gebhart/patrepeval huggingface dataset:
Recovery of infectious respiratory syncytial virus expressing an additional, foreign gene (1996)

A previous report described the recovery from cDNA of infectious recombinant respiratory syncytial virus (RSV) strain A2 (P. L. Collins, M. G. Hill, E. Camargo, H. Grosfeld, R. M. Chanock, and B. R. Murphy, Proc. Natl. Acad. Sci. USA, 92:11563-11567, 1995). Here, the system was used to construct recombinant RSV containing an additional gene encoding chloramphenicol acetyltransferase (CAT). The CAT coding sequence was flanked by RSV-specific gene-start and gene-end motifs, the transcription signals for the viral RNA-dependent RNA polymerase. The RSV-CAT chimeric transcription cassette was inserted into the region between the G and F genes of the complete cDNA-encoded positive-sense RSV antigenome, and infectious CAT-expressing recombinant RSV was recovered. Transcription of the inserted gene into the predicted subgenomic polyadenylated mRNA was demonstrated by Northern (RNA) blot hybridization analysis, and the encoded protein was detected by enzyme assay and by radioimmunoprecipitation. Quantitation of intracellular CAT, SH, G, and F mRNAs showed that the CAT mRNA was efficiently expressed and that the levels of the G and F mRNAs (which represent the genes on either side of the inserted CAT gene) were comparable to those expressed by a wild-type recombinant RSV. Consistent with this finding, the CAT-containing and wild-type viruses were very similar with regard to the levels of synthesis of the major viral proteins. Each of 25 RSV isolates obtained by plaque purification following eight serial passages expressed CAT, showing that the foreign gene was faithfully maintained in functional form. Analysis by reverse transcription and PCR did not reveal evidence of deletion of the foreign sequence. This finding demonstrated that the RSV genome can accept and maintain an increase in length of 762 nucleotides of foreign sequence and can be engineered to encode an additional, 11th mRNA. The presence of the additional gene resulted in a 10% decrease in plaque diameter and was associated with delay in virus growth and 20-fold decrease in virus yield in vitro. Thus, introduction of an additional gene into the RSV genome might represent a method of attenuation. The ability to express foreign genes by recombinant RSV has implications for basic studies as well as for the development of live recombinant vaccines.
Model based mask process correction and verification for advanced process nodes (2009)

The extension of optical lithography at 193nm wavelength to the 32nm node and beyond drives advanced resolution enhancement techniques that impose even tighter tolerance requirements on wafer lithography and etch as well as on mask manufacturing. The presence of residual errors in photomasks and the limitations of capturing those in process models for the wafer lithography have triggered development work for separately describing and correcting mask manufacturing effects. Long range effects - uniformity and pattern loading driven - and short range effects - proximity and linearity - contribute to the observed signatures. The dominating source of the short range errors is the etch process and hence it was captured with a variable etch bias model in the past [1]. The paper will discuss limitations and possible extensions to the approach for improved accuracy. The insertion of mask process correction into a post tapeout flow imposes strict requirements for runtime and data integrity. The paper describes a comprehensive approach for mask process correction including calibration and model building, model verification, mask data correction and mask data verification. Experimental data on runtime performance is presented. Flow scenarios as well as other applications of mask process correction for gaining operational efficiency in both tapeout and mask manufacturing are discussed.
CD25<sup>+</sup>CD4<sup>+</sup>regulatory T cells suppress CD4<sup>+</sup>T cell‐mediated pulmonary hyperinflammation driven by<i>Pneumocystis carinii</i>in immunodeficient mice (2002)

The CD4(+) T cell-mediated inflammatory response to Pneumocystis carinii (PC) critically contributes to the clinical severity of PC pneumonia. It has been suggested that lymphopenic conditions predispose individuals to this immunopathology, although the mechanisms remain poorly understood. Another set of evidence indicates that a subpopulation of CD4(+) T cells constitutively expressing the CD25 molecule prevent lymphopenia-induced autoimmunity and inflammatory bowel disease. We tested the ability of this CD25(+)CD4(+) population to regulate CD4(+) T cell-mediated inflammatory response to PC. Adoptive transfer of CD25(-)CD4(+) cells into PC-infected recombination-activating gene-2-deficient mice led to lethal pneumonia within 13 days post-transfer. PC infection appeared to trigger CD25(-)CD4(+) cells, since recipients with reduced PC load survived up to 5 weeks after transfer. In contrast, transfer of CD25(+)CD4(+) cells did not induce lethal pneumonia and prevented the development of the disease induced by CD25(-)CD4(+) cells. Furthermore, CD25(-)CD4(+) cells reduced the PC load in the lung, while CD25(+)CD4(+) cells suppressed this immune response. Our results indicate an essential role for CD25(+)CD4(+) T cells in the control of PC-driven immunopathology, and suggest that in immunocompromised hosts PC pneumonia may result from a deficiency in regulatory T cells.
FXII Antisense Oligonucleotide Mediated Depletion Results In Effective Anticoagulation without Bleeding Risk. (2010)

Abstract Abstract 1149 Human clinical efficacy has been demonstrated with antisense oligonucleotides (ASOs) in several disease indications, including dyslipidemia, cancer, diabetes and multiple sclerosis. Coagulation factors are attractive targets for antisense therapeutics for several reasons. The liver is principally responsible for production of coagulation factors and is an organ which is highly sensitive to ASO drugs. ASOs are highly specific, and thus we can selectively evaluate multiple coagulation factors to determine their roles in thrombosis, bleeding, and other processes. Employing antisense technology we selectively reduced levels of several individual clotting factors and compared the relative risk/benefit profiles. Antithrombotic activity was determined following ferric chloride induced thrombosis in the inferior vena cava and bleeding tendency was measured by blood volume loss following tail nick. ASOs targeting several clotting factors were studied, including factors FII, FVII, FIX, FXI and FXII. Previously we characterized the beneficial effects of targeting FXI, demonstrating antithrombotic effects without increased bleeding risk. Here, we describe the effects of targeting another member of the intrinsic pathway, FXII. FXII ASO treatment resulted in a dose-dependent and specific reduction in FXII mRNA levels in liver. These reductions in FXII levels correlated well with a prolongation of aPTT with no effects on PT prolongation. The anticoagulant effect of FXII ASO treatment also correlated well with antithrombotic activity in a FeCl3 induced IVC thrombosis mouse model across a wide dose range. In addition to the venous thrombosis model, FXII ASO treatment was effective across a wide dose range in a model of arterial thrombosis. Furthermore, FXII ASO treatment was well tolerated and no prolongation of tail bleeding time was observed at any dose tested, indicating a broad safety margin for FXII ASO targeting (in mice). In addition, FXII inhibition was protective in a mouse TF driven pulmonary embolism model. Inhibiting coagulation factors with ASOs is highly specific and offers an attractive approach to identifying optimal antithrombotic targets as well as human therapeutics for the treatment of coagulation related disorders with the potential for improved safety profiles. Disclosures: No relevant conflicts of interest to declare.
Hydrogen adsorption on some <i>a</i>-Ge1−<i>x</i>C<i>x</i>:H films prepared by radio-frequency sputtering (1988)

Auger and electron energy-loss spectroscopy (EELS) were used to study the interaction of hydrogen atoms with clean, Ar+ sputter-etched amorphous germanium (a-Ge), hydrogenated amorphous germanium (a-Ge:H), and some hydrogenated amorphous germanium carbide (a-Ge1−xCx:H) films prepared by rf sputtering. The EEL spectra indicate preferential sputtering of hydrogen bonded to germanium by ion etching in a-Ge:H as well as in a-Ge0.9C0.1:H and the creation of new surface Ge–H bonds following exposure to atomic hydrogen. No such information could be obtained from EELS studies for films containing 25 at. % or more carbon. However, Auger line-shape measurements of Ge and C in a-Ge1−xCx:H, before and after exposure to dissociated hydrogen, yield the same conclusions for x≤0.5. There is no evidence of preferential removal of hydrogen bonded to carbon by Ar+ etching or of formation of new C–H surface bonds in the alloy films by hydrogen adsorption. The preferential removal of hydrogen bonded to Ge but not to C may explain the relatively high density of bulk C–H bonds in rf sputter-deposited a-Ge1−xCx:H films.
Site-Specific Conjugation of Boron-Containing Dendrimers to Anti-EGF Receptor Monoclonal Antibody Cetuximab (IMC-C225) and Its Evaluation as a Potential Delivery Agent for Neutron Capture Therapy (2003)

The gene encoding EGFR often is amplified in human gliomas, and the receptor itself has been considered as a potential target for the specific delivery of therapeutic agents to brain tumors. The purpose of the present study was to investigate the use of the chimeric MoAb cetuximab (IMC-C225), which is directed against EGFR and EGFRvIII, as a boron delivery agent for neutron capture therapy (NCT) of brain tumors. As determined by 125I-cetuximab radioligand binding assays, F98 rat glioma cells, which had been transfected with the gene encoding EGFR (F98EGFR), expressed 1.60 +/- 0.13 x 10(5) receptor sites/cell with a Ka = 1.64 +/- 0.32 x 10(8) M-1). F98 cells transfected with the gene encoding a mutant form of EGFR, designated the F98EGFRvIII glioma, expressed 1.07 +/- 0.10 x 10(5) receptor sites/cell with a Ka = 2.18 +/- 0.54 x 10(9) M-1 compared to background levels expressed on F98 wild-type cells (F98WT). A heavily boronated, fifth generation polyamidoamine (PAMAM or "starburst") dendrimer, G5-B1100, was linked to oligosaccharide moieties, which were distant from antigen binding sites of cetuximab, by means of the heterobifunctional reagents N-succinimidyl 3-(2-pyridyldithio)propionate (SPDP) and N-(k-maleimidoundecanoic acid) hydrazide (KMUH). The resulting bioconjugate, designated C225-G5-B1100, was separated from the unconjugated dendrimer using a Sephacryl S-300 column. On the basis of the relative concentration ratios of boron and protein, there were approximately 1100 boron atoms per molecule of cetuximab with only a slight reduction of Ka. The localization of C225-G5-B1100 or G5-B1100 in rats bearing intracerebral implants of either F98EGFR or F98WT gliomas was determined 24 h following direct intratumoral (i.t.) injection at which time 92.3 +/- 23.3 micrograms B/g tumor was localized in F98EGFR gliomas versus 36.5 +/- 18.8 micrograms B/g tumor in F98WT gliomas and 13.4 +/- 6.1 micrograms in normal brain. In contrast, only 6.7 +/- 3.6 micrograms B/g tumor of G5-B1100 was localized in F98EGFR gliomas following i.t. injection, thereby demonstrating specific molecular targeting of EGFR. Based on these data, BNCT studies will be initiated in F98EGFR glioma bearing rats to evaluate C225-G5-B1100 for the treatment of intracerebral brain tumors.
PCR Amplification Kit (2004)

Analysis of length polymorphism at short tandem repeat (STR) loci utilizing the polymerase chain reaction (PCR) process has proven to be an ideal assay for human identification purposes. The short length of STR loci coupled with the amplification of target sequence through PCR allows for a robust, sensitive, and specific assay for highly polymorphic markers. A multiplex containing fifteen STR loci plus the gender-determining locus Amelogenin was developed to provide a single amplification/detection of all CODIS (Combined DNA Index System) STR loci (CSF1PO, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D21S11, FGA, TH01, TPOX, and vWA) as well as two internationally-accepted STRs (D2S1338 and D19S433). By incorporating five-dye fragment analysis technology and non-nucleotide linkers, previously optimized AmpFSTR R � kit primer sequences have been maintained. This kit has been developed in accordance with the standards of the forensic community as defined by the DNA Advisory Board. Validation studies were performed to include developmental validation, and the results support the use of the AmpFSTR R � Identifiler R � PCR Amplification Kit for human identity and parentage testing.
Who Received Loans? Home Owners’ Loan Corporation Lending and Discrimination in Philadelphia in the 1930s (2003)

The lending record of the Home Owners’ Loan Corporation (HOLC) has received little attention compared with HOLC’s residential security maps. Specifically, the extent to which HOLC practiced racial and ethnic discrimination in the process of making and servicing more than a million loans to homeowners during the Depression has not been carefully examined. Using primary sources including HOLC publications, newspaper articles, 1930 census data, and mortgage records from Philadelphia, this research shows that HOLC did make loans to African Americans, Jews, and immigrants. Evidence suggests, however, that HOLC supported racial segregation in the process of reselling properties acquired through foreclosure.
Effects of antiplatelet agents on platelet-induced thrombin generation (2002)

The ETP-method is a sensitive and reproducible method for the detection of drug effects on platelet-induced thrombin generation of high throughput, and can be recommended for studies on the pharmacodynamic profile of drugs interfering with platelet function.
Chemistry (Quagliano, James V.) (1964)

ADVERTISEMENT RETURN TO ISSUEPREVBook and Media Revie...Book and Media ReviewNEXTChemistry (Quagliano, James V.)P. Calvin Maybury Cite this: J. Chem. Educ. 1964, 41, 4, 231Publication Date (Print):April 1, 1964Publication History Received3 August 2009Published online1 April 1964Published inissue 1 April 1964https://doi.org/10.1021/ed041p231.1RIGHTS & PERMISSIONSArticle Views75Altmetric-Citations-LEARN 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 (1 MB) Get e-Alerts Get e-Alerts
Variational methods for the Dirichlet process (2004)

Variational inference methods, including mean field methods and loopy belief propagation, have been widely used for approximate probabilistic inference in graphical models. While often less accurate than MCMC, variational methods provide a fast deterministic approximation to marginal and conditional probabilities. Such approximations can be particularly useful in high dimensional problems where sampling methods are too slow to be effective. A limitation of current methods, however, is that they are restricted to parametric probabilistic models. MCMC does not have such a limitation; indeed, MCMC samplers have been developed for the Dirichlet process (DP), a nonparametric distribution on distributions (Ferguson, 1973) that is the cornerstone of Bayesian nonparametric statistics (Escobar & West, 1995; Neal, 2000). In this paper, we develop a mean-field variational approach to approximate inference for the Dirichlet process, where the approximate posterior is based on the truncated stick-breaking construction (Ishwaran & James, 2001). We compare our approach to DP samplers for Gaussian DP mixture models.
SNS Na+ channel expression increases in dorsal root ganglion neurons in the carrageenan inflammatory pain model (1998)

It has been suggested that hyperexcitability in dorsal root ganglion (DRG) neurons due to altered sodium channel expression contributes to some chronic pain syndromes. To understand the role of the voltage-gated sodium channel alpha-SNS in inflammatory pain, we investigated the expression of alpha-SNS mRNA and tetrodotoxin-resistant (TTX-R) sodium current in small DRG neurons, which include nociceptive cells, following injection of carrageenan into the hind paw of the rat using in situ hybridization and patch-clamp recording. alpha-SNS mRNA expression in DRG neurons projecting to the inflamed limb was significantly increased 4 days following carrageenan injection, compared with DRG neurons from the contralateral side or naive (uninjected) rats (mean +/- s.d. optical density ratio: ipsilateral/contralateral, 1.77 +/- 0.17; ipsilateral/naive, 1.88 +/- 0.36). The amplitude of the TTX-R sodium current in small DRG neurons projecting to the inflamed limb was significantly larger than on the contralateral side 4 days post-injection (31.7 +/- 3.3 vs 20.0 +/- 2.1 nA). The TTX-R current density was also significantly increased. These results demonstrate the increased expression of alpha-SNS sodium channels in small DRG neurons following injection of carrageenan into their projection field, and suggest that alpha-SNS is involved in the development of hyperexcitability associated with inflammation.
Session reconstruction for HTTP adaptive streaming: Laying the foundation for network-based QoE monitoring (2012)

HTTP Adaptive Streaming (HAS) is rapidly becoming a key video delivery technology for fixed and mobile networks. However, today there is no solution that allows network operators or CDN providers to perform network-based QoE monitoring for HAS sessions. We present a HAS QoE monitoring system, based on data collected in the network, without monitoring information from the client. To retrieve the major QoE parameters such as average quality, quality variation, rebuffering events and interactivity delay, we propose a technique called session reconstruction. We define a number of iterative steps and developed algorithms that can be used to perform HAS session reconstruction. Finally, we present the results of a working prototype for the reconstruction and monitoring of Microsoft Smooth Streaming HAS sessions that is capable of dealing with intermediate caching and user interactivity. We describe the main observations when using the platform to analyze more than a hundred HAS sessions.
The forces at work in colloidal self‐assembly: a review on fundamental interactions between colloidal particles (2008)

Abstract Colloidal particles with well‐defined sizes can self‐assemble into ordered, crystalline structures under non‐equilibrium conditions. This phenomenon originates from the various forces acting upon them. In this article, we provide an overview on the forces at work in a colloidal system, in particular, the roles of these forces at various stages in colloidal self‐assembly. Van der Waals, electrostatic, hydrodynamic, and capillary forces, as well as Brownian motions, are extensively discussed, whereas other types of interactions are briefly introduced and summarized. Copyright © 2008 Curtin University of Technology and John Wiley &amp; Sons, Ltd.
Susceptibility testing of Candida albicans and Aspergillus species by a simple microtiter menadione-augmented 3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2H-tetrazolium bromide assay (1995)

We describe a simple microtiter method for determining the susceptibility of Candida albicans and hyphal forms of Aspergillus fumigatus against antifungal agents. The assay measures mitochondrial respiration by determining reduction of 3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2H-tetrazolium bromide (MTT) to formazan, a process that is enhanced in the presence of menadione. C. albicans or conidial suspensions of A. fumigatus are seeded into microtiter plates. Hyphal outgrowth of Aspergillus spp. was achieved by a 12 to 14-h culture at 30 degrees C. Antifungal agents (amphotericin B, fluconazole, itraconazole) were added to the cultures for 24 h. Thereafter, incubations were continued for 3 h in the presence of MTT plus 0.1 mM menadione. Formazan formation was quantified photometrically after extraction of the formazan with acid isopropanol. Well-defined dose-response curves reflecting impairment of mitochondrial function by the antifungal agents were obtained. With C. albicans, the results correlated excellently with the MIC determinations performed according to the standard macrodilution procedure. In confirmation of a recent report, it was found that fluconazole was unable to exert its fungistatic action on a sensitive C. albicans strain in the presence of serum. The presented method can easily be integrated in the standard repertoire of a diagnostic microbiology laboratory and should prove useful as a means to assess the antifungal action of various agents on yeasts and filamentous fungi in the presence and absence of serum proteins or body fluids.
In Vitro Selection of Functional Nucleic Acids (1999)

In vitro selection allows rare functional RNA or DNA molecules to be isolated from pools of over 10(15) different sequences. This approach has been used to identify RNA and DNA ligands for numerous small molecules, and recent three-dimensional structure solutions have revealed the basis for ligand recognition in several cases. By selecting high-affinity and -specificity nucleic acid ligands for proteins, promising new therapeutic and diagnostic reagents have been identified. Selection experiments have also been carried out to identify ribozymes that catalyze a variety of chemical transformations, including RNA cleavage, ligation, and synthesis, as well as alkylation and acyl-transfer reactions and N-glycosidic and peptide bond formation. The existence of such RNA enzymes supports the notion that ribozymes could have directed a primitive metabolism before the evolution of protein synthesis. New in vitro protein selection techniques should allow for a direct comparison of the frequency of ligand binding and catalytic structures in pools of random sequence polynucleotides versus polypeptides.
Nursery research field day. (1980)

The Oklahoma Cooperative Extension Service periodically issues revisions to its publications. The most current edition is made available. For access to an earlier edition, if available for this title, please contact the Oklahoma State University Library Archives by email at libscua@okstate.edu or by phone at 405-744-6311.
Memory chip for 24-port global register file (2002)

The design of 256*32 bit 24-port global register file is discussed. An eight-read- and eight-write-port SRAM (static random-access memory) chip is proposed as a building block of such a global register file. Design trade-offs and performance measurements obtained from a 65 K+transistor, experimental, CMOS implementation of this SRAM chip are reported in detail.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>