gebhart/patrepeval huggingface dataset:
GENDER DIFFERENCE IN GRANULOCYTE DYNAMICS AND APOPTOSIS AND THE ROLE OF IL-18 DURING ENDOTOXIN-INDUCED SYSTEMIC INFLAMMATION (2009)

Delayed granulocyte apoptosis is implicated in persistent inflammation. Although it is known that males develop sepsis more easily than females, the mechanism for this is not fully understood. Serum IL-18 levels correspond to severity of systemic inflammation. The purpose of this study was to elucidate gender differences and the effects of IL-18 on granulocyte dynamics and apoptosis. Male and female wild-type (WT) and IL-18 knockout (KO) mice were injected intraperitoneally with LPS. Bone marrow cells, peripheral blood, and peritoneal cells were then collected at different times up to 24 h after injection. Apoptosis was assessed by annexin V staining using three-color flow cytometry with differentiated granulocyte-specific Gr-1, B-lymphocyte-specific B220, and macrophage-specific F4/80 antibodies. Male WT mice were more susceptible to endotoxin than female WT mice (survival rate, 41% in male WT and 84% in female WT). Male WT mice showed stronger responses than females in myeloid differentiation, release of myeloid cells from the bone marrow into the periphery, and migration into the inflammatory peritoneal cavity. Male mice also showed greater inhibition of granulocyte apoptosis in the peritoneal cavity, which might also contribute to the higher numbers of those cells present. A comparison between WT and KO mice revealed that the gender difference in these myeloid cells/granulocytes' behaviors was independent of endogenous IL-18. Nevertheless, levels of IL-18 in the blood of WT mice were significantly higher in males than in females after intraperitoneal LPS, and the survival rate was significantly higher in KO mice compared with WT mice only in males. This indicates that endogenous IL-18 production decreases survival only in males. Thus, excessive myeloid/granulocyte immunity independent of IL-18 and other IL-18-dependent life-threatening factors in males should be taken into account as therapeutic targets during systemic inflammatory states.
Structural properties of promoters: similarities and differences between prokaryotes and eukaryotes (2005)

During the process of transcription, RNA polymerase can exactly locate a promoter sequence in the complex maze of a genome. Several experimental studies and computational analyses have shown that the promoter sequences apparently possess some special properties, such as unusual DNA structures and low stability, which make them distinct from the rest of the genome. But most of these studies have been carried out on a particular set of promoter sequences or on promoter sequences from similar organisms. To examine whether the promoters from a wide variety of organisms share these special properties, we have carried out an analysis of sets of promoters from bacteria, vertebrates and plants. These promoters were analyzed with respect to the prediction of three different properties, such as DNA curvature, bendability and stability, which are relevant to transcription. All the promoter sequences are predicted to share certain features, such as stability and bendability profiles, but there are significant differences in DNA curvature profiles and nucleotide composition between the different organisms. These similarities and differences are correlated with some of the known facts about transcription process in the promoters from the three groups of organisms.
Guidelines for the Pharmacologic Treatment of Neurobehavioral Sequelae of Traumatic Brain Injury (2006)

There is currently a lack of evidence-based guidelines to guide the pharmacological treatment of neurobehavioral problems that commonly occur after traumatic brain injury (TBI). It was our objective to review the current literature on the pharmacological treatment of neurobehavioral problems after traumatic brain injury in three key areas: aggression, cognitive disorders, and affective disorders/anxiety/ psychosis. Three panels of leading researchers in the field of brain injury were formed to review the current literature on pharmacological treatment for TBI sequelae in the topic areas of affective/anxiety/ psychotic disorders, cognitive disorders, and aggression. A comprehensive Medline literature search was performed by each group to establish the groups of pertinent articles. Additional articles were obtained from bibliography searches of the primary articles. Group members then independently reviewed the articles and established a consensus rating. Despite reviewing a significant number of studies on drug treatment of neurobehavioral sequelae after TBI, the quality of evidence did not support any treatment standards and few guidelines due to a number of recurrent methodological problems. Guidelines were established for the use of methylphenidate in the treatment of deficits in attention and speed of information processing, as well as for the use of beta-blockers for the treatment of aggression following TBI. Options were recommended in the treatment of depression, bipolar disorder/mania, psychosis, aggression, general cognitive functions, and deficits in attention, speed of processing, and memory after TBI. The evidence-based guidelines and options established by this working group may help to guide the pharmacological treatment of the person experiencing neurobehavioral sequelae following TBI. There is a clear need for well-designed randomized controlled trials in the treatment of these common problems after TBI in order to establish definitive treatment standards for this patient population.
Poly(ethylene oxide)-Modified Poly(β-amino ester) Nanoparticles as a pH-Sensitive System for Tumor-Targeted Delivery of Hydrophobic Drugs. 1. In Vitro Evaluations (2005)

A representative poly(beta-amino ester) (PbAE) with biodegradable and pH-sensitive properties was used to formulate a nanoparticle-based dosage form for tumor-targeted paclitaxel delivery. The polymer undergoes rapid dissolution when the pH of the medium is less than 6.5 and hence is expected to release its contents at once within the acidic tumor microenvironment and endo/lysosome compartments of cells. PbAE nanoparticles were prepared by solvent displacement method and characterized for particle size, charge, and surface morphology. Pluronic F-108, a triblock copolymer of poly(ethylene oxide) (PEO) and poly(propylene oxide) (PPO), was blended with PbAE to induce surface modification of the nanoparticles. In vitro cellular uptake of tritiated [(3)H]-paclitaxel in solution form and as a nanoparticulate formulation was studied in MDA-MB-231 human breast adenocarcinoma cells grown in 12-well plates. We also examined the intracellular degradation pattern of the formulations within the cells by estimating the drug release profile. Cytotoxicity assay was performed on the formulations at different doses and time intervals. Nanoparticles prepared from poly(epsilon-caprolactone) (PCL) that do not display pH-sensitive release behavior were used as control. Spherical nanoparticles having positive zeta potential ( approximately 40 mV) were obtained in the size range of 150-200 nm with PbAE. The PEO chains of the Pluronic were well-anchored within the nanomatrix as determined by electron spectroscopy for chemical analysis (ESCA). The intracellular accumulation of paclitaxel within tumor cells was significantly higher when administered in the nanoparticle formulations as compared to aqueous solution. Qualitative fluorescent microscopy confirmed the rapid release of the payload into the cytosol in the case of PbAE nanoparticles, while the integrity of the PCL nanoparticles remained intact. The cytotoxicity assay results showed significantly higher tumoricidal activity of paclitaxel when administered in the nanoparticle formulations. The cell-kill effect was maximal for paclitaxel-loaded PbAE nanoparticles when normalized with respect to intracellular drug concentrations. Thus, PEO-modified PbAE nanoparticles show tremendous potential as novel carriers of cytotoxic agents for achieving improved drug disposition and enhanced efficacy.
Improved virological response to highly active antiretroviral therapy in HIV‐1‐infected patients carrying the CCR5 Δ32 deletion (2007)

CCR5 Delta32 heterozygous patients were more likely to have a virological response to HAART than wild-type patients at 6 and 12 months. However, this virological response did not produce better immunological and clinical responses. The long-term impact of the Delta32 deletion on survival in HIV-1-infected treated patients should be investigated in a meta-analysis.
AST-based multi-language plagiarism detection method (2013)

To detect plagiarism on programming course, the plagiarism detection method based on Abstract Syntax Tree (AST) is proposed. First, we parse source codes into the corresponding AST by syntax analyzer and a biology sequence matching algorithm is used to calculate the similarities of programs. Second, the AST features of similar parts of the programs are extracted and then space vectors of the features are obtained. Finally, we find “copy cluster” by clustering the vectors. Experimental results show that this method has a good effect on the detection of plagiarism and can also find the “copy cluster” accurately.
Inhibitors of anaplastic lymphoma kinase: a patent review (2010)

Multiple small-molecule ALK inhibitors have been reported with diverse chemical architecture, potency, kinase selectivity profiles and activity against potential resistance. The breadth of inhibitors combined with the recent discoveries of the involvement of ALK in lung, breast and colorectal cancers has kept the field advancing at a rapid pace.
Chemical Overcharge and Overdischarge Protection for Lithium-Ion Batteries (2004)

Rechargeable lithium-ion batteries suitable for the mass consumer market require robust safety and tolerance to repeated overdischarge and overcharge to avoid costly charge control circuitry and to allow simple replacement of individual cells by consumers. A chemical redox shuttle additive to the electrolyte is shown to provide this protection. The molecule, 2,5 ditertbutyl-1,4-dimethoxybenzene, provides overcharge and overdischarge protection for hundreds of charge-discharge cycles in both single cells and series-connected batteries. © 2004 The Electrochemical Society. All rights reserved.
Evidence for Budding of Human Immunodeficiency Virus Type 1 Selectively from Glycolipid-Enriched Membrane Lipid Rafts (2000)

A number of recent studies have demonstrated the significance of detergent-insoluble, glycolipid-enriched membrane domains or lipid rafts, especially in regard to activation and signaling in T lymphocytes. These domains can be viewed as floating rafts composed of sphingolipids and cholesterol which sequester glycosylphosphatidylinositol (GPI)-linked proteins, such as Thy-1 and CD59. CD45, a 200-kDa transmembrane phosphatase protein, is excluded from these domains. We have found that human immunodeficiency virus type 1 (HIV-1) particles produced by infected T-cell lines acquire the GPI-linked proteins Thy-1 and CD59, as well as the ganglioside GM1, which is known to partition preferentially into lipid rafts. In contrast, despite its high expression on the cell surface, CD45 was poorly incorporated into virus particles. Confocal fluorescence microscopy revealed that HIV-1 proteins colocalized with Thy-1, CD59, GM1, and a lipid raft-specific fluorescent lipid, DiIC(16)(3), in uropods of infected Jurkat cells. CD45 did not colocalize with HIV-1 proteins and was excluded from uropods. Dot immunoassay of Triton X-100-extracted membrane fractions revealed that HIV-1 p17 matrix protein and gp41 were present in the detergent-resistant fractions and that [(3)H]myristic acid-labeled HIV Gag showed a nine-to-one enrichment in lipid rafts. We propose a model for the budding of HIV virions through lipid rafts whereby host cell cholesterol, sphingolipids, and GPI-linked proteins within these domains are incorporated into the viral envelope, perhaps as a result of preferential sorting of HIV Gag to lipid rafts.
Charge-Mediated Recognition of N-Terminal Tryptophan in Aqueous Solution by a Synthetic Host (2005)

The molecular recognition of peptides and proteins in aqueous solution by designed molecules remains an elusive goal with broad implications for basic biochemical research and for sensors and separations technologies. This paper describes the recognition of N-terminal tryptophan in aqueous solution by the synthetic host cucurbit[8]uril (Q8). Q8 is known to form 1:1:1 heteroternary complexes with methyl viologen (MV) and a second aromatic guest. Here, the complexes of Q8.MV with (i) the four natural aromatic alpha-amino acids, (ii) four singly charged tryptophan derivatives, and (iii) four tryptophan-containing tripeptides were characterized by isothermal titration calorimetry, mass spectrometry, and UV-visible, fluorescence, and (1)H NMR spectroscopy. We find that Q8.MV binds Trp-Gly-Gly with high affinity (K(a) = 1.3 x 10(5) M(-1)), with 6-fold specificity over Gly-Trp-Gly, and with 40-fold specificity over Gly-Gly-Trp. Analysis of the nine indole-containing compounds suggests that peptide recognition is mediated by the electrostatic charge(s) proximal to the indole, and that the mode of binding is consistent for these compounds. Complex formation is accompanied by the growth of a visible charge-transfer band and the quenching of indole fluorescence. These optical properties, combined with the stability and selectivity of this system, are promising for applications in sensing and separating specific peptides.
Substrate Specificity of Tissue Type Plasminogen Activator (1995)

Tissue-type plasminogen activator (t-PA) is a remarkably specific protease: the only known substrate of this enzyme in vivo is a single peptide bond (Arg560-Val561) within the proenzyme plasminogen. Part of the substrate specificity of t-PA is due to a ternary interaction between fibrin, t-PA and plasminogen which reduces the Km of t-PA for plasminogen by a factor of 440. However, even in the absence of fibrin, t-PA continues to hydrolyze plasminogen more rapidly than does trypsin, a homologous serine protease. We have measured the extent of the specificity of t-PA for plasminogen by assaying t-PA and trypsin toward substrates modeled after the peptide sequence in plasminogen surrounding Arg560-Val561. Surprisingly, t-PA hydrolyzes these substrates with kcat/Km values which are 28,000-210,000-fold lower than those obtained using trypsin. Both the high activity toward plasminogen and the low activity toward peptides are also exhibited by the isolated protease domain. This suggests that the protease domain, in spite of its high homology to the nonspecific enzyme trypsin, is inherently specific for recognition of one or more structural features displayed by native plasminogen.
Ozonolysis of Vinylpyridines (1961)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTOzonolysis of VinylpyridinesR. H. CALLIGHAN and M. H. WILTCite this: J. Org. Chem. 1961, 26, 12, 4912–4914Publication Date (Print):December 1, 1961Publication History Published online1 May 2002Published inissue 1 December 1961https://pubs.acs.org/doi/10.1021/jo01070a032https://doi.org/10.1021/jo01070a032research-articleACS PublicationsRequest reuse permissionsArticle Views586Altmetric-Citations31LEARN 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
The Growth of MAT-LyLu Rat Prostatic Adenocarcinoma can be Prevented in Vivo by Polyamine Deprivation (1991)

The combination of inhibitors of ornithine decarboxylase and polyamine oxidase, and of antibiotics suitable for the (partial) decontamination of the gastrointestinal tract, with a polyamine deficient diet, is responsible for the almost complete inhibition of the growth of MAT-LyLu prostatic adenocarcinoma. In the tumor-bearing animals, erythrocyte spermidine levels were reduced, but spermine concentrations were increased. As has been previously observed, the increase in erythrocyte spermine level was associated with an enhancement of malignant cell death. Adriamycin administration did neither diminish tumor growth, nor potentiate the antitumor effect of polyamine deprivation treatment. Interruption of the polyamine deprivation treatment was accompanied by a significant enhancement of tumor growth. Since polyamine deprivation causes only reversible growth inhibition, it seems not appropriate as a monotherapy.
Oxidative upgrade of lignin – Recent routes reviewed (2013)

Lignin is the second most abundant natural polymer. Its use and targeted functionalisation within biomass refinery processes, however, still needs to be further explored and developed. The oxidative functionalisation, and thus valorisation of lignin, is a very promising way to go, since it holds the possibilities to yield highly functionalised, monomeric or oligomeric products that can serve as starting materials for other valorisation processes in the chemical and pharmaceutical industries. Gaining a profound knowledge about the structure of lignin, being able to analyse structural features, and understanding the mechanisms that guide the reactions leading to the oxidative derivatisation, depolymerisation and functionalisation of lignin samples from different renewable sources are key requirements for developing successful valorisation protocols for lignin. In this review, we wish to revisit, and set into context, some important achievements in the field of oxidatively upgrading lignin. We will focus on organometal catalyses (MTO, salen complexes, POMs), biomimetic catalyses (porphyrins), and enzymatic catalyses (laccase, peroxidase) for upgrading lignin and lignin model compounds. Details of mechanistic implications and means of potential manipulations of reaction outcomes are discussed.
LCX, leukemia-associated protein with a CXXC domain, is fused to MLL in acute myeloid leukemia with trilineage dysplasia having t(10;11)(q22;q23). (2002)

There are a limited number of reports of acute myeloid leukemia (AML) with t(10;11)(q22;q23). We showed that the MLL gene on 11q23 was fused to the LCX (leukemia-associated protein with a CXXC domain) gene on 10q22 in a de novoadult AML-M2 with trilineage dysplasia having t(10;11)(q22;q23). LCX consisted of at least 12 exons and was predicted to encode a 2136-amino-acid protein with an estimated molecular mass of 235.3 kDa. The LCX protein had a zinc-binding CXXC domain that MLL also contains within a methyltransferase domain, three nuclear localization signals, an alpha-helical coiled-coil region, and two homologous regions to CG2083 proteins of Drosophila melanogaster. We found approximately 12-, 9.5-, and 7.5-kb transcripts of LCX. Expression of the 7.5-kb transcript was detected in fetal heart, lung, and brain, and in adult skeletal muscle, thymus, and ovary. Expression of the 9.5-kb transcript was detected in fetal lung and brain and in adult ovary. Expression of the 12-kb transcript was detected in fetal heart and brain and in adult thymus and ovary. LCX was expressed in 8 of 22 leukemic cell lines, but not in EBV-induced normal B-cell lines. The MLL-LCX fusion protein lacked a CXXC domain of LCX, but retained an alpha-helical coiled-coil region at the COOH terminus, similar to MLL-SEPTING, MLL-CDCREL1, MLL-AF1p/Eps15, and MLL-AF6, which suggests that these fusion proteins are involved in the pathogenesis of 11q23-associated leukemia through similar mechanisms.
How to train your T cell: genetically engineered chimeric antigen receptor T cells versus bispecific T-cell engagers to target CD19 in B acute lymphoblastic leukemia (2015)

Antigen-specific T cell-based immunotherapy is getting its day in the sun. The contemporaneous development of two potent CD19-specific immunotherapeutic modalities for the treatment of B-cell malignancies provides exciting opportunities for patients, physicians and scientists alike. Patients with relapsed, refractory or poor-risk B-cell acute lymphoblastic leukemia (ALL) previously had few therapeutic options and now have two potential new lifelines. Physicians will have the choice between two powerful modalities and indeed could potentially enroll some patients on trials exploring both modalities if needed. For scientists interested in tumor immunology, the advent of chimeric antigen receptor T-cell therapy and of bispecific T-cell engagers (BiTEs) provides unprecedented opportunities to explore the promise and limitations of antigen-specific T-cell therapy in the context of human leukemia. In this article, we compare chimeric antigen receptor T cells and BiTEs targeting CD19 in B-cell ALL in the setting of the available clinical literature.
Development of atherosclerosis in genetically hyperlipidemic rabbits during chronic fish-oil ingestion. (1989)

The evidence for a reduction in cardiovascular mortality from fish oil is based on epidemiologic observations. To test whether fish-oil supplementation influences the development of atherosclerosis, we treated Watanabe heritable hyperlipidemic rabbits (WHHL), an inbred strain that spontaneously develops atherosclerosis, with 2.5 ml of MaxEPA fish-oil concentrate daily and compared them to a control group fed unsupplemented rabbit chow. Serial cholesterol and triglyceride levels were monitored as were plasma lipid hydroperoxides. The animals were given fish oil from the time of weaning until 1 year of age, when they were sacrificed and their aortas were compared for the extent of atherosclerosis. No significant differences in the cholesterol or triglyceride levels were noted between the two groups. Fatty acid hydroperoxide levels were also similar and were noted to increase from weaning (1.0 +/- 0.7 microM) to the time of sacrifice (1.8 +/- 1.5 microM, p less than 0.01). Fish oil had no influence on the extent of aortic atherosclerosis (25% +/- 14% surface area for controls vs. 28% +/- 19% for treated, p = NS), plaque thickness, or plaque volume after 1 year. We conclude that fish oil does not reduce the levels of serum cholesterol, lipid hydroperoxides, or aortic atherosclerosis in WHHL rabbits. The hypothesis that fish oil protects against atherosclerosis was not supported by this study.
Studies of membrane formation in Tetrahymena. The identification of membrane proteins and turnover rates in nongrowing cells. (1980)

Membrane proteins within cell fractions of Tetrahymena have been separated by polyacrylamide gel electrophoresis and the turnover of these proteins has been studied in nongrowing cells using double labeling procedures. Lactoperoxidase iodination and two-dimensional gel separations have revealed over 20 surface-labeled proteins, two of which are responsible for the single peak found in ciliary and nonciliary surface membranes. Turnover measurements show that there is heterogeneity in the rates at which membrane proteins turn over. The data suggest that larger proteins may turn over at higher rates in the microsomal fraction, as previously shown in mammalian cells. This was not found in the surface membrane fractions of Tetrahymena. However, membrane-associated cytoskeletal proteins had lower turnover rates than integral membrane proteins, and significant heterogeneity was found among the integral proteins measured. The implications of these findings for possible modes of membrane biogenesis in Tetrahymena are discussed.