gebhart/patrepeval huggingface dataset:
Synthesis and antimitogenic activities of four analogs of cyclosporin A modified in the 1-position (1986)

Cyclosporin A (CSA, 1), an immunosuppressive cyclic undecapeptide, contains a unique N-methylated amino acid, (2S,3R,4R,6E)-3-hydroxy-4-methyl-2-(N-methylamino)-6-octenoic++ + acid, called both C-9-ene and MeBmt [(4R)-N-methyl-4-butenyl-4-methylthreonine] that may be essential for the biological activity of CSA. In order to determine the minimal portion of MeBmt needed for antimitogenic activity, four analogues of CSA specifically modified in the 1-position have been synthesized. These are (MeThr1)CSA (4), (MeAbu1)CSA (5), (MeAbu1,Sar10)CSA (6), and [(MeLeu(3-OH)1)]CSA (7). The synthesis of analogues was carried out by forming a linear undecapeptide that was cyclized at the two non-N-methylated amino acids. The structure of cyclic analogues 4-7 and their corresponding precursors were established unequivocally by 1H NMR, FAB mass spectrometry, elemental analysis, and HPLC. The inhibition of Con A stimulated thymocytes by CSA (1), DH-CSA (2), 7, 4, 5, and 6 gave IC50's (nM) of 4, 10, 600, 8 X 10(3), 15 X 10(3), and 40 X 10(3), respectively. The increase in IC50 by modification of the side chain in MeBmt suggested the importance of this amino acid in the 1-position of CSA for full antimitogenic activity.
New Development in the Study of Amorphous Silicon Hydrogen Alloys: The Story of O (1978)

We present results of dark-conductivity, photoconductivity, photoluminescence, and optical-absorption experiments on films of sputtered oxygenated amorphous-silicon-hydrogen alloys ($a\ensuremath{-}{\mathrm{Si}}_{1\ensuremath{-}x}{\mathrm{H}}_{x}$). Films with oxygen (O) are shown to behave much more like glow-discharge-produced $a\ensuremath{-}{\mathrm{Si}}_{1\ensuremath{-}x}{\mathrm{H}}_{x}$ than do O-free films. O is found to enter the amorphous matrix predominantly in an Si-O-Si bridging configuration. Defects associated with the presence of H are shown to be likely centers for radiative recombination, while both O and H may be associated with locally deformable defects.
Transcriptional regulation by Fos and Jun in vitro: interaction among multiple activator and regulatory domains. (1991)

The proteins encoded by the proto-oncogenes c-fos and c-jun (Fos and Jun, respectively) form a heterodimeric complex that regulates transcription by interacting with the DNA-regulatory element known as the activator protein 1 (AP-1) binding site. Fos and Jun are members of a family of related transcription factors that dimerize via a leucine zipper structure and interact with DNA through a bipartite domain formed between regions of each protein that are rich in basic amino acids. Here we have defined other domains in the Fos-Jun heterodimer that contribute to transcriptional function in vitro. Although DNA-binding specificity is mediated by the leucine zipper and basic regions, Jun also contains a proline- and glutamine-rich region that functions as an ancillary DNA-binding domain but does not contribute directly to transcriptional activation. Transcriptional stimulation in vitro was associated with two regions in Fos and a single N-terminal activation domain in Jun. These activator regions were capable of operating independently; however, they appear to function cooperatively in the heterodimeric complex. The activity of these domains was modulated by inhibitory regions in Fos and Jun that repressed transcription in vitro. In the context of the heterodimer, the Jun activation domain was the major contributor to transcriptional stimulation and the inhibitory regions in Fos were the major contributors to transcriptional repression in vitro. Potentially, the inhibitory domains could serve a regulatory function in vivo. Thus, transcriptional regulation by the Fos-Jun heterodimer results from a complex integration of multiple activator and regulatory domains.
Analysis on Rate-Distortion Performance of Compressive Sensing for Binary Sparse Source (2009)

This paper proposes to use a bipartite graph to represent compressive sensing (CS). The evolution of nodes and edges in the bipartite graph, which is equivalent to the decoding process of compressive sensing, is characterized by a set of differential equations. One of main contributions in this paper is that we derive the close-form formulation of the evolution in statistics, which enable us to more accurately analyze the performance of compressive sensing. Based on the formulation, the distortion of random sampling and the rate needed to code measurements are analyzed briefly. Finally, numerical experiments verify our formulation of the evolution and the rate-distortion curves of compressive sensing are drawn to be compared with entropy coding.
Cloning of firefly luciferase cDNA and the expression of active luciferase in Escherichia coli. (1985)

A cDNA library was constructed from firefly (Photinus pyralis) lantern poly(A)+ RNA, using the Escherichia coli expression vector lambda gt11. The library was screened with anti-P. pyralis luciferase (Photinus luciferin:oxygen 4-oxidoreductase, EC 1.13.12.7) antibody, and several cDNA clones expressing luciferase antigens were isolated. One clone, lambda Luc1, contained 1.5 kilobase pairs of cDNA that hybridized to a 1.9- to 2.0-kilobase band on a nitrocellulose blot of electrophoretically fractionated lantern RNA. Hybridization of the cloned cDNA to lantern poly(A)+ RNA selected an RNA that directed the in vitro synthesis of a single polypeptide. This polypeptide comigrated with luciferase on NaDodSO4/PAGE and produced bioluminescence upon the addition of luciferin and ATP. A 1.8-kilobase-pair cDNA was isolated by probing the firefly cDNA library with the cDNA from lambda Luc1. This cDNA contained sufficient coding information to direct the synthesis of active firefly luciferase in E. coli.
Dynamic and Regulated Association of Caveolin with Lipid Bodies: Modulation of Lipid Body Motility and Function by a Dominant Negative Mutant (2003)

Caveolins are a crucial component of caveolae but have also been localized to the Golgi complex, and, under some experimental conditions, to lipid bodies (LBs). The physiological relevance and dynamics of LB association remain unclear. We now show that endogenous caveolin-1 and caveolin-2 redistribute to LBs in lipid loaded A431 and FRT cells. Association with LBs is regulated and reversible; removal of fatty acids causes caveolin to rapidly leave the lipid body. We also show by subcellular fractionation, light and electron microscopy that during the first hours of liver regeneration, caveolins show a dramatic redistribution from the cell surface to the newly formed LBs. At later stages of the regeneration process (when LBs are still abundant), the levels of caveolins in LBs decrease dramatically. As a model system to study association of caveolins with LBs we have used brefeldin A (BFA). BFA causes rapid redistribution of endogenous caveolins to LBs and this association was reversed upon BFA washout. Finally, we have used a dominant negative LB-associated caveolin mutant (cavDGV) to study LB formation and to examine its effect on LB function. We now show that the cavDGV mutant inhibits microtubule-dependent LB motility and blocks the reversal of lipid accumulation in LBs.
Characterization of the transcriptional regulation of the human MT1-MMP gene and association of risk reduction for focal-segmental glomerulosclerosis with two functional promoter SNPs (2008)

Genetic testing for MT1-MMP promoter SNPs could put renal biopsy results into new perspective. An independent study will be required to verify these findings and their possible diagnostic value for differentiation between certain renal diseases.
The Indoleamine 2,3-Dioxygenase Pathway Is Essential for Human Plasmacytoid Dendritic Cell-Induced Adaptive T Regulatory Cell Generation (2008)

Human plasmacytoid dendritic cells (PDCs) can drive naive, allogeneic CD4(+)CD25(-) T cells to differentiate into CD4(+)CD25(+)Foxp3(+) regulatory T cells (Tregs). However, the intracellular mechanism or mechanisms underlying PDC-induced Treg generation are unknown. In this study, we show that human PDCs express high levels of IDO, an intracellular enzyme that catabolizes tryptophan degradation. Triggering of TLR 9 with CpG oligodeoxynucleotides activates PDCs to up-regulate surface expression of B7 ligands and HLA-DR Ag, but also significantly increases the expression of IDO and results in the generation of inducible Tregs from CD4(+)CD25(-) T cells with potent suppressor cell function. Blocking IDO activity with the pharmacologic inhibitor 1-methyl-D-tryptophan significantly abrogates PDC-driven inducible Treg generation and suppressor cell function. Adding kynurenine, the immediate downstream metabolite of tryptophan, bypasses the 1-methyl-D-tryptophan effect and restores PDC-driven Treg generation. Our results demonstrate that the IDO pathway is essential for PDC-driven Treg generation from CD4(+)CD25(-) T cells and implicate the generation of kynurenine pathway metabolites as the critical mediator of this process.
High-Affinity Binding Proteins for N-Acetylchitooligosaccharide Elicitor in the Plasma Membranes from Wheat, Barley and Carrot Cells: Conserved Presence and Correlation with the Responsiveness to the Elicitor (2002)

Binding experiments as well as affinity labeling with an (125)I-labeled 2-(4-aminophenyl)ethylamino derivative of N-acetylchitooctaose revealed the presence of high-affinity binding sites/proteins for N-acetylchitooligosaccharide elicitor in the plasma membrane preparation from suspension-cultured carrot cells, barley cells and wheat leaves. Their binding specificity corresponded with the elicitor activity of N-acetylchitooligosaccharides and related sugars in these plant cells/tissues, and was similar to that reported for the binding site/protein previously reported for suspension-cultured rice cells. The molecular size of the binding proteins identified in carrot, barley and wheat was slightly smaller than that of rice. These plant cells were shown to respond to N-acetylchitooligosaccharides and generate reactive oxygen species, induced medium alkalinization, or previously shown to initiate lignification (wheat leaves, Barber et al. (1989) Physiol. Mol. Plant Pathol. 34: 3). No elicitor-binding protein nor the elicitor-induced cellular responses was detected for a cell line of tobacco BY-2 (BY-2T). On the other hand, another cell line of tobacco BY-2 (BY-2N) showed the presence of elicitor-binding protein and also elicitor-induced medium alkalinization. Thus, there was a good correlation between the existence of high-affinity binding proteins for the elicitor and elicitor-induced cellular responses among tested plant cells. These results indicated the wide distribution of N-acetylchitooligosaccharide elicitor-binding protein among various plants and added further support for the function of these plasma membrane proteins in the perception of the elicitor signal.
Characterization of a proline-rich cell wall protein gene family of soybean. A comparative analysis. (1990)

Further characterization of a proline-rich cell wall protein gene family from soybean (Glycine max (L.) Merr) has been accomplished by the isolation and sequence analysis of two additional genes, SbPRP2 and SbPRP3, which encode mRNAs of 1050 and 650 nucleotides in length, respectively. Like the proline-rich protein gene, SbPRP1, which was previously reported (Hong, J. C., Nagao, R. T., and Key, J. L. (1987) J. Biol. Chem. 262, 8367-8376), these two SbPRP genes encode proteins having a signal peptide sequence and repeats of Pro-Pro-Val-Tyr-Lys. The SbPRP2 gene encodes a protein of 26 kDa which contains a perfect alternating repeat of Pro-Pro-Val-Tyr-Lys and Pro-Pro-Val-Glu-Lys. The SbPRP3 encodes a 10-kDa protein which also contains Pro-Pro-Val-Tyr-Lys as a major amino acid repeat, but the overall amino acid sequence of this protein is more variable than that of SbPRP1 and SbPRP2. RNA blot analyses have demonstrated that there are marked differences in the pattern of expression of each SbPRP in various soybean tissues. In contrast, sequence analysis reveals that the SbPRP genes contain a high degree of sequence conservation. Nucleotide sequence homology extends 90 to 100 base pairs upstream of the transcription initiation site and includes typical CAT and TATA sequences. Approximately 80 base pairs of the 3'-noncoding sequence around the polyadenylation signal is also highly conserved. Therefore, the DNA sequence upstream of the 5'-conserved region is presumed to contain cis-elements accounting for the developmental and tissue specificity of gene expression. While the pentameric repeat structures occur in all SbPRP genes, the encoded proteins are predicted to be different in several features including basicity, substitutions of tyrosine and glutamic acid in the repeat, and the size of the mature protein.
The role of WT1 in Wilms tumorigenesis (1993)

Genetic alterations in tumor suppressor genes are believed to play an important role in the initiation of childhood and adult malignancies. Tumor-specific loss of heterozygosity for particular chromosomal regions has provided the starting point for the cloning of different tumor suppressor genes, including the Wilms tumor predisposing gene, WT1, at chromosome 11p13. This article reviews the pathology and genetics of Wilms tumor, the cloning of WT1, and the WT1 mutations reported thus far in 15 hereditary and nonhereditary Wilms tumors. The presence of constitutional WT1 mutations in 35 patients with the Denys-Drash syndrome (a syndrome consisting of nephropathy, intersex disorders, and Wilms tumor) is also described. To date, mutations in the WT1 gene have been found in less than 10% of Wilms tumors specimens examined and in greater than 95% of Denys-Drash patients. The possible significance of this observation with regard to both the cellular function of the WT1 protein and the involvement of alternative loci in the development of Wilms tumor is discussed.
Total synthesis of sialyl dimeric Lex (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTotal synthesis of sialyl dimeric LexK. C. Nicolaou, C. W. Hummel, and Y. IwabuchiCite this: J. Am. Chem. Soc. 1992, 114, 8, 3126–3128Publication Date (Print):April 1, 1992Publication History Published online1 May 2002Published inissue 1 April 1992https://pubs.acs.org/doi/10.1021/ja00034a063https://doi.org/10.1021/ja00034a063research-articleACS PublicationsRequest reuse permissionsArticle Views796Altmetric-Citations99LEARN 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
Apolipoprotein M associates to lipoproteins through its retained signal peptide (2008)

Apolipoprotein M (apoM) is predominantly associated with HDL. In this study, it was investigated whether apoM's uncleaved signal peptide is necessary for the protein's ability to associate with lipoproteins. ApoM with a cleavable signal peptide, Q22A, was expressed, together with wild-type apoM, in HEK293 cells. On size-exclusion chromatography, the elution profile of wild-type apoM was similar to that of human HDL-associated plasma apoM. In contrast, the size of the Q22A mutant corresponded to free, unassociated apoM. This strongly indicates that the signal peptide is indeed necessary for apoM's ability to associate with lipid.
Abstract 3716: Potent radiation enhancement with VX-984, a selective DNA-PKcs inhibitor for the treatment of NSCLC (2016)

Abstract Ionizing radiation (IR), which is widely used for the treatment of cancer, causes double-strand breaks (DSBs) in DNA. If left unrepaired, these DSBs are lethal to the cell. DNA-dependent protein kinase (DNA-PK) is a key enzyme in the non-homologous end joining (NHEJ) pathway that repairs DSBs caused by IR, or chemotherapeutic agents that cause DSBs such as doxorubicin. The goal of these studies was to characterize the radiation enhancing effects of VX-984, a selective and potent ATP-competitive inhibitor of the catalytic subunit of DNA-PK (DNA-PKcs), with a focus on non-small cell lung cancer (NSCLC) cells and tumor xenografts. VX-984 enhances the cytotoxicity of IR in a panel of cancer cell lines including NSCLC cell lines in vitro with dose enhancement factors (DEF) greater than 3. Notably, VX-984 combined with IR in normal human lung fibroblasts minimally enhanced the cytotoxicity compared to IR alone. Additionally, VX-984 decreased DNA-PKcs autophosphorylation on S2056 both in vitro and in vivo in NSCLC cells and attenuated the decay of the DNA damage markers γH2AX and pKAP1 in response to IR. In NSCLC PDX models VX-984, in combination with IR (2 Gy x 3), caused durable complete responses while IR alone only led to a delay in tumor growth, consistent with delayed DNA damage repair. In these models, the combination of VX-984 and IR was well tolerated. These data demonstrate that VX-984 is a potent radiation-enhancing agent and provide a strong rationale for the use of VX-984 in combination with IR for the treatment of NSCLC. Citation Format: Diane Boucher, Russell Hoover, Yuxin Wang, Yong Gu, David Newsome, Pamella Ford, Cameron Moody, Veronique Damagnez, Reiko Arimoto, Shawn Hillier, Mark Wood, William Markland, Brenda Eustace, Kevin Cottrell, Marina Penney, Brinley Furey, Kirk Tanner, John Maxwell, Paul Charifson. Potent radiation enhancement with VX-984, a selective DNA-PKcs inhibitor for the treatment of NSCLC. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3716.
Enhanced inhibition of colony formation of human renal cell carcinoma in soft agar by the combination of alpha-difluoromethylornithine and recombinant gamma-interferon. (1986)

We studied the inhibitory activity of alpha-difluoromethylornithine (DFMO) and alpha-, recombinant beta-, and recombinant-gamma-interferons (alpha-, rec-beta-, and rec-gamma-IFNs) on in vitro growth of 3 established human urogenital tumors (KO-RCC-1 from renal cell carcinoma, Bewo from choriocarcinoma of the uterus, and HT-1197 from transitional cell carcinoma of the urinary bladder) and 16 primary renal cell carcinomas obtained by nephrectomy. Treatment with DFMO together with rec-IFN-gamma synergistically inhibited KO-RCC-1 cell growth in monolayer culture and in soft agar. The other two established cell lines were less susceptible to this treatment. Combination of DFMO and rec-IFN-gamma was more inhibitory than that of DFMO and either IFN-alpha or rec-IFN-beta. The polyamine content in KO-RCC-1 cells was decreased to a greater extent by combined treatment with DFMO and rec-IFN-gamma than that in Bewo and HT-1197 cells. The effect of these agents in 11 of the 16 primary renal cell carcinomas, which could show clonal growth in double layer soft agar, was examined. More than 50% inhibition of colony growth was seen in only one case (9%) treated with 5 mM DFMO alone and in 2 cases (18%) treated with rec-IFN-gamma alone (1,000 units/ml) but in 10 of the 11 cases (91%) with the combined treatment. Our results indicate that combined treatment with DFMO and rec-IFN-gamma can be more effective than that with either agent individually in inhibiting cell growth of human renal cell carcinoma in vitro.
Caroverine in Tinnitus Treatment (1997)

This study was performed to examine whether a single infusion of caroverine, a quinoxaline-derivative, can be used successfully in the treatment of inner ear tinnitus. Microiontophoretical experiments in guinea-pigs have shown that caroverine acted as a potent competitive alpha-amino-3-hydroxy-5-methyl-4-isoxazone-proprionic acid (AMPA) receptor antagonist and, in higher dosages, a non-competitive N-methyl-d-aspartate (NMDA) antagonist. According to our working hypothesis of the pathophysiology of inner ear tinnitus (cochlear-synaptic tinnitus), these forms of tinnitus occur when the physiological activity of the NMDA and AMPA receptors at the subsynaptic membranes of inner hair cell afferents is disturbed. In total, 60 patients with inner ear tinnitus of assumed cochlear-synaptic pathophysiology were included in the study: after computerized randomization, 30 were treated with caroverine and 30 with placebo. For a response to have occurred, tinnitus had to show a reduction in both subjective rating and psychoacoustic measurement (tinnitus matching). In the caroverine group, 63.3% responded to therapy immediately after the infusion. In the placebo group, none of the patients treated showed a significant response according to the defined success criteria. The results confirm our working hypothesis on the genesis of cochlear-synaptic tinnitus.
Association between Hepatitis C Virus and Very-Low-Density Lipoprotein (VLDL)/LDL Analyzed in Iodixanol Density Gradients (2006)

Hepatitis C virus (HCV) RNA circulates in the blood of persistently infected patients in lipoviroparticles (LVPs), which are heterogeneous in density and associated with host lipoproteins and antibodies. The variability and lability of these virus-host complexes on fractionation has hindered our understanding of the structure of LVP and determination of the physicochemical properties of the HCV virion. In this study, HCV from an antibody-negative immunodeficient patient was analyzed using three fractionation techniques, NaBr gradients, isotonic iodixanol, and sucrose gradient centrifugation. Iodixanol gradients were shown to best preserve host lipoprotein-virus complexes, and all HCV RNA was found at densities below 1.13 g/ml, with the majority at low density, < or =1.08 g/ml. Immunoprecipitation with polyclonal antibodies against human ApoB and ApoE precipitated 91.8% and 95.0% of HCV with low density, respectively, suggesting that host lipoprotein is closely associated with HCV in a particle resembling VLDL. Immunoprecipitation with antibodies against glycoprotein E2 precipitated 25% of HCV with low density, providing evidence for the presence of E2 in LVPs. Treatment of serum with 0.5% deoxycholic acid in the absence of salt produced HCV with a density of 1.12 g/ml and a sedimentation coefficient of 215S. The diameters of these particles were calculated as 54 nm. Treatment of serum with 0.18% NP-40 produced HCV with a density of 1.18 g/ml, a sedimentation coefficient of 180S, and a diameter of 42 nm. Immunoprecipitation analysis showed that ApoB remained associated with HCV after treatment of serum with deoxycholic acid or NP-40, whereas ApoE was removed from HCV with these detergents.
Superconducting Magnet Technology for Accelerators (1984)

Following a major shortage of 99Mo in the 2009–2010 period, concern grew that the aging reactor production facilities needed to be replaced. Most producers were using highly enriched 235U (HEU) as the target material. The Organisation for Economic Co-...Read More