gebhart/patrepeval huggingface dataset:
Seed-Specific Over-Expression of an Arabidopsis cDNA Encoding a Diacylglycerol Acyltransferase Enhances Seed Oil Content and Seed Weight (2001)

We recently reported the cloning and characterization of an Arabidopsis (ecotype Columbia) diacylglycerol acyltransferase cDNA (Zou et al., 1999) and found that in Arabidopsis mutant line AS11, an ethyl methanesulfonate-induced mutation at a locus on chromosome II designated as Tag1 consists of a 147-bp insertion in the DNA, which results in a repeat of the 81-bp exon 2 in the Tag1 cDNA. This insertion mutation is correlated with an altered seed fatty acid composition, reduced diacylglycerol acyltransferase (DGAT; EC 2.3.1.20) activity, reduced seed triacylglycerol content, and delayed seed development in the AS11 mutant. The effect of the insertion mutation on microsomal acyl-coenzyme A-dependent DGAT is examined with respect to DGAT activity and its substrate specificity in the AS11 mutant relative to wild type. We demonstrate that transformation of mutant AS11 with a single copy of the wild-type Tag1 DGAT cDNA can complement the fatty acid and reduced oil phenotype of mutant AS11. More importantly, we show for the first time that seed-specific over-expression of the DGAT cDNA in wild-type Arabidopsis enhances oil deposition and average seed weight, which are correlated with DGAT transcript levels. The DGAT activity in developing seed of transgenic lines was enhanced by 10% to 70%. Thus, the current study confirms the important role of DGAT in regulating the quantity of seed triacylglycerols and the sink size in developing seeds.
Suppression of human immunodeficiency virus type 1 replication by CD8+ cells: evidence for HLA class I-restricted triggering of cytolytic and noncytolytic mechanisms (1997)

Although CD8+ lymphocytes in human immunodeficiency virus type 1 (HIV-1)-infected individuals have been demonstrated to suppress viral replication, the mechanisms of inhibition have not been defined precisely. A large body of evidence indicates that these cells act via soluble inhibitory factors, but the potential role of HLA class I-restricted cytolysis has remained controversial. Here we demonstrate that HIV-1-specific cytotoxic T lymphocytes (CTL) mediate antiviral suppression by both cytolytic and noncytolytic mechanisms. The predominant mechanism requires direct contact of CTL with the infected cells, is HLA class I restricted, and can achieve complete elimination of detectable virus in infected cell cultures. Inhibition occurs even at high multiplicities of infection or at ratios of CTL to CD4 cells as low as 1:1,000. The other mechanism is mediated by soluble inhibitory factors which are triggered in an antigen-specific and HLA-restricted fashion but then act without HLA restriction. These include MIP-1alpha, MIP-1beta, and RANTES, as well as a distinct factor(s) capable of inhibiting HIV-1 strains insensitive to these chemokines. These data indicate that HIV-1-specific CTL are potent mediators of HIV-1 suppression at cell ratios existing in vivo and demonstrate an antigen-specific trigger for CD8+ cell-derived soluble inhibitory factors. These results suggest that CTL play an important role in the observed antiviral activity of CD8+ cells from infected individuals.
Evaluation of different continuous cell lines in the isolation of mumps virus by the shell vial method from clinical samples (2001)

The Vero and LLC-MK2 cell lines are equally efficient at two and five days incubation for the isolation of the mumps virus from clinical samples, and the use of the shell vial method considerably shortens the time of aetiological diagnosis with higher specificity.
Polymer-assisted-deposition: a chemical solution route for a wide range of materials (2012)

In this tutorial article, the recent development of polymer assisted deposition (PAD) for the growth of a wide range of materials, in particular in thin films, is reviewed. Specifically, we describe the unique chemistry and processes of PAD for the deposition of metals, metal-oxides, metal-nitrides, metal-carbides, and their derived composites. Many examples are given not only to illustrate the powerfulness of PAD for high quality coatings, but also to give readers an opportunity to evaluate this technique for specific applications. The challenging issues related to PAD, based on the authors' experience, are also discussed in this review article.
Single-Locus Control of Saccharin Preference in Mice (1974)

VIDENCE for single-locus control of behavioral differences among inbred strains of mice is accumulating; examples include proneness to audiogenic seizure ' , avoidance learning', various activity measures, and vocalization' ' beginning with .096 percent W/V) and doubling succes- sively to 3.08 percent (W/V)). No differences were found between strains B and D in acuity threshold or aversion threshold. The B mice had a lower threshold for preference and drank more from the higher concentrations when the six solutions were simul- taneously presented. The F, hybrids responded like the B mice. The preference and avoidance thresholds are shown in Figure 1. Note that in comparison with the two other genotypes the area of preference for the D mice is restricted both with respect to range of concentrations (horizontal dimension) and to intensity of preference when it occurs (vertical dimension). This pattern sug- gests the complete dominance of the B strain's prefer- ence for saccharin. The hypothesis was further sup- ported by the response to saccharin of both strains and their hybrid during food deprivation s . Pelz et al. 9 also found large differences between inbred strains and feral mice in their preference for saccharin, and although they reported no data from crosses beyond the F,, their results are compatible with the hypothesis of single-locus regulation of preference for saccharin at moderate concentrations. This paper discusses the results of an experiment in which the genetics of preference were investigated in hybrids between B and D mice. Method
Combining ABCG2 Inhibitors with IMMU-132, an Anti–Trop-2 Antibody Conjugate of SN-38, Overcomes Resistance to SN-38 in Breast and Gastric Cancers (2016)

Sacituzumab govitecan (IMMU-132), an SN-38-conjugated antibody-drug conjugate, is showing promising therapeutic results in a phase I/II trial of patients with advanced Trop-2-expressing, metastatic, solid cancers. As members of the ATP-binding cassette (ABC) transporters confer chemotherapy resistance by active drug efflux, which is a frequent cause of treatment failure, we explored the use of known inhibitors of ABC transporters for improving the therapeutic efficacy of IMMU-132 by overcoming SN-38 resistance. Two human tumor cell lines made resistant to SN-38, MDA-MB-231-S120 (human breast cancer) and NCI-N87-S120 (human gastric cancer), were established by continuous exposure of the parental cells to stepwise increased concentrations of SN-38 and analyzed by flow cytometry for functional activities of ABCG2 and ABCB1, immunoblotting and qRT-PCR for the expression of ABCG2 at both protein and mRNA levels, and MTS assays for the potency of SN-38 alone or in combination with a modulator of ABC transporters. MDA-MB-231-S120 and NCI-N87-S120 displayed reduced sensitivity to SN-38 in vitro, with IC50 values approximately 50-fold higher than parental MDA-MB-231 and NCI-N87 cells. The increase in drug resistance of both S120 cell populations is associated with the expression of functional ABCG2, but not ABCB1. Importantly, treatment of both S120 sublines with known ABCG2 inhibitors (fumitremorgin C, Ko143, and YHO-13351) restored toxicity of SN-38, and the combination of YHO-13351 with IMMU-132 increased the median survival of mice bearing NCI-N87-S120 xenografts. These results provide a rationale for combination therapy of IMMU-132 and inhibitors of ABC transporters, such as YHO-13351. Mol Cancer Ther; 15(8); 1910-9. ©2016 AACR.
Carbon-13 Labeling for Quantitative Analysis of Molecular Movement in Heterogeneous Organic Materials Using Secondary Ion Mass Spectrometry (2007)

Secondary ion mass spectrometry (SIMS) is used to probe the movement of macromolecules in heterogeneous organic systems. Using 13C tracer labeling and two model systems, polystyrene/poly(2-vinylpyridine) (PS/P2VP) and polystyrene/poly(4-bromostyrene) (PS/P4BrS), the diffusion of 13C-labeled PS has been investigated near the respective heterogeneous interfaces using a CAMECA-IMS-6F magnetic sector mass spectrometer. 13C labeling has been shown to greatly minimize matrix effects (i.e., changes in secondary ion yields due to changing chemical environment) in heterogeneous systems. P2VP is a nitrogen-rich polymer (C7H7N monomer composition), making it an excellent model polymer for exploration of this technique for potential future use in biological applications, and probing the PS/P4BrS interface demonstrates the versatility of this technique for analysis of various heteroatom-containing materials. Results confirm that the 13C-labeling method does indeed allow for quantitative analysis of molecular movement in heterogeneous organic systems containing matrix-enhancing heteroatoms such as nitrogen. Therefore, extension of this method to more complicated biological systems involving multiple heteroatoms (oxygen, nitrogen, etc.), layers, and heterogeneous interfaces, as well as two- and three-dimensional profiling and imaging using SIMS, can be envisaged.
Computing parallel prefix and reduction using coterie structures (2003)

The efficient computation of region parameters in image understanding by a SIMD (single-instruction multiple-data) array requires that those regions be processed simultaneously. The difficulty is in orchestrating nonuniform data-dependent communication using only a single thread of control. The authors have found that, on reconfigurable broadcast meshes, coterie structures can be used to overcome this problem. They present a deterministic algorithm to compute parallel prefix in O(log N) communication steps for a number of real images and sketch a randomized reduction algorithm based on graph contraction that has O(log N) complexity for all images.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Human plasma P component: isolation and characterization (1978)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTHuman plasma P component: isolation and characterizationArthur R. Thompson and David L. EnfieldCite this: Biochemistry 1978, 17, 20, 4304–4311Publication Date (Print):October 1, 1978Publication History Published online1 May 2002Published inissue 1 October 1978https://pubs.acs.org/doi/10.1021/bi00613a030https://doi.org/10.1021/bi00613a030research-articleACS PublicationsRequest reuse permissionsArticle Views57Altmetric-Citations48LEARN 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
In vitro Cultivation and Experimental Inoculation of Sarcocystis falcatula and Sarcocystis neurona Merozoites into Budgerigars (Melopsittacus undulatus) (1997)

This is a report of the isolation and in vitro propagation of merozoites of Sarcocystis falcatula. Culture-derived S. falcatula merozoites remained infectious after several passages in tissue culture as determined by the susceptibility of experimentally inoculated Melopsittacus undulatus that died of pulmonary sarcocystosis after experimental inoculation. There was no obvious clinical disease or lesion when Sarcocystis neurona merozoites were used to inoculate M. undulatus. On the basis of the biological infectivity data, S. falcatula and S. neurona are not synonymous as suggested from limited molecular data.
The Influence of Neuroactive Steroid Lipophilicity on GABAAReceptor Modulation: Evidence for a Low-Affinity Interaction (2009)

Anesthetic steroids with actions at gamma-aminobutyric acid type A receptors (GABA(A)Rs) may access transmembrane domain binding site(s) directly from the plasma cell membrane. Accordingly, the effective concentration in lipid phase and the ability of the steroid to meet pharmacophore requirements for activity will both contribute to observed steady-state potency. Furthermore, onset and offset of receptor effects may be rate limited by lipid partitioning. Here we show that several GABA-active steroids, including naturally occurring neurosteroids, of different lipophilicity differ in kinetics and potency at GABA(A)Rs. The hydrophobicity ranking predicted relative potency of GABA(A)R potentiation and predicted current offset kinetics. Kinetic offset differences among steroids were largely eliminated by gamma-cyclodextrin, a scavenger of unbound steroid, suggesting that affinity differences among the analogues are dwarfed by the contributions of nonspecific accumulation. A 7-nitrobenz-2-oxa-1,3-diazole (NBD)-tagged fluorescent analogue of the low-lipophilicity alphaxalone (C17-NBD-alphaxalone) exhibited faster nonspecific accumulation and departitioning than those of a fluorescent analogue of the high-lipophilicity (3alpha,5alpha)-3-hydroxypregnan-20-one (C17-NBD-3alpha5alphaA). These differences were paralleled by differences in potentiation of GABA(A)R function. The enantiomer of C17-NBD-3alpha5alphaA, which does not satisfy pharmacophore requirements for steroid potentiation, exhibited identical fluorescence kinetics and distribution to C17-NBD-3alpha5alphaA, but was inactive at GABA(A)Rs. Simple simulations supported our major findings, which suggest that neurosteroid binding affinity is low. Therefore both specific (e.g., fulfilling pharmacophore requirements) and nonspecific (e.g., lipid solubility) properties contribute to the potency and longevity of anesthetic steroid action.
De Novo Synthesis of Tamiflu via a Catalytic Asymmetric Ring-Opening of meso-Aziridines with TMSN3 (2006)

An asymmetric ring-opening reaction of meso-aziridines with TMSN3 was developed using a catalyst prepared from Y(OiPr)3 and chiral ligand 2 in a 1:2 ratio. Excellent enantioselectivity was realized from a wide range of substrates with a practical catalyst loading. The products were efficiently converted to enantiomerically enriched 1,2-diamines, which are versatile chiral building blocks for pharmaceuticals and chiral ligands. This reaction was applied to a catalytic asymmetric synthesis of Tamiflu, a very important anti-influenza drug containing a chiral 1,2-diamino functionality.
RNA Interference of Signal Peptide-binding Protein SRP54 Elicits Deleterious Effects and Protein Sorting Defects in Trypanosomes (2002)

Trypanosomes are protozoan parasites that have a major impact on health. This family diverged very early from the eukaryotic lineage and possesses unique RNA processing mechanisms such as trans-splicing and RNA editing. The trypanosome signal recognition particle (SRP) has a unique composition compared with all known SRP complexes, because it contains two RNA molecules, the 7SL RNA and a tRNA-like molecule. RNA interference was utilized to elucidate the essentiality of the SRP pathway and its role in protein translocation in Trypanosoma brucei. The production of double stranded RNA specific for the signal peptide-binding protein SRP54 induced the degradation of the mRNA and a loss of the SRP54 protein. SRP54 depletion elicited inhibition in growth and cytokinesis, suggesting that the SRP pathway is essential. The translocation of four signal peptide-containing proteins was examined. Surprisingly, the proteins were translocated to the endoplasmic reticulum and properly processed. However, the surface EP procyclin, the lysosomal protein p67, and the flagellar pocket protein CRAM were mislocalized and accumulated in megavesicles, most likely because of a secondary effect on protein sorting. The translocation of these proteins to the endoplasmic reticulum under SRP54 depletion suggests that an alternative pathway for protein translocation exists in trypanosomes.
Enhancing and targeting nucleic acid delivery by magnetic force (2003)

Insufficient contact of inherently highly active nucleic acid delivery systems with target cells is a primary reason for their often observed limited efficacy. Physical methods of targeting can overcome this limitation and reduce the risk of undesired side effects due to non-target site delivery. The authors and others have developed a novel means of physical targeting, exploiting magnetic force acting on nucleic acid vectors associated with magnetic particles in order to mediate the rapid contact of vectors with target cells. Here, the principles of magnetic drug and nucleic acid delivery are reviewed, and the facts and potentials of the technique for research and therapeutic applications are discussed. Magnetically enhanced nucleic acid delivery - magnetofection - is universally applicable to viral and non-viral vectors, is extraordinarily rapid, simple and yields saturation level transfection at low dose in vitro. The method is useful for site-specific vector targeting in vivo. Exploiting the full potential of the technique requires an interdisciplinary research effort in magnetic field physics, magnetic particle chemistry, pharmaceutical formulation and medical application.
Response of the neonatal rat cardiomyocyte in culture to energy depletion: effects of cytokines, nitric oxide, and heat shock proteins. (1996)

Cytokines exert autocrine and paracrine effects on the heart, some of which may be mediated by inducible nitric oxide synthase (i-NOS) expression. We studied the effects of cytokine-mediated NO synthesis on cell injury in the presence of deoxyglucose (DOG) and cyanide (CV)(20 mM DOG and 2 mM CN) for up to 3 hours and during recovery (18 hours). The influence of heat shock protein-70 on the extent of myocyte damage was also assessed. IL-1 beta and gamma-IFN act synergistically to enhance NO synthesis by cardiac myocytes. When these cytokines are present, the rate of ATP depletion after DOG and CN is significantly greater than in their absence. When IL-1 beta and gamma-IFN are added with the NOS inhibitor, L-monomethyl-L-arginine (L-NMMA), or when a cytokine that does not produce NO (TNF-alpha) is present, the rate of ATP depletion is no different from the rate seen with DOG and CN alone. After recovery for 18 hours, myocytes that were exposed to IL-1 beta and gamma-IFN release more lactic dehydrogenase and have significantly lower levels of ATP. L-NMMA decreases lactic dehydrogenase release and maintains ATP at levels similar to metabolically inhibited cells in the absence of these cytokines. Consistent with the decreased recovery in ATP with cells incubated with DOG and CN plus IL-1 beta and gamma-IFN is a decrease in cytochrome oxidase activity. Decreases in cellular ATP correspond to increased levels of heat shock protein-70 measured in myocytes after 18 hours of recovery after metabolic inhibition in the presence of IL-1 beta and gamma-IFN. In contrast, prior induction of heat shock protein-70 reduces the rate of ATP depletion in myocytes treated with DOG and CN and maintains ATP at levels that are significantly higher than those seen in non-heat-shocked cells. Recovery of cells exposed to heat shock is also greater, as seen by decreased lactic dehydrogenase and citrate synthase release. The heat-shocked myocytes contain significantly more glycogen than the cells that were not heat shocked. The increased cellular glycogen is likely responsible for the greater lactate production and slower rates of ATP depletion in the heat-shocked, metabolically inhibited cells. Cell survival under conditions of metabolic inhibition is closely related to cellular ATP preservation.
Non-isotopical labeling of murine heterochromatin in situ by hybridization with in vitro-synthesized biotinylated gamma (major) satellite DNA. (1991)

Degenerate probe DNA, homologous to part of the 234-bp repeated mouse gamma (major) satellite DNA, was generated by primer-directed in vitro DNA amplification using the polymerase chain reaction with oligonucleotide primers that anneal in the most conserved parts of the repeat. Probe labeling with biotin was performed during DNA polymerization. In situ hybridization of probe DNA with metaphase chromosome preparations showed exclusive binding of probe molecules to the centromeric region of mouse chromosomes. We applied the probe DNA for labeling of mouse heterochromatin in metaphase chromosomes, as well as interphase cell nuclei, and compared results of probe visualization using avidin tagged with either fluorescein or alkaline phosphatase in combination with a chromogenic substrate.
Centralized Repair of Multiple Node Failures With Applications to Communication Efficient Secret Sharing (2018)

This paper considers a distributed storage system, where multiple storage nodes can be reconstructed simultaneously at a centralized location. This centralized multi-node repair (CMR) model is a generalization of regenerating codes that allow for bandwidth efficient repair of a single-failed node. This paper focuses on the tradeoff between the amount of data stored and repair bandwidth in the CMR model. In particular, repair bandwidth bounds are derived for the minimum storage multi-node repair (MSMR) and the minimum bandwidth multi-node repair (MBMR) operating points. The tightness of these bounds is analyzed via code constructions. The MSMR point is characterized by codes achieving this point under functional repair for the general set of CMR parameters, as well as with codes enabling exact repair for certain CMR parameters. The MBMR point, on the other hand, is characterized with exact repair codes for all CMR parameters for systems that satisfy a certain entropy accumulation property. Finally, the model proposed here is utilized for the secret sharing problem, where the codes for the multi-node repair problem are used to construct communication efficient secret sharing schemes with the property of bandwidth efficient share repair.
Ligand Discovery Using Small-Molecule Microarrays (2011)

Genome-wide association studies and genetic linkage studies have created a growing list of proteins related to disease. Small molecules can serve as useful probes of function for these proteins in a cellular setting or may serve as leads for therapeutic development. High-throughput and general binding assays may provide a path for discovering small molecules that target proteins for which little is known about structure or function or for which conventional functional assays have failed. One such binding assay involves small-molecule microarrays (SMMs) containing compounds that have been arrayed and immobilized onto a solid support. The SMMs can be incubated with a protein target of interest and protein-small molecule interactions may be detected using a variety of fluorescent readouts. Several suitable methods for manufacturing SMMs exist and different immobilization methods may be more or less preferable for any given application. Here, we describe protocols for covalent capture of small molecules using an isocyanate-coated glass surface and detection of binding using purified protein.