gebhart/patrepeval huggingface dataset:
Oligonucleotide Facilitators May Inhibit or Activate a Hammerhead Ribozyme (1996)

Facilitators are oligonucleotides capable of affecting hammerhead ribozyme activity by interacting with the substrate at the termini of the ribozyme. Facilitator effects were determined in vitro using a system consisting of a ribozyme with 7 nucleotides in every stem sequence and two substrates with inverted facilitator binding sequences. The effects of 9mer and 12mer RNA as well as DNA facilitators which bind either adjacent to the 3'- or 5'-end of the ribozyme were investigated. A kinetic model was developed which allows determination of the apparent dissociation constant of the ribozyme-substrate complex from single turnover reactions. We observed a decreased dissociation constant of the ribozyme-substrate complex due to facilitator addition corresponding to an additional stabilization energy of delta delta G=-1.7 kcal/mol with 3'-end facilitators. The cleavage rate constant was increased by 3'-end facilitators and decreased by 5'-end facilitators. Values for Km were slightly lowered by all facilitators and kcat was increased by 3'-end facilitators and decreased by 5'-end facilitators in our system. Generally the facilitator effects increased with the length of the facilitators and RNA provided greater effects than DNA of the same sequence. Results suggest facilitator influences on several steps of the hammerhead reaction, substrate association, cleavage and dissociation of products. Moreover, these effects are dependent in different manners on ribozyme and substrate concentration. This leads to the conclusion that there is a concentration dependence whether activation or inhibition is caused by facilitators. Conclusions are drawn with regard to the design of hammerhead ribozyme facilitator systems.
Phosphonic Acid-Functionalized Diblock Copolymer Nano-Objects via Polymerization-Induced Self-Assembly: Synthesis, Characterization, and Occlusion into Calcite Crystals (2015)

Dialkylphosphonate-functionalized and phosphonic acid-functionalized macromolecular chain transfer agents (macro-CTAs) are utilized for the reversible addition–fragmentation chain transfer (RAFT) dispersion polymerization of benzyl methacrylate (BzMA) at 20% w/w solids in methanol at 64 °C. Spherical, worm-like, and vesicular nano-objects could each be generated through systematic variation of the mean degree of polymerization of the core-forming PBzMA block when using relatively short macro-CTAs. Construction of detailed phase diagrams is essential for the reproducible targeting of pure copolymer morphologies, which were characterized using transmission electron microscopy (TEM) and dynamic light scattering (DLS). For nano-objects prepared using the phosphonic acid-based macro-CTA, transfer from methanol to water leads to the development of anionic surface charge as a result of ionization of the stabilizer chains, but this does not adversely affect the copolymer morphology. Given the well-known strong affinity of phosphonic acid for calcium ions, selected nano-objects were evaluated for their in situ occlusion within growing CaCO3 crystals. Scanning electron microscopy (SEM) studies provide compelling evidence for the occlusion of both worm-like and vesicular phosphonic acid-based nano-objects and hence the production of a series of interesting new organic–inorganic nanocomposites.
Quantitative Analysis of Cholesterol and Cholesterol Ester Mixtures Using Near-Infrared Fourier Transform Raman Spectroscopy (1996)

Near-infrared Fourier transform Raman spectroscopy is a rapid and nondestructive technique that can provide reliable qualitative in situ information about the chemistry of biological samples. We have combined this technique with partial least-squares (PLS) regression to perform a quantitative determination of free and esterified cholesterol in two synthetic sample series. In 66 ternary mixtures containing various proportions of cholesterol, cholesterol linoleate, and oleate, the standard errors of prediction were 1.27, 1.17, and 0.94%, respectively. For the second series of experiments concerning the sensitive problem of quantitative analysis of cholesterol palmitate and stearate mixtures, the standard error of prediction for 49 samples was 3.02%. It is also possible to extract quantitative information for a single component of the ternary mixtures independently. These results are of great importance when—as in the case of arterial samples—many chemical species are present. Comparison between Raman spectra of ternary mixtures and atherosclerotic rabbit aorta shows that many bands, assignable to free and esterified cholesterol, are easily observed in the aorta spectrum.
Production of a mouse monoclonal antibody reactive with a human nuclear antigen associated with cell proliferation (1983)

The production of a mouse monoclonal antibody, Ki-67, is described. The Ki-67 antibody recognized a nuclear antigen present in proliferating cells, but absent in resting cells. Immunostainings with Ki-67 revealed nuclear reactivity in cells of germinal centres of cortical follicles, cortical thymocytes, neck cells of gastrointestinal mucosa, undifferentiated spermatogonia and cells of a number of human cell lines. The Ki-67 antibody did not react with cells known to be in a resting stage, such as lymphocytes, monocytes, parietal cells and Paneth's cells of gastrointestinal mucosa, hepatocytes, renal cells, mature sperm cells, brain cells, etc. Expression of the antigen recognized by Ki-67 could be induced in peripheral blood lymphocytes after stimulation with phytohaemagglutinin, whereas it disappeared from HL-60 cells stimulated with phorbol esters to differentiate into mature macrophages in a resting stage. These findings suggest that Ki-67 is directed against a nuclear antigen associated with cell proliferation. A first series of immunostainings of tumour biopsies indicated that Ki-67 may be a potent tool for easy and quick evaluation of the proportion of proliferating cells in a tumour.
Physiology of sialic acid capsular polysaccharide synthesis in serogroup B Neisseria meningitidis (1983)

The pathway for biosynthesis of sialic acid capsular polysaccharide was examined in Neisseria meningitidis serogroup B strain M986 and in strain PRM102, an isogenic mutant defective in polysaccharide production. Strain PRM102 was found to possess only 25% of the level of sialyltransferase activity that was found in strain M986, but it had wild-type levels of both the N-acetylneuraminic acid (NANA) condensing enzyme and the CMP-NANA synthetase. A new meningococcal enzyme, a CMP-NANA hydrolase, was found in both meningococcal strains. This enzyme generated CMP and NANA from CMP-NANA, had a Km of 0.88 microM, had a Vmax of 10.75 nmol of NANA produced per h per mg of protein, and was completely inhibited by 45.3 microM CMP. The sialyltransferase, which also had CMP-NANA as substrate, was insensitive to CMP addition. Subcellular fractionation and purification of cytoplasmic and outer membranes on sucrose density gradients revealed that both the sialyltransferase and the CMP-NANA hydrolase were cytoplasmic membrane associated. The NANA condensing enzyme and the CMP-NANA synthetase were found to be cytosolic. A working hypothesis for the regulation of sialic acid polysaccharide synthesis was developed. The CMP-NANA hydrolase with its high affinity for CMP-NANA regulates polysaccharide formation by the sialyltransferase, whereas CMP, a product of both the sialyltransferase and the CMP-NANA hydrolase, modulates the activity of the hydrolase on the cytoplasmic membrane.
Synthesis of (±)-Calicheamicinone by Two Methods (1998)

Ketene acetal 25 was converted into silyl enol ether 20, which underwent a Diels−Alder reaction with methyl (E)-3-nitropropenoate to afford ketone 27. This was converted by two routes into (±)-calicheamicinone (1). In the first, modification of the nitro, ester, and allyl substituents gave ketone 38, which reacted stereoselectively with cerium trimethylsilylacetylide to place the acetylene unit syn to the nitrogen function (38 → 39). Further elaboration took the route as far as aldehyde 42. A slightly different series of reactions served to convert ketone 27 into tricyclic ketone 43. This also reacted with cerium trimethylsilylacetylide, but in the opposite stereochemical sense to 38, so as to place the acetylene unit anti to the nitrogen function (43 → 50). Further elaboration took this second route as far as lactone 44. Both 42 and 44 serve as advanced intermediates for the synthesis of (±)-calicheamicinone. The monoacetylenic aldehyde 42 reacted stereoselectively with cerium trimethylsilylacetylide to give the bis(acetylene) 53 as the major product. This was elaborated into lactone 60, which was desaturated (60 → 68) and methoxycarbonylated on nitrogen. The acetylenic silyl groups were then removed, so as to generate syn bis(acetylene) 72, and the terminal acetylenic hydrogens were replaced by iodine. The resulting diiodide 81 formed the cyclic enediyne 82 on reaction with (Z)-1,2-bis(trimethylstannyl)ethene in the presence of (Ph3P)4Pd, and the enediyne was converted into (±)-calicheamicinone. syn-Bis(acetylene) 72 was also synthesized from the other advanced intermediate (lactone 44), using, as a key step, free radical bromination of the derived unsaturated lactone 77. The resulting bromo lactones 78 were converted into an aldehyde ester 79, and this reacted stereoselectively with cerium trimethylsilylacetylide to give 80, convertible by the action of TBAF into 72.
Characterization of over‐the‐counter cough/cold medications by liquid chromatography/electrospray mass spectrometry (1995)

Abstract Electrospray ioniztion (ESI) high‐performance liquid chromatography/mass spectrometry (LC/MS) has been utilized for the characterization of the active ingredients in over‐the‐counter (OTC) cough and cold medications. The use of in‐source collision‐induced dissociation (CID) on a single quadrupole instrument produced spectra with characteristic fragment ions. The in‐source CID potential was rotated through different energies on alternate scans throughout the chromatographic run. The spectra across a given chromatographic peak were summed and averaged to give composite spectra which displayed molecular ions in addition to fragment ions, producing library searchable spectra of analytes with varying collisional stabilities, within a single chromatographic run. These spectra were then saved into a library which was created with the following OTC drugs, phenylpropanolamine, doxvlamine, pyrilamine, chlorpheniramine, brompheniramine, dextromethorphan, cyclizine, and clemastine. The active ingredients in commercial OTC remedies were detected and characterized using this created library. The method requires no derivatization and minimal sample preparation, is applicable to a range of analytes, and can be fully automated for multiple sample analyses.
Specific binding of lactoferrin to Aeromonas hydrophila (1991)

The interaction of lactoferrin (Lf) with Aeromonas hydrophila (n= 28) was tested in a 125I-labeled protein-binding assay. The mean percent binding values for human Lf (HLf) and bovine Lf (BLf) were 13.4±2.0 (SEM), and 17.5±2.7 (SEM), respectively. The Lf binding was characterized in type strain A. hydrophila subsp. hydrophila CCUG 14551. The HLf and BLf binding reached a complete saturation within 2 h. Unlabeled HLf and BLf displaced 125I-HLf binding in a dose-dependent manner, and more effectively by the heterologous (1 μg for 50% inhibition) than the homologous (10 μg for 50% inhibition) ligand. Apo- and holo-forms of HLf and BLf both inhibited more than 80%, while mucin caused approx. 50% inhibition of the HLf binding. Various other proteins (including transferrin) or carbohydrates did not block the binding. Two HLf-binding proteins with an estimated molecular masses of 40 kDa and 30 kDa were identified in a boiled-cell-envelope preparation, while the unboiled cell envelope demonstrated a short-ladder pattern at the top of the separating gel and a second band at approx. 60 kDa position. These data establish a specific interaction of Lf and the Lf-binding proteins seem to be porins in A. hydrophila.
The su(Hw) Insulator Can Disrupt Enhancer-Promoter Interactions When Located More than 20 Kilobases Away from the Drosophila achaete-scute Complex (1999)

Here we report that the su(Hw) insulator may not necessarily separate promoters from enhancers to allow inhibition of transcription by the su(Hw) protein. For this purpose we used the strains of Drosophila melanogaster which carry inversion of the region containing the yellow gene and the achaete-scute complex (AS-C). Despite the reverse orientation of the region, the AS-C enhancers continue to activate achaete and scute gene expression. The su(Hw) insulator, located more than 20 kb away from the inversion, facilitates strong suppression of achaete and scute gene expression, although is does not separate the promoters from the AS-C enhancers.
Serotonergic Anxiolytics in the Treatment of Panic Disorder: A Controlled Study With Buspirone (1989)

The efficacy of buspirone for panic disorder was tested in 60 patients who met Diagnostic and Statistical Manual of Mental Disorders (3rd ed.) criteria for panic disorder or agoraphobia with panic attacks. Patients were randomly assigned to treatment with buspirone (mean dose 29.5 mg/day), imipramine (mean dose 140 mg/day), or placebo, and treated for 8 weeks after a 4- to 7-day placebo lead-in period. Patients with 4 or fewer attacks per month and those without attacks at the baseline visit were excluded from panic frequency comparisons. Both buspirone and imipramine tended to be better than placebo on total number of panic attacks, global psychopathology, and the Hamilton Anxiety rating scale, but end point differences among treatments were not statistically significant. At the end of the study, 25% of the buspirone patients were panic-free, as were 7% of the imipramine patients and 14% of the placebo patients; again, these differences were not statistically significant. The results of this study were inconclusive, partly because of the relatively small number of patients (10-11) completing the study in each treatment group, and partly because of a robust placebo response in this population. Possible reasons for this high placebo response are discussed, as well as suggestions for changes in study design for future studies.
Studies of the relativistic electron source and related phenomena in Petawatt Laser matter interactions (1999)

The interaction of laser radiation with solid targets at 1 petawatt power and intensity up to 3x10{sup 20} Wcm{sup -2} has been studied with emphasis on relativistic electrons and high energy ions. Secondary effects including Bremsstrahlung radiation, nuclear interactions and heating have been characterized. A collimated beam of protons with up to 55 MeV energy is emitted normal to the rear surface of thin targets and its characteristics and origin are discussed. The significance of the data for radiography, fast ignition and proton beam applications is summarized.
Natriuretic peptides and acute renal failure (2003)

Atrial natriuretic peptides (ANPs) are a family of peptide hormones, e.g., ANP, long-acting natriuretic peptide, vessel dilator, and kaliuretic peptide synthesized by the ANP gene. Brain natriuretic peptide (BNP) and C-type natriuretic peptide are also members of this family but are synthesized by separate genes. Within the kidney, the ANP prohormone's posttranslational processing is different from that of other tissues, resulting in an additional four amino acids added to the NH2 terminus of ANP (e.g., urodilatin). Each of these natriuretic and diuretic peptides increases within the circulation with acute renal failure (ARF). Renal transplantation but not hemodialysis returns their circulating concentrations to those of healthy individuals. BNP and adrenomedullin, a 52-amino acid natriuretic peptide, have beneficial effects on glomerular hypertrophy and glomerular injury but do not improve tubular injury (i.e., acute tubular necrosis). Vessel dilator ameliorates acute tubular necrosis with regeneration of the brush borders of proximal tubules. Vessel dilator decreases mortality in ARF from 88 to 14% at day 6 of ARF, even when given 2 days after renal failure has been established.
Synthesis of Monodisperse Microparticles from Non‐Newtonian Polymer Solutions with Microfluidic Devices (2011)

Polymer solutions are useful precursors to synthesize microparticles with microfluidic devices, but most polymer solutions are incompatible with microfluidic emulsification due to their non-Newtonian flow characteristics. A technique is presented to form monodisperse particles from such solutions by surrounding them with a chaperoning Newtonian fluid and forcing both to pinch into preparticle drops. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
The use of graded InGaAs layers and patterned substrates to remove threading dislocations from GaAs on Si (1994)

We have investigated threading dislocation (TD) removal from GaAs films on Si by introduction of additional InGaAs graded strain layers in combination with growth on patterned substrates. The substrate patterns consisted of mesas with 10–34 μm widths. The mesa sidewalls were either overhanging (concave), leading to free sidewalls for the film on the mesas, or outward sloping (convex) sidewalls with {111} orientation. The dislocation structure was studied using transmission electron microscopy. It was found that the graded strained layers led to a reduction of dislocation density by a factor of ∼5 in films grown both on mesas with concave sidewalls and on unpatterned substrates. This reduction was due to dislocation reactions leading to annihilation of TDs. For films with graded strained layers on mesas with convex sidewalls, an additional factor of ∼3 reduction in TD density was observed in the part of the film that was grown on top of the mesas. In this case all mobile TDs (TDs associated with 60° misfit dislocations, i.e., TDs that could glide to relieve misfit stress) were removed from the film on top of the mesas to the regions above the sidewalls and only TDs associated with 90° misfit dislocations remained. We suggest that this is due to pinning of the TDs associated with 60° misfit dislocations at the mesa edges and we have presented an explanation for this pinning in terms of the stress conditions at the {111} oriented mesa edges. In addition, this leads us to suggest that in order to obtain minimum TD density it is imperative to prevent formation of 90° misfit dislocation during lattice mismatched heteroepitaxial growth.
Ron was wrong, Whit is right (2012)

Abstract. We performed a sanity check of public keys collected on the web. Our main goal was to test the validity of the assumption that different random choices are made each time keys are generated. We found that the vast majority of public keys work as intended. A more disconcerting finding is that two out of every one thousand RSA moduli that we collected offer no security. Our conclusion is that the validity of the assumption is questionable and that generating keys in the real world for “multiple-secrets ” cryptosystems such as RSA is significantly riskier than for “single-secret ” ones such as ElGamal or (EC)DSA which are based on Diffie-Hellman.
Requirements for Interleukin-4-Induced Gene Expression and Functional Characterization of Stat6 (1996)

Interleukin-4 (IL-4) stimulation leads to the activation of the signal transducer and activator of transcription 6 (Stat6). In this study, we present data relating to the functional properties of Stat6. Human embryonic kidney 293 cells were shown to be deficient of Stat6 yet express all other components of the IL-4 signaling cascade. This cell line was used for transient-transfection studies of wild-type and mutant Stat6 proteins. The wild-type protein was shown to activate a reporter construct carrying multiple copies of the IL-4 response element derived from the human immunoglobulin heavy-chain germ line epsilon promoter. Similarly, a truncated protein lacking 41 amino acids of the N terminus was fully active. However, removal of the C-terminal 186 amino acids completely abolished transcription activation. Amino acid substitutions were introduced into the putative DNA binding domain (VVI at positions 411 to 413), the SH2 domain (R-562), or the tyrosine (Y-641) which presumably becomes phosphorylated upon activation. All three of these Stat6 mutants were unable to activate transcription in 293 cells. Wild-type and mutant Stat6 derivatives were also expressed in insect cells, and purified proteins were analyzed in vitro for the ability to interact with both DNA and tyrosine-phosphorylated peptides derived from the IL-4 receptor alpha chain. Mutations within the DNA binding domain, the SH2 domain, or tyrosine 641 completely abolished DNA binding. In contrast, only the SH2 mutant failed to interact with tyrosine-phosphorylated peptides. The transdominant effects of all Stat6 derivatives were analyzed by using HepG2 cells, which express endogenous Stat6 protein. Differential effects were observed with various mutants, supporting the current model of the Jak/STAT activation cycle.
Fabrication of gated polycrystalline silicon field emitters (2002)

Polycrystalline silicon is currently being investigated as the cathode material for flat panel displays using field emission. Conventional silicon microfabrication techniques have been adapted to produce highly uniform arrays of gridded polysilicon field emitters.
Sensitization of TRPA1 by PAR2 contributes to the sensation of inflammatory pain (2007)

Proinflammatory agents trypsin and mast cell tryptase cleave and activate PAR2, which is expressed on sensory nerves to cause neurogenic inflammation. Transient receptor potential A1 (TRPA1) is an excitatory ion channel on primary sensory nerves of pain pathway. Here, we show that a functional interaction of PAR2 and TRPA1 in dorsal root ganglion (DRG) neurons could contribute to the sensation of inflammatory pain. Frequent colocalization of TRPA1 with PAR2 was found in rat DRG neurons. PAR2 activation increased the TRPA1 currents evoked by its agonists in HEK293 cells transfected with TRPA1, as well as DRG neurons. Application of phospholipase C (PLC) inhibitors or phosphatidylinositol-4,5-bisphosphate (PIP(2)) suppressed this potentiation. Decrease of plasma membrane PIP(2) levels through antibody sequestration or PLC-mediated hydrolysis mimicked the potentiating effects of PAR2 activation at the cellular level. Thus, the increased TRPA1 sensitivity may have been due to activation of PLC, which releases the inhibition of TRPA1 from plasma membrane PIP(2). These results identify for the first time to our knowledge a sensitization mechanism of TRPA1 and a novel mechanism through which trypsin or tryptase released in response to tissue inflammation might trigger the sensation of pain by TRPA1 activation.