gebhart/patrepeval huggingface dataset:
Use of lambda gt11 to isolate genes for two pseudorabies virus glycoproteins with homology to herpes simplex virus and varicella-zoster virus glycoproteins (1986)

A library of pseudorabies virus (PRV) DNA fragments was constructed in the expression cloning vector lambda gt11. The library was screened with antisera which reacted with mixtures of PRV proteins to isolate recombinant bacteriophages expressing PRV proteins. By the nature of the lambda gt11 vector, the cloned proteins were expressed in Escherichia coli as beta-galactosidase fusion proteins. The fusion proteins from 35 of these phages were purified and injected into mice to raise antisera. The antisera were screened by several different assays, including immunoprecipitation of [14C]glucosamine-labeled PRV proteins. This method identified phages expressing three different PRV glycoproteins: the secreted glycoprotein, gX; gI; and a glycoprotein that had not been previously identified, which we designate gp63. The gp63 and gI genes map adjacent to each other in the small unique region of the PRV genome. The DNA sequence was determined for the region of the genome encoding gp63 and gI. It was found that gp63 has a region of homology with a herpes simplex virus type 1 (HSV-1) protein, encoded by US7, and also with varicella-zoster virus (VZV) gpIV. The gI protein sequence has a region of homology with HSV-1 gE and VZV gpI. It is concluded that PRV, HSV, and VZV all have a cluster of homologous glycoprotein genes in the small unique components of their genomes and that the organization of these genes is conserved.
The separation of intracellular serum albumin from rat liver (1971)

1. Antibody precipitation of serum albumin from rat liver extracts yields impure preparations of the protein. 2. When rat liver is labelled with l-[1-(14)C]leucine, antibody precipitation of albumin leads to material that is contaminated with a protein or proteins of very high specific radioactivity. Only 10-25% of the radioactivity of the antibody precipitate is associated with serum albumin. 3. A chromatographic procedure is described that can be used to separate radiochemically pure serum albumin from antibody precipitates obtained from extracts of rat liver. 4. Extracellular albumin secreted by liver slices yields a precipitate with antibody which contains much less radioactive impurity. About 70-90% of the radioactivity is associated with serum albumin. Serum albumin separated by antibody precipitation from rat serum labelled in vivo was not contaminated with the radiochemical impurities associated with intracellular albumin. 5. A simple method is described of obtaining the content of serum albumin in rat liver extracts by the technique of isotope dilution and ion-exchange chromatography.
ADAM‐8 isolated from human osteoarthritic chondrocytes cleaves fibronectin at Ala271 (2009)

The results of this study identify ADAM-8 as a fibronectinase in human OA chondrocytes. Because ADAM-8 is capable of producing the fibronectin neoepitopes VRAA(271) and (272)VYQP in human OA cartilage, this enzyme may be an important mediator of cartilage catabolism.
Pharmacology and Therapeutic Applications of A3 Receptor Subtype (2003)

The present study summarizes the biological effects elicit upon A(3) adenosine receptor (A(3)AR) activation in normal and tumor cells. Anti-inflamatory response is mediated upon A(3)AR activation in neutrophils, eosinophils and macrophages via direct effect on cell degranulation or the production of anti-inflamatory cytokines. In basophils, which highly express A(3)AR, degranulation and mediator release upon receptor activation lead to pro-inflammatory effects resulting in bronchospasm and asthma. In other normal cells such as cardiomyocytes, neuronal cells and bone marrow cells A(1)AR activation induces cytoprotective effects in vitro. In vivo, A(3)AR agonists act as cardio- and neuroprotective agents and attenuate ischemic damage. Furthermore, agonists to A(3)AR induce granulocyte colony stimulating factor (G-CSF) production and myeloprotective effect in chemotherapy treated mice. Interestingly, A(3)AR agonists inhibit tumor cell growth both in vitro and in vivo through a cytostatic effect mediated via the de-regulation of the Wnt signaling pathway. The variety of activities elicit by A(3)AR agonists suggest their potential use as therapeutic agents in inflammation, brain/cardiac ischemia and cancer. Antagonists to A(3)AR may be implemented to the therapy of asthma and additional allergic conditions.
Dual function of MyD88 in inflammation and oncogenesis (2013)

These findings present a new dual function model for MyD88 implication in carcinogenesis making it a potential therapeutic target in cancer.
Discovery, Synthesis, and Bioactivity of Bis(heteroaryl)piperazines. 1. A Novel Class of Non-Nucleoside HIV-1 Reverse Transcriptase Inhibitors (1994)

A variety of analogues of 1-[4-methoxy-3,5-dimethylbenzyl]-4-[3-(ethylamino)-2-pyridyl]piperazine hydrochloride (U-80493E) were synthesized and evaluated for their inhibition of human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT). Replacement of the substituted aryl moiety with various substituted indoles provided bis(heteroaryl)piperazines (BHAPs) that were 10-100-fold more potent than U-80493E. The pyridyl portion of the lead molecule was found to be very sensitive to modifications. Extensive preclinical evaluations of several of these compounds led to the selection of 1-[(5-methoxyindol-2-yl)carbonyl]-4-[3-(ethylamino)-2- pyridyl]piperazine methanesulfonate (U-87201E, atevirdine mesylate) for clinical evaluation.
Growth and fabrication with single-walled carbon nanotube probe microscopy tips (2000)

Single-walled carbon nanotube (SWNT) probe microscopy tips were grown by a surface growth chemical vapor deposition method. Tips consisting of individual SWNTs (1.5–4 nm in diameter) and SWNT bundles (4–12 nm in diameter) have been prepared by design through variations in the catalyst and growth conditions. In addition to high-resolution imaging, these tips have been used to fabricate SWNT nanostructures by spatially controlled deposition of specific length segments of the nanotube tips.
Long-term gene delivery into the livers of immunocompetent mice with E1/E4-defective adenoviruses (1997)

We have compared the in vitro and in vivo behaviors of a set of isogenic E1- and E1/E4-defective adenoviruses expressing the lacZ gene of Escherichia coli from the Rous sarcoma virus long terminal repeat. Infection of tumor-derived established cell lines of human origin with the doubly defective adenoviruses resulted in (i) a lower replication of the viral backbone that correlated with reduced levels of E2A-specific RNA and protein, (ii) a significant shutoff of late gene and protein expression, and (iii) no apparent virus-induced cytotoxicity. Independently of the extent of the deletion, the additional inactivation of E4 from the viral backbone therefore drastically disabled the virus in vitro, with no apparent effect on transgene expression. A lacZ-transgenic model was used to compare the different recombinant adenoviruses in the livers of C57BL/6 mice. The immune response to the virally encoded beta-galactosidase was minimal in this model, as infusion of the E1-defective adenovirus resulted in a time course of transgene expression that mimicked that in immunodeficient (nu/nu) mice, with very little inflammation and necrosis in the liver. Administration of a doubly defective adenovirus to the transgenic animals led to long-term extrachromosomal persistence of viral DNA in the liver, with no detectable methylation of CpG dinucleotides. However, transient transgene expression was observed independently of the extent of the E4 deletion, suggesting that the choice of the promoter may be critical to maintain transgene expression from these attenuated adenovirus vectors.
MAP: mobile assistant programming for large scale communication networks (2002)

We have defined a new network programming model called mobile assistant programming (MAP) for development and execution of communication applications in large scale networks of heterogeneous computers. MAP assistants are high-level interpreted programs that can move between nodes, create clones and report results, Their execution is asynchronous and persistent to allow client disconnections and survival of node failures. We have implemented the mobile assistant programming model using the World-Wide Web framework and the scheme programming language. Our initial experience shows that the MAP model is a useful paradigm for programming communication applications in large scale networks.
Bioaccumulation of heavy metals by fimbrial designer adhesins (1999)

Naturally occurring adhesins bind to specific molecular targets in a lock-and-key fashion due to the composition of the binding domain of the adhesin. By introduction of random peptide libraries in a suitable surface exposed carrier protein it is possible to create and select designer adhesins with novel binding affinities. Type 1 fimbriae are surface organelles of Escherichia coli which mediate D-mannose sensitive binding to different host surfaces through the FimH adhesin, an integral part of these organelles. We have studied the ability of the FimH adhesin to display random peptide sequences. By serial selection and enrichment procedures specific sequences were identified which conferred the ability on recombinant cells to adhere to various metal oxides (PbO2, CoO, MnO2, Cr2O3). The properties inherent in these sequences permitted the distinct recognition of metals to varying degrees, indicating that this system allow for the isolation of peptide sequences with a variety of binding avidities. These studies demonstrate the potential and versatility of the FimH display system for presenting random peptide sequences. In addition, the possibility exists for the construction of microorganisms for the bioaccumulation of heavy metals from the environment.
Omega-3 fatty acids in ADHD and related neurodevelopmental disorders (2006)

Omega-3 fatty acids are dietary essentials, and are critical to brain development and function. Increasing evidence suggests that a relative lack of omega-3 may contribute to many psychiatric and neurodevelopmental disorders. This review focuses on the possible role of omega-3 in attention-deficit/hyperactivity disorder (ADHD) and related childhood developmental disorders, evaluating the existing evidence from both research and clinical perspectives. Theory and experimental evidence support a role for omega-3 in ADHD, dyslexia, developmental coordination disorder (DCD) and autism. Results from controlled treatment trials are mixed, but the few studies in this area have involved different populations and treatment formulations. Dietary supplementation with fish oils (providing EPA and DHA) appears to alleviate ADHD-related symptoms in at least some children, and one study of DCD children also found benefits for academic achievement. Larger trials are now needed to confirm these findings, and to establish the specificity and durability of any treatment effects as well as optimal formulations and dosages. Omega-3 is not supported by current evidence as a primary treatment for ADHD or related conditions, but further research in this area is clearly warranted. Given their relative safety and general health benefits, omega-3 fatty acids offer a promising complementary approach to standard treatments.
Characterization of the human gene encoding cytokeratin 17 and its expression pattern. (1992)

Among the members of the cytokeratin (CK) subfamily of intermediate filament (IF) proteins, CK 17 is remarkable as it is normally expressed in the basal cells of complex epithelia but not in stratified or simple epithelia. Because of its unusual expression pattern in normal and diseased states and because of the potential importance of CK 17 in tumor diagnosis, we have characterized the gene(s) and its cDNA-derived amino acid sequence. A cDNA clone encoding CK 17 was isolated from a HeLa cDNA library and used for the determination of the amino acid sequence, for studies of expression and for the screening of human genomic libraries. A number of lambda phage clones were isolated that covered three distinct, non-contiguous gene regions. Only one of these loci contains the functional CK 17 gene which is located only approximately 5 kbp 5'-upstream of the CK 16 gene, whereas the other two contain unprocessed CK 17 pseudogenes. Each of these genes is part of a larger CK type I gene locus the arrangement of which suggests that these genes and pseudogenes have arisen during evolution by duplication events comprising whole multigene loci. The functional CK 17 gene differs from the pseudogenes by the extent of methylation of certain DNA sequences in the 5'-upstream region. The 5 kbp CK 17 gene with 8 exons and 7 introns encodes a polypeptide of 432 amino acids with a calculated molecular weight of 48,000. Using S1-nuclease protection assays and RNAs from several cell lines we identified a single transcriptional start point 26 nucleotides down-stream from a TATA box element. Northern blot hybridization experiments showed a restricted pattern of CK 17 gene expression, supporting the notion that CK 17 synthesis is essentially regulated at the transcriptional level. From these findings and from immunohistological observations, CK 17 synthesis seems to be a marker of basal cell differentiation in complex epithelia and therefore indicative of a certain type of epithelial "stem cells".
[Study on the mechanism of alleviation of myocardial injury after early escharectomy en masse of several burns in rat]. (2006)

Early escharectomy en masse can significantly alleviate the myocardial injury after burns,which might be related to its effect in lowering the deletion rate of myocardial mtDNA at early postburn stage.
Effects of clipping and filtering on the performance of OFDM (2002)

Orthogonal frequency division multiplexing (OFDM) is an attractive technique for wireless communication applications. However, an OFDM signal has a large peak-to-mean envelope power ratio (PMEPR), which can result in significant distortion when transmitted through a nonlinear device, such as a transmitter power amplifier. We investigate, through extensive computer simulations, the effects of clipping and filtering on the performance of OFDM, including the power spectral density, the bit error rate, and the PMEPR. Our results show that clipping and filtering is a promising technique for the transmission of OFDM signals using realistic linear amplifiers.
Metabolism of Pyridine Compounds by Phthalate-Degrading Bacteria (1988)

Bacteria were isolated from marine sediments that grew aerobically on m-phthalate, p-phthalate, or dipicolinate (2,6-pyridine dicarboxylate [2,6-PDCA]). Strain OP-1, which grew on o-phthalate and was previously obtained from a marine source, was also studied. Intact cells of each organism demonstrated Na-dependent oxidation of their growth substrates. Strain PCC5M grew on dipicolinate but did not metabolize m-phthalate. The phthalate degraders, however, demonstrated Na-dependent metabolism of the appropriate PDCA analogs. 2,6-PDCA was transformed by strain CC9M when this strain was grown on m-phthalate, 2,5-PDCA was metabolized by strain PP-1 grown on p-phthalate, and 2,3-PDCA (quinolinate) was oxidized by strain OP-1 grown on o-phthalate. Spectral changes accompanying the Na-dependent transformations of the PDCA analogs suggest the formation of hydroxylated compounds. Metabolism probably occurred via phthalate hydroxylases; this is a previously unrecognized route for the environmental transformation of pyridine compounds. Hydroxylated products may feed into known pathways for the catabolism of pyridines or be photochemically degraded because of their absorbance in the solar actinic range (wavelengths > 300 nm). The results reinforce recent evidence for the broad potential of aromatic hydroxylase systems for the destruction of pollutants.
Engineering III - Phase 1 - 041 (2003)

Engineering III (Ph 1) (Bldg 041)\nCompletion Date: 2003\nSquare Feet: 41,000\nArchitect: MBT Architecture\nGeneral Contractor: Maino Construction Co Inc.\nConstruction System: Steel and masonry frame, masonry and glass curtain wall exterior\nArchitectural Style: Post-Modern\nCal Poly President: Warren J. Baker (1979-Present)\nPost-Modern architecture is a counter reaction to the strict and almost universal modernism of the mid-20th century. It reintroduces elements from historical building styles, although usually without their high level of detail. Common features include columns, pyramids, arches, obelisks, unusual or attention-getting shapes and rooflines, and combinations of stone and glass on the facade.
Paclitaxel pharmacokinetics and pharmacodynamics. (1995)

Paclitaxel (Taxol; Bristol-Myers Squibb Company, Princeton, NJ) displays nonlinear pharmacokinetics in humans. Both peak plasma paclitaxel concentrations and areas under the curve (AUCs) of the concentration versus time profiles will change disproportionately to changes in dose. Models that accurately describe the plasma paclitaxel profile contain two separate saturable processes, both described by Michaelis-Menten kinetics. Pharmacokinetic models using only linear components ultimately fail to describe adequately the disposition of paclitaxel in the body. The major toxicity of paclitaxel, neutropenia, appears to be related to the duration of time that plasma paclitaxel concentrations are at or above a threshold value. This relationship is well described by a sigmoid-Emax (maximum effect) model. Neutropenia is not directly related to either peak paclitaxel plasma concentration or to paclitaxel areas under the curve. A relationship between therapeutic efficacy and paclitaxel disposition is, as yet, undefined.
Regulatory use of endogenous retroviruses (2016)

Immunogenomics
Mammalian genomes contain many endogenous retroviruses (ERVs), which have a range of evolutionary ages. The propagation and maintenance of these genetic elements have been attributed to their ability to contribute to gene regulation. Chuong et al. demonstrate that some ERV families
Membrane-bound phospholipase A1 purified from Escherichia coli (1971)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMembrane-bound phospholipase A1 purified from Escherichia coliCarl J. Scandella and Arthur KornbergCite this: Biochemistry 1971, 10, 24, 4447–4456Publication Date (Print):November 1, 1971Publication History Published online1 May 2002Published inissue 1 November 1971https://pubs.acs.org/doi/10.1021/bi00800a015https://doi.org/10.1021/bi00800a015research-articleACS PublicationsRequest reuse permissionsArticle Views347Altmetric-Citations183LEARN 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
Loss of lamin B1 is a biomarker to quantify cellular senescence in photoaged skin (2017)

Skin ageing is an inevitable consequence of life and accelerated by exposure to ultraviolet (UV) rays. Senescence is an irreversible growth arrest and senescent cells accumulate in ageing tissues, at sites of age-related pathologies and in pre-neoplastic lesions. Conventionally, senescent cells have been detected by senescence associated-β-galactosidase (SA-β-gal) staining, a procedure that requires enzymatic activity, which is lost in fixed tissue samples. We previously demonstrated that loss of lamin B1 is a novel marker to identify senescent cells. Here, we demonstrate that loss of lamin B1 facilitates the detection and quantification of senescent cells upon UV-exposure in vitro and upon chronic UV-exposure and skin regeneration in vivo. Taken together, this marker enables the study of environmental conditions on tissue ageing and regeneration in vivo, serves as a diagnostic tool to distinguish senescent from proliferating cells in pre-neoplastic lesions, and facilitates investigating the role of senescent cells in various age-related pathologies.
Silencers, silencing, and heritable transcriptional states (1992)

Three copies of the mating-type genes, which determine cell type, are found in the budding yeast Saccharomyces cerevisiae. The copy at the MAT locus is transcriptionally active, whereas identical copies of the mating-type genes at the HML and HMR loci are transcriptionally silent. Hence, HML and HMR, also known as the silent mating-type loci, are subject to a position effect. Regulatory sequences flank the silent mating-type loci and mediate repression of HML and HMR. These regulatory sequences are called silencers for their ability to repress the transcription of nearby genes in a distance- and orientation-independent fashion. In addition, a number of proteins, including the four SIR proteins, histone H4, and an alpha-acetyltransferase, are required for the complete repression of HML and HMR. Because alterations in the amino-terminal domain of histone H4 result in the derepression of the silent mating-type loci, the mechanism of repression may involve the assembly of a specific chromatin structure. A number of additional clues permit insight into the nature of repression at HML and HMR. First, an S phase event is required for the establishment of repression. Second, at least one gene appears to play a role in the establishment mechanism yet is not essential for the stable propagation of repression through many rounds of cell division. Third, certain aspects of repression are linked to aspects of replication. The silent mating-type loci share many similarities with heterochromatin. Furthermore, regions of S. cerevisiae chromosomes, such as telomeres, which are known to be heterochromatic in other organisms, require a subset of SIR proteins for repression. Further analysis of the transcriptional repression at the silent mating-type loci may lend insight into heritable repression in other eukaryotes.
Infection of a human respiratory epithelial cell line with rhinovirus. Induction of cytokine release and modulation of susceptibility to infection by cytokine exposure. (1995)

Rhinovirus infections cause over one third of all colds and are a contributing factor to exacerbations of asthma. To gain insights into the early biochemical events that occur in infected epithelial cells, we develop, for the first time, a model in which a pure respiratory epithelial cell population can be routinely infected by rhinovirus. Viral infection was confirmed by demonstrating that viral titers of supernatants and lysates from infected cell increased with time and by PCR. Infection by rhinovirus 14 was inhibited by homotypic antiserum and by antibodies to intercellular adhesion molecule-1 (ICAM-1), the receptor for this virus. Susceptibility of epithelial cells to infection by rhinovirus 14 (but not rhinovirus 2, an ICAM-1 independent strain) can be increased by preexposure of cells to TNF alpha, whereas IFN gamma reduces susceptibility to infection by both rhinovirus strains. Rhinovirus infection per se does not markedly alter ICAM-1 expression on epithelial cells. Finally, we demonstrate that rhinovirus infection induced increased production of IL-8, IL-6, and GM-CSF from epithelial cells. Production of IL-8 correlated with viral replication during the first 24 h after infection. This model should provide useful insights into the pathogenesis of rhinovirus infections.