gebhart/patrepeval huggingface dataset:
Regulation of coagulation by a multivalent Kunitz-type inhibitor (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTRegulation of coagulation by a multivalent Kunitz-type inhibitorGeorge J. Broze, Jr., Thomas J. Girard, and William F. NovotnyCite this: Biochemistry 1990, 29, 33, 7539–7546Publication Date (Print):August 1, 1990Publication History Published online1 May 2002Published inissue 1 August 1990https://pubs.acs.org/doi/10.1021/bi00485a001https://doi.org/10.1021/bi00485a001research-articleACS PublicationsRequest reuse permissionsArticle Views425Altmetric-Citations262LEARN 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
Self-reproduction of chirality. Asymmetric synthesis of .beta.-aryl-.beta.-amino acids from enantiomerically pure dihydropyrimidinones (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSelf-reproduction of chirality. Asymmetric synthesis of .beta.-aryl-.beta.-amino acids from enantiomerically pure dihydropyrimidinonesJoseph P. Konopelski, Kent S. Chu, and George R. NegreteCite this: J. Org. Chem. 1991, 56, 4, 1355–1357Publication Date (Print):February 1, 1991Publication History Published online1 May 2002Published inissue 1 February 1991https://pubs.acs.org/doi/10.1021/jo00004a005https://doi.org/10.1021/jo00004a005research-articleACS PublicationsRequest reuse permissionsArticle Views475Altmetric-Citations57LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Visualization of unwinding activity of duplex RNA by DbpA, a DEAD box helicase, at single-molecule resolution by atomic force microscopy (2001)

The Escherichia coli protein DbpA is unique in its subclass of DEAD box RNA helicases, because it possesses ATPase-specific activity toward the peptidyl transferase center in 23S rRNA. Although its remarkable ATPase activity had been well defined toward various substrates, its RNA helicase activity remained to be characterized. Herein, we show by using biochemical assays and atomic force microscopy that DbpA exhibits ATP-stimulated unwinding activity of RNA duplex regardless of its primary sequence. This work presents an attempt to investigate the action of DEAD box proteins by a single-molecule visualization methodology. Our atomic force microscopy images enabled us to observe directly the unwinding reaction of a DEAD box helicase on long stretches of double-stranded RNA. Specifically, we could differentiate between the binding of DbpA to RNA in the absence of ATP and the formation of a Y-shaped intermediate after its progression through double-stranded RNA in the presence of ATP. Recent studies have questioned the designation of DbpA, in particular, and DEAD box proteins in general as RNA helicases. However, accumulated evidence and the results reported herein suggest that these proteins are indeed helicases that resemble in many aspects the DNA helicases.
Cationic Liposomes for Direct Gene Transfer in Therapy of Cancer and Other Diseasesa (1994)

Cationic liposomes can mediate efficient delivery of DNA and DNA/protein complex to mammalian cells in vitro and in vivo. Cationic cholesterol derivatives mixed with phosphatidylethanolamine and sonicated to form small unilamellar vesicles can complex with DNA and mediate the entry into the cytosol from the endosome compartment. One of the liposome formulations, DC-Chol liposomes, is used in a gene therapy clinical trial for melanoma. Recently, we exploited these cationic liposomes for the delivery of trans-activating protein factors to regulate and control the expression of delivered transgenes in a protein dose-dependent manner. Bacteriophage T7 RNA polymerase was co-delivered with a reporter gene under the control of T7 promoter to allow cytoplasmic expression of the gene. Human immunodeficiency virus-1 transactivating protein was also codelivered with a reporter gene under the control of HIV-1 long terminal repeat. Finally, human tumor cells selected for cis-platin resistance or isolated from patients who have failed cis-platin therapy are highly transfectable with cationic liposomes. These results suggest a serial therapy protocol with cis-platin and gene therapy for malignancy.
Squaric Acid Monoamide Mannosides as Ligands for the Bacterial Lectin FimH: Covalent Inhibition or Not? (2011)

Bacteria use long proteinaceous appendages, called fimbriae or pili, to adhere to the surfaces of their host cells. Widely distributed among the Enterobacteriacae are type 1 fimbriae that mediate mannose-specific bacterial adhesion through the lectin FimH, located at the fimbrial tips. It is possible to design synthetic mannosides such that they show high affinity for FimH and can thus inhibit mannose-specific bacterial adhesion in a competitive manner. It has been found that mannosidic squaric acid monoamides serve especially well as inhibitors of type 1 fimbriae-mediated bacterial adhesion, but it has remained unclear whether this effect is due to specific inhibition of the bacterial lectin FimH or to unspecific bioconjugation between the lectin's carbohydrate binding site and a squaric acid monoamide. A bioconjugation reaction would result in a covalently crosslinked squaric acid diamide. Here it is shown that covalent inhibition of FimH by mannosidic squaric acid derivatives is very unlikely and that compounds of this type serve rather as excellent specific candidates for low-molecular-weight inhibitors of bacterial adhesion. This has been verified by testing the properties of glycosidic squaric acid monoamides in diamide formation, by two different adhesion assays with a series of selected control compounds, and by molecular docking studies that further support the results obtained in the bioassays.
Adenosine: an endogenous inhibitor of neutrophil-mediated injury to endothelial cells. (1986)

Since adenosine and its analogue 2-chloroadenosine prevent neutrophils from generating superoxide anion in response to chemoattractants, we sought to determine whether these agents could inhibit neutrophil-mediated injury of endothelial cells. The chemoattractant N-formyl-methionyl-leucyl-phenylalanine (FMLP, 0.1 microM) enhanced the adherence of neutrophils to endothelial cells twofold (18 +/- 2% vs. 39 +/- 3% adherence, P less than 0.001) and caused substantial neutrophil-mediated injury to endothelial cells (2 +/- 2% vs. 39 +/- 4% cytotoxicity, P less than 0.001). 2-Chloroadenosine (10 microM) not only inhibited the adherence of stimulated neutrophils by 60% (24 +/- 2% adherence, P less than 0.001) but also diminished the cytotoxicity by 51% (20 +/- 4% cytotoxicity, P less than 0.002). Furthermore, depletion of endogenously released adenosine from the medium by adenosine deaminase-enhanced injury to endothelial cells by stimulated neutrophils (from 39 +/- 4% to 69 +/- 3% cytotoxicity, P less than 0.001). Indeed, in the presence of adenosine deaminase, even unstimulated neutrophils injured endothelial cells (19 +/- 4% vs. 2 +/- 2% cytotoxicity, P less than 0.001). These data indicate that engagement of adenosine receptors prevents both the adhesion of neutrophils and the injury they cause to endothelial cells. Adenosine inhibits injury provoked not only by cells that have been stimulated by chemoattractants but also by unstimulated cells. Based on this model of acute vascular damage we suggest that adenosine is not only a potent vasodilator, but plays the additional role of protecting vascular endothelium from damage by neutrophils.
Microbial assay of N2 fixation rate, a simple alternate for acetylene reduction assay (2018)

Nitrogen is an essential element for living creatures in every ecosystem but nitrogen cannot be absorbed by the plant itself directly from the atmosphere, so for nitrogen, plant depends on both free living and symbiotic microbes present in the soil. Nitrogen fixation potentiality of the soil thus reveals its fertility with respect to nitrogen. Researchers developed and modified techniques for measuring nitrogen fixation rate of the soil and acetylene reduction assay (ARA) technique became the most popular till now. At the same time this technique has few limitations especially for the researchers from third world country due to lack of special infrastructure in the laboratory and the most required instrument for this technique, gas chromatograph machine, is very expensive. Any alternation of this technique is deserved highly for the researchers from the developing countries. The present work/method explained a new approach for determination of nitrogen fixation rate and this new method was named as "Microbial bio-assay". In this technique nitrogen fixers were cultured in specific medium and condition and after required time of interval the amount of nitrogen fixed by them were calculated. Exploration of soil of the Sundarban mangrove ecosystem was performed regarding the microbial N<sub>2</sub> fixing capacity of that particular ecosystem. •The nitrogen fixation rate measured by acetylene reduction assay (ARA) was 1.13 times lower than the N<sub>2</sub> fixation rate measured by microbial bio-assay.•Microbial bio-assay can be used as an alternate of ARA method to measure N<sub>2</sub> fixation rate. The rates of N<sub>2</sub> fixation measured by both two methods were positively correlated with the population of N<sub>2</sub> fixing bacteria present in the soil of that particular ecosystem (R<sup>2</sup> = 0.85, p < 0.005, n = 85 for microbial bio-assay and R<sup>2</sup> = 0.78, p < 0.005, n = 85 for ARA).
Quantitative13C NMR Characterization of Milled Wood Lignins Isolated by Different Milling Techniques (2006)

Abstract Milled wood lignins (MWL) prepared from finely milled wood flour produced by different milling techniques were compared by quantitative 13C NMR. Wood meal produced in a Wiley mill was milled for either six weeks in a porcelain rotary mill with porcelain balls, or by two variations of our standard technique. Specifically the Wiley wood meal was milled for one week in the rotary mill followed by 48 h of vibratory ball‐milling with steel balls either in toluene or under a N2 atmosphere. Results showed that the vibratory‐milled samples were similar in structure with the exception that the preparation milled under N2 had higher aliphatic and phenolic hydroxyl contents. The rotary‐milled sample on the other hand had a much lower β‐O‐4′ and hydroxyl content along with a higher degree of condensation and oxidized side chain structures.
Ras/Raf/MEK/ERK and PI3K/PTEN/Akt/mTOR Inhibitors: Rationale and Importance to Inhibiting These Pathways in Human Health (2011)

The Ras/Raf/MEK/ERK and PI3K/PTEN/Akt/mTOR cascades are often activated by genetic alterations in upstream signaling molecules such as receptor tyrosine kinases (RTK). Integral components of these pathways, Ras, B-Raf, PI3K, and PTEN are also activated/inactivated by mutations. These pathways have profound effects on proliferative, apoptotic and differentiation pathways. Dysregulation of these pathways can contribute to chemotherapeutic drug resistance, proliferation of cancer initiating cells (CICs) and premature aging. This review will evaluate more recently described potential uses of MEK, PI3K, Akt and mTOR inhibitors in the proliferation of malignant cells, suppression of CICs, cellular senescence and prevention of aging. Ras/Raf/MEK/ERK and Ras/PI3K/PTEN/Akt/mTOR pathways play key roles in the regulation of normal and malignant cell growth. Inhibitors targeting these pathways have many potential uses from suppression of cancer, proliferative diseases as well as aging.
TREATMENT OF PREMATURE EJACULATION WITH PAROXETINE HYDROCHLORIDE AS NEEDED: 2 SINGLE-BLIND PLACEBO CONTROLLED CROSSOVER STUDIES (1999)

Paroxetine appears to be superior to placebo in the pharmacological treatment of premature ejaculation when administered on a chronic or as needed basis.
Detecting 20 nm Wide Defects in Large Area Nanopatterns Using Optical Interferometric Microscopy (2013)

Due to the diffraction limited resolution and the presence of speckle noise, visible laser light is generally thought to be impractical for finding deep subwavelength defects in patterned semiconductor wafers. Here, we report on a nondestructive low-noise interferometric imaging method capable of detecting nanoscale defects within a wide field of view using visible light. The method uses a common-path laser interferometer and a combination of digital image processing techniques to produce 70 μm by 27 μm panoramic phase and amplitude images of the test nanopattern. Significant noise reduction and high sensitivity are achieved, which enables successful detection of several different types of sparse defects with sizes on the order of 20 nm wide by 100 nm long by 110 nm tall.
Recombination in Vaccine and Circulating Strains of Porcine Reproductive and Respiratory Syndrome Viruses (2009)

Em2007, a porcine reproductive and respiratory syndrome virus (PRRSV) variant with a unique 68 aa deletion in Nsp2, was recently isolated in China. Phylogenetic and molecular evolutionary analyses indicated that Em2007 is a natural recombinant between a vaccine strain of PRRSV and circulating virus. We also tested its pathogenicity in piglets.
Fission yeast Hrp1, a chromodomain ATPase, is required for proper chromosome segregation and its overexpression interferes with chromatin condensation (2000)

Hrp1 of Schizosaccharomyces pombe is a member of the CHD protein family, characterized by a chromodomain, a Myb-like telobox-related DNA-binding domain and a SNF2-related helicase/ATPase domain. CHD proteins are thought to be required for modification of the chromatin structure in transcription, but the exact roles of CHD proteins are not known. Here we examine the sub-cellular localization and biochemical activity of Hrp1 and the phenotypes of hrp1 Delta and Hrp1-overexpressing strains. Fluorescence microscopy revealed that Hrp1 protein is targeted to the nucleus. We found that Hrp1 exhibited DNA-dependent ATPase activity, stimulated by both single- and double-stranded DNA. Overexpression of Hrp1 caused slow cell growth accompanied by defective chromosome condensation in anaphase resulting in a 'cut' (celluntimelytorn) phenotype and chromosome loss. The hrp1 Delta mutation also caused abnormal anaphase and mini-chromosome loss phenotypes. Electron micrographs demonstrated that aberrantly shaped nucleoli appeared in Hrp1-overexpressing cells. Therefore, these results suggest that Hrp1 may play a role in mitotic chromosome segregation and maintenance of chromatin structure by utilizing the energy from ATP hydrolysis.
Multiple Forms of Duck‐Egg‐White Lysozyme (1971)

Lysozyme was purified from pooled samples of Peking, Kaki and “wild‐type” duck eggwhites by gel filtration and ion‐exchange chromatography on Amberlite CG‐50. Two different lysozymes were found, called in relation with previous studies, duck‐lysozyme II and ducklysozyme III. The enzymes were shown to be pure by several criteria. The complete primary structures of the two duck lysozymes were established. The reduced and alkylated enzymes were subjected to digestion with trypsin. The structures of all the tryptic peptides were established. For both lysozymes, alignment of the tryptic peptides into a single chain containing 129 amino acids was determined from basic overlap peptides obtained by digestion of the enzyme with chymotrypsin. Six replacements were noted between the two duck lysozymes. Further comparisons were achieved with hen egg‐white and other lysozymes; the possibility of the existence of multiple alleles at one lysozyme locus is suggested for explaining the presence of multiple duck lysozymes.
Pharmacokinetics of prostaglandin E1 and its main metabolites after intracavernous injection and short-term infusion of prostaglandin E1 in patients with erectile dysfunction. (1997)

We found significant systemic concentrations of prostaglandin E1 and its metabolites after intracavernous injection. The systemic presence did not lead to significant changes in vital signs.
A low cost structured light system (2005)

The aim of this paper is to present the current development status of a low cost system for surface reconstruction with structured light. The acquisition system is composed of a single off-the-shelf digital camera and a pattern projector. A pattern codification strategy was developed to allow the pattern recognition automatically and a calibration methodology ensures the determination of the direction vector of each pattern. The experiments indicated that an accuracy of 0.5mm in depth could be achieved for typical applications.
Venous pooling and drainage affects photoplethysmographic signals at different vertical hand positions (2015)

The aim of the current work is to investigate the possibility of augmenting pulse oximetry algorithms to enable the estimation of venous parameters in peripheral tissues. In order to further understand the contribution of venous blood to the photoplethysmographic (PPG) signal, recordings were made from six healthy volunteer subjects during an exercise in which the right hand was placed in various positions above and below heart level. The left hand was kept at heart level as a control while the right hand was moved. A custom-made two-channel dual wavelength PPG instrumentation system was used to obtain the red and infrared plethysmographic signals from both the right and left index fingers simultaneously using identical sensors. Laser Doppler flowmetry signals were also recorded from an adjacent fingertip on the right hand. Analysis of all acquired PPG signals indicated changes in both ac and dc amplitude of the right hand when the position was changed, while those obtained from the left (control) hand remained relatively constant. Most clearly, in the change from heart level to 50cm below heart level there is a substantial decrease in both dc and ac amplitudes. This decrease in dc amplitude most likely corresponds to increased venous pooling, and hence increased absorption of light. It is speculated that the decrease in ac PPG amplitude is due to reduced arterial emptying during diastole due to increased downstream resistance due to venous pooling.
Somatic mutation theory of carcinogenesis: Why it should be dropped and replaced (2000)

The somatic mutation theory of carcinogenesis has been the dominant force driving cancer research during the 20th century. In brief, it proposes that successive DNA mutations in a single cell cause cancer (monoclonality). This theory places carcinogenesis at the cellular and subcellular hierarchical levels of biological complexity. Its basic premises are that (1) cancer is a defect of the control of cell proliferation and (2) the default state of metazoan cells is quiescence. These two premises have recently been contradicted by evidence. Supporters of the theory have dealt with these lacks of fit by incorporating ad hoc explanations similar to the use of epicycles in pre-Copernican astronomy. We propose the adoption of an alternative theory, the tissue organization field theory of carcinogenesis and neoplasia. Its basic premises are that (1) proliferation is the default state of all cells and (2) carcinogenesis and neoplasia are defects of tissue architecture. Carcinogens would act initially by disrupting the normal interactions that take place among cells in the parenchyma and stroma of an organ (the equivalent of the "morphogenetic fields" of developing organisms). Stroma appears as the primary target of carcinogens. Carcinogenesis and neoplasia occur entirely through emergent (supracellular) phenomena. Neoplastic cells may be reprogrammed to behave like "normal" cells within normal tissues. We argue that it is necessary to abandon the somatic mutation theory. Researchers will then become free to adopt alternative reliable premises to build a theory that explains carcinogenesis as another outcome, aberrant as it may be, of biological organization.
The yeast DHHC cysteine-rich domain protein Akr1p is a palmitoyl transferase (2002)

Protein palmitoylation has been long appreciated for its role in tethering proteins to membranes, yet the enzymes responsible for this modification have eluded identification. Here, experiments in vivo and in vitro demonstrate that Akr1p, a polytopic membrane protein containing a DHHC cysteine-rich domain (CRD), is a palmitoyl transferase (PTase). In vivo, we find that the casein kinase Yck2p is palmitoylated and that Akr1p function is required for this modification. Akr1p, purified to near homogeneity from yeast membranes, catalyzes Yck2p palmitoylation in vitro, indicating that Akr1p is itself a PTase. Palmitoylation is stimulated by added ATP. Furthermore, during the reaction, Akr1p is itself palmitoylated, suggesting a role for a palmitoyl-Akr1p intermediate in the overall reaction mechanism. Mutations introduced into the Akr1p DHHC-CRD eliminate both the trans- and autopalmitoylation activities, indicating a central participation of this conserved sequence in the enzymatic reaction. Finally, our results indicate that palmitoylation within the yeast cell is controlled by multiple PTase specificities. The conserved DHHC-CRD sequence, we propose, is the signature feature of an evolutionarily widespread PTase family.