gebhart/patrepeval huggingface dataset:
The Accessory Subunit of Xenopus laevis Mitochondrial DNA Polymerase γ Increases Processivity of the Catalytic Subunit of Human DNA Polymerase γ and Is Related to Class II Aminoacyl-tRNA Synthetases (1999)

Peptide sequences obtained from the accessory subunit of Xenopus laevis mitochondrial DNA (mtDNA) polymerase gamma (pol gamma) were used to clone the cDNA encoding this protein. Amino-terminal sequencing of the mitochondrial protein indicated the presence of a 44-amino-acid mitochondrial targeting sequence, leaving a predicted mature protein with 419 amino acids and a molecular mass of 47.3 kDa. This protein is associated with the larger, catalytic subunit in preparations of active mtDNA polymerase. The small subunit exhibits homology to its human, mouse, and Drosophila counterparts. Interestingly, significant homology to glycyl-tRNA synthetases from prokaryotic organisms reveals a likely evolutionary relationship. Since attempts to produce an enzymatically active recombinant catalytic subunit of Xenopus DNA pol gamma have not been successful, we tested the effects of adding the small subunit of the Xenopus enzyme to the catalytic subunit of human DNA pol gamma purified from baculovirus-infected insect cells. These experiments provide the first functional evidence that the small subunit of DNA pol gamma stimulates processive DNA synthesis by the human catalytic subunit under physiological salt conditions.
Synthesis of Optically Active Calanolides A and B (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis of Optically Active Calanolides A and BPrashant P. Deshpande, Frank Tagliaferri, Samuel F. Victory, Shija Yan, and David C. BakerCite this: J. Org. Chem. 1995, 60, 10, 2964–2965Publication Date (Print):May 1, 1995Publication History Published online1 May 2002Published inissue 1 May 1995https://pubs.acs.org/doi/10.1021/jo00115a007https://doi.org/10.1021/jo00115a007research-articleACS PublicationsRequest reuse permissionsArticle Views1027Altmetric-Citations34LEARN 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 (2)»Supporting Information Supporting Information Get e-Alerts
Enhanced Propellant Combustion with Nanoparticles (2003)

Enhanced burn rate results are presented for ammonium perchlorate/Al nanoparticle strand burners at atmospheric (and higher) pressure and for the comparative combustion in a high pressure closed vessel of a solid propellant containing 15% of either conventional micrometer-scale Al or nanometric Al. The burn rate at the smallest nanometric Al particle size appears to be asymptotically approaching an inverse particle-diameter-squared dependence.
Interferon-Induced and Double-Stranded RNA-Activated Enzymes: A Specific Protein Kinase and 2′,5′-Oligoadenylate Synthetases (1991)

Treatment of cells with interferon (IFN) results in the induction of two double-stranded RNA (dsRNA)-activated enzymes: a specific protein kinase and 2'-5' linked oligoadenylate [pppA(2'p5'A)n referred to as 2-5A] synthetases. The protein kinase, when activated by dsRNA, becomes autophosphorylated and catalyzes and phosphorylation of the protein synthesis initiation factor, eIF2. The 2-5A synthetases, when activated by dsRNA, form 2-5A molecules capable of activating a latent endoribonuclease that degrades RNA. By inhibiting initiation of protein synthesis or by degrading of RNA, these enzymes play key roles in two independent pathways that regulate overall protein synthesis.
Diagnosis of breast cancer using diffuse reflectance spectroscopy: Comparison of a Monte Carlo versus partial least squares analysis based feature extraction technique (2006)

The features extracted from the Monte Carlo based analysis were hemoglobin saturation, total hemoglobin concentration, beta-carotene concentration and the mean (wavelength averaged) reduced scattering coefficient. Beta-carotene concentration was positively correlated and the mean reduced scattering coefficient was negatively correlated with percent adipose tissue content in normal breast tissues. In addition, there was a statistically significant decrease in the beta-carotene concentration and hemoglobin saturation, and a statistically significant increase in the mean reduced scattering coefficient in malignant tissues compared to non-malignant tissues. The features extracted from the partial least squares analysis were a set of principal components. A subset of principal components showed that the diffuse reflectance spectra of malignant breast tissues displayed an increased intensity over wavelength range of 440-510 nm and a decreased intensity over wavelength range of 510-600 nm, relative to that of non-malignant breast tissues. The diagnostic performance of the classification algorithms based on both feature extraction techniques yielded similar sensitivities and specificities of approximately 80% for discriminating between malignant and non-malignant breast tissues. While both methods yielded similar classification accuracies, the model based approach provided insight into the physiological and structural features that discriminate between malignant and non-malignant breast tissues.
Regulation of extracellular matrix RNA levels in cultured smooth muscle cells (1989)

We have examined how the alpha 2(I), alpha 1(III), alpha 1(IV), and alpha 2(V) collagen genes as well as the thrombospondin and fibronectin genes are regulated by conditions that modulate the proliferation of smooth muscle cells in vitro. We find that smooth muscle cells (SMC) arrested by low serum containing media continue to express similar or slightly lower levels of mRNA for all the genes studied except type III collagen which exhibited a 5-fold increase. By contrast, when SMC are density-arrested, a coordinate increase in mRNA levels for all the extracellular matrix genes studied is observed. The increases range from approximately 1.5-fold for fibronectin to 5-fold for type III collagen. The mRNA levels for beta-tubulin and vimentin, however, are decreased in these density-arrested cells. Interestingly, the time course of increase for type IV collagen and fibronectin can be distinguished from the other extracellular matrix genes and best correlates with an increase in cell-cell contact. The increase in steady-state RNA levels for alpha 1(IV) collagen is not shared by fibroblasts similarly treated and may provide a useful marker for SMC in culture. Heparin, a potent inhibitor of SMC growth, increased the level of type III collagen mRNA about 2.5-fold and also increased the level of alpha 2(V) collagen and fibronectin. Transforming growth factor-beta is found to be a cell density-dependent modulator of SMC growth. Surprisingly, transforming growth factor-beta had little effect on most of the extracellular matrix genes studied. However, transforming growth factor-beta treatment of SMC increased thrombospondin mRNA levels about 4-fold, whereas type IV collagen mRNA exhibited a 2-fold increase. We conclude that type III collagen mRNA levels are positively and tightly coupled to SMC quiescence. The effect of cellular quiescence on other extracellular matrix mRNAs is complex but, in general, positive. This is particularly evident in SMC arrested by high cell density.
Eight-channel iTRAQ Enables Comparison of the Activity of Six Leukemogenic Tyrosine Kinases (2007)

There are a number of leukemogenic protein-tyrosine kinases (PTKs) associated with leukemic transformation. Although each is linked with a specific disease their functional activity poses the question whether they have a degree of commonality in their effects upon target cells. Exon array analysis of the effects of six leukemogenic PTKs (BCR/ABL, TEL/PDGFRbeta, FIP1/PDGFRalpha, D816V KIT, NPM/ALK, and FLT3ITD) revealed few common effects on the transcriptome. It is apparent, however, that proteome changes are not directly governed by transcriptome changes. Therefore, we assessed and used a new generation of iTRAQ tagging, enabling eight-channel relative quantification discovery proteomics, to analyze the effects of these six leukemogenic PTKs. Again these were found to have disparate effects on the proteome with few common targets. BCR/ABL had the greatest effect on the proteome and had more effects in common with FIP1/PDGFRalpha. The proteomic effects of the four type III receptor kinases were relatively remotely related. The only protein commonly affected was eosinophil-associated ribonuclease 7. Five of six PTKs affected the motility-related proteins CAPG and vimentin, although this did not correspond to changes in motility. However, correlation of the proteomics data with that from the exon microarray not only showed poor levels of correlation between transcript and protein levels but also revealed alternative patterns of regulation of the CAPG protein by different oncogenes, illustrating the utility of such a combined approach.
Teletext Signal Generation Equipment and Systems (1979)

Various systems for utilising the spare time in the vertical blanking interval of a normal television waveform have been proposed as a means of transmitting additional information for engineering tests and for other purposes. Broadly speaking, none of these systems have been viable for home use because of the cost of decoding the information. The advent of large scale integrated circuits (LSI) has changed this situation. In 1972 broadcasting authorities in the United Kingdom proposed systems for transmitting information in diqitally coded forms during the vertical blanking period for display on the home t.v. receiver. Initially these systems had slightly different technical parameters but as the result of development activity involvinq the broadcasting authorities and various receiver manufacturers a unified system was evolved and has been used by both authorities since 1974 (Reference 1.)
Telebuddies (2006)

In this paper we report on our work to enable "laid-back" social interactions using television as a primary interaction medium. By integrating semantic web techniques with interactive television we were able to create smart applications that can run as extensions of television shows and stimulate groups of users to communicate. Groups are based on the shared characteristics that can be found for subsets of spectators. Communication between spectators is brought about at two levels: direct communication like instant messaging and indirect communication like cooperating in a team to win a quiz. Our system does not necessarily require a new television format, but is able to reuse existing television shows and to "socialize" them so they can be re-broadcasted with support for group interaction.
Inhibition of DNA Binding Proteins by Oligonucleotide-Directed Triple Helix Formation (1989)

Oligonucleotides that bind to duplex DNA in a sequence-specific manner by triple helix formation offer an approach to the experimental manipulation of sequence-specific protein binding. Micromolar concentrations of pyrimidine oligodeoxyribonucleotides are shown to block recognition of double helical DNA by prokaryotic modifying enzymes and a eukaryotic transcription factor at a homopurine target site. Inhibition is sequence-specific. Oligonucleotides containing 5-methylcytosine provide substantially more efficient inhibition than oligonucleotides containing cytosine. The results have implications for gene-specific repression by oligonucleotides or their analogs.
Size Matters: Gold Nanoparticles in Targeted Cancer Drug Delivery (2012)

Cancer is the current leading cause of death worldwide, responsible for approximately one quarter of all deaths in the USA and UK. Nanotechnologies provide tremendous opportunities for multimodal, site-specific drug delivery to these disease sites and Au nanoparticles further offer a particularly unique set of physical, chemical and photonic properties with which to do so. This review will highlight some recent advances, by our laboratory and others, in the use of Au nanoparticles for systemic drug delivery to these malignancies and will also provide insights into their rational design, synthesis, physiological properties and clinical/preclinical applications, as well as strategies and challenges toward the clinical implementation of these constructs moving forward.
Validating in utero electroporation for the rapid analysis of gene regulatory elements in the murine telencephalon (2007)

With the ultimate goal of understanding how genetic modules have evolved in the telencephalon, we set out to modernize the functional analysis of cross-species cis-regulatory elements in mouse. In utero electroporation is rapidly replacing transgenesis as the method of choice for gain- and loss-of-function studies in the murine telencephalon, but the application of this technique to the analysis of transcriptional regulation has yet to be fully explored and exploited. To empirically define the developmental stages required to target specific populations of neurons in the dorsal telencephalon, or pallium, which gives rise to the neocortex in mouse, we performed a temporal and spatial analysis of the migratory properties of electroporated versus birth-dated cells. Next, we compared the activities of two known Ngn2 enhancers via transgenesis and in utero electroporation, demonstrating that the latter technique more faithfully reports the endogenous telencephalic expression pattern observed in an Ngn2lacZ knock-in line. Finally, we used this approach to test the telencephalic activities of a series of deletion constructs comprised of the zebrafish ER81 upstream regulatory region, allowing us to identify a previously uncharacterized enhancer that displays cross-species activity in the murine piriform cortex and lateral neocortex, yet not in more medial domains of the forebrain. Taken together, our data supports the contention that in utero technology can be exploited to rapidly examine the architecture and evolution of pallial-specific cis-regulatory elements.
Transfer of gene-corrected T cells corrects humoral and cytotoxic defects in patients with X-linked lymphoproliferative disease (2018)

These data demonstrate that autologous T-cell gene therapy corrects SAP-dependent defects and might offer an alternative therapeutic option for patients with X-linked lymphoproliferative disease 1.
Copy number variant detection in inbred strains from short read sequence data (2009)

We have developed an algorithm to detect copy number variants (CNVs) in homozygous organisms, such as inbred laboratory strains of mice, from short read sequence data. Our novel approach exploits the fact that inbred mice are homozygous at virtually every position in the genome to detect CNVs using a hidden Markov model (HMM). This HMM uses both the density of sequence reads mapped to the genome, and the rate of apparent heterozygous single nucleotide polymorphisms, to determine genomic copy number. We tested our algorithm on short read sequence data generated from re-sequencing chromosome 17 of the mouse strains A/J and CAST/EiJ with the Illumina platform. In total, we identified 118 copy number variants (43 for A/J and 75 for CAST/EiJ). We investigated the performance of our algorithm through comparison to CNVs previously identified by array-comparative genomic hybridization (array CGH). We performed quantitative-PCR validation on a subset of the calls that differed from the array CGH data sets.
Possible cell surface receptor for Friend murine leukemia virus isolated with viral envelope glycoprotein complexes (1980)

Water-soluble multimeric complexes of Friend leukemia virus envelope glycoprotein gp85 bind specifically to C57BL/6 mouse spleen leukocytes. Such complexes were used to isolate cell surface receptors for the virus, using an immunoprecipitation technique. The putative rceptor has a molecular weight of 14,000. Mouse H-2 histocompatibility antigens, which are receptors for Semliki Forest virus, are not receptors for Friend leukemia virus.
Chemical and Biological Folding Contribute to Temperature‐Sensitive ΔF508 CFTR Trafficking (2008)

Proteostasis (Balch WE, Morimoto RI, Dillin A, Kelly JW. Adapting proteostasis for disease intervention. Science 2008;319:916-919) refers to the biology that maintains the proteome in health and disease. Proteostasis is challenged by the most common mutant in cystic fibrosis, DeltaF508, a chloride channel [the cystic fibrosis transmembrane conductance regulator (CFTR)] that exhibits a temperature-sensitive phenotype for coupling to the coatomer complex II (COPII) transport machine for exit from the endoplasmic reticulum. Whether rescue of export of DeltaF508 CFTR at reduced temperature simply reflects energetic stabilization of the chemical fold defined by its primary sequence or requires a unique proteostasis environment is unknown. We now show that reduced temperature (30 degrees C) export of DeltaF508 does not occur in some cell types, despite efficient export of wild-type CFTR. We find that DeltaF508 export requires a local biological folding environment that is sensitive to heat/stress-inducible factors found in some cell types, suggesting that the energetic stabilization by reduced temperature is necessary, but not sufficient, for export of DeltaF508. Thus, the cell may require a proteostasis environment that is in part distinct from the wild-type pathway to restore DeltaF508 coupling to COPII. These results are discussed in the context of the energetics of the protein fold and the potential application of small molecules to achieve a proteostasis environment favoring export of a functional form of DeltaF508.
G Protein-Coupled Receptor 30 Localizes to the Endoplasmic Reticulum and Is Not Activated by Estradiol (2008)

The classical estrogen receptor (ER) mediates genomic as well as rapid nongenomic estradiol responses. In case of genomic responses, the ER acts as a ligand-dependent transcription factor that regulates gene expression in estrogen target tissues. In contrast, nongenomic effects are initiated at the plasma membrane and lead to rapid activation of cytoplasmic signal transduction pathways. Recently, an orphan G protein-coupled receptor, GPR30, has been claimed to bind to and to signal in response to estradiol. GPR30 therefore might mediate some of the nongenomic estradiol effects. The present study was performed to clarify the controversy about the subcellular localization of GPR30 and to gain insight into the in vivo function of this receptor. In transiently transfected cells as well as cells endogenously expressing GPR30, we confirmed that the receptor localized to the endoplasmic reticulum. However, using radioactive estradiol, we observed only saturable, specific binding to the classical ER but not to GPR30. Estradiol stimulation of cells expressing GPR30 had no impact on intracellular cAMP or calcium levels. To elucidate the physiological role of GPR30, we performed in vivo experiments with estradiol and G1, a compound that has been claimed to act as selective GPR30 agonist. In two classical estrogen target organs, the uterus and the mammary gland, G1 did not show any estrogenic effect. Taken together, we draw the conclusion that GPR30 is still an orphan receptor.
Domain Architecture of the Heme-Independent Yeast Cystathionine β-Synthase Provides Insights into Mechanisms of Catalysis and Regulation (2000)

Cystathionine beta-synthase from yeast (Saccharomyces cerevisiae) provides a model system for understanding some of the effects of disease-causing mutations in the human enzyme. The mutations, which lead to accumulation of L-homocysteine, are linked to homocystinuria and cardiovascular diseases. Here we characterize the domain architecture of the heme-independent yeast cystathionine beta-synthase. Our finding that the homogeneous recombinant truncated enzyme (residues 1-353) is catalytically active and binds pyridoxal phosphate stoichiometrically establishes that the N-terminal residues 1-353 compose a catalytic domain. Removal of the C-terminal residues 354-507 increases the specific activity and alters the steady-state kinetic parameters including the K(d) for pyridoxal phosphate, suggesting that the C-terminal residues 354-507 compose a regulatory domain. The yeast enzyme, unlike the human enzyme, is not activated by S-adenosyl-L-methionine. The truncated yeast enzyme is a dimer, whereas the full-length enzyme is a mixture of tetramer and octamer, suggesting that the C-terminal domain plays a role in the interaction of the subunits to form higher oligomeric structures. The N-terminal catalytic domain is more stable and less prone to aggregate than full-length enzyme and is thus potentially more suitable for structure determination by X-ray crystallography. Comparisons of the yeast and human enzymes reveal significant differences in catalytic and regulatory properties.
Characterization of thiL, Encoding Thiamin-monophosphate Kinase, in Salmonella typhimurium (1997)

Thiamin pyrophosphate is an essential cofactor that is synthesized de novo by Salmonella typhimurium. In bacteria, the end product of the de novo biosynthetic pathway is thiamin monophosphate, which is then phosphorylated by thiamin-monophosphate kinase (EC 2.7.4.16) to form thiamin pyrophosphate. We have isolated and characterized the thiL gene of S. typhimurium and showed that thiL is a 978-base pair open reading frame encoding a 35-kDa protein with thiamin-monophosphate kinase activity. thiL was located in the 10-centisome region of the S. typhimurium chromosome. We demonstrated that altered thiamin-monophosphate kinase activity resulted in decreased repression of transcription of thiamin pyrophosphate-regulated thiamin biosynthetic genes. In contrast to other thi loci, thiL is not transcriptionally regulated by thiamin pyrophosphate. This result is consistent with a dual role for ThiL in de novo biosynthesis and in salvage of exogenous thiamin.