gebhart/patrepeval huggingface dataset:
Synthesis of Functional Polymers by Atom Transfer Radical Polymerization (1998)

Atom Transfer Radical Polymerization (ATRP) provides an efficient way to conduct controlled/'living' radical polymerizations. The resulting polymers have predefined molecular weights and the molecular weight distributions are narrow. In addition, ATRP is particularly suitable for the preparation of well-defined polymers with side and chain-end functional groups. A large variety of monomers were polymerized using numerous halogenated initiators and macroinitiators containing hydroxy, amido, ester, epoxy, cyano, etc. groups. The chain-end halogen groups were converted to other functional groups such as azido and aminogroups.
Structure and specificity of antibody molecules (1975)

Abstract The structure of the Fab' fragment of a human myeloma protein (IgG1 (λ) New) has been determined by X-ray crystallographic analysis to a nominal resolution of 0.2 nm. Each of the structure subunits corresponding to the variable and to the constant homology regions of the light and heavy polypeptide chains contains two irregular (3-sheets which are roughly parallel to each other and surround a tightly packed interior of hydrophobic side chains. The regions of the hypervariable sequences in the light and heavy chains occur in close spatial proximity at one end of the molecule, defining the active site of IgG New. The role of these hypervariable regions in defining the size and shape of the active site of different immunoglobulins is discussed on the basis of the three-dimensional model of Fab' New. Several ligands that bind to the active centre of IgG New have been used to obtain crystalline ligand-Fab' New complexes which were investigated by difference Fourier maps. These studies are analysed in terms of the biological function and specificity of antibodies.
Intramolekularer Elektronentransfer in gemischtvalentem [1′,1′'′‐Dinaphthylmethyl‐(biferrocen)]ium‐triiodid: Struktur und Mößbauer‐Spektrum (1997)

Extrem empfindlich auf Änderungen im Kristallgitter reagieren die Elektronentransfergeschwindigkeiten in der Fe II /Fe III ‐Titelverbindung. Dies zeigen Mößbauer‐spektroskopische Untersuchungen an den beiden kristallographischen Modifikationen, in denen die Verbindung isoliert werden kann. Die Struktur von Kation und Anion in der triklinen Phase ist rechts gezeigt. magnified image
The Role of Matrix Stiffness in Hepatic Stellate Cell Activation and Liver Fibrosis (2005)

Liver fibrosis results primarily from the action of hepatic stellate cells, nonparenchymal cells of the liver that undergo transdifferentiation into fibrogenic, proliferative, and contractile myofibroblasts. Stellate cell transdifferentiation has been modeled by the culture of primary cells, a system that has yielded important information about factors determining the phenotype of these cells. Recent evidence suggests that the growth factor TGF-beta (acting through the cytoplasmic signaling intermediate Smad3) and the mechanical properties of the underlying matrix play particularly important roles in hepatic stellate cell transdifferentiation and that this transdifferentiation is a multistep process. The interrelationship between TGF-beta and matrix stiffness and the implications of the in vitro findings for liver fibrosis are now the subject of intensive investigation and will likely lead to important insights into the diagnosis and treatment of liver disease.
Enalapril maleate and a lysine analogue (MK‐521) in normal volunteers; relationship between plasma drug levels and the renin angiotensin system. (1982)

1 Two single doses of 10 mg each of the converting enzyme inhibitor enalapril maleate or MK-421 and of its lysine analogue (MK-521) were administered p.o. to twelve male volunteers. 2 The active diacid metabolite of MK-421 and the lysine analogue were determined by radioimmunoassay and MK-421 by the active metabolite method following in vitro hydrolysis. 3 Peak serum levels of MK-421, active metabolite and lysine analogue were reached within 1, 3 to 4, and 6 h respectively. Practically all MK-421 had disappeared from serum within 4 h. 4 A close correlation between percent inhibition of plasma converting enzyme activity and the serum concentration of active metabolite was observed ( r = 0.98, n = 171, P less than 0.001). Similarly, converting enzyme blockade as expressed by the ratio plasma angiotensin II/angiotensin I was closely correlated with serum active metabolite levels (r = 0.93, n = 15, P less than 0.001).
Vibrotactile identification of signal-processed sounds from environmental events (2009)

This study compared three different signal-processing principles (eight basic algorithms)-transposing, modulating, and filtering-to find the principle(s)/algorithm(s) that resulted in the best tactile identification of environmental sounds. The subjects were 19 volunteers (9 female/10 male) who were between 18 and 50 years old and profoundly hearing impaired. We processed sounds produced by 45 representative environmental events with the different algorithms and presented them to subjects as tactile stimuli using a wide-band stationary vibrator. We compared eight algorithms based on the three principles (one unprocessed, as reference). The subjects identified the stimuli by choosing among 10 alternatives drawn from the 45 events. We found that algorithm and subject were significant factors affecting the results (repeated measures analysis of variance, p < 0.001). We also found large differences between individuals regarding which algorithm was best. The test-retest variability was small (mean +/- 95% confidence interval = 8 +/- 3 percentage units), and no correlation was noted between identification score and individual vibratory thresholds. One transposing algorithm and two modulating algorithms led to significantly better results than did the unprocessed signals (p < 0.05). Thus, the two principles of transposing and modulating were appropriate, whereas filtering was unsuccessful. In future work, the two transposing algorithms and the modulating algorithm will be used in tests with a portable vibrator for people with dual sensory impairment (hearing and vision).
6-Diazo-5-oxo-L-norleucine, a New Tumor-inhibitory Substance.1a Preparation of L-, D- and DL-Forms1b (1958)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXT6-Diazo-5-oxo-L-norleucine, a New Tumor-inhibitory Substance.1a Preparation of L-, D- and DL-Forms1bHorace A. DeWald and Alexander M. MooreCite this: J. Am. Chem. Soc. 1958, 80, 15, 3941–3945Publication Date (Print):August 1, 1958Publication History Published online1 May 2002Published inissue 1 August 1958https://pubs.acs.org/doi/10.1021/ja01548a036https://doi.org/10.1021/ja01548a036research-articleACS PublicationsRequest reuse permissionsArticle Views577Altmetric-Citations23LEARN 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
Anti-Icing Superhydrophobic Coatings (2009)

We use nanoparticle-polymer composites to demonstrate the anti-icing capability of superhydrophobic surfaces and report direct experimental evidence that such surfaces are able to prevent ice formation upon impact of supercooled water both in laboratory conditions and in natural environments. We find that the anti-icing capability of these composites depends not only on their superhydrophobicity but also on the size of the particles exposed on the surface. The critical particle sizes that determine the superhydrophobicity and the anti-icing property are in two different length scales. The effect of particle size on ice formation is explained by using a classical heterogeneous nucleation theory. This result implies that the anti-icing property of a surface is not directly correlated with the superhydrophobicity, and thus, it is uncertain whether a superhydrophobic surface is anti-icing without detailed knowledge of the surface morphology. The result also opens up possibilities for rational design of anti-icing superhydrophobic surfaces by tuning surface textures in multiple length scales.
Functional diversity of cysteine residues in proteins and unique features of catalytic redox-active cysteines in thiol oxidoreductases. (2008)

Thiol-dependent redox systems are involved in regulation of diverse biological processes, such as response to stress, signal transduction, and protein folding. The thiol-based redox control is provided by mechanistically similar, but structurally distinct families of enzymes known as thiol oxidoreductases. Many such enzymes have been characterized, but identities and functions of the entire sets of thiol oxidoreductases in organisms are not known. Extreme sequence and structural divergence makes identification of these proteins difficult. Thiol oxidoreductases contain a redox-active cysteine residue, or its functional analog selenocysteine, in their active sites. Here, we describe computational methods for in silico prediction of thiol oxidoreductases in nucleotide and protein sequence databases and identification of their redox-active cysteines. We discuss different functional categories of cysteine residues, describe methods for discrimination between catalytic and noncatalytic and between redox and non-redox cysteine residues and highlight unique properties of the redox-active cysteines based on evolutionary conservation, secondary and three-dimensional structures, and sporadic replacement of cysteines with catalytically superior selenocysteine residues.
Glycerol-induced unraveling of the tight helical conformation of Escherichia coli type 1 fimbriae (1992)

Glycerol was found to unravel the helical conformation of Escherichia coli type 1 fimbriae without appreciable depolymerization. The linearized fimbrial polymers have a diameter of 2 nm, react strongly with a monoclonal antibody directed at an inaccessible epitope on native fimbriae, and display greater mannose-binding activity and trypsin sensitivity than native fimbriae. Removal of glycerol by dialysis results in spontaneous reassembly of the linear polymers into structures morphologically, antigenically, and functionally indistinguishable from native fimbriae.
Multifaceted Chemistry (1995)

Humanity's drive to uncover the secrets of life processes and to use this knowledge to improve human existence has led to spectacular advances in the biological and health sciences. Chemistry richly contributes to these advances by helping to increase our understanding of processes at the molecular level, and it provides many of the methods and techniques of biotechnology. However, chemistry is not just an adjunct of biology and biotechnology. It is and always will be a central science in its own right.
Distinct Function of Conserved Amino Acids in the Fingers of Saccharomyces cerevisiae DNA Polymerase α (2003)

Structural differences between class A and B DNA polymerases suggest that the motif B region, a wall of the catalytic pocket, may have evolved differentially in the two polymerase families. This study examines the function of the motif B residues in Saccharomyces cerevisiae DNA polymerase alpha (pol alpha). Effects of the mutations were determined by biochemical analysis and genetic complementation of a yeast strain carrying a temperature-sensitive pol alpha mutant. Many conserved residues were viable with a variety of substitutions. Among them, mutations at Asn-948 or Tyr-951 conferred up to 8-fold higher colony formation frequency in a URA3 forward mutation assay, and 79-fold higher trp1 reversion frequency was observed for Y951P in yeast. Purified Y951P was as accurate as wild type in DNA synthesis but approximately 6-fold less processive and 22-fold less active in vitro. Therefore, Y951P may increase the frequency of mutant colony formation because of its low level of DNA polymerase activity in yeast. Mutations at Lys-944 or Gly-952 were not viable, which is consistent with the observation that mutants with substitutions at Gly-952 have strongly reduced catalytic activity in vitro. Gly-952 may provide a space for the nascent base pair and thus may play an essential function in S. cerevisiae DNA pol alpha. These results suggest that class B DNA polymerases have a unique structure in the catalytic pocket, which is distinct from the corresponding region in class A DNA polymerases.
Functional inactivation of neutrophils with a Mac-1 (CD11b/CD18) monoclonal antibody protects against ischemia-reperfusion injury in rat liver (1993)

The role of neutrophil CD11b/CD18 (Mac-1) adhesion proteins in the pathogenesis of hepatic reperfusion injury was investigated in an experimental model. Male Fischer rats were treated with a CD11b monoclonal antibody or an isotype-matched IgM control antibody and subjected to 45 min of hepatic ischemic followed by 24 hr of reperfusion. Large numbers of neutrophils were present in postischemic liver lobes (1,241 +/- 64 polymorphonuclear cells/50 high-power fields) compared with numbers in baseline measurements (14 +/- 3 polymorphonuclear cells/50 high-power fields), and severe liver injury was observed after 24 hr of reperfusion (hepatic necrosis: 88% +/- 2%). Pretreatment with the CD11b antibody (two doses of 2 mg/kg each significantly attenuated liver injury and reduced the number of polymorphonuclear cells in the post-ischemic liver by 59%. Selective treatment with the antibody only during reperfusion was similarly effective. The increased spontaneous superoxide formation of neutrophils isolated from postischemic liver (1.05 +/- 0.11 nmol O2-/hr/10(6) cells) was reduced by 56% in neutrophils from CD11b antibody-treated animals. Flow cytometric analysis of CD11b/CD18 expression on circulating neutrophils demonstrated significant upregulation at all time points during reperfusion. Clone 17 also effectively inhibited neutrophil extravasation in a glycogen peritonitis model. Our data are consistent with a dual protective effect of the CD11b antibody in hepatic reperfusion injury in vivo (i.e., reduced accumulation of neutrophils and their functional inactivation).
Cloning and Characterization of the α(1,3/4) Fucosyltransferase of Helicobacter pylori (2000)

The gastric pathogen Helicobacter pylori can express the histo blood group antigens, which are on the surface of many human cells. Most H. pylori strains express the type II carbohydrates, Lewis X and Y, whereas a small population express the type I carbohydrates, Lewis A and B. The expression of Lewis A and Lewis X, as in the case of H. pylori strain UA948, requires the addition of fucose in alpha1,4 and alpha1,3 linkages to type I or type II carbohydrate backbones, respectively. This work describes the cloning and characterization of a single H. pylori fucosyltransferase (FucT) enzyme, which has the ability to transfer fucose to both of the aforementioned linkages in a manner similar to the human fucosyltransferase V (Fuc-TV). Two homologous copies of the fucT gene have been identified in each of the genomes sequenced. The characteristic adenosine and cytosine tracts in the amino terminus and repeated regions in the carboxyl terminus are present in the DNA encoding the two UA948fucT genes, but these genes also contain differences when compared with previously identified H. pylori fucTs. The UA948fucTa gene encodes an approximately 52-kDa protein containing 475 amino acids, whereas UA948fucTb does not encode a full-length FucT protein. In vitro, UA948FucTa appears to add fucose with a greater than 5-fold preference for type II chains but still retains significant activity using type I acceptors. The addition of the fucose to the type II carbohydrate acceptors, by UA948FucTa, does not appear to be affected by fucosylation at other sites on the carbohydrate acceptor, but the rate of fucose transfer is affected by terminal fucosylation of type I acceptors. Through mutational analysis we demonstrate that only FucTa is active in this H. pylori isolate and that inactivation of this enzyme eliminates expression of all Lewis antigens.
Graph-Based Multi-Surface Segmentation of OCT Data Using Trained Hard and Soft Constraints (2012)

Optical coherence tomography (OCT) is a well-established image modality in ophthalmology and used daily in the clinic. Automatic evaluation of such datasets requires an accurate segmentation of the retinal cell layers. However, due to the naturally low signal to noise ratio and the resulting bad image quality, this task remains challenging. We propose an automatic graph-based multi-surface segmentation algorithm that internally uses soft constraints to add prior information from a learned model. This improves the accuracy of the segmentation and increase the robustness to noise. Furthermore, we show that the graph size can be greatly reduced by applying a smart segmentation scheme. This allows the segmentation to be computed in seconds instead of minutes, without deteriorating the segmentation accuracy, making it ideal for a clinical setup. An extensive evaluation on 20 OCT datasets of healthy eyes was performed and showed a mean unsigned segmentation error of 3.05 ±0.54 μm over all datasets when compared to the average observer, which is lower than the inter-observer variability. Similar performance was measured for the task of drusen segmentation, demonstrating the usefulness of using soft constraints as a tool to deal with pathologies.
Chromosomal aberrations and micronucleus frequency in nurses occupationally exposed to cytotoxic drugs (1994)

In this study, we evaluated the effect of low level occupational exposure of nurses in a medical oncology unit in Cairo, Egypt, to anticancer drugs. Twenty nurses who constantly handled these drugs and 20 controls, matched according to age and sex, were examined. Metaphase chromosomes were studied. Percentages of metaphases with chromosomal aberrations were significantly higher (P < 0.001) in the exposed group (6.1 +/- 2.7) versus the controls (2.6 +/- 1.6). The detected chromosomal aberrations were in the form of chromatid gaps, chromatid breaks and acentric fragments. Micronucleated peripheral blood lymphocytes were also analyzed in cytochalasin B treated binucleated lymphocytes. There was significant increase in cells with micronuclei (P < 0.001) in nurses (10.05 +/- 4.71) in comparison to the matched control (5.42 +/- 2.22) (P < 0.001). Nurses exposed to the cytotoxic drugs for > or = 48 months showed a slightly higher frequency of cells with chromosomal aberrations as well as micronucleated cells than those exposed for < 48 months, but these differences were not statistically significant (P > 0.05).
Evidence of a New Role for the High-Osmolarity Glycerol Mitogen-Activated Protein Kinase Pathway in Yeast: Regulating Adaptation to Citric Acid Stress (2004)

Screening the Saccharomyces cerevisiae disruptome, profiling transcripts, and determining changes in protein expression have identified an important new role for the high-osmolarity glycerol (HOG) mitogen-activated protein kinase (MAPK) pathway in the regulation of adaptation to citric acid stress. Deletion of HOG1, SSK1, PBS2, PTC2, PTP2, and PTP3 resulted in sensitivity to citric acid. Furthermore, citric acid resulted in the dual phosphorylation, and thus activation, of Hog1p. Despite minor activation of glycerol biosynthesis, the inhibitory effect of citric acid was not due to an osmotic shock. HOG1 negatively regulated the expression of a number of proteins in response to citric acid stress, including Bmh1p. Evidence suggests that BMH1 is induced by citric acid to counteract the effect of amino acid starvation. In addition, deletion of BMH2 rendered cells sensitive to citric acid. Deletion of the transcription factor MSN4, which is known to be regulated by Bmh1p and Hog1p, had a similar effect. HOG1 was also required for citric acid-induced up-regulation of Ssa1p and Eno2p. To counteract the cation chelating activity of citric acid, the plasma membrane Ca(2+) channel, CCH1, and a functional vacuolar membrane H(+)-ATPase were found to be essential for optimal adaptation. Also, the transcriptional regulator CYC8, which mediates glucose derepression, was required for adaptation to citric acid to allow cells to metabolize excess citrate via the tricarboxylic acid (TCA) cycle. Supporting this, Mdh1p and Idh1p, both TCA cycle enzymes, were up-regulated in response to citric acid.
The tools for the job (2007)

Cloning and manipulating genes requires the ability to cut, modify and join genetic material (usually DNA, but sometimes RNA) and check the parameters of the molecules, such as size, that are being manipulated. We will assume knowledge of the structure of the materials involved (DNA, RNA and so on) and start by describing the tools available for manipulating them. Many of the tools involved are enzymes that have important physiological roles in cells. To understand why they are useful for our purposes, we should be aware of their normal roles, too.
Virological Response after Short-Term CCR5 Antagonist Exposure in HIV-Infected Patients: Frequency of Subjects with Virological Response and Associated Factors (2011)

The virological response after an 8-day maraviroc monotherapy has been proposed to be an alternative method to determine whether an CCR5 antagonist should be prescribed to HIV-infected patients. The frequency of patients eligible for a combined antiretroviral therapy which includes maraviroc on the basis of the result of this clinical test is not well-known at the moment. In the same way, clinical and immunovirological factors associated with the virological response after antagonist exposure need to be determined. Ninety consecutive HIV-infected patients were exposed to an 8-day maraviroc monotherapy. The virological response was considered positive if either a reduction of ≥1-log(10) HIV RNA copies/ml or an undetectable viral load (<40 HIV RNA copies/ml) was achieved. CXCR4- and CCR5-tropic virus levels were determined by using patients' viral isolates and multiple rounds of infection of indicator cell lines (U87-CXCR4 and U87-CCR5). The frequency of patients with a positive virological response was 72.2% (94.7% and 66.2% for treatment-naïve and pretreated patients, respectively). The positive response rates dramatically decreased in patients with lower CD4(+) T-cell counts. The CXCR4-tropic virus level was the only variable independently associated with the virological response after short-term maraviroc exposure. Lower CD4(+) T-cell strata were associated with higher CXCR4-tropic virus levels. These results support the suggestion that CCR5 antagonists should be an early treatment option before the expansion of CXCR4-tropic strains.