gebhart/patrepeval huggingface dataset:
Primary Structure of ω‐Hordothionin, a Member of a Novel Family of Thionins from Barley Endosperm, and Its Inhibition of Protein Synthesis in Eukaryotic and Prokaryotic Cell‐Free Systems (1996)

A new sulfur-rich basic polypeptide, so called omega-hordothionin, has been isolated from barley endosperm by extractions with NaCl and ammonium bicarbonate followed by reverse-phase high performance liquid chromatography. Purified omega-hordothionin was found to be homogeneous by SDS/polyacrylamide gel electrophoresis, N-terminal amino-acid sequencing and electrospray-ionization mass spectrometric analysis. The complete primary structure of omega-hordothionin was determined by automatic degradation of the intact molecule and peptides obtained by proteolytic cleavage. Omega-hordothionin consists of a single polypeptide chain of 48 amino acids with a molecular mass of 5508 Da deduced from its amino acid sequence, which fully coincides with the 5508.2 Da determined by electrospray-ionization mass spectrometry. The isolated polypeptide showed a characteristic composition with a high content of basic amino acids (five arginine residues, two lysine residues and six histidine residues) and eight cysteine residues, and has strong sequence identity (66%) with the sorghum SI alpha 1 alpha-amylase inhibitor. Omega-hordothionin, like gamma-hordothionin, exhibited translation inhibitory activity on both eukaryotic cell-free systems from mammalian (rat liver and rabbit reticulocyte lysates) and prokaryotic cell-free systems (Escherichia coli). However, in contrast to gamma-hordothionin, omega-hordothionin did not inhibit plant systems such as Triticum aestivum, Cucumis sativus, Vicia sativa and Hordeum vulgare. Gamma-hordothionin also inhibited the alpha-amylase activity from human saliva, while omega-hordothionin and the other different genetic variants of thionins, alpha-hordothionin and beta-hordothionin, failed to show any inhibitory effect.
Characterization of cDNA clones for porcine α(l,3)galactosyl transferase: The enzyme generating the Galα(l,3)Gal epitope (1994)

Abstract: Galoα(l,3)Gal is a terminal carbohydrate found on many glycosylated cell surface molecules of species other than humans and Old World monkeys, and is produced by the α(l,3)galactosyl transferase enzyme's adding galactose to a substrate. We have previously shown, by the transfection of COS cells with the cloned mouse α(l,3)galactosyl transferase, that most human anti‐pig antibodies react with Galα(l,3)Gal. Using cross‐species hybridization with the mouse α(l,3)galactosyl transferase cDNA, bacteriophage λ, gt11 and λgt10 pig cDNA libraries were screened and overlapping clones isolated which encode the pig α(l,3)galactosyl transferase. Sequencing of the clones demonstrated a single open reading frame coding for a protein with high homology to murine (75% identity) and bovine (82% identity) α(l,3)galactosyl transferases. Southern blot analysis shows the porcine α(l,3)galactosyl transferase gene to be a single copy gene, and northern analysis demonstrated an mRNA of 3.9 kb. After splicing the clones to produce a single full length clone, transfection of Galα(l,3)Gal ‐ COS cells led to strong reactivity with human serum and with the IB4 lectin (which reacts only with Galα(l,3)Gal), indicating that the expression of the transferase led to the expression of Galα(l,3)Gal. The cloning of the cDNA gene for the pig α(l,3)galactosyl transferase is the first step in the production of a transgenic pig lacking the transferase and therefore the Galα(l,3)Gal epitope; such animals could serve as donors for human transplantation.
Bacterial endotoxin and current concepts in the diagnosis and treatment of endotoxaemia (1990)

Microbiology Society journals contain high-quality research papers and topical review articles. We are a not-for-profit publisher and we support and invest in the microbiology community, to the benefit of everyone. This supports our principal goal to develop, expand and strengthen the networks available to our members so that they can generate new knowledge about microbes and ensure that it is shared with other communities.
Methods for Derivation of Human Embryonic Stem Cells (2005)

The expanded blastocysts, developed from 2PN-stage embryos, are generally divided into three categories: a good blastocyst containing a large and distinguishable inner cell mass (ICM), a blastocyst with a small and distinct ICM, and a blastocyst with a poorly defined ICM. In this study, we introduce methods for the derivation of human embryonic stem cells (hESCs) depending on the quality of the blastocysts. An immunosurgical method was used for the good expanded blastocysts. This method, however, raises the probability of ICM loss in cases of hESC derivation from blastocysts with smaller or indistinct ICMs. Furthermore, this method is also associated with a risk of the contamination of the hESCs with animal pathogens. To overcome these shortcomings, the partial- or whole-embryo culture method was used. For blastocysts with no visible ICM, the whole-embryo culture method was used to establish hESCs via the seeding of the entire blastocyst without its zona pellucida directly on a STO feeder layer. However, trophectodermal overgrowth tends to hinder the expansion of the ICM during the initial steps of hESC derivation. Therefore, the partial-embryo culture method was developed to establish hESCs from blastocysts with smaller ICMs. The surgical isolation of the region containing the ICM with an ultra-fine glass pipette alleviates trophectoderm overgrowth. This method is also applicable to blastocysts with large and distinct ICMs, and the efficiency of this method is comparable to that of the immunosurgical method.
Role of the nucleoside transport function in the transport and salvage of purine nucleobases. (1986)

Genetic deficiencies in the nucleoside transport function markedly altered the abilities of cultured mutant S49 T lymphoblasts to transport, incorporate, and salvage exogenous hypoxanthine. The concentrations of exogenous hypoxanthine required to reverse azaserine toxicity and replenish azaserine-depleted nucleoside triphosphate pools in AE1 cells, a nucleoside transport-deficient clone, were about 10-fold higher than those required for wild type cells. In a similar fashion, guanine could reverse mycophenolic acid toxicity in wild type but not in AE1 cells. Surprisingly, a second nucleoside transport-deficient clone, 80-5D2, which had lost 80-90% of its ability to transport nucleosides, required lower hypoxanthine concentrations than the wild type parent to reverse these azaserine-mediated effects. The addition of submicromolar concentrations of either p-nitrobenzylthioinosine or dipyridamole, two potent inhibitors of nucleoside transport, to wild type cells mimicked the phenotype of the AE1 cells with respect to hypoxanthine. AE1 cells or p-nitrobenzylthioinosine-treated wild type cells could only transport hypoxanthine at 10-25% the rate of untreated wild type cells, whereas 80-5D2 cells could transport hypoxanthine more efficiently. Adenine transport was also diminished in AE1 and FURD-80-3-6 cells, but not to sufficiently low levels to interfere with their ability to salvage adenine to overcome azaserine toxicity. These studies on S49 cells altered in their nucleoside transport capacity provide powerful genetic evidence that purine nucleobases share a common transport function with nucleosides in these mammalian T lymphoblasts.
Hydroxylated Codeine Derivatives (1958)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTHydroxylated Codeine DerivativesLEWIS J. SARGENT, LOUIS H. SCHWARTZMAN, and LYNDON F. SMALLCite this: J. Org. Chem. 1958, 23, 9, 1247–1251Publication Date (Print):September 1, 1958Publication History Published online1 May 2002Published inissue 1 September 1958https://pubs.acs.org/doi/10.1021/jo01103a003https://doi.org/10.1021/jo01103a003research-articleACS PublicationsRequest reuse permissionsArticle Views269Altmetric-Citations11LEARN 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
Homogeneous Biocatalysis in Organic Solvents and Water-Organic Mixtures (2003)

Biocatalysis in non-aqueous media has undergone tremendous development during the last decade, and numerous reactions have been introduced and optimized for synthetic applications. In contrast to aqueous enzymology, biotransformations in organic solvents offer unique industrially attractive advantages, such as: drastic changes in the enantioselectivity of the reaction, the reversal of the thermodynamic equilibrium of hydrolysis reactions, suppression of water-dependent side reactions, and resistance to bacterial contamination. Currently, the field is dominated by heterogeneous biocatalysis based primarily on lyophilized enzyme powders, cross-linked crystals, and enzymes immobilized on inert supports that are mainly applied in enantioselective synthesis. However, low reaction rates are an inherent problem of the heterogeneous biocatalysis, while the homogeneous systems have the advantage that the elimination of diffusional barriers of substrates and products between organic and water phases results in an increase in the reaction rate. Here the discussion is focused on the correlation between activity and structure of the intact enzymes dissolved in neat organic solvents, as well as modifications of natural enzymes, which make them soluble and catalytically active in non-aqueous environment. Factors that influence conformation and stability of the enzymes are also discussed. Current developments in non-aqueous biocatalysts that combine advantages of protein modification and immobilization, i.e., HIP plastics, enzyme chips, ionic liquids, are introduced. Finally, engineering enzymes for biotransformations in non-conventional media by directed evolution is summarized.
Biological Decomposition of Solid Wood (1984)

Decomposition of wood is an important part of the carbon cycle of nature. Decomposition is caused by fungi, insects, and marine borers that use the wood as food or shelter, or both. Lignin in wood provides a physical barrier to enzymatic decomposition of cellulose and hemicelluloses. This barrier is breached mechanically by insects and marine borers, biochemically by white- and soft-rot fungi, and possibly by small nonenzyme catalysts in the case of brown-rot fungi. Cellulose is degraded by endo- and exo-glucanases and β-glucosidases, hemicelluloses by endo-glycanases and glycosidases, lignin by nonspecific enzymes, and perhaps by nonenzymatic, oxidative agents. Rapid strength loss occurs with all decay fungi, but especially with brown-rot fungi. Strength loss due to insect attack is roughly proportional to the amount of wood removed. Fungal decomposition of wood can be prevented by keeping it below its fiber-saturation moisture content (approximately 27% of its dry weight) and by using the heart-wood of naturally durable woods (species) or preservative-treated wood. Useful application of wood-decomposing fungi is limited currently to production of edible mushrooms. Potential applications include biological pulping, pretreatment for enzymatic conversion of wood to sugars, and waste treatment. Many aspects of wood biodecomposition have not been researched adequately.
HDAC-regulated myomiRs control BAF60 variant exchange and direct the functional phenotype of fibro-adipogenic progenitors in dystrophic muscles (2014)

Fibro-adipogenic progenitors (FAPs) are important components of the skeletal muscle regenerative environment. Whether FAPs support muscle regeneration or promote fibro-adipogenic degeneration is emerging as a key determinant in the pathogenesis of muscular diseases, including Duchenne muscular dystrophy (DMD). However, the molecular mechanism that controls FAP lineage commitment and activity is currently unknown. We show here that an HDAC-myomiR-BAF60 variant network regulates the fate of FAPs in dystrophic muscles of mdx mice. Combinatorial analysis of gene expression microarray, genome-wide chromatin remodeling by nuclease accessibility (NA) combined with next-generation sequencing (NA-seq), small RNA sequencing (RNA-seq), and microRNA (miR) high-throughput screening (HTS) against SWI/SNF BAF60 variants revealed that HDAC inhibitors (HDACis) derepress a "latent" myogenic program in FAPs from dystrophic muscles at early stages of disease. Specifically, HDAC inhibition induces two core components of the myogenic transcriptional machinery, MYOD and BAF60C, and up-regulates the myogenic miRs (myomiRs) (miR-1.2, miR-133, and miR-206), which target the alternative BAF60 variants BAF60A and BAF60B, ultimately directing promyogenic differentiation while suppressing the fibro-adipogenic phenotype. In contrast, FAPs from late stage dystrophic muscles are resistant to HDACi-induced chromatin remodeling at myogenic loci and fail to activate the promyogenic phenotype. These results reveal a previously unappreciated disease stage-specific bipotency of mesenchimal cells within the regenerative environment of dystrophic muscles. Resolution of such bipotency by epigenetic intervention with HDACis provides a molecular rationale for the in situ reprogramming of target cells to promote therapeutic regeneration of dystrophic muscles.
Efficacy of Neoadjuvant Cisplatin in Triple-Negative Breast Cancer (2010)

PURPOSE Cisplatin is a chemotherapeutic agent not used routinely for breast cancer treatment. As a DNA cross-linking agent, cisplatin may be effective treatment for hereditary BRCA1-mutated breast cancers. Because sporadic triple-negative breast cancer (TNBC) and BRCA1-associated breast cancer share features suggesting common pathogenesis, we conducted a neoadjuvant trial of cisplatin in TNBC and explored specific biomarkers to identify predictors of response. PATIENTS AND METHODS Twenty-eight women with stage II or III breast cancers lacking estrogen and progesterone receptors and HER2/Neu (TNBC) were enrolled and treated with four cycles of cisplatin at 75 mg/m(2) every 21 days. After definitive surgery, patients received standard adjuvant chemotherapy and radiation therapy per their treating physicians. Clinical and pathologic treatment response were assessed, and pretreatment tumor samples were evaluated for selected biomarkers. Results Six (22%) of 28 patients achieved pathologic complete responses, including both patients with BRCA1 germline mutations;18 (64%) patients had a clinical complete or partial response. Fourteen (50%) patients showed good pathologic responses (Miller-Payne score of 3, 4, or 5), 10 had minor responses (Miller-Payne score of 1 or 2), and four (14%) progressed. All TNBCs clustered with reference basal-like tumors by hierarchical clustering. Factors associated with good cisplatin response include young age (P = .001), low BRCA1 mRNA expression (P = .03), BRCA1 promoter methylation (P = .04), p53 nonsense or frameshift mutations (P = .01), and a gene expression signature of E2F3 activation (P = .03). CONCLUSION Single-agent cisplatin induced response in a subset of patients with TNBC. Decreased BRCA1 expression may identify subsets of TNBCs that are cisplatin sensitive. Other biomarkers show promise in predicting cisplatin response.
An 802.11a/b/g/n Digital Fractional- $N$ PLL With Automatic TDC Linearity Calibration for Spur Cancellation (2017)

A fractional-N digital phase-locked loop (PLL) architecture with low fractional spur is presented in this paper. A 2-D Vernier time-to-digital convertor (TDC) is implemented to achieve wide detection range with fine resolution. The TDC is calibrated automatically utilizing the ramp signal generated from the fractional-N accumulator for optimal linearity. A digi-phase spur cancellation technique with automatic TDC gain tracking is also implemented to further suppress the fractional spurs. The chip also includes an improved multimodulus divider (MMD) structure that overcomes the glitch problem during division ratio toggling associated with the prior art MMDs, enabling carrier synthesis across wide frequency range continuously. As part of an 802.11a/b/g/n transceiver, the DPLL can provide coverage for both 2.4/5 G WiFi bands. The proposed fractional-N DPLL is implemented in a 55-nm CMOS technology. The DPLL achieves a largest fractional spur level of -55 dBc without using a sigma-delta modulator and an in-band phase noise of -107 dBc/Hz (0.55 ps integrated jitter) while consuming 9.9 mW.
Enhancement of bismuth antibacterial activity with lipophilic thiol chelators (1997)

The antibacterial properties of bismuth are greatly enhanced when bismuth is combined with certain lipophilic thiol compounds. Antibacterial activity was enhanced from 25- to 300-fold by the following seven different thiols, in order of decreasing synergy: 1,3-propanedithiol, dimercaprol (BAL), dithiothreitol, 3-mercapto-2-butanol, beta-mercaptoethanol, 1-monothioglycerol, and mercaptoethylamine. The dithiols produced the greatest synergy with bismuth at optimum bismuth-thiol molar ratios of from 3:1 to 1:1. The monothiols were generally not as synergistic and required molar ratios of from 1:1 to 1:4 for optimum antibacterial activity. The most-active mono- or dithiols were also the most soluble in butanol. The intensity of the yellow formed by bismuth-thiol complexes reflected the degree of chelation and correlated with antibacterial potency at high molar ratios. The bismuth-BAL compound (BisBAL) was active against most bacteria, as assessed by broth dilution, agar diffusion, and agar dilution analyses. Staphylococci (MIC, 5 to 7 microM Bi3+) and Helicobacter pylori (MIC, 2.2 microM) were among the most sensitive bacteria. Gram-negative bacteria were sensitive (MIC, < 17 microM). Enterococci were relatively resistant (MIC, 63 microM Bi3+). The MIC range for anaerobes was 15 to 100 microM Bi3+, except for Clostridium difficile (MIC, 7.5 microM). Bactericidal activity averaged 29% above the MIC. Bactericidal activity increased with increasing pH and/or increasing temperature. Bismuth-thiol solubility, stability, and antibacterial activity depended on pH and the bismuth-thiol molar ratio. BisBAL was stable but ineffective against Escherichia coli at pH 4. Activity and instability (reactivity) increased with increasing alkalinity. BisBAL was acid soluble at a molar ratio of greater than 3:2 and alkaline soluble at a molar ratio of less than 2:3. In conclusion, certain lipophilic thiol compounds enhanced bismuth antibacterial activity against a broad spectrum of bacteria. The activity, solubility, and stability of BisBAL were strongly dependent on the pH, temperature, and molar ratio. Chelation of bismuth with certain thiol agents enhanced the solubility and lipophilicity of this cationic heavy metal, thereby significantly enhancing its potency and versatility as an antibacterial agent.
Inhibition of CD39 Enzymatic Function at the Surface of Tumor Cells Alleviates Their Immunosuppressive Activity (2014)

The ectonucleotidases CD39 and CD73 hydrolyze extracellular adenosine triphosphate (ATP) and adenosine diphosphate (ADP) to generate adenosine, which binds to adenosine receptors and inhibits T-cell and natural killer (NK)-cell responses, thereby suppressing the immune system. The generation of adenosine via the CD39/CD73 pathway is recognized as a major mechanism of regulatory T cell (Treg) immunosuppressive function. The number of CD39⁺ Tregs is increased in some human cancers, and the importance of CD39⁺ Tregs in promoting tumor growth and metastasis has been demonstrated using several in vivo models. Here, we addressed whether CD39 is expressed by tumor cells and whether CD39⁺ tumor cells mediate immunosuppression via the adenosine pathway. Immunohistochemical staining of normal and tumor tissues revealed that CD39 expression is significantly higher in several types of human cancer than in normal tissues. In cancer specimens, CD39 is expressed by infiltrating lymphocytes, the tumor stroma, and tumor cells. Furthermore, the expression of CD39 at the cell surface of tumor cells was directly demonstrated via flow cytometry of human cancer cell lines. CD39 in cancer cells displays ATPase activity and, together with CD73, generates adenosine. CD39⁺CD73⁺ cancer cells inhibited the proliferation of CD4 and CD8 T cells and the generation of cytotoxic effector CD8 T cells (CTL) in a CD39- and adenosine-dependent manner. Treatment with a CD39 inhibitor or blocking antibody alleviated the tumor-induced inhibition of CD4 and CD8 T-cell proliferation and increased CTL- and NK cell-mediated cytotoxicity. In conclusion, interfering with the CD39-adenosine pathway may represent a novel immunotherapeutic strategy for inhibiting tumor cell-mediated immunosuppression.
Comparative Virulence of Streptococcus pneumoniae Strains with Insertion-Duplication, Point, and Deletion Mutations in the Pneumolysin Gene (1999)

Pneumolysin is a 471-amino-acid toxin produced by Streptococcus pneumoniae which has both cytolytic and complement activation properties. We have constructed a derivative of the type 2 S. pneumoniae strain D39 in which the portion of the pneumolysin gene encoding amino acids 55 to 437 has been deleted in-frame. The virulence of this strain (DeltaPly) was compared with those of wild-type D39, a pneumolysin insertion-duplication mutant (PLN-A), and a derivative (PdT) carrying a toxin gene with three point mutations known to abolish both cytolytic activity and complement activation. PdT was intermediate in virulence between D39 and either PLN-A or DeltaPly in a mouse intraperitoneal challenge model. This provides unequivocal evidence that pneumolysin has an additional property that is not abolished by point mutations which reduce cytotoxicity and complement activation to virtually undetectable levels.