gebhart/patrepeval huggingface dataset:
Potential DNA Vaccine Integration into Host Cell Genome (1995)

Studies have been designed to examine the potential integration of DNA vaccines into the host cell genome. This is of concern because of the possibility of insertional mutagenesis resulting in the inactivation of tumor suppressor genes or the activation of oncogenes. The requirements for adequate testing were determined to be (1) a method to purify host cell genomic DNA from nonintegrated free plasmid, (2) a sensitive method to detect integrated plasmid in the purified genomic DNA, and (3) stringent methods to avoid contamination. These requirements were fulfilled by agarose-gel electrophoresis, the polymerase chain reaction, and separation of each activity with stringent handling procedures, respectively. An exploratory experiment was carried out in which mice were injected with 100 micrograms of vaccine plasmid DNA in each quadriceps. Examination of quadriceps and 12 other tissues at several time points failed to reveal any evidence of integration at a sensitivity level that could detect 1 to 7.5 integrations in 150,000 nuclei. A worst-case scenario determined that this would be at least 3 orders of magnitude below the spontaneous mutation frequency.
Rapid detection of Serpulina hyodysenteriae in diagnostic specimens by PCR (1994)

A PCR assay for the detection of Serpulina hyodysenteriae in diagnostic specimens was developed on the basis of sequence analysis of a recombinant clone designated pRED3C6. Clone pRED3C6, which contained a 2.3-kb DNA fragment unique to S. hyodysenteriae, was identified by screening a plasmid library of S. hyodysenteriae isolate B204 genomic DNA in Escherichia coli by colony immunoblot with the mouse monoclonal antibody 10G6/G10, which was produced against cell-free supernatant antigens from the same isolate. Southern blot analysis of HindIII-digested genomic DNA of S. hyodysenteriae serotypes 1 through 7 and of four weakly beta-hemolytic intestinal spirochetes, including Serpulina innocens, with the 2.3-kb DNA fragment of pRED3C6 indicated that the cloned sequence was present exclusively in the seven serotypes of S. hyodysenteriae. An oligonucleotide primer pair for PCR amplification of a 1.55-kb fragment and an internal oligonucleotide probe were designed and synthesized on the basis of sequence analysis of the 2.3-kb DNA fragment of pRED3C6. Purified genomic DNAs from reference isolates of S. hyodysenteriae serotypes 1 through 9, S. innocens, weakly beta-hemolytic intestinal spirochetes belonging to genotypic groups distinct from those of reference Serpulina spp., other cultivable reference isolates of the order Spirochaetales, and enteric bacteria including Escherichia coli, Salmonella spp., Campylobacter spp., and Bacteroides vulgatus were amplified with the oligonucleotide primer pair in a hot-start PCR. The 1.55-kb products were obtained only in the presence of genomic DNA from each of the nine serotypes of S. hyodysenteriae. The specificity of the 1.55-kb products for S. hyodysenteriae was confirmed on the basis of production of a restriction endonuclease pattern of the PCR products identical to the predicted restriction map analysis of pRED3C6 and positive hybridization signal with the S. hyodysenteriae-specific internal oligonucleotide probe. By using total DNA obtained from normal swine feces inoculated with decreasing concentrations of S. hyodysenteriae cells, the sensitivity of the PCR assay was calculated to be between 1 and 10 organisms per 0.1 g of feces. The PCR assay was 1,000 times more sensitive than conventional culture of dysenteric feces on selective medium. There was complete agreement between the results of PCR assays and anaerobic culture on selective agar medium with diagnostic specimen (n = 9) obtained from six farms on which there were cases with clinical signs suggestive of swine dysentery. Detection of S. hyodysenteriae by PCR amplification of DNA has great potential for rapid identification of S. hyodysenteriae in diagnostic specimens.
HDAC6 and Ovarian Cancer (2013)

The special class IIb histone deacetylase, HDAC6, plays a prominent role in many cellular processes related to cancer, including oncogenesis, the cell stress response, motility, and myriad signaling pathways. Many of the lessons learned from other cancers can be applied to ovarian cancer as well. HDAC6 interacts with diverse proteins such as HSP90, cortactin, tubulin, dynein, p300, Bax, and GRK2 in both the nucleus and cytoplasm to carry out these cancerous functions. Not all pro-cancer interactions of HDAC6 involve deacetylation. The idea of using HDAC6 as a target for cancer treatment continues to expand in recent years, and more potent and specific HDAC6 inhibitors are required to effectively down-regulate the tumor-prone cell signaling pathways responsible for ovarian cancer.
SOME PRELIMINARY THOUGHTS ON LONG RANGE PLANNING FOR THE FEDERAL JUDICIARY (1992)

Considers the "mission" of the federal courts. There is no single, objectively correct conception of the role of the federal courts and that attempting to develop a once-and-for all conception would be a waste of time and could, in-fact, prevent the Long-Range Planning Committee of the Judicial Conference from achieving its potential. Next is a discussion of the conception of long-range planning, in terms of a relatively short event horizon (somewhat arbitrarily set at five years) and the absolutely wide-open scope of the range of proposals that are relevant to the work of this Committee (basically anything and everything). Then there is a description of preliminary thoughts on the role of the Committee to be a kind of permanent Federal Courts Study Committee modelled after comparable Congressional committees. Lastly, this statement will touch briefly on some of the organizational and operational relationships and attitudes that the author deems important as you begin the enterprise of judicial branch planning.
Azaglycosylation of complex stannyl alkoxides with glycal-derived iodo sulfonamides: a straightforward synthesis of sialyl-Lewis X antigen and other oligosaccharide domains (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAzaglycosylation of complex stannyl alkoxides with glycal-derived iodo sulfonamides: a straightforward synthesis of sialyl-Lewis X antigen and other oligosaccharide domainsSamuel J. Danishefsky, Koshi Koseki, David A. Griffith, Jacquelyn Gervay, John M. Peterson, Frank E. McDonald, and Takeshi OriyamaCite this: J. Am. Chem. Soc. 1992, 114, 21, 8331–8333Publication Date (Print):October 1, 1992Publication History Published online1 May 2002Published inissue 1 October 1992https://doi.org/10.1021/ja00047a078RIGHTS & PERMISSIONSArticle Views490Altmetric-Citations71LEARN 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 InReddit PDF (373 KB) Get e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
High-Frequency C-Type Virus Induction by Inhibitors of Protein Synthesis (1974)

When inhibitors of protein synthesis are added to BALB/c mouse cells in culture, induction of naturally integrated C-type RNA virus occurs in a high percentage of cells. The action of protein synthesis inhibitors differs from that of halogenated pyrimidines, another class of virus inducers, in their effects on biologically distinguishable viruses. The use of such inhibitors to study integrated virus expression provides a means for studying gene regulation in mammalian cells.
Micromachined Dual Input Axis Angular Rate Sensor (1996)

The need for inexpensive yet reliable angular rate sensors in fields ranging from automotive to consumer electronics has sparked prolific micromachined angular rate sensor research. The vast majority of research has focused on single input axis angular rate sensors based upon either translational resonance, such as tuning forks, or structural mode resonance, such as vibrating rings. However, this work presents an entirely novel approach based on angular resonance of a rotating rigid rotor suspended by torsional springs. The inherent symmetry of the circular design allows angular rate measurement about two axes simultaneously. Using a commercial micro-accelerometer production process, two versions of a fully integrated, 660 m diameter dual input axis angular rate sensor have been designed, fabricated, and tested. Minimum detectable signals as small as 1.2 /sec over a 25 Hz bandwidth were achieved with untuned rate sensors having mismatched mode frequencies. However, with mode frequency tuning the performance was improved to 10 /min over an equivalent bandwidth.
Binding of specific peroxidase-labeled antibody to placental-type phosphatase on tumor-derived membrane fragments. (1980)

Monospecific antiserum to human placental alkaline phosphatase was purified by immunoabsorption and labeled with horseradish peroxidase. The binding of this labeled antibody to membrane fragments prepared from placental and tumor tissue was measured using agarose gel filtration to separate bound antibody. The antibody bound only to membrane fragments which contained placental phosphatase, and the amount bound varied in the order ascitic fluid membrane fragments greater than tumor extracts greater than placental extracts. Absorption of the antibody with crude placental membrane yielded a population of antibody which reacted with tumor tissue and pure placental enzyme, but only slightly with placental membranes. These results are interpreted to suggest that some antigenic sites are exposed in tumor tissue membranes which are not in placental membranes.
Genomes and Characterization of Phages Bcep22 and BcepIL02, Founders of a Novel Phage Type in Burkholderia cenocepacia (2011)

Within the Burkholderia cepacia complex, B. cenocepacia is the most common species associated with aggressive infections in the lungs of cystic fibrosis patients, causing disease that is often refractive to treatment by antibiotics. Phage therapy may be a potential alternative form of treatment for these infections. Here we describe the genome of the previously described therapeutic B. cenocepacia podophage BcepIL02 and its close relative, Bcep22. Phage Bcep22 was found to contain a circularly permuted genome of 63,882 bp containing 77 genes; BcepIL02 was found to be 62,714 bp and contains 76 predicted genes. Major virion-associated proteins were identified by proteomic analysis. We propose that these phages comprise the founding members of a novel podophage lineage, the Bcep22-like phages. Among the interesting features of these phages are a series of tandemly repeated putative tail fiber genes that are similar to each other and also to one or more such genes in the other phages. Both phages also contain an extremely large (ca. 4,600-amino-acid), virion-associated, multidomain protein that accounts for over 20% of the phages' coding capacity, is widely distributed among other bacterial and phage genomes, and may be involved in facilitating DNA entry in both phage and other mobile DNA elements. The phages, which were previously presumed to be virulent, show evidence of a temperate lifestyle but are apparently unable to form stable lysogens in their hosts. This ambiguity complicates determination of a phage lifestyle, a key consideration in the selection of therapeutic phages.
Properties of SiGe oxides grown in a microwave oxygen plasma (1995)

Thin oxide on strained Si1−xGex surface has been grown using a nonelectron cyclotron resonance mode microwave plasma at low temperatures (150–200 °C). An optimized post-oxidation and post-metal annealing cycle has resulted in very low fixed oxide charge density (1.78×1010/cm2) and moderately low interface trap density (2.9×1011/cm2 eV). A controlled in situ hydrogen-plasma treatment to Si1−xGex has been found to be useful in improving the electrical properties of the oxide. The high electron injection phenomena of metal oxide semiconductor capacitors has been used for charge trapping studies of sites normally present in the SiGe oxides. From the position and the extent of current ledge observed as a function of ramped gate voltage, the capture cross section and the total number of traps have been determined.
国語教育学の研究動向と展望 : 全国大学国語教育学会『国語科教育』掲載論文を中心に (2003)

本稿では, 全国大学国語教育学会誌『国語科教育』に掲載された1998年から2002年までの論文を中心として, 国語教育学の研究動向を把握し, 研究の展望を行った。研究動向の特徴としては, 1)国語教育史の研究においてリテラシー形成過程の史的研究の蓄積が見られること, 2)比較国語教育学において記述研究だけでなく「比較」研究への足がかりが認められること, 3)授業研究・教師研究・学習者研究・発達研究それぞれについて実証的な研究方法の開拓がおこなわれたこと, 4)国語科における教材価値についての吟味・検討が進められたこと, 5)リテラシーを育む足場として国語科カリキュラムの構成原理を追及する研究が進められたこと, 等をあげることができる。蓄積された研究成果を国語科の教員養成・教師教育カリキュラムに反映させることと, カリキュラム研究としてリテラシー教育の再構築をめざす研究を進めていくことが大きな課題である。
Elevation of hepatic glutathione S-transferase activities and protection against mutagenic metabolites of benzo(a)pyrene by dietary antioxidants. (1978)

Abstract Addition of either 2(3)-tert-butyl-4-hydroxyanisole (BHA) or 1,2-dihydro-6-ethoxy-2,2,4-trimethylquinoline (ethoxyquin) to the diet greatly decreases the levels of mutagenic metabolites of benzo(a)pyrene in CD-1 mice. (R. P. Batzinger, S-Y. L. Ou, and E. Bueding, Cancer Res., 38:000, 1978). The mutagenic activity of the urinary metabolites of benzo(a)pyrene is markedly reduced in the presence of glutathione together with the liver cytosols of rats or mice fed on a diet containing BHA. The liver cytosols of mice and rats maintained on control diets are much less effective in this respect. Dietary BHA causes increases in mouse and rat hepatic glutathione S-transferase (EC 2.5.1.18) specific activities with 1,2-dichloro-4-nitrobenzene, 1-chloro-2,4-dinitrobenzene, p-nitrobenzylchloride, and Δ5-androstene-3,17-dione. In the mouse the increases are larger (5- to 10-fold) and are dependent on the dose and duration of administration of BHA. Increases in these glutathione S-transferase specific activities were also observed in mouse hepatic cytosols after feeding of ethoxyquin. Direct addition of reduced glutathione and purified glutathione S-transferases A and B obtained from rat liver to the mutagenicity assay system mimicked the effect of the rodent cytosols. Since BHA and ethoxyquin are known to reduce the neoplastic effects of a variety of potent carcinogens, we suggest that the protective effects of these antioxidants may be accounted for, at least in part, by their ability to elevate the glutathione S-transferases. These enzymes inactivate arene oxides and other hydrophobic electrophiles by catalyzing their conjugation with glutathione.
Rhodobacter capsulatus porphobilinogen synthase, a high activity metal ion independent hexamer (2004)

The evidence presented in this paper supports the unusual position of the R. capsulatus PBGS as not requiring any metal ions for function. Unlike other wild-type PBGS, the R. capsulatus protein is a hexamer with an unusually high specific activity when compared to other octameric PBGS proteins.
Insertion loss reduction between single-mode fibers and diffused channel waveguides (1988)

Methods of reducing the insertion loss between single-mode fibers and graded-index channel waveguides, namely, annealing and backdiffusion, are analyzed theoretically and compared. Mode mismatch and misalignment losses are calculated to determine the best method and the optimal conditions for their use. The main result of this paper is that, in the single-mode regime, there is no apparent advantage in using backdiffusion instead of the simpler annealing process, in contrast with the multimode case. In the coupling loss calculation, a numerical simulation of waveguide formation by potassium-sodium ion exchange in glass is used for illustration.
CheckCell (2014)

Testing and static analysis can help root out bugs in programs, but not in data. This paper introduces data debugging , an approach that combines program analysis and statistical analysis to automatically find potential data errors. Since it is impossible to know a priori whether data are erroneous, data debugging instead locates data that has a disproportionate impact on the computation. Such data is either very important, or wrong. Data debugging is especially useful in the context of data-intensive programming environments that intertwine data with programs in the form of queries or formulas. We present the first data debugging tool, CheckCell, an add-in for Microsoft Excel. CheckCell identifies cells that have an unusually high impact on the spreadsheet's computations. We show that CheckCell is both analytically and empirically fast and effective. We show that it successfully finds injected typographical errors produced by a generative model trained with data entry from 169,112 Mechanical Turk tasks. CheckCell is more precise and efficient than standard outlier detection techniques. CheckCell also automatically identifies a key flaw in the infamous Reinhart and Rogoff spreadsheet.
Dielectric and Piezoelectric Properties of the Morphotropic Phase Boundary Composition in the (0.8− x ) Pb(Mg 1/3 Ta 2/3 )O 3 −0.2PbZrO 3 − x PbTiO 3 Ternary System (2008)

Morphotropic phase boundary (MPB) compositions separating rhombohedral and tetragonal phases in the (1− x − y )Pb(Mg 1/3 Ta 2/3 )O 3 – y PbZrO 3 – x PbTiO 3 (PMT–PZ–PT100 x ) ternary solid solution system were characterized using X‐ray diffraction and dielectric, piezoelectric properties. This work focused on compositions with a PZ content fixed at y =0.2, with an MPB composition found to be located at x =0.4. Piezoelectric coefficients and dielectric permittivity were found to be on the order of d 33 =580 pC/N and 4100, respectively. Acceptor modification using manganese was found to induce a “hardening” effect in 0.4PMT–0.2PZ–0.4PT, with decreased piezoelectric coefficients d 33 and dielectric loss and increased mechanical quality factor Q . Piezoelectric coefficients d 33 , Q values, and dielectric loss were found to be 500 pC/N, 2000, and 0.4%, respectively, for 0.4PMT–0.2PZ–0.4PT with MnO 2 dopant levels around 0.5 wt%. The figure of merit (product of Q and d 33 ) was found to be on the order of 1 × 10 6 , significantly higher when compared with other hard piezoelectric PZT materials. Specifically, the PMT–PZ–PT materials may be attractive candidates for high‐power ultrasonic applications, particularly fine‐scale components that require relating high permittivities.
Demonstration of hydrogenase in extracts of the homoacetate-fermenting bacterium Clostridium thermoaceticum (1982)

Cell-free extracts of the homoacetate-fermenting bacterium Clostridium thermoaceticum were shown to catalyze the hydrogen-dependent reduction of various artificial electron acceptors. The activity of the hydrogenase was optimal at pH 8.5 to 9 and was extremely sensitive to aeration. EDTA did not significantly reduce the liability of the enzymic activity to oxidation (aeration). At 50 degrees C, when both methyl viologen and hydrogen were at saturating concentrations with respect to hydrogenase, the specific activity of cell-free extracts approximated 4 mumol of H2 oxidized per min per mg of protein; fourfold higher specific activities were obtained when benzyl viologen was utilized as an electron acceptor. Activity stains of polyacrylamide gels demonstrated the presence of a single hydrogenase band, suggesting that the catalytic activity in cell extracts was due to a single enzyme. The activity was stable for at least 32 min at 55 degrees C but was slowly inactivated at 70 degrees C. NAD, NADP, flavin adenine dinucleotide, flavin mononucleotide, and ferredoxin were not significantly reduced, but possible reduction of the particulate b-type cytochrome of C. thermoaceticum was observed. NaCl, sodium dodecyl sulfate, iodoacetamide, and CO were shown to inhibit catalysis. A kinetic study is presented, and the possible physiologic roles for hydrogenase in C. thermoaceticum ar discussed.
A Major Role for Perifornical Orexin Neurons in the Control of Glucose Metabolism in Rats (2009)

Hypothalamic orexin plays an important role in EGP, most likely by changing the hypothalamic output to the autonomic nervous system. Disturbance of this pathway may result in unbalanced glucose homeostasis.
Association of single nucleotide polymorphisms in the leptin gene with carcass and meat quality traits of beef cattle1 (2005)

Calpastatin (CAST) is a naturally occurring protein that inhibits the normal tenderization of meat as it ages postmortem. A SNP was identified in the CAST gene (a G to C substitution) and genotyped on crossbred commercially fed heifers (n = 163), steers (n = 226), and bulls (n = 61) from beef feedlots, and steers (n = 178) from a University of Guelph feeding trial. The association of the CAST SNP with carcass and meat quality traits was studied. Carcass traits included fat, lean, and bone yield; grade fat; LM area; and HCW. Meat quality traits included marbling grade; i.m. fat content of LM; tenderness evaluation of LM (Warner-Bratzler shear force) at 2, 7, 14, and 21 d of postmortem aging; and tenderness evaluation of semitendinosus muscle at 7 d of postmortem aging. The mixed model used in the analyses included fixed effects of CAST genotype, sex, slaughter group, and breed composition (linear covariate); sire was a random effect. For the analysis of shear force, i.m. fat content of LM was also included in the model as a linear covariate. Shear force measures were analyzed within days of postmortem aging and by repeated measures analysis. The CAST SNP allele C was more frequent (63%) in the crossbred population than allele G. The CAST SNP was associated with shear force across days of postmortem aging (P = 0.005); genotype CC yielded beef that was more tender than GG (-0.32 kg +/- 0.13), and CG had intermediate tenderness. The corresponding average allele substitution effect (G to C substitution) was also highly significant (-0.15 +/- 0.05 kg, P = 0.002). A lower percentage of unacceptably tough steaks (shear force > 5.7 kg) at 2 and 7 d postmortem was associated with an increasing number of C alleles (P < or = 0.05). At 7 d postmortem, the percentage of unacceptably tough steaks decreased by 24 and 35%, respectively, for animals carrying 1 and 2 copies of the C allele relative to animals with no C alleles. However, genotype CC had a greater fat yield (+1.44 +/- 0.56%; P = 0.037) than genotype GG, with a corresponding allele substitution effect of 0.67 +/- 0.27% (P = 0.015). Therefore, the CAST SNP allele C was associated with increased LM tenderness across days of postmortem aging and, importantly for the beef industry, had a significant reduction in the percentage of steaks rated unacceptably tough by consumers based on an assumed threshold level.