gebhart/patrepeval huggingface dataset:
Novel reference genes for quantifying transcriptional responses of <it>Escherichia coli </it>to protein overexpression by quantitative PCR (2011)

&lt;p&gt;Abstract&lt;/p&gt; &lt;p&gt;Background&lt;/p&gt; &lt;p&gt;Accurate interpretation of quantitative PCR (qPCR) data requires normalization using constitutively expressed reference genes. Ribosomal RNA is often used as a reference gene for transcriptional studies in &lt;it&gt;E. coli&lt;/it&gt;. However, the choice of reliable reference genes has not been systematically validated. The objective of this study is to identify a set of reliable reference genes for transcription analysis in recombinant protein over-expression studies in &lt;it&gt;E. coli&lt;/it&gt;.&lt;/p&gt; &lt;p&gt;Results&lt;/p&gt; &lt;p&gt;In this study, the meta-analysis of 240 sets of single-channel Affymetrix microarray data representing over-expressions of 63 distinct recombinant proteins in various &lt;it&gt;E. coli &lt;/it&gt;strains identified twenty candidate reference genes that were stably expressed across all conditions. The expression of these twenty genes and two commonly used reference genes, &lt;it&gt;rrsA &lt;/it&gt;encoding ribosomal RNA 16S and ihfB, was quantified by qPCR in &lt;it&gt;E. coli &lt;/it&gt;cells over-expressing four genes of the 1-Deoxy-D-Xylulose 5-Phosphate pathway. From these results, two independent statistical algorithms identified three novel reference genes &lt;it&gt;cysG&lt;/it&gt;, &lt;it&gt;hcaT&lt;/it&gt;, and &lt;it&gt;idnT &lt;/it&gt;but not &lt;it&gt;rrsA &lt;/it&gt;and &lt;it&gt;ihfB &lt;/it&gt;as highly invariant in two &lt;it&gt;E. coli &lt;/it&gt;strains, across different growth temperatures and induction conditions. Transcriptomic data normalized by the geometric average of these three genes demonstrated that genes of the lycopene synthetic pathway maintained steady expression upon enzyme overexpression. In contrast, the use of rrsA or ihfB as reference genes led to the mis-interpretation that lycopene pathway genes were regulated during enzyme over-expression.&lt;/p&gt; &lt;p&gt;Conclusion&lt;/p&gt; &lt;p&gt;This study identified &lt;it&gt;cysG/hcaT/idnT &lt;/it&gt;to be reliable novel reference genes for transcription analysis in recombinant protein producing &lt;it&gt;E. coli&lt;/it&gt;.&lt;/p&gt;
Effect of chelators on copper metabolism and copper pools in mouse hepatocytes (1989)

Disorders of copper storage are usually treated by chelation therapy. It is generally thought that the chelators act by mobilizing copper from the liver, hence allowing excretion in the urine. This paper has examined the effect of chelators on copper uptake and storage in mouse hepatocytes. Penicillamine, a clinically important chelator, does not block the uptake of copper or remove copper from hepatocytes. Two other copper chelators, sar and diamsar, which form very stable and kinetically inert Cu2+ complexes by encapsulating the metal ion in an organic cage, were shown to block copper accumulation by the cells and to remove up to 80% of cell-associated copper. They also removed most (approximately 80%) of the 64Cu accumulated by the cells in 30 min, but released only a small percentage (less than 20%) of that accumulated over 18 h. The results show that copper in the hepatocyte can be divided into at least two pools, an easily accessible one, and another, not removable even after long-term incubation with any of the chelators. Most of the copper normally found in the cell appeared to be associated with the former pool.
[Effects of adjuvant hyaluronidase in tumors refractory to chemotherapy. Review of the literature and pharmacokinetics of cisplatin after regional administration in animals and humans]. (1997)

Several clinical studies have recently suggested that topical or systemic adjuvant hyaluronidase may increase the therapeutic index of anticancer drugs. In cases of disease progression, further objective responses have been observed after the association of hyaluronidase to the previously employed drugs. Some evidences suggest that hyaluronidase improves local diffusion as well as tissue and tumor uptake of the associated drugs. Hence, plasma and tissue concentrations of platinum following administration of cisplatin alone and associated with hyaluronidase have been investigated in 20 rats after intraperitoneal injection and in 10 patients with colorectal liver metastases and local progression of the disease after regional and systemic chemotherapy with intraarterial cisplatin and intravenous 5-fluorouracil. Three out of six refractory patients treated with hepatic intraarterial cisplatin + hyaluronidase showed one minor response and two stable diseases, respectively, without any apparent increase of treatment related toxicity. In turn, adjuvant hyaluronidase increased both the extent distribution and lasting time of cisplatin in the body and reduced plasma levels of total and free platinum originating from cisplatin, without any modification of either unbound fraction of platinum or total body clearance. Hence, adjuvant hyaluronidase seems to increase tissue extraction of cisplatin and, particularly, liver extraction after intraarterial administration in man. These results encourage further studies aimed to determine the clinical role of adjuvant hyaluronidase in patients refractory to regional chemotherapy.
2-Pyrones. XVIII. 5-Aroyl-2-pyrones and 5-Aroyl-2-pyridones (1956)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXT2-Pyrones. XVIII. 5-Aroyl-2-pyrones and 5-Aroyl-2-pyridonesRichard H. Wiley and S. C. SlaymakerCite this: J. Am. Chem. Soc. 1956, 78, 11, 2393–2398Publication Date (Print):June 1, 1956Publication History Published online1 May 2002Published inissue 1 June 1956https://pubs.acs.org/doi/10.1021/ja01592a014https://doi.org/10.1021/ja01592a014research-articleACS PublicationsRequest reuse permissionsArticle Views287Altmetric-Citations21LEARN 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
Reducing the peak to average ratio of multicarrier GSM and edge signals (2003)

In conventional base station solutions, the carriers transmitted are combined after the power amplifiers. An alternative to this is to combine the carriers in the digital domain. The major drawback of the digital carrier combining is a strongly varying envelope of the composite signal. The high PAR, sets strict requirements for the linearity of the power amplifier. High linearity requirements for the power amplifier leads to low power efficiency and therefore to high power consumption. In this paper, the possibility of reducing the PAR by clipping is investigated in two cases, GSM and EDGE.
Polysaccharides : structural diversity and functional versatility (1998)

Progress in structural characteristics of functional polysaccharides supramolecular structure of polysaccharides x-ray diffraction study of polysaccharides hydrogen bonds in various cellulose derivatives computer modelling of polysaccharide-polysaccharide interactions bacterial polysaccharides related to mammalian structures bacterial polysaccharides - components screening of polysaccharide-producing microorganisms, factors influencing the production, and recovery of microbial polysaccharides hemicelluloses - structure and properties characterization and properties of hyaluronic acid (hyaluronan) agar pectin macromolecular properties of xanthan inclusion complexes of the cyclodextrins synthetic glycopolymers - new tools for glycobiology stereoselective syntheses using carbohydrates as carriers of chiral information structural complexes of chitosan polysaccharides as support for enzyme and cell immobilization bioencapsulation of living cells by entrapment in polysaccharide gels hydrothermal degradation and fractionation of saccharides and polysaccharides conversion of cellulosic feedstocks into useful products polysaccharide surfactants - structure, syntheses and surface-active properties structure and properties of membranes from polysaccharide derivatives cellulose derivatives as liquified-crystalline phase enzymatic hydrolysis of hemicellulose and cellulose acid hydrolysis of hemicellulose and cellulose - theory and applications polysaccharides in peat - biotechnological applications polysaccharides from biomass via thermomechanical process surface modification of polysaccharides under cold plasma conditions.
The ventilatory responsiveness to CO2 below eupnoea as a determinant of ventilatory stability in sleep (2004)

Sleep unmasks a highly sensitive hypocapnia-induced apnoeic threshold, whereby apnoea is initiated by small transient reductions in arterial CO(2) pressure (P(aCO(2))) below eupnoea and respiratory rhythm is not restored until P(aCO(2)) has risen significantly above eupnoeic levels. We propose that the 'CO(2) reserve' (i.e. the difference in P(aCO(2)) between eupnoea and the apnoeic threshold (AT)), when combined with 'plant gain' (or the ventilatory increase required for a given reduction in P(aCO(2))) and 'controller gain' (ventilatory responsiveness to CO(2) above eupnoea) are the key determinants of breathing instability in sleep. The CO(2) reserve varies inversely with both plant gain and the slope of the ventilatory response to reduced CO(2) below eupnoea; it is highly labile in non-random eye movement (NREM) sleep. With many types of increases or decreases in background ventilatory drive and P(aCO(2)), the slope of the ventilatory response to reduced P(aCO(2)) below eupnoea remains unchanged from control. Thus, the CO(2) reserve varies inversely with plant gain, i.e. it is widened with hyperventilation and narrowed with hypoventilation, regardless of the stimulus and whether it acts primarily at the peripheral or central chemoreceptors. However, there are notable exceptions, such as hypoxia, heart failure, or increased pulmonary vascular pressures, which all increase the slope of the CO(2) response below eupnoea and narrow the CO(2) reserve despite an accompanying hyperventilation and reduced plant gain. Finally, we review growing evidence that chemoreceptor-induced instability in respiratory motor output during sleep contributes significantly to the major clinical problem of cyclical obstructive sleep apnoea.
Functional impairment of natural killer cells in active ulcerative colitis: reversion of the defective natural killer activity by interleukin 2. (1992)

We have studied the functional characteristics and clinical importance of the natural killer (NK) cytotoxicity of peripheral blood mononuclear cells (PBMNC) from patients with ulcerative colitis. Normal NK activity was observed in PBMNC from patients with inactive disease, but a pronounced decrease was found in those with active disease. Clinical change from active to inactive disease was associated with enhancement of the depressed NK activity. The impairment of NK cytotoxicity found in patients with active disese could not be ascribed to a deficient number of NK cells as the amounts of HNK-1+, CD16+ (Leu 11), and CD11b (OKM1) cells in PBMNC were within normal ranges. This defective cytotoxic PBMNC activity was normalised by short term (18 hour) incubation with recombinant interleukin 2 (rIL-2). Moreover, long term (5 day) incubation of these effector cells with rIL-2 induced strong cytotoxic activity against NK resistant and NK sensitive target cells in patients with active and inactive disease. We also found that both precursors and effectors of cytotoxic activity promoted by short term and long term incubation with rIL-2 of PBMNC from the patients showed the phenotype of NK cells (CD16+, CD3-). Taken together, these results show that active ulcerative colitis is associated with a defective function of NK cells that is found to be normal in the inactive stage of the disease. The possible pathogenic and therapeutic implications of these findings are discussed.
Autophagy in Health and Disease: A Double-Edged Sword (2004)

Autophagy, the process by which cells recycle cytoplasm and dispose of excess or defective organelles, has entered the research spotlight largely owing to the discovery of the protein components that drive this process. Identifying the autophagy genes in yeast and finding orthologs in other organisms reveals the conservation of the mechanism of autophagy in eukaryotes and allows the use of molecular genetics and biology in different model systems to study this process. By mostly morphological studies, autophagy has been linked to disease processes. Whether autophagy protects from or causes disease is unclear. Here, we summarize current knowledge about the role of autophagy in disease and health.
Immunophenotyping of leukemias using a cluster of differentiation antibody microarray. (2001)

Different leukemias express on their plasma membranes particular subsets of the 247 defined cluster of differentiation (CD) antigens, which may resemble those of precursor cells along the lineages of differentiation to mature myeloid and lymphoid leukocytes. The extent of use of CD antigen expression (immunophenotyping) for identification of leukemias has been constrained by the technique used, flow cytometry, which commonly specifies only three CD antigens in any one assay. Currently, leukemias and lymphomas are diagnosed using a combination of morphology, immunophenotype, cytochemistry, and karyotype. We have developed a rapid, simple procedure, which enables concurrent determination of 50 or more CD antigens on leukocytes or leukemia cells in a single analysis using a microarray of antibodies. A suspension of cells is applied to the array, and cells only bind to antibody dots for which they express the corresponding CD antigen. For patients with significantly raised leukocyte counts, the resulting dot pattern then represents the immunophenotype of those cells. For patients at earlier stages of disease, the diagnosis depends on recognition of dot patterns distinct from the background of normal leukocytes. Distinctive and reproducible dot patterns have been obtained for normal peripheral blood leukocytes, chronic lymphocytic leukemia (CLL), hairy cell leukemia, mantle cell lymphoma, acute myeloid leukemia, and T-cell acute lymphoblastic leukemia. The consensus pattern for CD antigen expression found on CLL cells taken from 20 patients in descending order of cells bound was CD44, HLA-DR, CD37, CD19, CD20, CD5, CD52, CD45RA, CD22, CD24, CD45, CD23, CD21, CD71, CD11c, and CD9. The antigens that provided the best discrimination between CLL and normal peripheral blood leukocytes were CD19, CD20, CD21, CD22, CD23, CD24, CD25, and CD37. Results obtained for the expression of 48 CD antigens from the microarray compared well with flow cytometry. The microarray enables extensive immunophenotyping, and the intact cells captured on antibody dots can be further characterized using soluble, fluorescently labeled antibodies.
T cell antigen receptor phosphorylation induced by an anti-receptor antibody. (1987)

In previous studies we demonstrated that the antigen receptor complex on murine T cells is phosphorylated after antigen or mitogen activation. After the clonotypic structures bind antigen, the invariant subunits or CD3 molecules are the target of dual kinase activation. The antigen receptor CD3-gamma-chain subunit is phosphorylated on serine residues by activated protein kinase C and the p21 subunit is phosphorylated by a tyrosine kinase. Herein we demonstrate that another mechanism of receptor activation by the stimulatory monoclonal antibody 145-2C11, which binds the CD3-epsilon chain, results in a similar pattern of kinase activation and receptor phosphorylation.
Human papillomavirus type distribution in anal cancer and anal intraepithelial lesions (2008)

A systematic review was conducted of HPV type distribution in anal cancer and anal high-grade and low-grade squamous intraepithelial lesions (HSIL and LSIL). A Medline search of studies using PCR or hybrid capture for HPV DNA detection was completed. A total of 1,824 cases were included: 992 invasive anal cancers, 472 HSIL cases and 360 LSIL cases. Crude HPV prevalence in anal cancer, HSIL, and LSIL was 71, 91 and 88%, respectively. HPV16/18 prevalence was 72% in invasive anal cancer, 69% in HSIL and 27% in LSIL. The HPV 16 and/or 18 prevalence in invasive anal cancer cases was similar to that reported in invasive cervical cancer. If ongoing clinical trials show efficacy in preventing anal HPV infection and associated anal lesions, prophylactic HPV vaccines may play an important role for the primary prevention of these cancers in both genders.
Synthesis, Biological Evaluation, and Structure Analysis of a Series of New 1,5-Anhydrohexitol Nucleosides (1995)

In view of the selective anti-HSV activity of 1,5-anhydro-2,3-dideoxy-2- (5-iodouracil-1-yl)-D-arabino-hexitol, a series of novel 1,5-anhydrohexitol nucleosides were synthesized and evaluated for their inhibitory activity against several viruses. The 5-iodouracil 3 and the 5-ethyluracil 4 derivatives are highly selective TK-dependent inhibitors of HSV-1 and HSV-2. Broad anti-herpes virus activity was noticed for 5-fluorocytosine 6 and 2,6-diaminopurine 10 analogues. From a transport study of 3, using the thymidine influx competition method, one can conclude that intracellular uptake of this compound most probably occurs by passive diffusion. X-ray analysis of compounds 3 and 9 showed that the heterocyclic base of 1,5-anhydrohexitol pyrimidine and purine is placed in the axial position and that the sugar ring adopts a slightly distorted chair conformation.
Development and Testing of an Electro-Mechanical Relay to Detect Fallen Distribution Conductors (1982)

If undetected by phase or ground overcurrent relaying methods, fallen distribution conductors or high impedance faults may be a fire hazard and a threat to public safety. Four promising relay schemes to detect these faults are evaluated using both digital and analog techniques and one scheme was chosen for prototype construction. In the light of economic and performance data, a prototype Ratio Ground Relay has been constructed for installation and testing on six Pennsylvania Power and Light distribution feeders.
Gene expression analysis using single molecule detection (2003)

Recent developments of single molecule detection techniques and in particular the introduction of fluorescence correlation spectroscopy (FCS) led to a number of important applications in biological research. We present a unique approach for the gene expression analysis using dual-color cross-correlation. The expression assay is based on gene-specific hybridization of two dye-labeled DNA probes to a selected target gene. The counting of the dual-labeled molecules within the solution allows the quantification of the expressed gene copies in absolute numbers. As detection and analysis by FCS can be performed at the level of single molecules, there is no need for any type of amplification. We describe the gene expression assay and present data demonstrating the capacity of this novel technology. In order to prove the gene specificity, we performed experiments with gene-depleted total cDNA. The biological application was demonstrated by quantifying selected high, medium and low abundant genes in cDNA prepared from HL-60 cells.
Antibody-Dependent and -Independent Protection following Intranasal Immunization of Mice with Rotavirus Particles (1999)

The ability to elicit protective immune responses after intranasal immunization with rotavirus particles, either with or without the attenuated Escherichia coli heat-labile enterotoxin LT(R192G) as an adjuvant, was examined in the adult mouse model. BALB/c mice were administered one or two inoculations of psoralen/UV-inactivated, triple-layered (tl) or double-layered (dl) purified rotavirus particles. Four weeks after immunization, mice were challenged with the murine rotavirus strain EDIM, and the shedding of rotavirus antigen was quantified. Rotaviruses used for immunization included EDIM and heterotypic simian (RRV), bovine (WC3), and human (89-12) strains. tl EDIM stimulated both systemic and intestinal rotavirus antibody responses and complete protection with as little as one 1-microgram dose. Inclusion of LT(R192G) (10 micrograms) significantly increased rotavirus antibody responses and reduced antigen concentrations needed for full protection. Both dl EDIM and heterotypic dl and tl particles stimulated protection, but they did so less than tl EDIM at comparable concentrations, either with or without LT(R192G). When B-cell-deficient microMt mice were immunized with tl EDIM particles, protection was reduced to levels similar to those induced with dl EDIM and heterotypic particles in BALB/c mice. However, dl EDIM particles induced similar levels of protection in both mouse strains. The protection stimulated by tl or dl EDIM particles was not diminished by CD8 cell depletion prior to immunization in either strain of mice. These results indicate that tl EDIM induced immunity at least partially through responses to its outer capsid proteins, presumably by stimulation of serotype-specific neutralizing antibody. In contrast, the other particles stimulated protection primarily by an antibody-independent mechanism. Finally, depletion of CD8 cells had no effect on protection by either mechanism.
Application of Complex Macromolecular Architectures for Advanced Microelectronic Materials (2002)

The distinctive features of well-defined, three-dimensional macromolecules with topologies designed to enhance solubility and amplify end-group functionality facilitated nanophase morphologies in mixtures with organosilicates and ultimately nanoporous organosilicate networks. Novel macromolecular architectures including dendritic and star-shaped polymers and organic nanoparticles were prepared by a modular approach from several libraries of building blocks including various generations of dendritic initiators and dendrons, selectively placed to amplify functionality and/or arm number, coupled with living polymerization techniques. Mixtures of an organosilicate and the macromolecular template were deposited, cured, and the phase separation of the organic component, organized the vitrifying organosilicate into nanostructures. Removal of the sacrificial macromolecular template, also denoted as porogen, by thermolysis, yielded the desired nanoporous organosilicate, and the size scale of phase separation was strongly dependent on the chain topology. These materials were designed for use as interlayer, ultra-low dielectric insulators for on-chip applications with dielectric constant values as low as 1.5. The porogen design, chemistry and role of polymer architecture on hybrid and pore morphology will be emphasized.