gebhart/patrepeval huggingface dataset:
Dityrosine Formation in Calmodulin:  Cross-Linking and Polymerization Catalyzed by Arthromyces Peroxidase (1996)

We employ bovine brain calmodulin, a protein that is subject to photoactivated dityrosine formation [Malencik, D. A., & Anderson, S. R. (1987) Biochemistry 26, 695; (1994) Biochemistry 33, 13363], as a model for the development of an efficient enzyme-catalyzed protein cross-linking technique. Key steps in the elaboration of the procedure are (1) identification of a peroxidase, from Arthromyces ramosus, that catalyzes dityrosine production in proteins that are not acted on by other common peroxidases, (2) monitoring of the intrinsic fluorescence of dityrosine to determine optimum reaction conditions, achieved with calmodulin in solutions containing boric acid-sodium borate (concentration > or = 0.2 M), approximately pH 8.3, approximately 40 degrees C, and (3) quenching of the reaction with reduced glutathione. Arthromyces peroxidase is the only common peroxidase able to catalyze significant dityrosine production in calmodulin, through a reaction that is largely intermolecular. Gel filtration yields fractions (accounting for approximately 40% of the initial calmodulin) that represent differing mobility ranges in NaDodSO4 polyacrylamide gel electrophoresis and contain close to the maximum possible amounts of dityrosine. The various fractions undergo Ca2+-dependent conformational changes detected in sedimentation velocity and/or fluorescence anisotropy measurements. Most of the samples stimulate the Ca2+-dependent activity of smooth muscle myosin light chain kinase. In catalytic assays utilizing the synthetic phosphatic acceptor peptide, the average activities range from 50 to 100% of that determined for native calmodulin. However, only the least polymerized fraction and the photogenerated calmodulin dimers significantly enhance the p-nitrophenylphosphatase activity of calcineurin. The ability to prepare soluble calmodulin polymers that retain a substantial degree of biological activity and exhibit the intense visible fluorescence of dityrosine illustrates the potential usefulness of Arthromyces peroxidase in the zero-length cross-linking of proteins.
Heparanase activity expressed by platelets, neutrophils, and lymphoma cells releases active fibroblast growth factor from extracellular matrix. (1990)

Incubation of platelets, neutrophils, and lymphoma cells with Descemet's membranes of bovine corneas and with the extracellular matrix (ECM) produced by cultured corneal endothelial cells resulted in release of basic fibroblast growth factor (bFGF), which stimulated the proliferation of 3T3 fibroblasts and vascular endothelial cells. Similar requirements were observed for release of endogenous bFGF stored in Descemet's membrane and of exogenous bFGF sequestered by the subendothelial ECM. Release of ECM-resident bFGF by platelets, neutrophils, and lymphoma cells was inhibited by carrageenan lambda, but not by protease inhibitors, in correlation with the inhibition of heparanase activity expressed by these cells. Degradation of the ECM-heparan sulfate side chains by this endo-beta-D-glucuronidase is thought to play an important role in cell invasion, particularly in the extravasation of blood-borne tumor cells and activated cells of the immune system. We propose that both heparanase and ECM-resident bFGF may modulate the cell response to contact with its local environment. Heparanase-mediated release of active bFGF from storage in basement membranes provides a novel mechanism for a localized induction of neovascularization in various normal and pathological processes, such as wound healing, inflammation, and tumor development.
Nanopore Based Sequence Specific Detection of Duplex DNA for Genomic Profiling (2010)

We demonstrate a purely electrical method for the single-molecule detection of specific DNA sequences, achieved by hybridizing double-stranded DNA (dsDNA) with peptide nucleic acid (PNA) probes and electrophoretically threading the DNA through sub-5 nm silicon nitride pores. Bis-PNAs were used as the tagging probes in order to achieve high affinity and sequence specificity. Sequence detection is performed by reading the ion current traces of individual translocating DNA molecules, which display a characteristic secondary blockade level, absent in untagged molecules. The potential for barcoding DNA is demonstrated through nanopore analysis of once-tagged and twice-tagged DNA at different locations on the same genomic fragment. Our high-throughput, long-read length method can be used to identify key sequences embedded in individual DNA molecules, without the need for amplification or fluorescent/radio labeling. This opens up a wide range of possibilities in human genomics as well as in pathogen detection for fighting infectious diseases.
Typhoid fever & vaccine development: a partially answered question. (2012)

Typhoid fever is a systemic disease caused by the human specific Gram-negative pathogen Salmonella enterica serovar Typhi (S. Typhi). The extra-intestinal infections caused by Salmonella are very fatal. The incidence of typhoid fever remains very high in impoverished areas and the emergence of multidrug resistance has made the situation worse. To combat and to reduce the morbidity and mortality caused by typhoid fever, many preventive measures and strategies have been employed, the most important being vaccination. In recent years, many Salmonella vaccines have been developed including live attenuated as well as DNA vaccines and their clinical trials have shown encouraging results. But with the increasing antibiotic resistance, the development of potent vaccine candidate for typhoid fever is a need of the hour. This review discusses the latest trends in the typhoid vaccine development and the clinical trials which are underway.
Runtime compilation techniques for data partitioning and communication schedule reuse (1993)

Article Free Access Share on Runtime compilation techniques for data partitioning and communication schedule reuse Authors: R. Ponnusamy Computer Scince Department, University of Maryland, College Park, MD and Northeast Parallel architectures Center, Syracuse University, Syracuse, NY Computer Scince Department, University of Maryland, College Park, MD and Northeast Parallel architectures Center, Syracuse University, Syracuse, NYView Profile , J. Saltz Computer Scince Department, University of Maryland, College Park, MD Computer Scince Department, University of Maryland, College Park, MDView Profile , A. Choudhary View Profile Authors Info & Claims Supercomputing '93: Proceedings of the 1993 ACM/IEEE conference on SupercomputingDecember 1993 Pages 361–370https://doi.org/10.1145/169627.169752Published:01 December 1993Publication History 80citation386DownloadsMetricsTotal Citations80Total Downloads386Last 12 Months27Last 6 weeks3 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
The effect of pH on the polymer degradation and drug release from PLGA‐mPEG microparticles (2008)

Abstract In vitro drug release and degradation mechanism of Poly ( dl ‐lactide‐ co ‐glycolic acid)‐ methoxypoly (ethyleneglycol) (PLGA‐mPEG) microparticles were investigated under different pH conditions. Methotrexate(MTX), an antirheumatic drug, was employed as the model drug. In polyester‐based microparticle system, two main issues involved in degradation were water uptake and the carboxylic groups produced by chain scission. Polymer composition was identified to be responsible for the odd degradation behavior in different releasing media. Because of the exposure of mPEG chains at the particle surface, microparticle degradation showed apparent different mechanism under the investigated releasing conditions. At pH 10.08, microparticles exhibited rapid weight loss but slower molecular weight decrease, and the degradation pattern was close to surface degradation. At pH 7.4, microparticles underwent heterogeneous bulk degradation. However, at pH 1.2, it showed fastest molecular weight decrease while slowest weight loss, and homogeneous degradation was observed. Particle agglomeration was also seen in acidic environment. Fourier transform infrared (FTIR) spectrum results indicated the crystallization of drugs under the low pH condition. Drug release was dependent on transport paths and drug property. These two factors were highly controlled by the polymer degradation and drug solubility in the releasing media as well as drug crystallinity. © 2008 Wiley Periodicals, Inc. J Appl Polym Sci, 2008
An asymmetric synthesis of MK-0417. Observations on oxazaborolidine-catalyzed reductions (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAn asymmetric synthesis of MK-0417. Observations on oxazaborolidine-catalyzed reductionsTodd K. Jones, Julie J. Mohan, Lyndon C. Xavier, Thomas J. Blacklock, David J. Mathre, Paul Sohar, E. Tracy Turner Jones, Robert A. Reamer, F. E. Roberts, and E. J. J. GrabowskiCite this: J. Org. Chem. 1991, 56, 2, 763–769Publication Date (Print):January 1, 1991Publication History Published online1 May 2002Published inissue 1 January 1991https://pubs.acs.org/doi/10.1021/jo00002a050https://doi.org/10.1021/jo00002a050research-articleACS PublicationsRequest reuse permissionsArticle Views1738Altmetric-Citations143LEARN 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
Analysis of zinc-fingers and homeoboxes (ZHX)-1-interacting proteins: molecular cloning and characterization of a member of the ZHX family, ZHX3 (2003)

Human zinc-fingers and homeoboxes (ZHX) 1, a transcriptional repressor, was originally cloned as an interacting protein with the activation domain of the A subunit of nuclear factor-Y (NF-YA). As the first step in investigating the mechanism by which ZHX1 acts as a transcriptional repressor, we conducted a search of ZHX1-interacting proteins using a yeast two-hybrid system. Nuclear proteins such as ZHX1, transcriptional co-factors and DNA-binding proteins, zyxin, androgen-induced aldose reductase and eleven-nineteen lysine-rich leukaemia gene, as well as some unknown proteins, were cloned. Molecular cloning and determination of the nucleotide sequence of the full-length cDNA encoding a novel protein revealed that it consists of 956 amino acid residues and contains two zinc-finger (Znf) motifs and five homeodomains (HDs) as well as ZHX1. We concluded that the protein forms the ZHX family with ZHX1 and denoted it ZHX3. ZHX3 not only dimerizes with both ZHX1 and ZHX3, but also interacts with the activation domain of the NF-YA. Further analysis revealed that ZHX3 is a ubiquitous transcriptional repressor that is localized in nuclei and functions as a dimer. Lastly, the dimerization domain, the interaction domain with NF-YA, and the repressor domain are mapped to a region including the HD1 region, and two nuclear localization signals are mapped to the N-terminal through Znf1 and the HD2 region, respectively.
<title>Electrically stimulated bilayer hydrogels as muscles</title> (1999)

Muscle-like actuators have been made from bilayers of crosslinked polyacrylamide and polyacrylic acid hydrogels sandwiched between electrodes. The polyacrylic acid responds to applied positive polarity field by contracting and expelling water which is taken up by the polyacrylamide layers. Previous studies have shown that the effective swelling modulus of polyacrylamide is much lower than polyacrylic acid. Hence the polyacrylamide acts as a sponge. As the polyacrylic acid layer contracts in the x, y and z directions the polyacrylamide is also pulled in on x and y, so that the whole stack becomes narrower and expands along the z- axis. Reversing the field reverses this effect with a time constant of about 1 minute for 1 mm thick layers with a thickness change of about 10%. Linear changes up to 50% have been obtained. Other gel actuators either transfer water across a sheet and so bend, or contract by expelling water. This new system shows a linear contraction and expansion without a volume change and so can be run (sealed) in a dry environment.
fbfB , a Gene Encoding a Putative Galactose Oxidase, Is Involved in Stigmatella aurantiaca Fruiting Body Formation (1998)

Stigmatella aurantiaca is a gram-negative bacterium which forms, under conditions of starvation in a multicellular process, characteristic three-dimensional structures: the fruiting bodies. For studying this complex process, mutants impaired in fruiting body formation have been induced by transposon insertion with a Tn5-derived transposon. The gene affected (fbfB) in one of the mutants (AP182) was studied further. Inactivation of fbfB results in mutants which form only clumps during starvation instead of wild-type fruiting bodies. This mutant phenotype can be partially rescued, if cells of mutants impaired in fbfB function are mixed with those of some independent mutants defective in fruiting before starvation. The fbfB gene is expressed about 14 h after induction of fruiting body formation as determined by measuring beta-galactosidase activity in a merodiploid strain harboring the wild-type gene and an fbfB-delta trp-lacZ fusion gene or by Northern (RNA) analysis with the Rhodobacter capsulatus pufBA fragment fused to fbfB as an indicator. The predicted polypeptide FbfB has a molecular mass of 57.8 kDa and shows a significant homology to the galactose oxidase (GaoA) of the fungus Dactylium dendroides. Galactose oxidase catalyzes the oxidation of galactose and primary alcohols to the corresponding aldehydes.
The MARCKS family of cellular protein kinase C substrates. (1993)

Stimulation of membrane polyphosphoinositol turnover is one of the most commonly employed signal transduction systems in normal physiology.The two second messengers generated by this reaction include inositol 1,4,5-trisphosphate, which can transiently elevate intracellular calcium levels, and diacylglycerols, which can activate most isoforms of protein kinase C (PKC).' Activation of members of this family of a t least 10 isoenzymes leads to a wide variety of physiological effects, including synthesis of macromolecules, activation of transport systems, secretion of hormones, contraction of muscle, and many others.However, the molecular steps between the activation of PKC and the resultant biological responses are largely unknown.One approach to elucidating these molecular pathways is to study direct cellular substrates for PKC in the hope that the knowledge gained will help to explain downstream events.This review will focus on one class of PKC substrates of which the prototype is the myristoylated, alanine-rich C kinase substrate or MARCKS protein.This protein, also referred to as 87 kDa, 80K, phosphomyristin, etc. has been employed for at least a decade as an indicator or marker for PKC activation in intact cells; early studies of this type have been reviewed previously (1,2).This review will concentrate on data that have accrued since the elucidation of the primary sequence of the protein, particularly potential structure:function relationships.
Cloned Transgenic Swine Via In Vitro Production and Cryopreservation1 (2006)

It has been notoriously difficult to successfully cryopreserve swine embryos, a task that has been even more difficult for in vitro-produced embryos. The first reproducible method of cryopreserving in vivo-produced swine embryos was after centrifugation and removal of the lipids. Here we report the adaptation of a similar process that permits the cryopreservation of in vitro-produced somatic cell nuclear transfer (SCNT) swine embryos. These embryos develop to the blastocyst stage and survive cryopreservation. Transfer of 163 cryopreserved SCNT embryos to two surrogates produced 10 piglets. Application of this technique may permit national and international movement of cloned transgenic swine embryos, storage until a suitable surrogate is available, or the long-term frozen storage of valuable genetics.
Photolabeling of Prostaglandin Endoperoxide H Synthase-1 with 3-Trifluoro-3-(m-[125I]iodophenyl)diazirine as a Probe of Membrane Association and the Cyclooxygenase Active Site (1996)

Previous studies of the crystal structure of the ovine prostaglandin endoperoxide H synthase-1 (PGHS-1)/S-flurbiprofen complex (Picot, D., Loll, P. J., and Garavito, R. M. (1994) Nature 367, 243-249) suggest that the enzyme is associated with membranes through a series of four amphipathic helices located between residues 70 and 117. We have used the photoactivatable, hydrophobic reagent 3-trifluoro-3-(m-[125I]iodophenyl)diazirine ([125I]TID) which partitions into membranes and other hydrophobic domains to determine which domains of microsomal PGHS-1 are subject to photolabeling. After incubation of ovine vesicular gland microsomes with [125I]TID, ovine PGHS-1 was one of the major photolabeled proteins. Proteolytic cleavage of labeled PGHS-1 at Arg277 with trypsin established that [125I]TID was incorporated into both the 33-kDa tryptic peptide containing the amino terminus and the 38-kDa tryptic peptide containing the carboxyl terminus. This pattern of photolabeling was not affected by the presence of 20 mM glutathione, indicating that the photolabeling observed for PGHS-1 was not due to the presence of [125I]TID in the aqueous phase. However, nonradioactive TID as well as two inhibitors, ibuprofen and sulindac sulfide, which bind the cyclooxygenase active site of PGHS-1, prevented the labeling of the 38-kDa carboxyl-terminal tryptic peptide. These results suggest that [125I]TID can label both the cyclooxygenase active site in the tryptic 38-kDa fragment and a membrane binding domain located in the 33-kDa fragment. Cleavage of photolabeled PGHS-1 with endoproteinase Lys-C yielded a peptide containing residues 25-166 which was labeled with [125I]TID. This peptide contains the putative membrane binding domain of ovine PGHS-1. Our results provide biochemical support for the concept developed from the crystal structure that PGHS-1 binds to membranes via four amphipathic helices located near the NH2 terminus of the protein.
Clinical Importance of Myeloid Antigen Expression in Adult Acute Lymphoblastic Leukemia (1987)

To determine the clinical importance of immunophenotypes in adult acute lymphoblastic leukemia (ALL), we prospectively studied 76 patients with this condition. Before treatment, lymphoblasts were tested for reactivity with monoclonal antibodies to B-cell, T-cell, and myeloid (My) antigens. Unexpectedly, myeloid antigens (MCS-2 or MY9) were identified in 25 patients (33 percent), usually in conjunction with B-cell or T-cell antigens. Among My+ patients, 15 (60 percent) expressed B-cell antigens (B+T-My+); all 6 tested had rearranged immunoglobulin genes. Five patients (20 percent) expressed T-cell antigens (B-T+My+), and one My+ patient expressed both B-cell and T-cell antigens. Only myeloid antigens (B-T-My+) were expressed in four patients (16 percent); three who were tested had germ-line immunoglobulin and T-cell-receptor gene configurations. Although no significant differences in presenting clinical features were found, My+ patients had fewer complete remissions than My- patients (35 vs. 76 percent, P less than 0.01). No differences in response or survival were observed between My+ and My- patients expressing T-cell antigens. However, among those expressing B-cell antigens, My+ patients had fewer complete remissions (29 vs. 71 percent, P = 0.02) and shorter survival (P = 0.03; median, 8.1 vs. greater than 26 months). These findings indicate that expression of myeloid antigen identifies a high-risk group of patients with adult ALL for whom alternative forms of treatment should be investigated.
Real-world rates of hematology lab abnormalities and associated cost among metastatic pancreatic cancer (mPC) therapeutic regimens. (2020)

670 Background: Low hematologic counts are a common, costly side effect of chemotherapy. This observational study examines rates and associated cost to treat. Methods: Data on adverse events (AEs) were extracted from the clinical Flatiron Health database for mPC patients (pts) from 01/2014-01/2019. Anemia, neutropenia, and lymphopenia occurrence was assessed via diagnosis codes and structured lab data. Costs due to AEs were derived from a claims analysis of mPC pts from 2013-2017 in Medicare Limited Data Set claims. Mean adjusted incremental costs (ICs) were estimated by comparing 30-day costs of pts with and without AEs, with controls selected among pts without AEs with the same regimen and line of therapy, when at least 80 cases/controls were identified. Results: 4592 treated mPC pts were identified (median age at diagnosis: 68y, IQR: 61 – 75). 1138 pts were treated with FOLFIRINOX (FFX) in first-line (1L), 2295 pts with 1L gemcitabine plus nab-paclitaxel (gem-nab), 218 pts with second-line (2L) FOLFOX, 56 pts with 2L FOLFIRI, and 178 pts with 2L liposomal irinotecan (nal-IRI) based therapy. Observed rates of anemia and neutropenia are shown in the table below. Lymphopenia rates were similar across regimens and ICs were not statistically significant. ICs for patients with any grade anemia were $3864, $3818, $3536, $3978, and $2963 for FFX, gem-nab, FOLFOX, FOLFIRI, and nal-IRI treated pts, respectively. ICs for pts with any grade neutropenia were $2382 for FFX, $2440 for gem-nab, $2688 for FOLFOX, $3551 for FOLFIRI and $2307 for nal-IRI. Conclusions: Any grade anemia ICs ranged from $2963 [$1544, $4400] (nal-IRI) to $3978 [$2241, $5817] (FOLFIRI), and any grade neutropenia ICs ranged from $2307 [$703, $4313] (nal-IRI) to $3551 [$1227, $6039] (FOLFIRI). Pts treated with nal-IRI had similar any grade AE rates but lower ICs, which suggest lower severity of AEs. These results are consistent with Flatiron Health’s lower rates of grades 3+ neutropenia and anemia. [Table: see text]
Requirement of RSF and FACT for Transcription of Chromatin Templates in Vitro (1998)

Transcription of naked DNA in vitro requires the general transcription factors and RNA polymerase II. However, this minimal set of factors is not sufficient for transcription when the DNA template is packaged into chromatin. Here, a factor that facilitates activator-dependent transcription initiation on chromatin templates was purified. This factor, remodeling and spacing factor (RSF), has adenosine triphosphate-dependent nucleosome-remodeling and spacing activities. Polymerases that initiate transcription with RSF can only extend their transcripts in the presence of FACT (facilitates chromatin transcription). Thus, the minimal factor requirements for activator-dependent transcription on chromatin templates in vitro have been defined.