin-affinity chromatography. Two glycoproteins, with affinity for concanavalin A, were found to be common to both infective (trypomastigote) and non-infective (epimastigote) forms: protein 1 (90 kDa, pI 5.5-6.5) and protein 2 (80 kDa, pI 5.3-6.3). In epimastigotes a specific concanavalin-A-binding surface glycoprotein (70 kDa, pI 5.5) was identified. Trypomastigote forms, on the other hand, presented several specific iodinatable surface components: glycoproteins 3(85 kDa, pI 5.5), 4 (85 kDa, pI 5.0), 6 (100 kDa, pI 6.5), 7 (120 kDa, pI 6.3), 8 (68 kDa, pI 6.7) and several minor high-molecular-mass acid proteins, all containing glucose and/or mannose, and glycoprotein 5 (85 kDa, pI 6.3-7.5), containing N-acetyl-D-glucosamine (Tc-85). Proteins 1, 2 and 5 were the only ones which gave clear evidence of charge heterogeneity. Most of the surface proteins of trypomastigote forms, the exception being proteins 3, 4 and 8, were removed by treatment with trypsin. This proteolytic treatment results in 90% inhibition of the in vitro vertebrate-cell-invasion capacity of the parasites. Upon reincubation in culture medium for 4 h, the trypsin-removed glycoproteins are again detected, an observation that correlates well with the recovery of the cell-penetration capacity observed in the same period.
Synthesis and purification of large amounts of RNA oligonucleotides. (1991)

Biophysical studies of RNA oligonucleotides require milligram amounts of RNA of specific length and sequence. Transcription from synthetic DNA templates using T7 RNA polymerase is a convenient method for synthesis of RNA oligonucleotides ranging in size from 9 to about 45 nucleotides. Here we present methods that make the large-scale synthesis of RNA oligonucleotides practical. This paper describes a rapid method for isolating T7 RNA polymerase free from RNases for use in transcription reactions. Protocols are also described for purification of the desired RNA oligonucleotide from the other products of transcription.