gebhart/patrepeval huggingface dataset:
Antiviral activity of the novel immune modulator 7-thia-8-oxoguanosine. (1990)

A novel thiazolopyrimidine nucleoside, 5-amino-3-beta-D-ribofuranosylthiazolo[4,5-d]pyrimidine-2,7(3H,6H) -dione (7-thia-8-oxoguanosine), was evaluated for antiviral activity in rodent models, and at 50-200 mg/kg prevented death in mice inoculated intraperitoneally (i.p.) with Semliki Forest, San Angelo, and banzi viruses when administered i.p. before virus challenge. Similarly, the nucleoside was effective against an intranasal challenge of rat coronavirus in suckling rats, with activity present when treatment started as late as 4 h after virus inoculation. Protection was observed against herpes type 1 and murine cytomegalovirus (both inoculated i.p.) infections, and encephalitis induced by intracerebral inoculation of a human coronavirus in mice. Friend leukemia virus splenomegaly was more severe in drug-treated animals than in placebos. This immune modulator is promising for the treatment of animal and human diseases.
Combining topical negative pressure and a Bogota bag for managing a difficult laparostomy (2004)

A patient with a severe intra-abdominal infection required a laparostomy. A Bogota bag was combined with topical negative pressure therapy, saving nursing time and enabling successful management of wound fluid.
Broad-Spectrum Protection against Tombusviruses Elicited by Defective Interfering RNAs in Transgenic Plants (1999)

We have designed a DNA cassette to transcribe defective interfering (DI) RNAs of tomato bushy stunt virus (TBSV) and have investigated their potential to protect transgenic Nicotiana benthamiana plants from tombusvirus infections. To produce RNAs with authentic 5' and 3' termini identical to those of the native B10 DI RNA, the DI RNA sequences were flanked by ribozymes (RzDI). When RzDI RNAs transcribed in vitro were mixed with parental TBSV transcripts and inoculated into protoplasts or plants, they became amplified, reduced the accumulation of the parental RNA, and mediated attenuation of the lethal syndrome characteristic of TBSV infections. Analysis of F1 and F2 RzDI transformants indicated that uninfected plants expressed the DI RNAs in low abundance, but these RNAs were amplified to very high levels during TBSV infection. By two weeks postinoculation with TBSV, all untransformed N. benthamiana plants and transformed negative controls died. Although infection of transgenic RzDI plants initially induced moderate to severe symptoms, these plants subsequently recovered, flowered, and set seed. Plants from the same transgenic lines also exhibited broad-spectrum protection against related tombusviruses but remained susceptible to a distantly related tombus-like virus and to unrelated viruses.
Channel allocation algorithms for multi-carrier systems (2005)

This study focuses on orthogonal channel allocation strategies, yielding multiuser diversity with a deterministic channel, for use in an N-user system with N parallel sub-channels. The techniques are applicable, for instance, in orthogonal frequency division multiple-access (OFDMA) systems with dynamic sub-carrier allocation. We show that multiuser diversity, and thus an increase of aggregate data rates with the size of the user population, can still be successfully achieved even under a hard fairness constraint. Furthermore, we provide algorithms which perform channel allocation yielding a variable-rate with constant power and fixed-rate with variable power. We show the effect of system bandwidth (and thus sub-channel correlation) on multiuser diversity. The techniques considered here do not require phase information in the channel allocation process, which, from a practical point-of-view, is particularly important for time-division duplex systems exploiting channel reciprocity.
The Size of the Nucleus Increases as Yeast Cells Grow (2007)

It is not known how the volume of the cell nucleus is set, nor how the ratio of nuclear volume to cell volume (N/C) is determined. Here, we have measured the size of the nucleus in growing cells of the budding yeast Saccharomyces cerevisiae. Analysis of mutant yeast strains spanning a range of cell sizes revealed that the ratio of average nuclear volume to average cell volume was quite consistent, with nuclear volume being approximately 7% that of cell volume. At the single cell level, nuclear and cell size were strongly correlated in growing wild-type cells, as determined by three different microscopic approaches. Even in G1-phase, nuclear volume grew, although it did not grow quite as fast as overall cell volume. DNA content did not appear to have any immediate, direct influence on nuclear size, in that nuclear size did not increase sharply during S-phase. The maintenance of nuclear size did not require continuous growth or ribosome biogenesis, as starvation and rapamycin treatment had little immediate impact on nuclear size. Blocking the nuclear export of new ribosomal subunits, among other proteins and RNAs, with leptomycin B also had no obvious effect on nuclear size. Nuclear expansion must now be factored into conceptual and mathematical models of budding yeast growth and division. These results raise questions as to the unknown force(s) that expand the nucleus as yeast cells grow.
A Spectral Factorization Approach to Pseudo-QMF Design (1993)

A new approach to the design of M-channel pseudoquadrature-mirror-filter (QMF) banks is presented. In this approach, the prototype filter is obtained as a spectral factor of a 2Mth band filter. This completely eliminates the need for optimization whereas in conventional pseudo-QMF designs, the main computational effort is in optimization of the prototype. As in the conventional approach, the aliasing cancellation (AC) constraint ensures that all the significant aliasing terms are canceled. The overall transfer function T(z) of the analysis/synthesis system has a linear phase and an approximately “flat” magnitude response in the frequency region ε ≤ ω ≤ (π - ε), where ε depends on the transition bandwidth of the prototype and 0 &lt; ε &lt; (π/2M). Three design examples are included.
Ruthenium catalysed cross metathesis with fluorinated olefins (2001)

The E-selective cross metathesis (CM) of fluorinated olefins with various functionalised alkenes in good to excellent yields is reported.
Molecular Cloning and Expression of Human cDNAs Encoding a Novel DNA Ligase IV and DNA Ligase III, an Enzyme Active in DNA Repair and Recombination (1995)

Three distinct DNA ligases, I to III, have been found previously in mammalian cells, but a cloned cDNA has been identified only for DNA ligase I, an essential enzyme active in DNA replication. A short peptide sequence conserved close to the C terminus of all known eukaryotic DNA ligases was used to search for additional homologous sequences in human cDNA libraries. Two different incomplete cDNA clones that showed partial homology to the conserved peptide were identified. Full-length cDNAs were obtained and expressed by in vitro transcription and translation. The 103-kDa product of one cDNA clone formed a characteristic complex with the XRCC1 DNA repair protein and was identical with the previously described DNA ligase III. DNA ligase III appears closely related to the smaller DNA ligase II. The 96-kDa in vitro translation product of the second cDNA clone was also shown to be an ATP-dependent DNA ligase. A fourth DNA ligase (DNA ligase IV) has been purified from human cells and shown to be identical to the 96-kDa DNA ligase by unique agreement between mass spectrometry data on tryptic peptides from the purified enzyme and the predicted open reading frame of the cloned cDNA. The amino acid sequences of DNA ligases III and IV share a related active-site motif and several short regions of homology with DNA ligase I, other DNA ligases, and RNA capping enzymes. DNA ligases III and IV are encoded by distinct genes located on human chromosomes 17q11.2-12 and 13q33-34, respectively.
Protective effects of inhaled ipratropium bromide on bronchoconstriction induced by adenosine and methacholine in asthma (1992)

Although adenosine-induced bronchoconstriction is mainly due to mast cell mediator release, vagal reflexes have also been implicated in this response. We have investigated the effect of a specific muscarinic-receptor antagonist, ipratropium bromide, on methacholine- and adenosine-induced bronchoconstriction in a randomized, placebo-controlled, double-blind study of 12 asthmatic subjects. Airway response was evaluated as forced expiratory volume in one second (FEV1). Inhaled ipratropium bromide (40 micrograms), administered 20 min prior to bronchoprovocation, increased the provocation dose of inhaled methacholine and adenosine required to reduce FEV1 by 20% from baseline (PD20) from 0.11 to 0.79 mg (p less than 0.01) and from 0.57 to 1.27 mg (p less than 0.01), respectively. The mean baseline FEV1 values after administration of ipratropium bromide were significantly higher than after placebo administration (p less than 0.05). However, there was no correlation between the degree of bronchodilatation and dose-ratios for methacholine and adenosine. The findings of the present study implicate vagal reflexes in the bronchospastic response induced by inhaled adenosine in asthma.
Identification and Functional Characterization of Human Cd4+Cd25+ T Cells with Regulatory Properties Isolated from Peripheral Blood (2001)

A subpopulation of peripheral human CD4(+)CD25(+) T cells that expresses CD45RO, histocompatibility leukocyte antigen DR, and intracellular cytotoxic T lymphocyte-associated antigen (CTLA) 4 does not expand after stimulation and markedly suppresses the expansion of conventional T cells in a contact-dependent manner. After activation, CD4(+)CD25(+) T cells express CTLA-4 on the surface detectable for several weeks. These cells show a G1/G0 cell cycle arrest and no production of interleukin (IL)-2, IL-4, or interferon (IFN)-gamma on either protein or mRNA levels. The anergic state of CD4(+)CD25(+) T cells is not reversible by the addition of anti-CD28, anti-CTLA-4, anti-transforming growth factor beta, or anti-IL-10 antibody. However, the refractory state of CD4(+)CD25(+) T cells was partially reversible by the addition of IL-2 or IL-4. These data demonstrate that human blood contains a resident T cell population with potent regulatory properties.
Selective expression of Ly-6G on myeloid lineage cells in mouse bone marrow. RB6-8C5 mAb to granulocyte-differentiation antigen (Gr-1) detects members of the Ly-6 family. (1993)

Mouse Ly-6 proteins are characterized by lineage-restricted patterns of expression on lymphoid cells. A mAb (1A8) was produced to Ly-6G, a newly described member of the Ly-6 locus. Based on selective reactivity to cloned Ly-6 gene products expressed in EL4J cells, 1A8 was determined to be specific for Ly-6G. Furthermore, mAb to other Ly-6 specificities did not bind to Ly-6G-transfected EL4J cells, indicating that Ly-6G is distinct from other serologically defined Ly-6 specificities. FACS analysis using 1A8 demonstrated that Ly-6G was expressed in bone marrow but not substantially on other lymphoid tissues, including activated T and B cells. In the bone marrow, Ly-6G expression was primarily restricted to the cells with more forward angle light scatter, which are mostly granulocytes. The RB6-8C5 mAb, previously described to detect a myeloid-restricted Ag (Gr-1) on more differentiated granulocytes, also reacted with Ly-6G- and Ly-6C-transfected EL4J cells. Both 1A8 and RB6-8C5 selectively precipitate a M(r) 21 to 25 kDa, glycosylphosphatidylinositol-anchored protein. Collectively, these data indicate that the Gr-1 Ag is a member of the Ly-6 family and further link expression of individual Ly-6 genes with distinct lineages in mouse bone marrow cells.
Predicting therapeutic nanomedicine efficacy using a companion magnetic resonance imaging nanoparticle (2015)

Therapeutic nanoparticles (TNPs) have shown heterogeneous responses in human clinical trials, raising questions of whether imaging should be used to identify patients with a higher likelihood of NP accumulation and thus therapeutic response. Despite extensive debate about the enhanced permeability and retention (EPR) effect in tumors, it is increasingly clear that EPR is extremely variable; yet, little experimental data exist to predict the clinical utility of EPR and its influence on TNP efficacy. We hypothesized that a 30-nm magnetic NP (MNP) in clinical use could predict colocalization of TNPs by magnetic resonance imaging (MRI). To this end, we performed single-cell resolution imaging of fluorescently labeled MNPs and TNPs and studied their intratumoral distribution in mice. MNPs circulated in the tumor microvasculature and demonstrated sustained uptake into cells of the tumor microenvironment within minutes. MNPs could predictably demonstrate areas of colocalization for a model TNP, poly(d,l-lactic-co-glycolic acid)-b-polyethylene glycol (PLGA-PEG), within the tumor microenvironment with >85% accuracy and circulating within the microvasculature with >95% accuracy, despite their markedly different sizes and compositions. Computational analysis of NP transport enabled predictive modeling of TNP distribution based on imaging data and identified key parameters governing intratumoral NP accumulation and macrophage uptake. Finally, MRI accurately predicted initial treatment response and drug accumulation in a preclinical efficacy study using a paclitaxel-encapsulated NP in tumor-bearing mice. These approaches yield valuable insight into the in vivo kinetics of NP distribution and suggest that clinically relevant imaging modalities and agents can be used to select patients with high EPR for treatment with TNPs.
Molecular characterization of the CAN1 locus in Saccharomyces cerevisiae. A transmembrane protein without N-terminal hydrophobic signal sequence. (1985)

The complete DNA sequence of the CAN1 locus of the yeast Saccharomyces cerevisiae is presented. The predicted primary translation product consists of 590 amino acids. From the hydropathic profile of the amino acid sequence (as calculated by the algorithm of Kyte and Doolittle (Kyte, J., and Doolittle, R. F. (1982) J. Mol. Biol. 157, 105-132)), one can divide the protein into two distinct regions. The 93-amino acid long N-terminal domain is extremely hydrophilic and does not exhibit any cleavable signal sequence. The rest of the protein (from amino acids 94 to 590) shows features typical for an integral membrane protein. The proposal for the N terminus of the primary translation product is based on results obtained by S1 mapping, insertion mutagenesis, and gene fusion experiments.
Quantitative precipitation of short oligonucleotides with low concentrations of cetyltrimethylammonium bromide (1989)

Journal Article Quantitative precipitation of short oligonucleotides with low concentrations of cetyltrimethylammonium bromide Get access Jean-Pierre Jost, Jean-Pierre Jost Friedrich Miescher-InstitutPO Box 2543, CH-4002 Basel, Switzerland Search for other works by this author on: Oxford Academic PubMed Google Scholar Josef Jirieny, Josef Jirieny Friedrich Miescher-InstitutPO Box 2543, CH-4002 Basel, Switzerland Search for other works by this author on: Oxford Academic PubMed Google Scholar Hanspeter Saluz Hanspeter Saluz Friedrich Miescher-InstitutPO Box 2543, CH-4002 Basel, Switzerland Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 17, Issue 5, 11 March 1989, Page 2143, https://doi.org/10.1093/nar/17.5.2143 Published: 11 March 1989 Article history Received: 05 January 1989 Published: 11 March 1989
The estimation of distances between specific backbone-labeled sites in DNA using fluorescence resonance energy transfer (1992)

A series DNA helices of twenty-four base pairs has been prepared for the study of fluorescence resonance energy transfer. Each of the DNA helices contains two phosphorothioate diesters (one in each strand) at pre-selected sites for introduction of the desired donor and acceptor fluorophores. The phosphorothioate-containing oligodeoxynucleotides have been prepared as pure Rp or Sp derivatives or as deastereomeric mixtures. Fluorescein and eosin are employed as the respective donor and acceptor fluorophores. A series of donor-acceptor pairs was generated by labeling of the appropriate phosphorothioate diester with the desired fluorophore and annealing the two complementary DNA strands (one containing the acceptor and one containing the donor fluorophore) to form the double-stranded helix. The 24-mer helices containing two covalently attached fluorophores exhibited some thermal destabilization and the extent of this destabilization was dependent upon the stereochemical orientation of the fluorophore. The Sp derivatives direct the fluorophore out, away from the the DNA helix, while the Rp derivatives direct the fluorophore toward the major groove. As expected, the Sp labeled duplexes were more stable than the corresponding Rp labeled sequences. However, all of the duplex structures formed were stable under the conditions used to measure energy transfer. Energy transfer could be observed with these complexes from the quenching of the donor fluorescence in the presence of the acceptor fluorophore. Using Förster's theories, distances separating the fluorophores could be calculated that were generally in reasonable agreement with the distances expected in an idealized B-form DNA helix. However anomalous results were obtained for one donor/acceptor pair where the expected distance was less than 20 A. Fluorescence anisotropy values determined in solutions of varying viscosity were quite high suggesting that the fluorophores did not experience complete freedom of movement when attached to the DNA helix.
Efficient CRISPR/Cas9-Mediated Genome Editing in Mice by Zygote Electroporation of Nuclease (2015)

The clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein (Cas) system is an adaptive immune system in bacteria and archaea that has recently been exploited for genome engineering. Mutant mice can be generated in one step through direct delivery of the CRISPR/Cas9 components into a mouse zygote. Although the technology is robust, delivery remains a bottleneck, as it involves manual injection of the components into the pronuclei or the cytoplasm of mouse zygotes, which is technically demanding and inherently low throughput. To overcome this limitation, we employed electroporation as a means to deliver the CRISPR/Cas9 components, including Cas9 messenger RNA, single-guide RNA, and donor oligonucleotide, into mouse zygotes and recovered live mice with targeted nonhomologous end joining and homology-directed repair mutations with high efficiency. Our results demonstrate that mice carrying CRISPR/Cas9-mediated targeted mutations can be obtained with high efficiency by zygote electroporation.
Mechanistic Study of Partial Oxidation of Methane to Syngas Using In Situ Time‐Resolved FTIR and Microprobe Raman Spectroscopies (2002)

In situ time-resolved Fourier transform infrared (FTIR) and microprobe Raman spectroscopies were used to characterize the reaction mechanisms of the partial oxidation of methane to syngas over SiO(2)- and gamma-Al(2)O(3)-supported rhodium and ruthenium catalysts. The interaction of both pure methane and a methane/oxygen mixture at a stoichiometric feed ratio with an oxygen-rich catalyst surface led to the formation of CO2 and H(2)O as the primary products. For the H(2)-pretreated samples, the reaction mechanisms with the catalysts differ. Only Rh/SiO(2) is capable of catalyzing the direct oxidation of methane to syngas, while syngas formation over Rh/gamma-Al(2)O(3), Ru/SiO(2), and Ru/gamma-Al(2)O(3) can be achieved mainly via a combustion-reforming scheme. The significant difference in the mechanisms for partial oxidation of methane to syngas over the catalysts can be correlated to the differences in the concentration of oxygen species (O(2-)) on the catalyst surface during the reaction, mainly due to the difference in the nature of the metals and supports.
Complex Effects of In Vitro Hyperoxia on Alveolar Macrophage Arachidonic Acid Metabolism (1990)

Metabolites of arachidonic acid (AA) released into bronchoalveolar lavage fluid of animals exposed to hyperoxia have previously been implicated as mediators of pulmonary oxygen toxicity. The alveolar macrophage (AM) represents an important potential source of these eicosanoids. We have therefore investigated the effects of in vitro hyperoxia (95% O2/5% CO2) versus normoxia (95% air/5% CO2) on the metabolism of AA in the AM of the rat. Exposure to 95% O2 for up to 72 h did not impair the viability or affect the protein content of cultured AMs. Hyperoxia for 24 to 72 h increased the accumulation of free AA liberated from endogenous stores in cultures of resting AMs. Despite this increase in free AA, no changes in synthesis of thromboxane B2, prostaglandin (PG) E2, PGF2 alpha, leukotriene (LT) B4, or LTC4 were observed in resting AMs exposed to hyperoxia for up to 72 h. This was not due to degradation of eicosanoids in hyperoxia. However, formation of cyclooxygenase metabolites from exogenously supplied AA was reduced in hyperoxia-incubated AMs, suggesting that hyperoxia inhibited the cyclooxygenase enzyme. In AMs stimulated with calcium ionophore A23187, both AA release and synthesis of cyclooxygenase and lipoxygenase eicosanoids were augmented after incubation in hyperoxia for 24 to 72 h. The increase in A23187-stimulated LTB4 synthesis caused by hyperoxia was inhibited by the antioxidants catalase, superoxide dismutase, and the intracellular cysteine loading agent L-2-oxothiazolidine-4-carboxylic acid, suggesting that the augmentation by hyperoxia of A23187-induced AA metabolism was mediated by reactive oxygen metabolites. Thus, hyperoxia has complex effects on AA metabolism in the AM, which include the ability to augment the release of AA and formation of bioactive eicosanoids. These findings support a possible role for eicosanoid synthesis by the AM in the pathogenesis of oxygen toxicity of the lung.