gebhart/patrepeval huggingface dataset:
An <sup>1</sup>H NMR determination of the three‐dimensional structures of mirror‐image forms of a Leu‐5 variant of the trypsin inhibitor from <i>Ecballium elaterium</i> (EETI‐II) (1994)

The 3-dimensional structures of mirror-image forms of a Leu-5 variant of the trypsin inhibitor Ecballium elaterium (EETI-II) have been determined by 1H NMR spectroscopy and simulated annealing calculations incorporating NOE-derived distance constraints. Spectra were assigned using 2-dimensional NMR methods at 400 MHz, and internuclear distances were determined from NOESY experiments. Three-bond spin-spin couplings between C alpha H and amide protons, amide exchange rates, and the temperature dependence of amide chemical shifts were also measured. The structure consists largely of loops and turns, with a short region of beta-sheet. The Leu-5 substitution produces a substantial reduction in affinity for trypsin relative to native EETI-II, which contains an Ile at this position. The global structure of the Leu-5 analogue studied here is similar to that reported for native EETI-II (Heitz A, Chiche L, Le-Nguyen D, Castro B, 1989, Biochemistry 28:2392-2398) and to X-ray and NMR structures of the related proteinase inhibitor CMTI-I (Bode W et al., 1989, FEBS Lett 242:285-292; Holak TA et al., 1989a, J Mol Biol 210:649-654; Holak TA, Gondol D, Otlewski J, Wilusz T, 1989b, J Mol Biol 210:635-648; Holak TA, Habazettl J, Oschkinat H, Otlewski J, 1991, J Am Chem Soc 113:3196-3198). The region near the scissile bond is the most disordered part of the structure, based on geometric superimposition of 40 calculated structures. This disorder most likely reflects additional motion being present in this region relative to the rest of the protein. This motional disorder is increased in the Leu-5 analogue relative to the native form and may be responsible for its reduced trypsin binding. A second form of the protein synthesized with all (D) amino acids was also studied by NMR and found to have a spectrum identical with that of the (L) form. This is consistent with the (D) form being a mirror image of the (L) form and not distinguishable by NMR in an achiral solvent (i.e., H2O). The (D) form has no activity against trypsin, as would be expected for a mirror-image form.
Preliminary investigation of topical nitroglycerin formulations containing natural wound healing agent in diabetes‐induced foot ulcer (2013)

Nitroglycerin (NTG) is an organic nitrate rapidly denitrated by enzymes to release free radical nitric oxide and shows improved wound healing and tissue protection from oxidative damage. The purpose of this study was to evaluate whether topical application of NTG in the form of gel/ointment along with a natural wound healing agent, aloe vera, would bring about wound healing by using diabetes-induced foot ulcer model and rat excision wound model. All these formulations were evaluated for pH, viscosity, drug content and ex vivo diffusion studies using rat skin. Based on ex vivo permeation studies, the formulation consisting of carbopol 974p as a gelling agent and aloe vera was found to be suitable. The in vivo study used streptozotocin-induced diabetic foot ulcer and rat excision wound models to analyse wound healing activity. The wound size in animals of all treated groups was significantly reduced compared with that of the diabetic control and marketed treated animals. This study showed that the gel formed with carbopol 974p (1%) and aloe vera promotes significant wound healing and closure in diabetic rats compared with the commercial product and provides a promising product to be used in diabetes-induced foot ulcer.
Superoxide Is Produced by the Reduced Flavin in Mitochondrial Complex I (2011)

NADH:ubiquinone oxidoreductase (complex I) is a major source of reactive oxygen species in mitochondria and a contributor to cellular oxidative stress. In isolated complex I the reduced flavin is known to react with molecular oxygen to form predominantly superoxide, but studies using intact mitochondria contend that superoxide may result from a semiquinone species that responds to the proton-motive force (Δp) also. Here, we use bovine heart submitochondrial particles to show that a single mechanism describes superoxide production by complex I under all conditions (during both NADH oxidation and reverse electron transfer). NADH-induced superoxide production is inhibited by complex I flavin-site inhibitors but not by inhibitors of ubiquinone reduction, and it is independent of Δp. Reverse electron transfer (RET) through complex I in submitochondrial particles, driven by succinate oxidation and the Δp created by ATP hydrolysis, reduces the flavin, leading to NAD(+) and O(2) reduction. RET-induced superoxide production is inhibited by both flavin-site and ubiquinone-reduction inhibitors. The potential dependence of NADH-induced superoxide production (set by the NAD(+) potential) matches that of RET-induced superoxide production (set by the succinate potential and Δp), and they both match the potential dependence of the flavin. Therefore, both NADH- and RET-induced superoxide are produced by the flavin, according to the same molecular mechanism. The unified mechanism describes how reactive oxygen species production by complex I responds to changes in cellular conditions. It establishes a route to understanding causative connections between the enzyme and its pathological effects and to developing rational strategies for addressing them.
The Notch Ligands, Jagged and Delta, Are Sequentially Processed by α-Secretase and Presenilin/γ-Secretase and Release Signaling Fragments (2003)

The cleavage of Notch by presenilin (PS)/gamma-secretase is a salient example of regulated intramembrane proteolysis, an unusual mechanism of signal transduction. This cleavage is preceded by the binding of protein ligands to the Notch ectodomain, activating its shedding. We hypothesized that the Notch ligands, Delta and Jagged, themselves undergo PS-mediated regulated intramembrane proteolysis. Here, we show that the ectodomain of mammalian Jagged is cleaved by an A disintegrin and metalloprotease (ADAM) 17-like activity in cultured cells and in vivo, similar to the known cleavage of Drosophila Delta by Kuzbanian. The ectodomain shedding of ligand can be stimulated by Notch and yields membrane-tethered C-terminal fragments (CTFs) of Jagged and Delta that accumulate in cells expressing a dominant-negative form of PS or treated with gamma-secretase inhibitors. PS forms stable complexes with Delta and Jagged and with their respective CTFs. PS/gamma-secretase then mediates the cleavage of the latter to release the Delta and Jagged intracellular domains, a portion of which can enter the nucleus. The ligand CTFs compete with an activated form of Notch for cleavage by gamma-secretase and can thus inhibit Notch signaling in vitro. The soluble Jagged intracellular domain can activate gene expression via the transcription factor AP1, and this effect is counteracted by the co-expression of the gamma-secretase-cleaved product of Notch, Notch intracellular domain. We conclude that Delta and Jagged undergo ADAM-mediated ectodomain processing followed by PS-mediated intramembrane proteolysis to release signaling fragments. Thus, Notch and its cognate ligands are processed by the same molecular machinery and may antagonistically regulate each other's signaling.
Compatibility of Resin-Coated Proppants With Crosslinked Fracturing Fluids (1992)

Summary This paper describes the additive interaction and/or compatibility of various resin-coated proppants (RCP's) with low-, neutral-, and high-pH water-based fracturing fluids. Solutions are provided for those fluids exhibiting compatibility problems with RCP's.
Clinical Trials Testing Cardiovascular Benefits of Antioxidant Supplementation (2002)

Self-selected supplementation of vitamin E has been associated with reduced coronary events and atherosclerotic progression, but the evidence from clinical trials is controversial. ASAP was a 6-year randomized trial to study the effect of supplementation with vitamin E plus slow-release vitamin C on carotid atherosclerotic progression in 520 hypercholesterolemic men and women aged 45-69 years. The supplementation reduced the progression of carotid atherosclerosis by 26% (P = 0.014), by 33% (P = 0.024) in men and 14% (not significant) in women. The effect was larger in subjects with low baseline vitamin C or atherosclerotic plaques. In the Harvard IVUS trial, the combined supplementation with vitamins E and C significantly inhibited the progression of coronary atherosclerosis in one year. These data confirm that the supplementation with a combination of vitamins E and C can retard atherosclerotic progression. The findings of completed trials testing the effect on cardiovascular events are less consistent. The major on-going clinical trials include the SU.VI.MAX, WHS, WACS and WAVE studies. These involve in total over 80,000 subjects, who are treated with antioxidative supplements for years. The results of these studies will become available during 2003-2006. They may provide the necessary additional information concerning the effect of antioxidants on cardiovascular events.
Polymer microstructured fibers by one-step extrusion (2007)

For the first time to our knowledge, polymer-based microstructured fibers with complex cross-sections are directly produced via melt extrusion. Two principal types of fibers were fabricated: a microstructured fiber of a single polymer with a hexagonal array of air holes and a bicomponent fiber consisting of approximately 60 coaxial rings. From the latter, strong visible iridescence was observed and is shown to exhibit a mechanochromic response. This approach, the mainstay of the textile trade for decades, offers a means of continuous high-volume low-cost manufacturing of polymer (and conceivably soft-glass) fibers. For example, in the present effort, 128 coaxially microstructured fibers were fabricated simultaneously at rates exceeding 1200 m/min from industrially mainstream polymers. This approach offers an important step forward towards commoditizing microstructured fibers and open new doors for optical engineering in fashion, marking/identification, and numerous military applications.
Tight-Binding Photonic Molecule Modes of Resonant Bispheres (1999)

We observe coherent resonant coupling of optical whispering-gallery modes in fluorescence from dye doped polymer bispheres with diameters ranging from 2 to $5\ensuremath{\mu}\mathrm{m}$. By monitoring the frequencies of fluorescence peaks of individual spheres, we sort out two spheres with appropriate size matching and bring them into contact. Wave optics calculation also gives good agreement with the experiment. By taking into account harmonic coupling of the whispering-gallery modes, the obtained features of normal mode splitting are well explained by the tight-binding photon picture.
Regulation of 11β‐hydroxysteroid dehydrogenase type 1 and glucose‐stimulated insulin secretion in pancreatic islets of Langerhans (2004)

Levels of 11beta-HSD1 in islets from ob/ob mice are positively regulated by DHC and could be lowered by a selective 11beta-HSD1 inhibitor and a glucocorticoid receptor antagonist. Increased levels of 11beta-HSD1 were associated with impaired GSIS.
An explanation-based, visual debugger for one-way constraints (2004)

This paper describes a domain-specific debugger for one-way constraint solvers. The debugger makes use of several new techniques. First, the debugger displays only a portion of the dataflow graph, called a <i>constraint slice</i>, that is directly related to an incorrect variable. This technique helps the debugger scale to a system containing thousands of constraints. Second, the debugger presents a visual representation of the solver's data structures and uses color encodings to highlight changes to the data structures. Finally, the debugger allows the user to point to a variable that has an unexpected value and ask the debugger to suggest reasons for the unexpected value. The debugger makes use of information gathered during the constraint satisfaction process to generate plausible suggestions. Informal testing has shown that the explanatory capability and the color coding of the constraint solver's data structures are particularly useful in locating bugs in constraint code.
Memory fault diagnosis by syndrome compression (2001)

In this paper we present a data compression technique that can be used to speed up the transmission of diagnosis data from the embedded RAM with built-in self-diagnosis (BISD) support. The proposed approach compresses the faulty-cell address and March syndrome to about 28% of the original size under the March-17N diagnostic test algorithm. The key component of the compressor is a novel syndrome-accumulation circuit, which can be realized by a content-addressable memory. Experimental results show that the area overhead is about 0.9% for a 1Mb SRAM with 164 faults. The proposed compression technique reduces the time for diagnostic test, as well as the tester storage capacity requirement.
Initial Approaches to Artificial Cellulase Systems for Conversion of Biomass to Ethanol (1996)

The process of converting low-value biomass to ethanol via fermentation depends keenly on the development of economic biocatalysts to achieve effective depolymerization of the cellulosic content of biomass. This process has few features in common with contemporary large-scale uses of cellulases, such as food processing and detergent augmentation. Cellulase preparations used in an ethanolfrom-biomass process must hydrolyze crystalline cellulose completely, operate effectively at mildly acidic pH, withstand process stress, and they need not be derived from microorganisms that are generally recognized as safe (GRAS). Furthermore, the ideal cellulase complex used in biomass processing should be highly active on the intended feedstock and obtainable at the lowest possible cost. Clearly, the ability to "engineer" cellulase systems in anticipation of each application is key to successful optimization and commercialization. To achieve this goal, we are collaborating with other researchers to purify individual cellulase enzymes and their genes from a variety of bacteria and fungi. We are also comparing purified cellulases, both individually and in mixtures, using key criteria, to design and assemble optimized, use-specific, artificial cellulase systems that can be produced by recombinant host microorganisms on an industrial scale. This paper describes both strategies and progress to date.
Measuring user confidence in smartphone security and privacy (2012)

In order to direct and build an effective, secure mobile ecosystem, we must first understand user attitudes toward security and privacy for smartphones and how they may differ from attitudes toward more traditional computing systems. What are users' comfort levels in performing different tasks? How do users select applications? What are their overall perceptions of the platform? This understanding will help inform the design of more secure smartphones that will enable users to safely and confidently benefit from the potential and convenience offered by mobile platforms.
Comparison of ID8 MOSE and VEGF-modified ID8 cell lines in an immunocompetent animal model for human ovarian cancer. (2006)

Attempts to develop novel immunotherapeutic mouse models have been hampered by the lack of an adequate in vivo system. This study was performed to establish an immunocompetent mouse model for the testing of immunotherapy concepts. The in vivo system was based on a svngeneic mouse ovarian surface epithelium (MOSE) cancer, physiologically and biologically closely resembling human epithelial ovarian cancer. In addition, a more aggressive variant containing a mutated form of vascular epithelial growth factor was also evaluated. The growth patterns of these ovarian cancer cells in mice were compared to the established, highly aggressive 4T1 breast cancer model. A clinically-relevant tool for the study of different growth patterns in ovarian cancer, with potential significance for the development of novel immunological methods, was successfully developed.
A Dual-Pulse Repetition Frequency Scheme for Mitigating Velocity Ambiguities of the NOAA P-3 Airborne Doppler Radar (2000)

To mitigate some of the deleterious effects of the relatively small unambiguous Doppler velocity range (Nyquist interval) of airborne X-band Doppler radars, a technique has been developed to extend this interval. This technique, termed the batch-mode dual-PRF (pulse repetition frequency) technique, utilizes two batches of pulses that are each averaged to produce two velocity estimates at each range bin, with each batch at a different sampling rate. Comparison of the two velocity estimates produces a difference velocity that is used to dealias the second estimate within an extended velocity range that is larger than the Nyquist velocities of either of the two original samples. In this implementation, the choices of the two PRFs are restricted to ratios of 3/2 or 4/3 of the lowest PRF.
Pharmacokinetics and tissue distribution of the nonadecapeptide Moli1901 in rats and mice (2003)

1. Administration of aerosolized, radiolabelled Moli1901 (duramycin, 2622U90), a 19 amino acid polycyclic peptide, to rats resulted in the deposition of high amounts of radiolabel in the respiratory tract, with deposited radiolabel persisting almost unchanged through 7 days after dosing. Little to no radiolabel was present in the bloodstream of these rats. 2. Rats absorbed little radiolabel after p.o. administration, with nearly all of the dose excreted in the faeces by 2 days after dosing. 3. At 7 days following an intravenous dose, rats excreted 54% of the radiolabel in faeces and 5.4% in the urine, with 44% remaining in the carcass, primarily in the liver (33%). 4. Following an intratracheal instillation dose to rats, radiolabel was eliminated from the pulmonary system with a half-life of 64 days. Excretion was almost exclusively via faeces, with an elimination half-life of 52 days. Plasma and blood concentrations in these animals were uniformly <1 ng eq. ml(-1) at all sampling times. 5. Results in mice given intravenous and oral doses were consistent with those observed in rats. 6. Prolonged retention of Moli1901 in pulmonary tissue supports its use in the treatment of respiratory diseases.
Distance Encoded Product Quantization (2014)

Many binary code embedding techniques have been proposed for large-scale approximate nearest neighbor search in computer vision. Recently, product quantization that encodes the cluster index in each subspace has been shown to provide impressive accuracy for nearest neighbor search. In this paper, we explore a simple question: is it best to use all the bit budget for encoding a cluster index in each subspace? We have found that as data points are located farther away from the centers of their clusters, the error of estimated distances among those points becomes larger. To address this issue, we propose a novel encoding scheme that distributes the available bit budget to encoding both the cluster index and the quantized distance between a point and its cluster center. We also propose two different distance metrics tailored to our encoding scheme. We have tested our method against the-state-of-the-art techniques on several well-known benchmarks, and found that our method consistently improves the accuracy over other tested methods. This result is achieved mainly because our method accurately estimates distances between two data points with the new binary codes and distance metric.
Self-assembly of poly(<i>o</i>-methoxyaniline) hollow nanospheres from a polymeric acid solution (2009)

Self-assembled poly(o-methoxyaniline) (POMA) hollow nanospheres were prepared in a solution of poly(methyl vinyl ether-alt-maleic acid) (PMVEA) by oxidative polymerization using ammonium persulfate as the oxidant. The weight ratio of PMVEA to o-methoxyaniline in the solution had a significant effect on the morphology of the poly(o-methoxyaniline) nanospheres as determined by scanning electron microscopy. The diameter of the hollow nanospheres decreased from 440 to 210 nm with an increase in the PMVEA concentration from 1% to 5%. Freeze-fracture transmission electron microscopy results showed the presence of spherical micelles composed of PMVEA/ o-methoxyaniline prior to polymerization, which also decreased in size as more PMVEA was added to the solution, and can act as soft templates for the formation of the hollow POMA nanospheres. The POMA/PMVEA hollow nanospheres were characterized by means of Fourier transform infrared, UV-visible, x-ray photoelectron spectroscopy, elemental analysis and conductivity measurements.
Shared Subgenome Dominance Following Polyploidization Explains Grass Genome Evolutionary Plasticity from a Seven Protochromosome Ancestor with 16K Protogenes (2013)

Modern plant genomes are diploidized paleopolyploids. We revisited grass genome paleohistory in response to the diploidization process through a detailed investigation of the evolutionary fate of duplicated blocks. Ancestrally duplicated genes can be conserved, deleted, and shuffled, defining dominant (bias toward duplicate retention) and sensitive (bias toward duplicate erosion) chromosomal fragments. We propose a new grass genome paleohistory deriving from an ancestral karyotype structured in seven protochromosomes containing 16,464 protogenes and following evolutionary rules where 1) ancestral shared polyploidizations shaped conserved dominant (D) and sensitive (S) subgenomes, 2) subgenome dominance is revealed by both gene deletion and shuffling from the S blocks, 3) duplicate deletion/movement may have been mediated by single-/double-stranded illegitimate recombination mechanisms, 4) modern genomes arose through centromeric fusion of protochromosomes, leading to functional monocentric neochromosomes, 5) the fusion of two dominant blocks leads to supradominant neochromosomes (D + D = D) with higher ancestral gene retention compared with D + S = D (i.e., fusion of blocks with opposite sensitivity) or even S + S = S (i.e., fusion of two sensitive ancestral blocks). A new user-friendly online tool named "PlantSyntenyViewer," available at http://urgi.versailles.inra.fr/synteny-cereal, presents the refined comparative genomics data.
A comparative study of the utilization of ether- and ester-linked phospholipid-containing liposomes by J774.E1 macrophage cell-line infected with Leishmania mexicana mexicana amastigotes. (1994)

The macrophage cell-line J774.E1 and Leishmania m. mexicana infection was used to investigate the uptake of liposomes, which differed in their bulk phospholipid: ester- or ether-analogue of phosphatydilcholine (PC). The receptor-mediated uptake of both species of liposomes, containing native or acetylated LDL as ligands was also evaluated. Uninfected and infected J774.E1 cell-line accumulated more ester- and ether-liposomes alone than mixed type (50:50, ester/ether). The utilization was significantly enhanced when both types of liposomes contained native LDL. The highest uptake was recorded for liposomes bearing acetylated LDL by infected J774.E1 cells. Accumulation of ester- and ether-liposomes with the same ligand was not markedly affected by different chemical nature of PC. Finally, ether-liposomes alone possessed certain activity against Leishmania m. mexicana amastigotes. The results presented here demonstrated the usefulness of ether-liposomes with specific ligands in site-specific delivery of antileishmanial compounds in vitro.