gebhart/patrepeval huggingface dataset:
Human monocytes support factor X activation by factor VIIa, independent of tissue factor: implications for the therapeutic mechanism of high- dose factor VIIa in hemophilia [see comments] (1994)

High doses of recombinant factor VIIa are useful in managing bleeding in hemophiliacs with inhibitors. Whether this therapeutic effect of factor VIIa is dependent on tissue factor (TF) is a matter of debate. We examined the ability of freshly isolated human monocytes (which lack TF) to support the activation of coagulation-factor X by factor VIIa. The rate of factor-X activation by factor VIIa was accelerated in the presence of monocytes compared with the rate of X activation in solution. This activation of factor X on monocytes was saturable with a K1/2 of about 400 to 600 pmol/L factor VIIa. The rate of activation was not inhibited by an excess of inhibitory anti-TF antibody or a Gla-containing fragment of prothrombin. In contrast to monocytes, an endothelial cell line did not support activation of factor X by factor VIIa. Our findings suggest that at least one cell type can accelerate activation for factor X by factor VIIa in the absence of TF. This activity requires higher concentrations of factor VIIa than does the TF mechanism. The concentrations of VIIa required are of a similar order of magnitude to those required for a therapeutic effect of VIIa in bleeding hemophiliacs with inhibitors.
RNA editing with CRISPR-Cas13 (2017)

Nucleic acid editing holds promise for treating genetic disease, particularly at the RNA level, where disease-relevant sequences can be rescued to yield functional protein products. Type VI CRISPR-Cas systems contain the programmable single-effector RNA-guided ribonuclease Cas13. We profiled type VI systems in order to engineer a Cas13 ortholog capable of robust knockdown and demonstrated RNA editing by using catalytically inactive Cas13 (dCas13) to direct adenosine-to-inosine deaminase activity by ADAR2 (adenosine deaminase acting on RNA type 2) to transcripts in mammalian cells. This system, referred to as RNA Editing for Programmable A to I Replacement (REPAIR), which has no strict sequence constraints, can be used to edit full-length transcripts containing pathogenic mutations. We further engineered this system to create a high-specificity variant and minimized the system to facilitate viral delivery. REPAIR presents a promising RNA-editing platform with broad applicability for research, therapeutics, and biotechnology.
Coupling the phosphotransferase system and the methyl-accepting chemotaxis protein-dependent chemotaxis signaling pathways of Escherichia coli. (1995)

Chemotactic responses in Escherichia coli are typically mediated by transmembrane receptors that monitor chemoeffector levels with periplasmic binding domains and communicate with the flagellar motors through two cytoplasmic proteins, CheA and CheY. CheA autophosphorylates and then donates its phosphate to CheY, which in turn controls flagellar rotation. E. coli also exhibits chemotactic responses to substrates that are transported by the phosphoenolpyruvate (PEP)-dependent carbohydrate phosphotransferase system (PTS). Unlike conventional chemoreception, PTS substrates are sensed during their uptake and concomitant phosphorylation by the cell. The phosphoryl groups are transferred from PEP to the carbohydrates through two common intermediates, enzyme I (EI) and phosphohistidine carrier protein (HPr), and then to sugar-specific enzymes II. We found that in mutant strains HPr-like proteins could substitute for HPr in transport but did not mediate chemotactic signaling. In in vitro assays, these proteins exhibited reduced phosphotransfer rates from EI, indicating that the phosphorylation state of EI might link the PTS phospho-relay to the flagellar signaling pathway. Tests with purified proteins revealed that unphosphorylated EI inhibited CheA autophosphorylation, whereas phosphorylated EI did not. These findings suggest the following model for signal transduction in PTS-dependent chemotaxis. During uptake of a PTS carbohydrate, EI is dephosphorylated more rapidly by HPr than it is phosphorylated at the expense of PEP. Consequently, unphosphorylated EI builds up and inhibits CheA autophosphorylation. This slows the flow of phosphates to CheY, eliciting an up-gradient swimming response by the cell.
Upconversion Nanoparticles: Design, Nanochemistry, and Applications in Theranostics (2014)

ADVERTISEMENT RETURN TO ISSUEReviewNEXTUpconversion Nanoparticles: Design, Nanochemistry, and Applications in TheranosticsGuanying Chen*†‡, Hailong Qiu†‡, Paras N. Prasad*‡§, and Xiaoyuan Chen*∥View Author Information† School of Chemical Engineering and Technology, Harbin Institute of Technology, Harbin, Heilongjiang 150001, China‡ Department of Chemistry and the Institute for Lasers, Photonics, and Biophotonics, University at Buffalo, State University of New York, Buffalo, New York 14260, United States§ Department of Chemistry, Korea University, Seoul 136-701, Korea∥ Laboratory of Molecular Imaging and Nanomedicine, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland 20892-2281, United States*E-mail: [email protected]*E-mail: [email protected]*E-mail: [email protected]Cite this: Chem. Rev. 2014, 114, 10, 5161–5214Publication Date (Web):March 10, 2014Publication History Received5 August 2013Published online10 March 2014Published inissue 28 May 2014https://doi.org/10.1021/cr400425hCopyright © 2014 American Chemical SocietyRIGHTS & PERMISSIONSACS AuthorChoiceArticle Views75082Altmetric-Citations1907LEARN 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 InReddit PDF (60 MB) Get e-AlertsSUBJECTS:Biological imaging,Ions,Lanthanides,Luminescence,Nanoparticles Get e-Alerts
PET Studies with Carbon-11 Radioligands in Neuropsychopharmacological Drug Development (2001)

A basic problem in the discovery and development of novel drugs to be used in the treatment of neurological and psychiatric disorders is the absence of relevant in vitro or in vivo animal models that can yield results which can be extrapolated to man. Drug research now benefits from the fast development of functional imaging techniques such as positron emission tomography (PET) which trace radiolabelled molecules directly in the human brain. PET uses molecules that are labelled with short-lived radionuclides and injected intravenously into experimental animals, human volunteers or patients. The most frequent approach is to study how an unlabelled drug inhibits specific binding of a well characterised selective PET radioligand. The alternative direct approach is to radiolabel a new potential drug and to trace its uptake, anatomical distribution and binding in brain. Furthermore, the effects of a novel drug on physiological-biochemical parameters, such as glucose metabolism or blood flow, can also be assessed. The demonstration of quantitative relationships between drug binding in vivo and drug effects in patients is used to validate targets for drug action, to correlate pharmacological and physiological effects, and to optimise clinical treatment.
Decellularized extracellular matrix derived from human adipose tissue as a potential scaffold for allograft tissue engineering (2011)

Decellularized tissues composed of extracellular matrix (ECM) have been clinically used to support the regeneration of various human tissues and organs. Most decellularized tissues so far have been derived from animals or cadavers. Therefore, despite the many advantages of decellularized tissue, there are concerns about the potential for immunogenicity and the possible presence of infectious agents. Herein, we present a biomaterial composed of ECM derived from human adipose tissue, the most prevalent, expendable, and safely harvested tissue in the human body. The ECM was extracted by successive physical, chemical, and enzymatic treatments of human adipose tissue isolated by liposuction. Cellular components including nucleic acids were effectively removed without significant disruption of the morphology or structure of the ECM. Major ECM components were quantified, including acid/pepsin-soluble collagen, sulfated glycosaminoglycan (GAG), and soluble elastin. In an in vivo experiment using mice, the decellularized ECM graft exhibited good compatibility to surrounding tissues. Overall results suggest that the decellularized ECM containing biological and chemical cues of native human ECM could be an ideal scaffold material not only for autologous but also for allograft tissue engineering.
Compared with Cyclosporine, ISATX247 Significantly Prolongs Renal-Allograft Survival in a Nonhuman Primate Model (2004)

Allografts in monkeys treated with ISATX247 survived significantly longer than those treated with cyclosporine. On the basis of survival times and degree of calcineurin inhibition, ISATX247 is a more potent immunosuppressive agent than cyclosporine in this nonhuman primate model of renal-allograft transplantation.
Enantioselective reduction of pentoxifylline to lisofylline using whole‐cell Lactobacillus kefiri biotransformation (2007)

Lisofylline (LSF) is a drug candidate that has been under investigation for acute respiratory distress syndrome, acute lung injury, septic shock and mucositis. As LSF is not commercially available in our country, we produced it for pharmacokinetic studies. In the present work whole-cell reduction of pentoxifylline [1-(5-oxohexyl)-3,5-dimethylxanthine] to LSF [1-(5R-hydroxyhexyl)-3,5-dimethylxanthine] using Lactobacillus kefiri DSM 20587 was investigated. Glucose or 2-propanol was used as a co-substrate to regenerate the NADPH cofactor. The reaction conditions were optimized. The influence of different concentrations of co-substrates on the yield and enantioselectivity of the biotransformation of pentoxifylline into LSF were tested. Maximum yield (100%) of biotransformation was reached in the presence of glucose as a co-substrate. At glucose concentrations of 675 and 900 mM the bioreduction of pentoxifylline proceeded highly enantioselectively (enantiomeric excess for the R enantiomer of 98%).
Design considerations for three-terminal optically addressed MQW spatial light modulators (1986)

Although current developments in multiple quantum well (MQW) device technology show great promise, problems remain when considered in the larger framework of processing element (PE) arrays. Spatial light modulation requires many small modulator cells (25 × 25 μ m 2 ) with low switching energy (&lt;20 fJ/ μ m 2 ), low driving voltage (&lt;20 V), good dynamic range (&gt; 10 dB), and integrable into large arrays (&gt;100 × 100 PEs) with a technology compatible with detector fabrication. For digital optical processors to become viable, spatial light modulators with at least 10 4 processing elements operating at 100-MHz frame rate are required. Assuming ideal detection efficiency, a unity power gain, and operation near thermal limits, this frame rate results in an impractical input light power density of 100 W/cm 2 for a modulator array consuming 10 fJ/ μ m 2 . To ease the optical power requirements a power gain of several hundred must be achieved. For an acceptable dynamic range the processing elements should be three-terminal devices consisting of physically separated detectors and MQW modulators and should be biased at lower energies than the energy corresponding to the excitonic absorption peak. This is in contrast to two-terminal optical bistable devices using the self-electroabsorption effect and operable only with low dynamic range. A detector with high gain is also essential for weak signals to produce larger photocurrents than the currents generated in the MQW modulator. GaAs/GaAIAs heterojunction bipolar phototransistors may be good candidates to perform the required detection functions, because of their compatibility with GaAs/GaAIAs MQW modulator technology.
Effects of plasma kallikrein deficiency on haemostasis and thrombosis in mice: Murine Ortholog of the Fletcher Trait (2012)

Plasma kallikrein is a multifunctional serine protease involved in contact activation of coagulation. Deficiency in humans is characterised by prolonged activated partial thromboplastin time (aPTT); however, the balance between thrombosis and haemostasis is not fully understood. A study of plasma kallikrein-deficient mice revealed increased aPTT, without prolonged bleeding time. Prekallikrein antisense oligonucleotide (ASO) treatment in mice suggested potential for a positive therapeutic index. The current goal was to further define the role of plasma kallikrein in coagulation. Blood pressure and heart rate were normal in plasma kallikrein-deficient mice, and mice were completely protected from occlusion (100 ± 1.3% control flow) in 3.5% FeCl<sub>3</sub> -induced arterial thrombosis versus heterozygotes (20 ± 11.4%) and wild-type littermates (8 ± 0%). Vessels occluded in 8/8 wild-type, 7/8 heterozygotes, and 0/8 knockouts. Anti-thrombotic protection was less pronounced in 5% FeCl<sub>3</sub>-induced arterial injury. Integrated blood flow was 8 ± 0% control in wild-type and heterozygotes, and significantly (p<0.01) improved to 43 ± 14.2% in knockouts. The number of vessels occluded was similar in all genotypes. Thrombus weight was significantly reduced in knockouts (−47%) and heterozygotes (−23%) versus wild-type in oxidative venous thrombosis. Average tail bleeding time increased modestly in knockout mice compared to wild-type. Average renal bleeding times were similar in all genotypes. These studies confirm and extend studies with prekallikrein ASO, and demonstrate that plasma kallikrein deletion prevents occlusive thrombus formation in mice with a minimal role in provoked bleeding. Additional support for the significance of the intrinsic pathway in the coagulation cascade is provided, as well as for a potential new anti-thrombotic approach.
Isolation of four major glycoprotein families (ZP1, ZP2, ZP3, ZP4) of porcine zona pellucida and characterization of antisera raised to each glycoprotein family. (1991)

Porcine zona pellucida (ZP) contains antigens which cross-react with man, and anti porcine ZP antibody was found to exhibit a strong blocking effect on human sperm-ZP interaction. Previously, we found that porcine ZP was composed of four major glycoprotein families (ZP1, ZP2, ZP3, ZP4). In this study, each of the glycoprotein families was isolated by O'Farrell's two-dimensional electrophoresis and injected into mice to obtain antisera to each component. All the mouse antisera had high titers of antibodies to porcine and human ZP in an immunofluorescent staining test. Western blot analysis showed that although the antisera most strongly reacted with the corresponding components of porcine ZP, each glycoprotein family also possessed antigens which cross-reacted with each other. The antisera to ZP1, ZP3 and ZP4 strongly inhibited human sperm-ZP interaction but antiserum to ZP2 had no inhibitory effect on it.
Targeting Several CAG Expansion Diseases by a Single Antisense Oligonucleotide (2011)

To date there are 9 known diseases caused by an expanded polyglutamine repeat, with the most prevalent being Huntington's disease. Huntington's disease is a progressive autosomal dominant neurodegenerative disorder for which currently no therapy is available. It is caused by a CAG repeat expansion in the HTT gene, which results in an expansion of a glutamine stretch at the N-terminal end of the huntingtin protein. This polyglutamine expansion plays a central role in the disease and results in the accumulation of cytoplasmic and nuclear aggregates. Here, we make use of modified 2'-O-methyl phosphorothioate (CUG)n triplet-repeat antisense oligonucleotides to effectively reduce mutant huntingtin transcript and protein levels in patient-derived Huntington's disease fibroblasts and lymphoblasts. The most effective antisense oligonucleotide, (CUG)(7), also reduced mutant ataxin-1 and ataxin-3 mRNA levels in spinocerebellar ataxia 1 and 3, respectively, and atrophin-1 in dentatorubral-pallidoluysian atrophy patient derived fibroblasts. This antisense oligonucleotide is not only a promising therapeutic tool to reduce mutant huntingtin levels in Huntington's disease but our results in spinocerebellar ataxia and dentatorubral-pallidoluysian atrophy cells suggest that this could also be applicable to other polyglutamine expansion disorders as well.
Affinity Capillary Electrophoresis−Mass Spectrometry for Screening Combinatorial Libraries (1996)

A new methodology, affinity capillary electrophoresis−mass spectrometry (ACE-MS), is introduced as a solution-based approach for screening combinatorial libraries for drug leads. The method allows on-line, one-step selection and structural identification of candidate ligands. ACE-MS is demonstrated using the binding of vancomycin to libraries of all-d-tri- and tetrapeptides as a model system. Peptide libraries of different forms of Fmoc-DDXX and Fmoc-EXX containing up to 361 compounds were successfully employed to determine interacting structural motifs. A consensus structure of the strongest interacting peptides consisted of d-Ala at the C-terminus and an aromatic amino acid in the penultimate position. Ligands with this structure bound more strongly to the receptor than the known ligand, d-Ala-d-Ala. A 1000 peptide library was also screened directly by ACE-MS. It was found that, for this and potentially larger libraries, incorporating an affinity solid phase extraction step prior to ACE-MS was effective in both removing a large number of non-interacting species as well as preconcentrating sample components for sequence determination by MS.
Hydrolysis of a Model for the 5‘-Cap of mRNA by Dinuclear Copper(II) and Zinc(II) Complexes. Rapid Hydrolysis by Four Copper(II) Ions (1999)

Two bis(triazacyclononane) ligands, 1,3-bis(1,4,7-triaza-1-cyclononyl)-p-xylene (pXTD) and 1,3-bis(1,4,7-triaza-1-cyclononyl)-m-xylene (mXTD), form stable dinuclear Cu(II) complexes (Cu(2)L). At pH 7.3, the predominant species are bis(hydroxide) complexes (Cu(2)L(OH)(2)(2+)) as determined by equilibrium modeling of pH-potentiometric measurements. Several dinuclear and mononuclear Cu(II) complexes and a dinuclear Zn(II) complex promote the hydrolysis of GpppG, a model for the 5'-cap of mRNA. At 0.125 mM complex, both Cu(2)(pXTD) and Cu(2)(mXTD) promote hydrolysis of GpppG approximately 100-fold more rapidly than does the monomeric Cu(TACN) complex (0.250 mM) at pH 7.3 and 37 degrees C (TACN = 1,4,7-triazacyclononane). The dependence of the rate constant on dinuclear Cu(II) complex concentration suggests that Cu(2)(pXTD) promotes hydrolysis through both a 1:1 complex (Cu(2)L-GpppG) and a 2:1 complex ((Cu(2)L)(2)-GpppG). The 2:1 complex is 20-fold more reactive than the 1:1 complex; a first-order rate constant of 1.1 x 10(-)(4) s(-)(1) is determined for hydrolysis of the 2:1 complex. Cu(2)(mXTD) effectively promotes the hydrolysis of GpppG only through a 2:1 complex which hydrolyzes with a first-order rate constant of 4.3 x 10 (-)(5) s(-)(1). Cu(2)(pXTD) binds as a 1:1 complex to m(7)GpppG with a binding constant of 27 000 M(-)(1) as determined by use of fluorescence spectroscopy. Two Cu(2)(mXTD) complexes bind stepwise to m(7)GpppG with binding constants of 5300 and 12 000 M(-)(1) for the first complex and second complex, respectively.
Galectins in the tumor endothelium: opportunities for combined cancer therapy (2007)

Galectins are emerging as a family of proteins that play an important role in several steps of tumorigenesis. Evidence is accumulating that galectins are expressed by the tumor endothelium, where they contribute to different steps of tumor progression such as immune escape and metastasis. Recent studies have identified an important role for galectins in tumor angiogenesis. Moreover, it has been shown that galectins in the endothelium can be targeted for therapeutic applications. This opens a window of opportunity for the development of tumor-type independent treatment strategies. This review focuses on the expression of galectins in the tumor endothelium, their contribution to tumor progression, and their application in tumor-type independent cancer therapy.
Expression of Programmed Death 1 Ligands by Murine T Cells and APC (2002)

Programmed death 1 (PD-1) is a new member of the CD28/CTLA-4 family, which has been implicated in the maintenance of peripheral tolerance. Two ligands for PD-1, namely, B7-H1 (PD-L1) and B7-DC (PD-L2), have recently been identified as new members of the B7 family but their expression at the protein level remains largely unknown. To characterize the expression of B7-H1 and B7-DC, we newly generated an anti-mouse B7-H1 mAb (MIH6) and an anti-mouse B7-DC mAb (TY25). MIH6 and TY25 immunoprecipitated a single molecule of 43 and 42 kDa from the lysate of B7-H1 and B7-DC transfectants, respectively. Flow cytometric analysis revealed that B7-H1 was broadly expressed on the surface of mouse tumor cell lines while the expression of B7-DC was rather restricted. PD-1 was expressed on anti-CD3-stimulated T cells and anti-IgM plus anti-CD40-stimulated B cells at high levels but was undetectable on activated macrophages or DCs. B7-H1 was constitutively expressed on freshly isolated splenic T cells, B cells, macrophages, and dendritic cells (DCs), and up-regulated on T cells by anti-CD3 stimulation on macrophages by LPS, IFN-gamma, GM-CSF, or IL-4, and on DCs by IFN-gamma, GM-CSF, or IL-4. In contrast, B7-DC expression was only inducible on macrophages and DCs upon stimulation with IFN-gamma, GM-CSF, or IL-4. The inducible expression of PD-1 ligands on both T cells and APCs may suggest new paradigms of PD-1-mediated immune regulation.
The CCPN data model for NMR spectroscopy: Development of a software pipeline (2005)

To address data management and data exchange problems in the nuclear magnetic resonance (NMR) community, the Collaborative Computing Project for the NMR community (CCPN) created a "Data Model" that describes all the different types of information needed in an NMR structural study, from molecular structure and NMR parameters to coordinates. This paper describes the development of a set of software applications that use the Data Model and its associated libraries, thus validating the approach. These applications are freely available and provide a pipeline for high-throughput analysis of NMR data. Three programs work directly with the Data Model: CcpNmr Analysis, an entirely new analysis and interactive display program, the CcpNmr FormatConverter, which allows transfer of data from programs commonly used in NMR to and from the Data Model, and the CLOUDS software for automated structure calculation and assignment (Carnegie Mellon University), which was rewritten to interact directly with the Data Model. The ARIA 2.0 software for structure calculation (Institut Pasteur) and the QUEEN program for validation of restraints (University of Nijmegen) were extended to provide conversion of their data to the Data Model. During these developments the Data Model has been thoroughly tested and used, demonstrating that applications can successfully exchange data via the Data Model. The software architecture developed by CCPN is now ready for new developments, such as integration with additional software applications and extensions of the Data Model into other areas of research.