gebhart/patrepeval huggingface dataset:
Induction of differentiation of acute promyelocytic leukemia cells by a cytidine deaminase-resistant analogue of 1-beta-D-arabinofuranosylcytosine, 1-(2-deoxy-2-methylene-beta-D-erythro-pentofuranosyl)cytidine. (2001)

Since the establishment of all-trans retinoic acid (ATRA) differentiation therapy, the prognosis of acute promyelocytic leukemia (APL) has improved, and APL has become a curable subtype of acute myelocytic leukemia. Complete remission can be achieved with ATRA alone, but disease-free survival is still too short because of relapse. To overcome this drawback, ATRA has been used in combination with chemotherapeutic agents such as 1-beta-D-arabinofuranosylcytosine (araC) and daunorubicin. However, growth of the APL cell lines NB4 and HT93 is less sensitive to araC than to that of other myeloid leukemia cell lines such as HL-60 and U937. ATRA effectively induced granulocytic differentiation of NB4 and HT93 cells, whereas araC did not, even in a high concentration. A cytidine deaminase-resistant analogue of araC, 1-(2-deoxy-2-methylene-beta-D-erythro-pentofuranosyl)cytidine (DMDC), inhibited the growth of NB4 and HT-93 cells and was also effective on HL-60 and U937 cells. The promyelocytic cell lines were induced to differentiate by DMDC and other cytidine deaminase-resistant analogues. Among them, DMDC was the most potent in inducing differentiation and inhibiting the growth of NB4 cells. The ATRA-induced differentiation of NB4 cells was not augmented by araC, whereas combined treatment with ATRA and DMDC had more than additive effects in inducing the differentiation of NB4 cells. Similar results were observed in a primary culture of leukemia cells that had been freshly isolated from APL patients. These results suggest that DMDC may play a role in the treatment of APL.
Retrohoming of a Mobile Group II Intron in Human Cells Suggests How Eukaryotes Limit Group II Intron Proliferation (2015)

Mobile bacterial group II introns are evolutionary ancestors of spliceosomal introns and retroelements in eukaryotes. They consist of an autocatalytic intron RNA (a "ribozyme") and an intron-encoded reverse transcriptase, which function together to promote intron integration into new DNA sites by a mechanism termed "retrohoming". Although mobile group II introns splice and retrohome efficiently in bacteria, all examined thus far function inefficiently in eukaryotes, where their ribozyme activity is limited by low Mg2+ concentrations, and intron-containing transcripts are subject to nonsense-mediated decay (NMD) and translational repression. Here, by using RNA polymerase II to express a humanized group II intron reverse transcriptase and T7 RNA polymerase to express intron transcripts resistant to NMD, we find that simply supplementing culture medium with Mg2+ induces the Lactococcus lactis Ll.LtrB intron to retrohome into plasmid and chromosomal sites, the latter at frequencies up to ~0.1%, in viable HEK-293 cells. Surprisingly, under these conditions, the Ll.LtrB intron reverse transcriptase is required for retrohoming but not for RNA splicing as in bacteria. By using a genetic assay for in vivo selections combined with deep sequencing, we identified intron RNA mutations that enhance retrohoming in human cells, but <4-fold and not without added Mg2+. Further, the selected mutations lie outside the ribozyme catalytic core, which appears not readily modified to function efficiently at low Mg2+ concentrations. Our results reveal differences between group II intron retrohoming in human cells and bacteria and suggest constraints on critical nucleotide residues of the ribozyme core that limit how much group II intron retrohoming in eukaryotes can be enhanced. These findings have implications for group II intron use for gene targeting in eukaryotes and suggest how differences in intracellular Mg2+ concentrations between bacteria and eukarya may have impacted the evolution of introns and gene expression mechanisms.
Correction of Ornithine Transcarbamylase Deficiency in Adult spf ash Mice and in OTC-Deficient Human Hepatocytes with Recombinant Adenoviruses Bearing the CAG Promoter (1996)

Ornithine transcarbamylase (OTC) deficiency, the most common and severe inborn error of the urea cycle in humans, remains without adequate treatment, and mortality rates are high. Adenoviral vectors provide an efficient system for gene delivery, but there are problems, including toxicity. Efficient promoters that reduce the amount of vector required for treatment need to be developed. We constructed two recombinant adenoviral vectors, AdexCAGhOTC and AdexSR alpha hOTC, which harbor the human OTC gene under transcriptional control of CAG (a modified chicken beta-actin promoter with CMV-IE enhancer) and SR alpha (the SV40 early promoter with the R segment and part of the US segment of the HTLV-1 LTR), respectively. Each was tested in adult spf(ash) mice, an animal model of human OTC deficiency, and in primary human hepatocytes with OTC deficiency. Spf(ash) mice have a pronounced orotic aciduria as seen in humans. A complete recovery of hepatic OTC activity with minimal tissue damage was observed in these animals following the intravenous administration of AdexCAGhOTC alone. Western blot analysis confirmed hepatic OTC expression and normalization of orotic aciduria was evident for 60 days. Enzyme activities of primary human hepatocytes infected with AdexCAGhOTC were 10-40 times higher than those with AdexSR alpha hOTC. Thus, the adenoviral vector with an efficient promoter such as CAG, can be given further consideration for possible gene therapy in humans with OTC deficiency.
Matched field inversion of broadband data using the freeze bath method (1999)

This paper presents a statistical freeze bath method for geoacoustic inversion that emphasizes the search for a distribution of models that fit the data well. Contrary to simulated annealing optimization, the freeze bath samples the multidimensional model parameter space at constant freeze probability, corresponding to fixed temperatures for each parameter. The sampling process uses a heat bath algorithm as a Boltzmann sampling tool to carry out a global search over the model parameter space. The conventional heat bath algorithm is modified to sample on a fuzzy grid in order to access the entire range of parameter values. The inversion provides a set of good models that indicates how well the model parameters are constrained by the data, and reveals the degree of correlation between parameters. The efficiency of the search process is improved by reparameterizing the original model parameters to a new set based on the eigenvectors of the model covariance matrix. The inversion performance of the freeze bath is demonstrated using simulated data for a simple geoacoustic model. The method is applied to shallow water broadband data obtained during the Haro Strait geoacoustic tomography experiment to estimate a geoacoustic profile at the site.
Bioadhesive Drug Delivery (1991)

Bioadhesive drug delivery systems adhere to the mucin-network and/or underlying epithelial layer of mucosal surfaces. Mucus is a continuous network of cross-linked glycoproteins which, at physiological pH, carries a substantial negative charge due to the presence of sialic acid and sulfonic acid residues. The glycocalyx (polysaccharide-containing structures) on the external surface of cells is partly responsible for the adhesive properties of the cell and carries a net negative charge as well. Bioadhesion begins with establishment of intimate contact between the polymer and substrate. This is followed by bond formation and interpenetration/interdiffusion of polymer and substrate. Any increase in contact area and establishment of physical entanglement at the interface strengthens the force of bioadhesion. Thus, factors that favor intimacy of contact, increased bond formation and enhanced physical entanglement will potentially increase bioadhesive strength. Bioadhesive polymers can be used in drug delivery to localize delivery systems at specific sites for either local treatment or for prolonged delivery of drug in a route of administration that would otherwise cause rapid removal of the system.
3′- O -modified nucleotides as reversible terminators for pyrosequencing (2007)

Pyrosequencing is a method used to sequence DNA by detecting the pyrophosphate (PPi) group that is generated when a nucleotide is incorporated into the growing DNA strand in polymerase reaction. However, this method has an inherent difficulty in accurately deciphering the homopolymeric regions of the DNA templates. We report here the development of a method to solve this problem by using nucleotide reversible terminators. These nucleotide analogues are modified with a reversible chemical moiety capping the 3'-OH group to temporarily terminate the polymerase reaction. In this way, only one nucleotide is incorporated into the growing DNA strand even in homopolymeric regions. After detection of the PPi for sequence determination, the 3'-OH of the primer extension products is regenerated through different deprotection methods. Using an allyl or a 2-nitrobenzyl group as the reversible moiety to cap the 3'-OH of the four nucleotides, we have synthesized two sets of 3'-O-modified nucleotides, 3'-O-allyl-dNTPs and 3'-O-(2-nitrobenzyl)-dNTPs as reversible terminators for pyrosequencing. The capping moiety on the 3'-OH of the DNA extension product is efficiently removed after PPi detection by either a chemical method or photolysis. To sequence DNA, templates containing homopolymeric regions are immobilized on Sepharose beads, and then extension-signal detection-deprotection cycles are conducted by using the nucleotide reversible terminators on the DNA beads to unambiguously decipher the sequence of DNA templates. Our results establish that this reversible-terminator-pyrosequencing approach can be potentially developed into a powerful methodology to accurately determine DNA sequences.
CPG70 Is a Novel Basic Metallocarboxypeptidase with C-terminal Polycystic Kidney Disease Domains from Porphyromonas gingivalis (2002)

In a search for a basic carboxypeptidase that might work in concert with the major virulence factors, the Arg- and Lys-specific cysteine endoproteinases of Porphyromonas gingivalis, a novel 69.8-kDa metallocarboxypeptidase CPG70 was purified to apparent homogeneity from the culture fluid of P. gingivalis HG66. Carboxypeptidase activity was measured by matrix-assisted laser desorption ionization-mass spectrometry using peptide substrates derived from a tryptic digest of hemoglobin. CPG70 exhibited activity with peptides containing C-terminal Lys and Arg residues. The k(cat)/K(m) values for the hydrolysis of the synthetic dipeptides FA-Ala-Lys and FA-Ala-Arg by CPG70 were 99 and 56 mm(-1)s(-1), respectively. The enzyme activity was strongly inhibited by the Arg analog (2-guanidinoethylmercapto)succinic acid and 1,10-phenanthroline. High resolution inductively coupled plasma-mass spectrometry demonstrated that 1 mol of CPG70 was associated with 0.6 mol of zinc, 0.2 mol of nickel, and 0.2 mol of copper. A search of the P. gingivalis W83 genomic data base (TIGR) with the N-terminal amino acid sequence determined for CPG70 revealed that the enzyme is an N- and C-terminally truncated form of a predicted 91.5-kDa protein (PG0232). Analysis of the deduced amino acid sequence of the full-length protein revealed an N-terminal signal sequence followed by a pro-segment, a metallocarboxypeptidase catalytic domain, three tandem polycystic kidney disease domains, and an 88-residue C-terminal segment. The catalytic domain exhibited the highest sequence identity with the duck metallocarboxypeptidase D domain II. Insertional inactivation of the gene encoding CPG70 resulted in a P. gingivalis isogenic mutant that was avirulent in the murine lesion model under the conditions tested.
Secondary structure prediction of human SAA1. Presumptive identification of calcium and lipid binding sites. (1986)

Serum amyloid A protein (SAA), an apolipoprotein of high density lipoprotein (HDL), is an acute phase protein thought to be the precursor of amyloid fibrils in reactive systemic (AA) amyloidosis. A prediction of the secondary structure of the human serum amyloid protein SAA1(alpha) is presented. The prediction was based upon one-dimensional Fourier analysis of the amino acid sequence together with sequence matching to known structural motifs. The results were compared with those from prediction algorithms based upon statistical techniques. Our findings are consistent with available experimental data. They include the putative identification of the amino-terminal 11 residues as the functionally important lipid-binding site of SAA and of a likely, neutral, calcium-binding sequence: Gly48-Pro49-Gly50-Gly51. Sequence comparisons between SAA and protein tyrosine kinases, phospholipases A2 and delta-crystallin, all of which bind both calcium and phospholipid, revealed significant homologies that support our proposals concerning structure-function relationships in SAA.
The Archaeology of Israelite Society in Iron Age II. By Avraham Faust (2015)

&#x0D; &#x0D; &#x0D; The Archaeology of Israelite Society in Iron Age II. By Avraham Faust. Translated by Ruth Ludlum. Winona Lake: Eisenbrauns, 2012. Pp. xviii + 328, illus. $49.50.&#x0D; &#x0D; &#x0D;
Copyright protection for electronic publishing over computer networks (1995)

One of the major challenges faced by electronic publishing is that of preventing individuals from easily copying and illegally distributing electronic documents. The authors explore the use of cryptographic protocols to discourage the distribution of illicit electronic copies, and propose an architecture and two separate strategies for making electronic document distribution secure.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Sequence-Based Rendezvous for Dynamic Spectrum Access (2008)

In the context of dynamic spectrum access (DSA), rendezvous refers to the ability of two or more radios to meet and establish a link on a common channel. In decentralized networks, this is often accomplished by each radio visiting potential channels in random fashion, in a process that we call blind random rendezvous. In this work, we propose the use of sequences that determine the order with which radios visit potentially available channels. Through sequence-based rendezvous, it is possible to: (i) establish an upper bound to the time to rendezvous (TTR); (ii) establish a priority order for channels in which rendezvous occurs; (Hi) reduce the expected TTR as compared to random rendezvous. We provide an example of a family of sequences and derive the expected time-to- rendezvous using this method. We also describe how the method can be adopted when one or more primary users are detected in the channels of interest.
Multiplex Picodroplet Digital PCR to Detect KRAS Mutations in Circulating DNA from the Plasma of Colorectal Cancer Patients (2013)

This work demonstrates the clinical utility of multiplex dPCR to screen for multiple mutations simultaneously with a sensitivity sufficient to detect mutations in circulating DNA obtained by noninvasive blood collection.
Recombinase‐mediated cassette exchange ( RMCE ) for monoclonal antibody expression in the commercially relevant CHOK1SV cell line (2015)

To meet product quality and cost parameters for therapeutic monoclonal antibody (mAb) production, cell lines are required to have excellent growth, stability, and productivity characteristics. In particular, cell line generation stability is critical to the success of a program, especially where high cell line generation numbers are required for large in-market supply. However, a typical process for developing such cell lines is laborious, lengthy, and costly. In this study, we applied a FLP/FRT recombinase-mediated cassette exchange (RMCE) system to build a site-specific integration (SSI) system for mAb expression in the commercially relevant CHOK1SV cell line. Using a vector with a FRT-flanked mAb expression cassette, we generated a clonal cell line with good productivity, long-term production stability, and low mAb gene-copy number indicating the vector was located in a 'hot-spot.' A SSI host cell line was made by removing the mAb genes from the 'hot-spot' by RMCE, creating a 'landing pad' containing two recombination cassettes that allow targeting of one or two copies of recombinant genes. Cell lines made from this host exhibited excellent growth and productivity profiles, and stability for at least 100 generations in the absence of selection agents. Importantly, while clones containing two copies had higher productivity than single copy clones, both were stable over many generations. Taken together, this study suggests the use of FLP-based RMCE to develop SSI host cells for mAb production in CHOK1SV offers significant savings in both resources and overall cell line development time, leading to a shortened 'time-to-clinic' for therapeutic mAbs.
Immunotoxins (1985)

Exhausted CD8 T (Tex) cells are a distinct cell lineage that arise during chronic infections and cancers in animal models and humans. Tex cells are characterized by progressive loss of effector functions, high and sustained inhibitory receptor expression, ...Read More
Bypass of Senescence After Disruption of p21 CIP1/WAF1 Gene in Normal Diploid Human Fibroblasts (1997)

Most somatic cells die after a finite number of cell divisions, a phenomenon described as senescence. The p21(CIP1/WAF1) gene encodes an inhibitor of cyclin-dependent kinases. Inactivation of p21 by two sequential rounds of targeted homologous recombination was sufficient to bypass senescence in normal diploid human fibroblasts. At the checkpoint between the prereplicative phase of growth and the phase of chromosome replication, cells lacking p21 failed to arrest the cell cycle in response to DNA damage, but their apoptotic response and genomic stability were unaltered. These results establish the feasibility of using gene targeting for genetic studies of normal human cells.
Starch : properties and potential (1987)

Starch Availability and Utilization Starch Granule Structure and Function: A Physiochemical Approach Morphology and Composition of Starch Physically Modified Starches Starch Biomass A Chemical Feedstock for Enzyme and Fermentation Processes.
Stimulatory action of protein kinase Cɛ isoform on the slow component of delayed rectifier K+ current in guinea‐pig atrial myocytes (2007)

The present study provides experimental evidence to suggest that, in native guinea-pig cardiac myocytes, activation of PKC contributes to alpha(1)-adrenoceptor-mediated potentiation of I (Ks) and that epsilon is the isoform predominantly involved in this PKC action.
Peroxidatic oxidation of catecholamines. A kinetic electron spin resonance investigation using the spin stabilization approach. (1984)

Using spin stabilization, ESR measurements have been made of o-semiquinone production from the horseradish peroxidase-H2O2 oxidation of catecholamine substrates. The termination rate constant for semiquinones stabilized with Zn2+ at pH 5 is about 10(4) times smaller than for uncomplexed semiquinones at neutral pH. Stabilization allows steady state concentrations of semiquinones to be obtained. The duration of the steady state is dependent upon the concentrations of enzyme, hydrogen peroxide, and catecholamine substrate. The relative reactivity of the substrates 3,4-dihydroxyphenylalanine, norepinephrine, and dopamine at pH 5 is 1:8:40. The effects of phenol and ascorbate were studied and shown to be consistent with scavenging of phenoxyl radicals by catecholamine and semiquinone radicals by ascorbate, respectively.
Novel sponge-derived amino acids. 12. Tryptophan-derived pigments and accompanying sesterterpenes from Fascaplysinopsis reticulata (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTNovel sponge-derived amino acids. 12. Tryptophan-derived pigments and accompanying sesterterpenes from Fascaplysinopsis reticulataCarlos Jimenez, Emilio Quinoa, Madeline Adamczeski, Lisa M. Hunter, and Phillip CrewsCite this: J. Org. Chem. 1991, 56, 10, 3403–3410Publication Date (Print):May 1, 1991Publication History Published online1 May 2002Published inissue 1 May 1991https://pubs.acs.org/doi/10.1021/jo00010a041https://doi.org/10.1021/jo00010a041research-articleACS PublicationsRequest reuse permissionsArticle Views575Altmetric-Citations88LEARN 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
A Small Viral RNA Is Required for in Vitro Packaging of Bacteriophage φ29 DNA (1987)

A small RNA of Bacillus subtilis bacteriophage phi 29 is shown to have a novel and essential role in viral DNA packaging in vitro. This requirement for RNA in the encapsidation of viral DNA provides a new dimension of complexity to the attendant protein-DNA interactions. The RNA is a constituent of the viral precursor shell of the DNA-packaging machine but is not a component of the mature virion. Studies of the sequential interactions involving this RNA molecule are likely to provide new insight into the structural and possible catalytic roles of small RNA molecules. The phi 29 assembly in extracts and phi 29 DNA packaging in the defined in vitro system were strongly inhibited by treatment with the ribonucleases A or T1. However, phage assembly occurred normally in the presence of ribonuclease A that had been treated with a ribonuclease inhibitor. An RNA of approximately 120 nucleotides co-purified with the phi 29 precursor protein shell (prohead), and this particle was the target of ribonuclease action. Removal of RNA from the prohead by ribonuclease rendered it inactive for DNA packaging. By RNA-DNA hybridization analysis, the RNA was shown to originate from a viral DNA segment very near the left end of the genome, the end packaged first during in vitro assembly.