gebhart/patrepeval huggingface dataset:
Polymerase recognition of synthetic oligodeoxyribonucleotides incorporating degenerate pyrimidine and purine bases (1998)

A universal base that is capable of substituting for any of the four natural bases in DNA would be of great utility in both mutagenesis and recombinant DNA experiments. This paper describes the properties of oligonucleotides incorporating two degenerate bases, the pyrimidine base 6H,8H-3,4-dihydropyrimido[4,5-c][1,2]oxazin-7-one and the purine base N6-methoxy-2,6-diaminopurine, designated P and K, respectively. An equimolar mixture of the analogues P and K (called M) acts, in primers, as a universal base. The thermal stability of oligonucleotide duplexes were only slightly reduced when natural bases were replaced by P or K. Templates containing the modified bases were copied by Taq polymerase; P behaved as thymine in 60% of copying events and as cytosine in 40%, whereas K behaved as if it were guanine (13%) or adenine (87%). The dUTPase gene of Caenorhabditis elegans, which we have found to contain three nonidentical homologous repeats, was used as a model system to test the use of these bases in primers for DNA synthesis. A pair of oligodeoxyribonucleotides, each 20 residues long and containing an equimolar mixture of P and K at six positions, primed with high specificity both T7 DNA polymerase in sequencing reactions and Taq polymerase in PCRs; no nonspecific amplification was obtained on genomic DNA of C. elegans. Use of P and K can significantly reduce the complexity of degenerate oligonucleotide mixtures, and when used together, P and K can act as a universal base.
Clinical Observations with AN-1792 Using TAPIR Analyses (2005)

Clinical observations with AN-1792 using tissue amyloid plaque immunoreactivity (TAPIR) analyses established for the first time evidence in humans that antibodies against beta-amyloid-related epitopes are capable of slowing progression in Alzheimer's disease. Antibodies derived upon TAPIR assay selection may specifically target the pathologic neoepitopes of aggregated A beta species present in amyloid plaques and some of their aggregated, protofibrillar and low molecular weight oligomeric precursors. We briefly summarize here how the proof of concept was established and why it provides the basis for a potential cure for Alzheimer's disease.
Phosphorylation of Connexin43 on Serine368 by Protein Kinase C Regulates Gap Junctional Communication (2000)

Phorbol esters (e.g., TPA) activate protein kinase C (PKC), increase connexin43 (Cx43) phosphorylation, and decrease cell-cell communication via gap junctions in many cell types. We asked whether PKC directly phosphorylates and regulates Cx43. Rat epithelial T51B cells metabolically labeled with (32)P(i) yielded two-dimensional phosphotryptic maps of Cx43 with several phosphopeptides that increased in intensity upon TPA treatment. One of these peptides comigrated with the major phosphopeptide observed after PKC phosphorylation of immunoaffinity-purified Cx43. Purification of this comigrating peptide and subsequent sequencing indicated that the phosphorylated serine was residue 368. To pursue the functional importance of phosphorylation at this site, fibroblasts from Cx43(-/-) mice were transfected with either wild-type (Cx43wt) or mutant Cx43 (Cx43-S368A). Intercellular dye transfer studies revealed different responses to TPA and were followed by single channel analyses. TPA stimulation of T51B cells or Cx43wt-transfected fibroblasts caused a large increase in the relative frequency of approximately 50-pS channel events and a concomitant loss of approximately 100-pS channel events. This change to approximately 50-pS events was absent when cells transfected with Cx43-S368A were treated with TPA. These data strongly suggest that PKC directly phosphorylates Cx43 on S368 in vivo, which results in a change in single channel behavior that contributes to a decrease in intercellular communication.
Avian Influenza Vaccination in Chickens and Pigs with Replication-Competent Adenovirus–Free Human Recombinant Adenovirus 5 (2010)

Protective immunity to avian influenza (AI) virus can be elicited in chickens by in ovo or intramuscular vaccination with replication-competent adenovirus (RCA)-free human recombinant adenovirus serotype 5 (Ad5) encoding AI virus H5 (AdTW68.H5) or H7 (AdCN94.H7) hemagglutinins. We evaluated bivalent in ovo vaccination with AdTW68.H5 and AdCN94.H7 and determined that vaccinated chickens developed robust hemagglutination inhibition (HI) antibody levels to both H5 and H7 AI strains. Additionally, we evaluated immune responses of 1-day-old chickens vaccinated via spray with AdCN94.H7. These birds showed increased immunoglobulin A responses in lachrymal fluids and increased interleukin-6 expression in Harderian gland-derived lymphocytes. However, specific HI antibodies were not detected in the sera of these birds. Because pigs might play a role as a "mixing vessel" for the generation of pandemic influenza viruses we explored the use of RCA-free adenovirus technology to immunize pigs against AI virus. Weanling piglets vaccinated intramuscularly with a single dose of RCA-free AdTW68.H5 developed strong systemic antibody responses 3 wk postvaccination. Intranasal application of AdTW68.H5 in piglets resulted in reduced vaccine coverage, i.e., 33% of pigs (2/6) developed an antibody response, but serum antibody levels in those successfully immunized animals were similar to intramuscularly vaccinated animals.
Nanovalves (2007)

Abstract This article features both molecular and supramolecular chemistry involving: i) stimuli‐induced nanoscale movements within mechanically interlocked molecules; ii) the fabrication of mesoporous silica substrates; and iii) the integration of the mechanically interlocked molecular/supramolecular actuators to act as gatekeepers at the entrances to the silica nanopores into which guest dye molecules can be uploaded and released on demand from the mesoporous silica substrates. The supramolecular actuators are based on two [2]pseudorotaxanes—that is, 1:1 complexes that can be dissociated by external inputs, such as acid/base cycles, electrons, and light. The molecular actuators are based on bistable [2]rotaxanes and can be operated mechanically by using either redox chemistry or electrochemistry. After these pseudorotaxanes and bistable rotaxanes have been attached covalently to the orifices of the silica nanopores, stimuli‐controlled mechanical movements within these mechanically interlocked molecules can be harnessed to close and open the nanopores. Therefore, these mechanically interlocked molecules have been employed as nanovalves for controlled sequestering and release of guest dye molecules into and out of the mesoporous silica substrates. These actuators can be regarded as the prototypes of highly controllable drug‐delivery systems.
Expression of a Chimeric Polygalacturonase Gene in Transgenic rin (Ripening Inhibitor) Tomato Fruit Results in Polyuronide Degradation but Not Fruit Softening (1989)

James J. Giovannoni, Dean DellaPenna, Alan B. Bennett, Robert L. Fischer, Expression of a Chimeric Polygalacturonase Gene in Transgenic rin (Ripening Inhibitor) Tomato Fruit Results in Polyuronide Degradation but Not Fruit Softening, The Plant Cell, Vol. 1, No. 1 (Jan., 1989), pp. 53-63
Catalyst Evaluation for Catalytic Biomass Pyrolysis (2000)

Commercial catalysts, including zeolites (HZSM-5), fluid catalytic cracking (FCC) catalysts, transition metal catalysts (Fe/Cr), and aluminas, were successfully evaluated in a fixed bed catalytic reactor using a mixture of model compounds to simulate biomass flash pyrolysis vapors. Successful criteria including the stability index (SI), the water generation (WG), and the loss of organics (LO) were introduced to monitor the effect of catalysts and ascertain major changes in the obtained liquid product composition. SI being a measure of the effective carbonyls reduction after catalytic cracking reached 100% in the case of HZSM-5 catalysts, leading to the selective production of aromatic hydrocarbons. Transition metal catalysts (Fe/Cr) lead to the selective production of phenol and light phenolics. Comparable trends were obtained using solid biomass in the catalytic fixed bed reactor.
Inhibition by heparin of thrombin-catalyzed activation of the factor VIII-von Willebrand factor complex. (1994)

The activation of factor VIII (fVIII) by thrombin is associated with heavy chain cleavages at Arg372 and Arg740 and light chain cleavage at Arg1689. In a defined, plasma-free assay of fVIII activation and at physiological ionic strength and pH, heparin inhibited the rate of activation of either human or porcine fVIII by thrombin in either the presence or absence of von Willebrand factor (vWf). The inhibitory effect of heparin was associated with inhibition of all three thrombin-catalyzed bond cleavages. At plasma concentrations of fVIII (approximately 1 nM) and vWf (approximately 35 nM), the rate of fVIII activation was inhibited by 50% at approximately 0.1 unit/ml heparin, which is below the normal range of heparin concentrations in plasma during therapeutic anticoagulation (0.2-0.7 unit/ml). We propose that, in addition to catalyzing the inhibition of thrombin and other intrinsic pathway coagulation proteases by antithrombin, heparin functions as an anticoagulant by direct inhibition of the activation of the fVIII-vWf complex by thrombin.
Morphological assessment of renal arteries after radiofrequency catheter-based sympathetic denervation in a porcine model (2012)

Catheter-based application of radiofrequency energy resulted in circumscribed transmural injury within the arterial wall affecting autonomic nerve fascicles delayed to treatment. Acute loss of endothelialization resulted in thrombus formation leaving kidney perfusion apparently unimpaired.
A Prospective Rater- and Subject-Blinded Study Comparing the Efficacy of IncobotulinumtoxinA and OnabotulinumtoxinA to Treat Crow's Feet (2014)

IncobotulinumtoxinA and onabotulinumtoxinA (1:1 dose conversion ratio) were well tolerated, showing comparable efficacy and duration of treatment effect for crow's feet.
The Cedar file system (1988)

The Cedar File System (CFS) is a workstation file system that provides access to both a workstation's local disk and to remote file servers via a single hierarchical name space. CFS supports a group of cooperating programmers by allowing them to both manage local naming environments and to share consistent versions of collections of software.
Representation and Recognition of Events in Surveillance Video Using Petri Nets (2005)

Detection of events is an essential task in surveillance applications. This task requires finding a general event representation method and developing efficient recognition algorithms dealing with this representation. In this paper, we describe an interactive system for querying surveillance video about events. The queries may not be known in advance and have to be composed from primitive events and previously defined queries. We propose using Petri nets as both representation and recognition methods. The Petri net representation for users' queries is derived automatically from simpler event nets. Recognition is then performed by tokens moving through the Petri nets.
Gaps in the Ablation Line as a Potential Cause of Recovery From Electrical Isolation and Their Visualization Using MRI (2011)

Conduction block can occur across discontinuous ablation lines. Moreover, with recovery of conductivity over time, ablation lines with large gaps exhibiting acute conduction block may recover propagation in the gap over time, allowing recurrences of arrhythmias. The ability to see gaps acutely using MRI will allow for targeting these sites for ablation.
Direct Photolithography on Optical Fiber End (2002)

New photolithography techniques have been developed for fabricating an arbitrary structure on the optical fiber end. One technique consists of preparing a uniform resist film on the optical fiber end. The area of the fiber end is too small to apply the normal spin coating method. The surface tension of the resist strongly disturbs the film uniformity. The spray coating technique can be used to prepare a thin uniform resist film reducing the effect of the surface tension. Another technique is for transferring the arbitrary pattern aligned to the fiber core. The mask including the arbitrary pattern and the alignment guide hole is prepared using the self-aligning method. These techniques are promising for fabricating the microlens which improves the coupling efficiency between the laser diode and the fiber. The effect of the fabricated lens on the optical fiber end is confirmed.
Repair of defined single base-pair mismatches in Escherichia coli (1985)

Heteroduplexes with single base-pair mismatches of known sequence were prepared by annealing separated strands of bacteriophage lambda DNA and used to transfect Escherichia coli. Each of the eight possible single base-pair mismatches was constructed. Genetic analysis of the progeny phages obtained from transfected bacteria indicates that the E. coli mismatch repair system does not recognize (or does not repair) all single base-pair mismatches with equal efficiency. In particular, the A.G, C.T, and C.C mismatches appear to be less repaired than any others. The mutator character of mismatch repair-deficient mutants suggests that such unrepaired mismatches should occur infrequently during E. coli DNA replication.
The Variation Tendency Analysis on Contribution Rate to Economic Growth by Production Factor Input in China (2013)

The economic growth is influenced by two factors, input of production factors and social production efficiency. The input of production factors is the premise and foundation of economic growth. The previous academic studies generally use the production functions to derive quantitative description of contributions and all kinds of production factors input have contributed to economic growth. Based on translog production function, measuring the contribution rate of capital, labour and energy to economic growth in China, will absolutely be able to reveal their variation trendencies, as well as the changing path of the growth model in China.
Mono-, di- and tetra-nuclear ruthenium(II) complexes containing 2,2′-p-phenylenebis(imidazo[4,5-f ]phenanthroline): synthesis, characterization and third-order non-linear optical properties (2001)

Mono-, di- and tetra-nuclear ruthenium(II) complexes containing 2,2′-p-phenylenebis(imidazo[4,5-f ]phenanthroline) (H2bpib) have been synthesized and characterized. Electrochemical and UV/Vis data show that the first redox process in these complexes is bipyridine based and the metal–metal interaction in di- and tetra-nuclear complexes is very weak. Resonance Raman spectra provide direct evidence for a low-energy bipyridine to H2bpib charge-transfer transition. Furthermore, the non-linear optical properties of the ruthenium(II) complexes were investigated by Z-scan techniques with 12 ns laser pulses at 540 nm, and all of them exhibit both NLO absorption and self-defocusing effect. The corresponding effective NLO susceptibilities |χ3| of the complexes are 5.76 × 10−12–21.06 × 10−12 esu.
Time-resolved Raman studies of the decay of the longitudinal optical phonons in wurtzite GaN (1998)

Decay of the longitudinal-optical (LO) phonons in wurtzite GaN has been studied by subpicosecond time-resolved Raman spectroscopy. Our experimental results show that among the various possible decay channels, the LO phonons in wurtzite GaN decay primarily into a large wave-vector TO and a large wave-vector LA or TA phonon. These experimental results are consistent with the recent theoretical calculations of the phonon dispersion curves for wurtzite GaN.
Noise in Gene Expression Determines Cell Fate in Bacillus subtilis (2007)

Random cell-to-cell variations in gene expression within an isogenic population can lead to transitions between alternative states of gene expression. Little is known about how these variations (noise) in natural systems affect such transitions. In Bacillus subtilis, noise in ComK, the protein that regulates competence for DNA uptake, is thought to cause cells to transition to the competent state in which genes encoding DNA uptake proteins are expressed. We demonstrate that noise in comK expression selects cells for competence and that experimental reduction of this noise decreases the number of competent cells. We also show that transitions are limited temporally by a reduction in comK transcription. These results illustrate how such stochastic transitions are regulated in a natural system and suggest that noise characteristics are subject to evolutionary forces.
Decreased differentiation of erythroid cells exacerbates ineffective erythropoiesis in β-thalassemia (2008)

In beta-thalassemia, the mechanism driving ineffective erythropoiesis (IE) is insufficiently understood. We analyzed mice affected by beta-thalassemia and observed, unexpectedly, a relatively small increase in apoptosis of their erythroid cells compared with healthy mice. Therefore, we sought to determine whether IE could also be characterized by limited erythroid cell differentiation. In thalassemic mice, we observed that a greater than normal percentage of erythroid cells was in S-phase, exhibiting an erythroblast-like morphology. Thalassemic cells were associated with expression of cell cycle-promoting genes such as EpoR, Jak2, Cyclin-A, Cdk2, and Ki-67 and the antiapoptotic protein Bcl-X(L). The cells also differentiated less than normal erythroid ones in vitro. To investigate whether Jak2 could be responsible for the limited cell differentiation, we administered a Jak2 inhibitor, TG101209, to healthy and thalassemic mice. Exposure to TG101209 dramatically decreased the spleen size but also affected anemia. Although our data do not exclude a role for apoptosis in IE, we propose that expansion of the erythroid pool followed by limited cell differentiation exacerbates IE in thalassemia. In addition, these results suggest that use of Jak2 inhibitors has the potential to profoundly change the management of this disorder.
Chemokine (C-C Motif) Ligand 2 Engages CCR2+ Stromal Cells of Monocytic Origin to Promote Breast Cancer Metastasis to Lung and Bone (2009)

Metastatic spread of cancer to distant vital organs, including lung and bone, is the overwhelming cause of breast cancer mortality and morbidity. Effective treatment of systemic metastasis relies on the identification and functional characterization of metastasis mediators to multiple organs. Overexpression of the chemokine (C-C motif) ligand 2 (CCL2) is frequently associated with advanced tumor stage and metastatic relapse in breast cancer. However, the functional mechanism of CCL2 in promoting organ-specific metastasis of breast cancer has not been rigorously investigated. Here, we used organ-specific metastatic sublines of the MDA-MB-231 human breast cancer cell line to demonstrate that overexpression of CCL2 promotes breast cancer metastasis to both lung and bone. Conversely, blocking CCL2 function with a neutralizing antibody reduced lung and bone metastases. The enhancement of lung and bone metastases by CCL2 was associated with increased macrophage infiltration and osteoclast differentiation, respectively. By performing functional assays with primary cells isolated from the wild type, CCL2 and CCR2 knock-out mice, we showed that tumor cell-derived CCL2 depends on its receptor CCR2 (chemokine, CC motif, receptor 2) expressed on stromal cells to exert its function in promoting macrophage recruitment and osteoclast differentiation. Overall, these data demonstrated that CCL2-expressing breast tumor cells engage CCR2(+) stromal cells of monocytic origin, including macrophages and preosteoclasts, to facilitate colonization in lung and bone. Therefore, CCL2 and CCR2 are promising therapeutic targets for simultaneously inhibiting lung and bone metastasis of breast cancer.
A rice cab gene promoter contains separate cis-acting elements that regulate expression in dicot and monocot plants. (1992)

The major light-harvesting chlorophyll a/b binding proteins of the photosynthetic apparatus are encoded by families of nuclear cab genes. The expression of most cab genes is tissue specific and photoregulated in angiosperms. In transgenic tobacco plants, expression of the reporter gene beta-glucuronidase (GUS) is photoregulated and tissue specific from 5' upstream sequences of the rice cab1R gene; deletion of sequences upstream from position -170 with respect to the transcription start site eliminates the enhanced and photoregulated expression in the transgenic plants. Using an in situ transient expression assay, we have determined that the sequence OCT-R, an octamer repeat that lies within the -269 to -170 region of cab1R, is essential for photoregulated expression of the chimeric GUS gene in leaf cells of maize and rice but is not required for expression in illuminated tobacco leaves. Conversely, box III*- and G-box-like sequences found near OCT-R in cab1R are necessary for high-level transient expression of the reporter gene in tobacco leaf tissue but are not required for transient expression in maize or rice leaves.
Growth of Multilayer Films of Fixed and Variable Charge Density Polyelectrolytes:  Effect of Mutual Charge and Secondary Interactions (2003)

We report on the effect of mutual polyelectrolyte charge and secondary interactions on the formation of polyelectrolyte multilayer films of a lowly charged copolymer of acrylamide and [3-(2-methylpropionamido)propyl]trimethylammonium chloride, AM-MAPTAC 10 (10 mol % of cationic monomers), and poly(acrylic acid) (PAA). These multilayer films were constructed on planar substrates by the sequential adsorption of AM-MAPTAC 10 and PAA at different pH conditions. Surface plasmon resonance spectroscopy (SPRS), quartz crystal microbalance (QCM), and atomic force microscopy (AFM) were employed to follow the film formation process. While AM-MAPTAC 10 is permanently charged, the ionization of PAA is adjusted by changing the pH of the adsorption solutions. In contrast with previous studies, it is shown that multilayer formation with one polyelectrolyte with a charge density of 10 mol % is possible. However, the multilayer growth follows a different pattern depending on the relative charge density of PAA. At low pH, where PAA is only lowly ionized, the films show an exponential-like growth, with a gradual increase of the thickness and adsorbed mass per layer with increasing layer number. At neutral to alkaline pH, where PAA approaches full ionization, multilayer growth proceeds via a series of adsorption−desorption steps, with immersion in PAA solutions leading to partial removal of the underlying AM-MAPTAC 10 layer. The obtained results are discussed in terms of an interplay between electrostatic and secondary interactions within the films and matching of the charge density of the polyelectrolytes employed to construct the films.