gebhart/patrepeval huggingface dataset:
CDK inhibitors: positive and negative regulators of G1-phase progression (1999)

Mitogen-dependent progression through the first gap phase (G1) and initiation of DNA synthesis (S phase) during the mammalian cell division cycle are cooperatively regulated by several classes of cyclin-dependent kinases (CDKs) whose activities are in turn constrained by CDK inhibitors (CKIs). CKIs that govern these events have been assigned to one of two families based on their structures and CDK targets. The first class includes the INK4 proteins (inhibitors of CDK4), so named for their ability to specifically inhibit the catalytic subunits of CDK4 and CDK6. Four such proteins [p16 (Serrano et al. 1993), p15 (Hannon and Beach 1994), p18 (Guan et al. 1994; Hirai et al. 1995), and p19 (Chan et al. 1995; Hirai et al. 1995)] are composed of multiple ankyrin repeats and bind only to CDK4 and CDK6 but not to other CDKs or to D-type cyclins. The INK4 proteins can be contrasted with more broadly acting inhibitors of the Cip/Kip family whose actions affect the activities of cyclin D-, E-, and A-dependent kinases. The latter class includes p21 (Gu et al. 1993; Harper et al. 1993; El-Deiry et al. 1993; Xiong et al. 1993a; Dulic et al. 1994; Noda et al. 1994), p27 (Polyak et al. 1994a,b; Toyoshima and Hunter 1994), and p57 (Lee et al. 1995; Matsuoka et al. 1995), all of which contain characteristic motifs within their amino-terminal moieties that enable them to bind both to cyclin and CDK subunits (Chen et al. 1995, 1996; Nakanishi et al. 1995; Warbrick et al. 1995; Lin et al. 1996; Russo et al. 1996). Based largely on in vitro experiments and in vivo overexpression studies, CKIs of the Cip/Kip family were initially thought to interfere with the activities of cyclin D-, E-, and A-dependent kinases. More recent work has altered this view and revealed that although the Cip/Kip proteins are potent inhibitors of cyclin Eand A-dependent CDK2, they act as positive regulators of cyclin Ddependent kinases. This challenges previous assumptions about how the G1/S transition of the mammalian cell cycle is governed, helps explain some enigmatic features of cell cycle control that also involve the functions of the retinoblastoma protein (Rb) and the INK4 proteins, and changes our thinking about how either p16 loss or overexpression of cyclin D-dependent kinases contribute to cancer. Here we focus on the biochemical interactions that occur between CKIs and cyclin Dand E-dependent kinases in cultured mammalian cells, emphasizing the manner by which different positive and negative regulators of the cell division cycle cooperate to govern the G1-to-S transition. To gain a more comprehensive understanding of the biology of CDK inhibitors, readers are encouraged to refer to a rapidly emerging but already extensive literature (for review, see Elledge and Harper 1994; Sherr and Roberts 1995; Chellappan et al. 1998; Hengst and Reed 1998a; Kiyokawa and Koff 1998; Nakayama 1998; Ruas and Peters 1998).
Effects of icosapent ethyl on lipid and inflammatory parameters in patients with diabetes mellitus-2, residual elevated triglycerides (200–500 mg/dL), and on statin therapy at LDL-C goal: the ANCHOR study (2013)

Clinicaltrials.gov Identifier NCT01047501.
Cell penetration by transportan (1998)

Transportan is a 27 amino acid‐long peptide containing 12 functional amino acids from the amino terminus of the neuropeptide galanin and mastoparan in the carboxyl terminus, connected via a lysine. Transportan is a cell‐penetrating peptide as judged by indirect immunofluorescence using N ε13 ‐biotinyl‐transportan. The internalization of biotinyl‐transportan is energy independent and takes place efficiently at 37°,4°, and 0°C. Cellular uptake of transportan is probably not mediated by endocytosis, since it cannot be blocked by treating the cells with phenylarsine oxide or hyperosmolar sucrose solution and is nonsaturable. The kinetics of internalization was studied with the aid of the 125 I‐labeled peptide. At 37°C, the maximal intracellular concentration is reached in about 20 min. The internalized transportan is protected from trypsin. The cell‐penetrating ability of transportan is not restricted by cell type, but seems to be a general feature of this peptide. In Bowes' melanoma cells, transportan first localizes in the outer membrane and cytoplasmatic membrane structures. This is followed by a redistribution into the nuclear membrane and uptake into the nuclei where transportan concentrates in distinct substructures, probably the nucleoli.—Pooga, M., Hällbrink, M., Zorko, M., Langel, Ü. Cell penetration of transportan FASEB J. 12, 67–77 (1998)
A non-anticoagulant synthetic pentasaccharide reduces inflammation in a murine model of kidney ischemia-reperfusion injury (2006)

Fondaparinux is a synthetic pentasaccharide that selectively inhibits factor Xa (FXa) in an antithrombin-dependent fashion. This newly developed anticoagulant is used in the prevention and treatment of venous thromboembolism. Recently, we showed that fondaparinux reduces inflammation and protects the kidney from ischemia-reperfusion (I/R) injury. However, the relative contributions of the anticoagulant and anti-inflammatory activities of fondaparinux to the observed protection is unknown. To address this, we chemically modified fondaparinux to abolish its affinity for antithrombin and analyzed the effect of this non-anticoagulant (NAC)-pentasaccharide on binding of U937 cells to P-selectin in vitro and on inflammation in a murine model of kidney I/R injury. NAC-pentasaccharide was as effective as fondaparinux at inhibiting the binding of U937 cells to P-selectin. In addition, NAC-pentasaccharide significantly reduced IL-6 and MIP-2 expression and injury in the kidney I/R model. These findings indicate that the anti-inflammatory activity of fondaparinux can be dissociated from its anticoagulant activity and that NAC-pentasaccharide is protective in kidney I/R injury.
Bispecific antibodies and ADCs (2011)

The malleability and versatility of antibodies present both promise and challenges for researchers developing the molecules as therapeutics. The potential for introducing new functionality by engin...
Aromatic van der Waals Clusters:  Structure and Nonrigidity (1996)

More than a dozen cases of nonrigid van der Waals clusters are presented and discussed to demonstrate that cluster nonrigidity is a general phenomenon in all weakly bound systems. The interplay of structure and nonrigidity complicates cluster research and mandates a dynamical approach to cluster properties in which multiple stable configurations coexist and interconvert, and large amplitude nuclear motions are the rule rather than the exception. Empirical potential energy surface calculations are employed to yield physical insight into the structure and dynamics of nonrigid clusters, and molecular symmetry group theory is applied to analyze spectroscopic manifestations of cluster nonrigidity. Empirical potentials of various forms are successful in predicting most cluster structures, as well as estimating the potential surface barrier heights hindering the interconversion between different local minimum-energy structures. Such calculational approaches also emphasize the importance of large amplitude motion for one or more of the cluster vibrational degrees of freedom. The limits of these empirical calculations are discussed, and recent attempts to derive cluster structure and properties by ab initio techniques are reviewed. The aromatic/small molecule clusters considered in this presentation display two types of nonrigidity: local nonrigidity in which large amplitude motion involves the rotation of one of the molecular constituents, and global nonrigidity in which large amplitude motion involves displacement of the centers of mass of the molecular constituents. The former motion interchanges equivalent atoms, and the latter motion interchanges cluster conformations. The potential surface barriers for these large amplitude motions tend to increase with constituent molecule complexity.
X-ray analysis of a complex of Escherichia coli uracil DNA glycosylase (EcUDG) with a proteinaceous inhibitor. The structure elucidation of a prokaryotic UDG (1998)

Uracil-DNA glycosylase (UDG), a key highly conserved DNA repair enzyme involved in uracil excision repair, was discovered in Escherichia coli . The Bacillus subtilis bacteriophage, PBS-1 and PBS-2, which contain dUMP residues in their DNA, express a UDG inhibitor protein, Ugi which binds to UDG very tightly to form a physiologically irreversible complex. The X-ray analysis of the E. coli UDG ( Ec UDG)-Ugi complex at 3.2 A resolution, leads to the first structure elucidation of a bacterial UDG molecule. This structure is similar to the enzymes from human and viral sources. A comparison of the available structures involving UDG permits the delineation of the constant and the variable regions of the molecule. Structural comparison and mutational analysis also indicate that the mode of action of the enzyme from these sources are the same. The crystal structure shows a remarkable spatial conservation of the active site residues involved in DNA binding in spite of significant differences in the structure of the enzyme-inhibitor complex, in comparison with those from the mammalian and viral sources. Ec UDG could serve as a prototype for UDGs from pathogenic prokaryotes, and provide a framework for possible drug development against such pathogens with emphasis on features of the molecule that differ from those in the human enzyme.
Junction fabrication by shadow evaporation without a suspended bridge (2011)

We present a novel shadow evaporation technique for the realization of junctions and capacitors. The design by e-beam lithography of strongly asymmetric undercuts on a bilayer resist enables in situ fabrication of junctions and capacitors without the use of the well-known suspended bridge (Dolan 1977 Appl. Phys. Lett. 31 337-9). The absence of bridges increases the mechanical robustness of the resist mask as well as the accessible range of the junction size, from 10(-2) µm(2) to more than 10(4) µm(2). We have fabricated Al/AlO(x)/Al Josephson junctions, phase qubit and capacitors using a 100 kV e-beam writer. Although this high voltage enables a precise control of the undercut, implementation using a conventional 20 kV e-beam is also discussed. The phase qubit coherence times, extracted from spectroscopy resonance width, Rabi and Ramsey oscillation decays and energy relaxation measurements, are longer than the ones obtained in our previous samples realized by standard techniques. These results demonstrate the high quality of the junction obtained by this bridge-free technique.
A short-chain methotrexate polyglutamate as outcome parameter in rheumatoid arthritis patients receiving methotrexate. (2012)

MTXPG2 seems to be a potential indicator for clinical response and may serve as a marker for drug monitoring.
Two ro (ss‐a) autoantibody responses in systemic lupus erythematosus (1988)

Autoantibodies to Ro (SS-A), La (SS-B), and Sm/nuclear RNP were quantitated by enzyme-linked immunosorbent assay in 106 white patients with systemic lupus erythematosus. Two Ro autoantibody subgroups were identified that differed quantitatively, genetically, and clinically. The subgroup having anti-Ro only demonstrated significantly lower mean anti-Ro levels than did the subgroup with concomitant anti-La and showed a strong association with the linked HLA alleles DR2 and DQw1. The anti-Ro with anti-La subgroup was associated with the linked HLA alleles B8, DR3, DRw52, and DQw2 (DR3 was primary), and this subgroup consisted of patients with older ages at disease onset, sicca complex, and less renal involvement. Overall, the relative risk (RR) for having anti-Ro was highest in HLA-DR2/DR3 heterozygotes compared with non-DR2/DR3 heterozygotes (RR 15) and all other DR combinations (RR 7), suggesting a compound effect of 2 immune responses. Heterozygotes for HLA-DQw1/DQw2 demonstrated significantly higher mean levels of anti-Ro, which may be indicative of trans gene interaction at HLA-DQ. These data suggest the hypothesis that HLA genes exert their major effects on Ro/La autoantibody subsets of systemic lupus erythematosus.
Increased isobutanol production in Saccharomyces cerevisiae by overexpression of genes in valine metabolism (2011)

Overexpression of genes ILV2, ILV3, ILV5, and BAT2 in valine metabolism led to an increase in isobutanol production in S. cerevisiae. Additional overexpression of ILV6 in the ILV2 ILV3 ILV5 overexpression strain had a negative effect, presumably by increasing the sensitivity of Ilv2 to valine inhibition, thus weakening the positive impact of overexpression of ILV2, ILV3, and ILV5 on isobutanol production. Aerobic cultivations of the ILV2 ILV3 ILV5 overexpression strain and the reference strain showed that supplying amino acids in cultivation media gave a substantial improvement in isobutanol production for the reference strain, but not for the ILV2 ILV3 ILV5 overexpression strain. This result implies that other constraints besides the enzyme activities for the supply of 2-ketoisovalerate may become bottlenecks for isobutanol production after ILV2, ILV3, and ILV5 have been overexpressed, which most probably includes the valine inhibition to Ilv2.
A Genetically Engineered P450 Monooxygenase: Construction of the Functional Fused Enzyme between Rat Cytochrome P450c and NADPH-Cytochrome P450 Reductase (1987)

A hybrid cDNA encoding a fused enzyme consisting of rat cytochrome P450c and rat NADPH-cytochrome P450 reductase was constructed by combining the cytochrome P450c cDNA with the cDNA fragment encoding the protease-solubilized moiety of the NADPH-cytochrome P450 reductase. The hybrid cDNA was inserted between the yeast alcohol dehydrogenase I promoter and terminator of the expression vector pAAH5 to yield expression plasmid pAMP19. Saccharomyces cerevisiae AH22 cells transformed with the expression plasmid pAMP19 produced a 130-kD protein reactive with both anti-cytochrome P450c Ig and antireductase Ig. The yeast cells containing the fused enzyme exhibited about four times higher monooxygenase activity toward 7-ethoxycoumarin than those containing rat cytochrome P450c alone. The fused enzyme was purified from the yeast microsomal fraction by sequential chromatography with DEAE-cellulose and 2',5'-ADP Sepharose 4B columns. The preparation had an apparent molecular weight of 130 kD and the same sequence of the 10 amino-terminal amino acids as that of rat cytochrome P450c. Spectral properties of the fused enzyme indicated the presence of a protoheme, flavin adenine dinucleotide, and flavin mononucleotide in the molecule. The reaction mechanism of the fused enzyme followed first-order kinetics. These results clearly indicate that the fused enzyme is a new self-catalytic P450 monooxygenase. Trypsin treatment of yeast microsomes containing the fused enzyme suggested that the P450 moiety is embedded in the microsomal membrane with the reductase moiety lying on the cytoplasmic side.
Effects of Anticytokine Therapy in a Mouse Model of Chronic Asthma (2004)

The relative contribution of Th2 and Th1 cytokines to the pathogenesis of lesions of chronic asthma remains poorly understood. To date, therapeutic inhibition of Th2 cytokines has proved disappointing. We used a clinically relevant model of chronic allergic asthma in mice to compare the effects of administering neutralizing antibodies to interleukin (IL)-13, IL-5, and interferon-gamma (IFN-gamma) to animals with established disease. As has been observed in clinical studies, anti-IL-5 inhibited both inflammation and remodeling but had no effect on airway responsiveness to methacholine. Anti-IL-13 effectively suppressed eosinophil recruitment and accumulation of chronic inflammatory cells in the airways. This treatment also partially suppressed changes of airway wall remodeling, including goblet cell hyperplasia/metaplasia and subepithelial fibrosis, but had limited ability to inhibit airway hyperreactivity (AHR). In contrast, treatment with anti-IFN-gamma markedly suppressed AHR. This antibody inhibited accumulation of chronic inflammatory cells but did not affect eosinophil recruitment or changes of remodeling. We conclude that inhibition of IL-5 is beneficial and that inhibition of IL-13 has considerable potential as a therapeutic strategy in chronic asthma, that IFN-gamma may play an important role in the pathogenesis of AHR, and that co-operative interaction between Th2 and Th1 cytokines contributes to the pathogenesis of the lesions of chronic asthma.
Oxidation of Steroids. IV. Methyl Δ9(11)-Lithocholenate and Methyl 9α,11α-Oxidolithocholanate1,2 (1951)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTOxidation of Steroids. IV. Methyl Δ9(11)-Lithocholenate and Methyl 9α,11α-Oxidolithocholanate1,2Louis F. Fieser and Srinivasa RajagopalanCite this: J. Am. Chem. Soc. 1951, 73, 1, 118–122Publication Date (Print):January 1, 1951Publication History Published online1 May 2002Published inissue 1 January 1951https://pubs.acs.org/doi/10.1021/ja01145a043https://doi.org/10.1021/ja01145a043research-articleACS PublicationsRequest reuse permissionsArticle Views123Altmetric-Citations16LEARN 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
Nitric oxide inhibits uterine contractility during pregnancy but not during delivery (1993)

Nitric Oxide mediates various biological phenomena, including vascular smooth muscle relaxation. In the present study, we sought to determine if an L-arginine nitric oxide-relaxation system is present in the uterus and if it modulates contractility during pregnancy. The substrate and a donor of nitric oxide and nitric oxide gas caused substantial relaxation of the spontaneous contractility of tissues from the rat uterus in vitro during pregnancy. Inhibitors of nitric oxide synthase and soluble guanylate cyclase reversed the relaxation effects of L-arginine. Nitric oxide was produced by the uterus in organ culture. Relaxation effects of L-arginine on the pregnant rat uterus were diminished at the time of spontaneous labor and postpartum. Nitric oxide production was also substantially reduced during labor. These results show that an L-arginine-nitric oxide-relaxation system is present in the uterus and it inhibits contractility during pregnancy but not during labor.
A monoclonal cytolytic T-lymphocyte response observed in a melanoma patient vaccinated with a tumor-specific antigenic peptide encoded by geneMAGE-3 (2001)

Vaccination of melanoma patients with tumor-specific antigens recognized by cytolytic T lymphocytes (CTL) produces significant tumor regressions in a minority of patients. These regressions appear to occur in the absence of massive CTL responses. To detect low-level responses, we resorted to antigenic stimulation of blood lymphocyte cultures in limiting dilution conditions, followed by tetramer analysis, cloning of the tetramer-positive cells, and T-cell receptor (TCR) sequence analysis of the CTL clones that showed strict specificity for the tumor antigen. A monoclonal CTL response against a MAGE-3 antigen was observed in a melanoma patient, who showed partial rejection of a large metastasis after treatment with a vaccine containing only the tumor-specific antigenic peptide. Tetramer analysis after in vitro restimulation indicated that about 1/40,000 postimmunization CD8(+) blood lymphocytes were directed against the antigen. The same TCR was present in all of the positive microcultures. TCR evaluation carried out directly on blood lymphocytes by PCR amplification led to a similar frequency estimate after immunization, whereas the TCR was not found among 2.5 x 10(6) CD8(+) lymphocytes collected before immunization. Our results prove unambiguously that vaccines containing only a tumor-specific antigenic peptide can elicit a CTL response. Even though they provide no information about the effector mechanisms responsible for the observed reduction in tumor mass in this patient, they would suggest that low-level CTL responses can initiate tumor rejection.
Digital Color Halftoning (1999)

This guide is aimed at professionals in the field of digital colour imaging who want to understand the halftone process or design halftone equipment and processes for research and development purposes. It is also suitable as a textbook for undergraduates and graduates in printing and graphic arts.
Recombinant factor VIIa partially reverses the inhibitory effect of fondaparinux on thrombin generation after tissue factor activation in platelet rich plasma and whole blood (2004)

Fondaparinux (Arixtra), a specific AT-dependent FXa inhibitor, is effective and safe in the prevention and treatment of venous thromboembolism, but some major hemorrhagic events may occur. No specific antidote to fondaparinux has been proposed. Recombinant FVIIa (Novoseven) could be used as an haemostatic treatment, but this option has not been well documented. We studied the effect of rFVIIa (1 micro g/ml) on the inhibition of thrombin generation induced by fondaparinux (0.1 micro g/ml to 1 micro g/ml). Coagulation was triggered in platelet rich plasma (PRP) or in whole blood by recalcification in the presence of diluted thromboplastin. In PRP thrombin generation was assessed using the thrombinoscope assay. In whole blood, prothrombin activation was assessed by measuring the kinetics of F(1+2) formation using an ELISA assay. Fondaparinux at concentrations equal or greater than 0.5 micro g/ml prolonged the initiation phase of thrombin generation, and reduced the velocity of prothrombin activation. It also decreased by 60% the endogenous thrombin potential. In the presence of fondaparinux (0.5 micro g/ml to 1 micro g/ml) rFVIIa accelerated the initiation phase of thrombin generation, but it did not significantly increase the endogenous thrombin potential. However, rFVIIa did not completely reverse the inhibitory effect of fondaparinux on the parameters of thrombin generation and prothrombin activation. This study shows that rFVIIa accelerates thrombin generation, but does not completely reverse the inhibitory effect of fondaparinux on thrombin generation. The potential clinical use of rFVIIa as haemostatic treatment of major bleedings related to fondaparinux has to be evaluated.