gebhart/patrepeval huggingface dataset:
Titelbild: Angew. Chem. 7/2002 (2002)

Das Titelbild zeigt je ein Beispiel für einen Cu2(μ-O)2- und Fe2(μ-O)2-Komplex mit dem rautenförmigen M2(μ-O)2-Kern sowie ein Multimetallenzym (Hydroxylase-Baustein der Methan-Monooxygenase, im Hintergrund), das nicht zur Gruppe der Häm-Proteine gehört. Obwohl solche rautenförmigen M2(μ-O)2-Kerne bei mehrwertigen Mangankomplexen schon länger bekannt sind, wurden sie erst kürzlich bei synthetischen Kupfer- und Eisenkomplexen nachgewiesen. Trotz unterschiedlicher Elektronenstrukturen, die durch experimentelle und theoretische Untersuchungen bestätigt wurden, zeigen Cu2(μ-O)2- und Fe2(μ-O)2-Kerne analoge kovalente Metall-Oxo-Bindungen und eine ähnliche Neigung zum Abstrahieren von Wasserstoffatomen bei Substraten. Die Kenntnisse über die Biokatalyse wurden durch die Isolierung und die umfassende Charakterisierung der Cu2(μ-O)2- und Fe2(μ-O)2-Komplexe wesentlich erweitert. Insbesondere haben die Untersuchungsergebnisse zur Entwicklung neuer mechanistischer Vorstellungen geführt, wie Nichthäm-Multimetallenzyme, z. B. Methan-Monooxygenase, Fettsäure-Desaturase und Tyrosinase, Disauerstoffmoleküle aktivieren und damit viele unterschiedliche organische Umwandlungen katalysieren. Weitere Einzelheiten erfahren Sie im Aufsatz von L. Que, Jr. und W. B. Tolman auf Seite 1160 ff.
Isolation and sequence of cDNA clones encoding rat phosphatidylinositol transfer protein (1989)

Phosphatidylinositol (PtdIns) transfer protein is a cytosolic protein that catalyzes the transfer of PtdIns between membranes. It is expressed in organisms from yeast to man, and activity has been found in all animal tissues examined. Using antibodies prepared against bovine brain PtdIns transfer protein, lambda gt11 rat brain cDNA libraries were screened and several clones isolated. DNA sequence analysis showed that the cDNAs encoded a polypeptide of 271 amino acids with a mass of 31,911 Da. Comparison of the deduced amino acid sequence with N-terminal sequence data obtained for the intact purified bovine brain protein and rat lung phospholipid transfer protein verified that the cDNAs were PtdIns transfer protein clones. The predicted protein shows no significant sequence similarity to other known (phospholipid)-binding proteins. DNA blot hybridization suggests that the rat genome may contain more than one gene encoding PtdIns transfer protein. RNA blot hybridization reveals that the PtdIns transfer protein gene is expressed at low levels in a wide variety of rat tissues; all tissues examined showed a major mRNA component of 1.9 kilobases and a minor component of 3.4 kilobases. The isolation of clones encoding rat PtdIns transfer protein will greatly facilitate studies of the structure and function of PtdIns transfer proteins and their role in lipid metabolism.
PIKT: Problem Informant/Killer Tool (2000)

MicroRNAs (miRNAs) are a class of 21-24 nucleotide non-coding RNAs that down-regulate gene expression by cleaving or inhibiting the translation of target gene transcripts. miRNAs have been extensively analyzed in a few model plant species such as Arabidopsis, rice and Populus, and partially investigated in other non-model plant species. However, only a few conserved miRNAs have been identified in Chinese cabbage, a common and economically important crop in Asia. To identify novel and conserved miRNAs in Chinese cabbage (Brassica rapa L. ssp. pekinensis) we constructed a small RNA library. Using high-throughput Solexa sequencing to identify microRNAs we found 11,210 unique sequences belonging to 321 conserved miRNA families and 228 novel miRNAs. We ran a Blast search with these sequences against the Chinese cabbage mRNA database and found 2,308 and 736 potential target genes for 221 conserved and 125 novel miRNAs, respectively. The BlastX search against the Arabidopsis genome and GO analysis suggested most of the targets were involved in plant growth, metabolism, development and stress response. This study provides the first large scale-cloning and characterization of Chinese cabbage miRNAs and their potential targets. These miRNAs add to the growing database of new miRNAs, prompt further study on Chinese cabbage miRNA regulation mechanisms, and help toward a greater understanding of the important roles of miRNAs in Chinese cabbage.
tert-Butyloxycarbonyl and benzyloxycarbonyl amino acid fluorides. New, stable rapid-acting acylating agents for peptide synthesis (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTtert-Butyloxycarbonyl and benzyloxycarbonyl amino acid fluorides. New, stable rapid-acting acylating agents for peptide synthesisLouis A. Carpino, El-Sayed M. E. Mansour, and Dean Sadat-AalaeeCite this: J. Org. Chem. 1991, 56, 8, 2611–2614Publication Date (Print):April 1, 1991Publication History Published online1 May 2002Published inissue 1 April 1991https://pubs.acs.org/doi/10.1021/jo00008a005https://doi.org/10.1021/jo00008a005research-articleACS PublicationsRequest reuse permissionsArticle Views1322Altmetric-Citations113LEARN 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
Site-Specific Chemical Modification Procedures (2003)

Identification of important or essential residues in proteins and peptides is an overall goal in understanding the mechanism of an enzyme or the binding affinity of a peptide ligand to its receptor. Most early attempts to accomplish this relied on chemical modification of amino acid residues in the native peptide or protein (1). Selectivity of chemical modification reagents has always been the largest problem to overcome when this approach is taken. Isolation of the desired product from the heterogeneous mixture of components and determination of the modified residue or residues become very labor-intensive processes.
P02.82. Correction of the Omega-3 Index in women with metabolic syndrome by adding omega-3 supplements to a Mediterranean-style diet (2012)

Methods One trial and one case series are reported here. The trial was a 12-week multicenter study (N=56) testing the effects of MLG diet on the O3I, and the case series was conducted in the offices of two physicians and included 21 women who were given, in addition to a MLG diet recommendation, one of two omega-3 supplements for approximately 12 weeks. One supplement (N=12) provided 1980 mg EPA+DHA per day (High DHA, Metagenics Inc.), and the other supplement (N=9) provided 2880 mg EPA+DHA daily (EPA-DHA 720, Metagenics Inc.). RBC fatty acid profiles were determined by gas chromatography and CVD risk factors by standard laboratory methods.
Studies on autoantibodies to deoxyribonucleic acid and deoxyribonucleoprotein with enzyme-immunoassay (ELISA). (1981)

Simple, rapid, quantitative, and reproducible ELISA procedures were developed for the determination of antibodies to DNA and NP in human sera. The results are reported in International Units per milliliter, based on the WHO reference preparation of anti-nuclear factor serum. The results of both tests are significantly correlated with anti-dsDNA values obtained by an RIA (Farr technic) and by the Crithidia luciliae IF assay. The anti-DNA and anti-NP ELISA test results were more frequently positive in SLE sera than were screening tests for anti-dsDNA by the Crithidia procedure or anti-NP detection by a latex agglutination test. Parallel tests in 284 sera from patients for anti-DNA and anti-NP by ELISA showed a significant correlation between the two antibody values. However, 17% of the specimens were positive for antibodies to one antigen but not the other, whereas other specimens showed a strong predominance of one antibody over the other. Absorption studies confirmed the differing antibody specificities measured by the two assays. The ELISA anti-DNA results were inhibited by native DNA, NP, and denatured DNA in increasing order of efficiency. In contrast, the antibodies against NP were strongly inhibited by NP but only very slightly by dsDNA or denatured DNA. Other antigens, including histones, ribonucleic acid, extractable nuclear antigens, and aggregated human IgG, inhibited only slightly or not at all in either assay.
Regulation of Microtubule Dynamics and Myogenic Differentiation by Murf, a Striated Muscle Ring-Finger Protein (2000)

The RING-finger domain is a novel zinc-binding Cys-His protein motif found in a growing number of proteins involved in signal transduction, ubiquitination, gene transcription, differentiation, and morphogenesis. We describe a novel muscle-specific RING-finger protein (MURF) expressed specifically in cardiac and skeletal muscle cells throughout pre- and postnatal mouse development. MURF belongs to the RING-B-box-coiled-coil subclass of RING-finger proteins, characterized by an NH(2)-terminal RING-finger followed by a zinc-finger domain (B-box) and a leucine-rich coiled-coil domain. Expression of MURF is required for skeletal myoblast differentiation and myotube fusion. The leucine-rich coiled-coil domain of MURF mediates association with microtubules, whereas the RING-finger domain is required for microtubule stabilization and an additional region is required for homo-oligomerization. Expression of MURF establishes a cellular microtubule network that is resistant to microtubule depolymerization induced by alkaloids, cold and calcium. These results identify MURF as a myogenic regulator of the microtubule network of striated muscle cells and reveal a link between microtubule organization and myogenesis.
Reappearance of cardiac presynaptic sympathetic nerve terminals in the transplanted heart: correlation between PET using (11)C-hydroxyephedrine and invasively measured norepinephrine release. (2001)

Results of invasively measured NE release and noninvasive (11)C-HED PET are well correlated. This study further supports the usefulness of PET as a noninvasive approach for detection of reappearance of catecholamine uptake sites after heart transplantation.
PANTHER: a browsable database of gene products organized by biological function, using curated protein family and subfamily classification (2003)

The PANTHER database was designed for high-throughput analysis of protein sequences. One of the key features is a simplified ontology of protein function, which allows browsing of the database by biological functions. Biologist curators have associated the ontology terms with groups of protein sequences rather than individual sequences. Statistical models (Hidden Markov Models, or HMMs) are built from each of these groups. The advantage of this approach is that new sequences can be automatically classified as they become available. To ensure accurate functional classification, HMMs are constructed not only for families, but also for functionally distinct subfamilies. Multiple sequence alignments and phylogenetic trees, including curator-assigned information, are available for each family. The current version of the PANTHER database includes training sequences from all organisms in the GenBank non-redundant protein database, and the HMMs have been used to classify gene products across the entire genomes of human, and Drosophila melanogaster. The ontology terms and protein families and subfamilies, as well as Drosophila gene c;assifications, can be browsed and searched for free. Due to outstanding contractual obligations, access to human gene classifications and to protein family trees and multiple sequence alignments will temporarily require a nominal registration fee. PANTHER is publicly available on the web at http://panther.celera.com.
Regulation of vascular endothelial growth factor transcription by endothelial PAS domain protein 1 (EPAS1) and possible involvement of EPAS1 in the angiogenesis of renal cell carcinoma (2001)

These results suggest that endogenous VEGF can be up-regulated transcriptionally by EPAS1, and EPAS1 may be involved in the angiogenesis of RCC.
Controlled Synthesis of Amphiphilic Block Copolymers with Pendant N-Acetyl-d-glucosamine Residues by Living Cationic Polymerization and Their Interaction with WGA Lectin (1999)

Amphiphilic block copolymers of vinyl ethers (VEs) having pendant N-acetyl-d-glucosamine (GlcNAc) residues were synthesized by living cationic polymerization of isobutyl VE (IBVE) and a VE carrying 3,4,6-tri-O-acetyl-2-deoxy-2-phthalimido-β-d-glucose (1). Sequential block copolymerization of 1 and IBVE was conducted by the CF3COOH/EtAlCl2 initiating system in the presence of added base (1,4-dioxane) to yield the precursor block copolymer with a narrow molecular weight distribution (M̄w/M̄n ∼ 1.1) and a regulated segment composition. Deprotection and subsequent N-acetylation of the precursor polymers afforded the GlcNAc-carrying amphiphilic block copolymers with a well-controlled structure. The interaction of the resultant GlcNAc-carrying block copolymer with wheat germ agglutinin (WGA) lectin, which is known to specifically recognize GlcNAc and its oligomers, was investigated. The association constants were evaluated by measuring the changes in fluorescence intensity of WGA observed upon addition of the GlcNAc-carrying polymer to an aqueous solution of WGA. It was clearly demonstrated that the GlcNAc-carrying polymers show a significant increase in binding affinity toward WGA lectin compared to GlcNAc and its oligomers.
Inhibition of diabetic nephropathy by a decoy peptide corresponding to the “handle” region for nonproteolytic activation of prorenin (2004)

We found that when a site-specific binding protein interacts with the "handle" region of the prorenin prosegment, the prorenin molecule undergoes a conformational change to its enzymatically active state. This nonproteolytic activation is completely blocked by a decoy peptide with the handle region structure, which competitively binds to such a binding protein. Given increased plasma prorenin in diabetes, we examined the hypothesis that the nonproteolytic activation of prorenin plays a significant role in diabetic organ damage. Streptozotocin-induced diabetic rats were treated with subcutaneous administration of handle region peptide. Metabolic and renal histological changes and the renin-Ang system components in the plasma and kidneys were determined at 8, 16, and 24 weeks following streptozotocin treatment. Kidneys of diabetic rats contained increased Ang I and II without any changes in renin, Ang-converting enzyme, or angiotensinogen synthesis. Treatment with the handle region peptide decreased the renal content of Ang I and II, however, and completely inhibited the development of diabetic nephropathy without affecting hyperglycemia. We propose that the nonproteolytic activation of prorenin may be a significant mechanism of diabetic nephropathy. The mechanism and substances causing nonproteolytic activation of prorenin may serve as important therapeutic targets for the prevention of diabetic organ damage.
Cancer-associated myofibroblasts possess various factors to promote endometrial tumor progression. (2001)

Myofibroblastic invasion associated with malignant epithelial cells of endometrial cancer as well as other cancers is often found in the interstitium. To assess the myofibroblastic-epithelial interaction, frozen sections from a total of 10 endometrial cancers with or without invasive myofibroblasts were immunohistochemically examined. Interestingly, the invasive myofibroblasts adjacent to malignant epithelial cells showed frequently intensive positive staining of several growth factors such as vascular endothelial growth factor (VEGF), insulin-like growth factor I, and epidermal growth factor, the cognate receptors such as Fetal liver kinase-1/Kinase Insert Domain-containing receptor/VEGF receptor-2, fms-like tyrosine kinase-1/VEGF receptor-1, and epidermal growth factor receptor, several cell cycle regulators such as cyclins and cyclin dependent kinases, and estrogen receptor alpha. Moreover, we indicated that the majority of the myofibroblasts as well as cancer epithelial cells are proliferating because of their positive staining of proliferating cell nuclear antigen and Ki-67. Furthermore, the myofibroblasts were also positive of hypoxia-inducible factor 1 alpha, which is a marker protein of hypoxia, probably followed by activation of VEGF-Flk-1 and VEGF-fms-like tyrosine kinase-1 signals, which could initiate angiogenesis. These findings suggest directly that the myofibroblasts might participate in the progression of tumor cells in terms of cancer cell growth stimulation and also activated initiation of angiogenesis.
Renal Cell Carcinomas Produce IL-6, IL-10, IL-11, and TGF-β1 in Primary Cultures and Modulate T Lymphocyte Blast Transformation (1997)

We investigated the immunomodulatory capacity of primary cultures of renal cell carcinomas (RCC) by assessing production of cytokines and modulation of mitogen-induced T lymphocyte blast transformation. The results clearly show that immunomodulatory capacity is a common feature of RCC and that in vitro these tumors can produce interleukin-10 (IL-10) up to 20 ng/ml, IL-6 up to 35 micrograms/ml (> 250 kU/ml in the B9 system), IL-11 up to 15 micrograms/ml, and transforming growth factor-beta 1 (TGF-beta 1) up to 22 ng/ml. Furthermore, these tumors have the capacity to modulate T cell blast transformation over two orders of magnitude in each direction. The correlations of the immunologic properties of tumor cell cultures with the conventional classification of tumors (histology, cytology, staging, grading, presence of metastases, and secondary tumors) are analyzed. The significance of these findings for modulation of local immunity by RCC as well as for patient outcome is discussed.
A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force‐field parameter sets 53A5 and 53A6 (2004)

Successive parameterizations of the GROMOS force field have been used successfully to simulate biomolecular systems over a long period of time. The continuing expansion of computational power with time makes it possible to compute ever more properties for an increasing variety of molecular systems with greater precision. This has led to recurrent parameterizations of the GROMOS force field all aimed at achieving better agreement with experimental data. Here we report the results of the latest, extensive reparameterization of the GROMOS force field. In contrast to the parameterization of other biomolecular force fields, this parameterization of the GROMOS force field is based primarily on reproducing the free enthalpies of hydration and apolar solvation for a range of compounds. This approach was chosen because the relative free enthalpy of solvation between polar and apolar environments is a key property in many biomolecular processes of interest, such as protein folding, biomolecular association, membrane formation, and transport over membranes. The newest parameter sets, 53A5 and 53A6, were optimized by first fitting to reproduce the thermodynamic properties of pure liquids of a range of small polar molecules and the solvation free enthalpies of amino acid analogs in cyclohexane (53A5). The partial charges were then adjusted to reproduce the hydration free enthalpies in water (53A6). Both parameter sets are fully documented, and the differences between these and previous parameter sets are discussed.
Day-Night Dip and Early-Morning Surge in Blood Pressure in Hypertension (2012)

We investigated the relationship between the day-night blood pressure (BP) dip and the early morning BP surge in an cohort of 3012 initially untreated subjects with essential hypertension. The day-night reduction in systolic BP showed a direct association with the sleep trough (r = 0.564; P < 0.0001) and the preawakening (r = 0.554; P < 0.0001) systolic BP surge. Over a mean follow-up period of 8.44 years, 268 subjects developed a major cardiovascular event (composite of cardiovascular death, nonfatal myocardial infarction, nonfatal stroke, and heart failure requiring hospitalization) and 220 subjects died. In a Cox model, after adjustment for predictive covariates, including age, sex, diabetes mellitus, cigarette smoking, total cholesterol, left ventricular hypertrophy on ECG, estimated glomerular filtration rate, and average 24-hour systolic BP, a blunted sleep trough (≤ 19.5 mm Hg; quartile 1) and preawakening (≤ 9.5 mm Hg; quartile 1) BP surge was associated with an excess risk of events (hazard ratio, 1.66 [95% CI, 1.14-2.42]; P = 0.009; hazard ratio, 1.71 [95% CI, 1.12-2.71]; P = 0.013). After adjustment for the same covariates, neither the dipping pattern nor the measures of early morning BP surge were independent predictors of mortality. In conclusion, in initially untreated subjects with hypertension, a blunted day-night BP dip was associated with a blunted morning BP surge and vice versa. In these subjects, a blunted morning BP surge was an independent predictor of cardiovascular events, whereas an excessive BP surge did not portend an increased risk of events.
Adhesion molecules as therapeutic targets for autoimmune diseases and transplant rejection (2003)

Inflammatory disorders such as autoimmune diseases and graft rejection are mediated by activated leukocytes, particularly T lymphocytes, which penetrate the inflamed tissue and perpetuate or amplify the immune reaction. In an unstimulated state, leukocytes do not readily adhere to the vascular endothelium. However, inflammatory signals induce the expression of proteins on the endothelial cell surface that promote the adhesion and extravasation of activated immune cells from the circulation into the underlying tissues. Key among these molecules are P- and E-selectin, intercellular adhesion molecule-1 (ICAM-1) and vascular cell adhesion molecule-1 (VCAM-1) on the endothelial cells, and their respective counter receptors, P-selectin glycoprotein ligand-1 (PSGL-1), leukocyte function-associated antigen-1 (LFA-1) and very late antigen-4 (VLA-4), on the leukocytes. In vitro blockade of these molecules inhibits the adhesion of leukocytes. In many cases there is attenuation of leukocyte activation as well. Adhesion blockade in animal models prevents or ameliorates graft rejection and disease severity in autoimmune models. Clinical studies with humanised monoclonal antibodies which interfere with LFA-1/ICAM-1 or VLA-4/VCAM-1 interactions have shown significant efficacy and good safety profiles in autoimmune disease, including psoriasis, multiple sclerosis and inflammatory bowel disease. Thus, adhesion blockade is emerging as a useful therapeutic strategy in several inflammatory settings.
The organization of the human immunoglobulin lambda gene locus. (1995)

To elucidate the complex structure of the human immunoglobulin lambda gene locus, a 1020-kb contig was constructed using 184 cosmid clones and one bacterial artificial chromosome (BAC) clone. A high-resolution physical map of this contig revealed that the entire lambda gene locus is 911 kb in length. It contains seven constant region (C lambda) gene segments and 69 unique EcoRI-HindIII segments that hybridize to variable region gene (V lambda) probes. The VpreB gene, BCRL4, and gamma-glutamyl transpeptidase gene (GGT)-like sequences are also located within the lambda gene locus. Hybridization analysis suggested that the lambda gene locus has undergone extensive amplification events in evolution.