gebhart/patrepeval huggingface dataset:
Structural basis for multifunctional roles of mammalian aminopeptidase N (2012)

Mammalian aminopeptidase N (APN) plays multifunctional roles in many physiological processes, including peptide metabolism, cell motility and adhesion, and coronavirus entry. Here we determined crystal structures of porcine APN at 1.85 Å resolution and its complexes with a peptide substrate and a variety of inhibitors. APN is a cell surface-anchored and seahorse-shaped zinc-aminopeptidase that forms head-to-head dimers. Captured in a catalytically active state, these structures of APN illustrate a detailed catalytic mechanism for its aminopeptidase activity. The active site and peptide-binding channel of APN reside in cavities with wide openings, allowing easy access to peptides. The cavities can potentially open up further to bind the exposed N terminus of proteins. The active site anchors the N-terminal neutral residue of peptides/proteins, and the peptide-binding channel binds the remainder of the peptides/proteins in a sequence-independent fashion. APN also provides an exposed outer surface for coronavirus binding, without its physiological functions being affected. These structural features enable APN to function ubiquitously in peptide metabolism, interact with other proteins to mediate cell motility and adhesion, and serve as a coronavirus receptor. This study elucidates multifunctional roles of APN and can guide therapeutic efforts to treat APN-related diseases.
The Methodology for Evaluating the Safety of Operations at the Uncontrolled Aerodromes (2014)

<span style="line-height: 115%; font-family: 'Times New Roman','serif'; font-size: 9pt; mso-fareast-font-family: Calibri; mso-ansi-language: EN-GB; mso-fareast-language: EN-US; mso-bidi-language: AR-SA; mso-fareast-theme-font: minor-latin;" lang="EN-GB">The objective of this methodology is to determine the general procedure for the evaluation of safety indicators for operation at uncontrolled aerodromes. The basis of this assessment is to determine the processes that take place at the aerodrome and finding critical points in these processes. They are determined on the basis of observations at aerodromes and are based on current legislation. The result of applying this methodology to aerodrome operations is the identification of several indicators, which monitoring and the adoption of safety measures can enhance safety at these uncontrolled aerodromes in the Czech Republic.</span>
Effect of limited amplitude and rate of flap motion on vane-controlled gust alleviation system (1972)

An airplane (light transport type) is assumed to be in level flight (no pitching) through atmospheric turbulence which has a mean-square vertical gust intensity of 9.3 (m/sec)sq. The power spectral density of the vertical acceleration due to gusts is examined with and without a gust-alleviation system in operation. The gust-alleviation system consisted of wing flaps that were used in conjunction with a vane mounted ahead of the airplane to sense the vertical gust velocity. The primary purpose of this study was to examine the change in the effectiveness of the gust-alleviation system when the flap motion is limited in amplitude and rate. The alleviation system was very effective if no restrictions were placed on flap motion (rate and amplitude). Restricting the flap amplitude to 0.5 radian did not appreciably change the effectiveness. However, restricting the flap rate did reduce the gust alleviation, and restricting the flap rate to 0.25 rad/sec actually caused the alleviation system to increase the vertical acceleration above that for the no-alleviation situation. Based upon this analysis, rate limiting appears to be rather significant in gust-alleviation systems designed for passenger comfort.
Zigzag Connected Autotransformer Based Controlled AC-DC Converter for Pulse Multiplication (2007)

This paper deals with the analysis and design of a non-isolated 36-pulse controlled AC-DC converter for medium power rating drives, field winding supply of large alternators, magnet power supplies, etc. It consists of pulse multiplication in non-isolated 12-pulse AC-DC converter to get 36-pulse converter characteristics without employing zero-sequence blocking transformer (ZSBT). The proposed converter employs a zigzag connected autotransformer, which results in near equal leakage reactance in series with each thyristor bridge. The volt-ampere rating of the autotransformer is small and the converter meets IEEE-519 standard power-quality requirements over wide range of firing angle.
Water Treatment Using Discharge on the Surface of a Bubble in Water (2005)

Abstract Summary: A new method for water treatment utilizing radicals produced by a discharge on the surface of a bubble in water is proposed and this method is applied to the de‐color of indigo solution whose original color is blue. The discharge of this method begins at the crossing points of mesh electrode, acrylic resin spacer, and bubbling gas (i.e., called a triple junction where there is a weak point for the electrical breakdown in the electrical power devices). This weak point for the electrical breakdown is used very actively for the surface discharge. The discharge process on the surface of the bubble in water is also observed using a wire‐to‐plane electrode system to fix the observation region of discharge (type‐A reactor). The streamer length estimated by photographs increased linearly with the applied voltage. The energy consumption of discharge for type‐B reactor with a mesh‐to‐plane electrode in oxygen is about 0.09 J when the applied voltage is 20 kV. Production efficiency of the H 2 O 2 concentration of about 27 mg · L −1 in oxygen (46 mg · L −1 in helium) has been obtained when the repetition rate of discharge operated by a pulsed‐power generator, the peak value of applied voltage, and the discharge period are 100 pps (pulsed power generator), 25 kV and 60 min, respectively. De‐colorization rate of indigo solution for different discharge periods. magnified image De‐colorization rate of indigo solution for different discharge periods.
Predominance of cyclooxygenase 1 over cyclooxygenase 2 in the generation of proinflammatory prostaglandins in autoantibody‐driven K/BxN serum–transfer arthritis (2008)

These findings challenge previous paradigms of distinct "housekeeping" versus inflammatory functions of the COX isoforms and highlight the potential pathogenic contribution of prostanoids synthesized via COX-1, in particular PGI2, to inflammatory arthritis.
Adenosine decreases permeability of in vitro endothelial monolayers (1993)

The addition of adenosine to perfusates flowing through an in vitro cell-column model of the vasculature decreases the permeability of cell column fetal bovine aortic endothelial monolayers. At 10(-4) M adenosine, cell monolayer permeability to the paracellular tracers polyethylene glycol (mol wt 900) and cyanocobalamin (mol wt 1,355) is significantly decreased within 15 min. In continuous treatments with adenosine for up to 30 min, the permeability reduction is maintained, and removal of adenosine returns permeability to baseline levels within 15 min. The effect of adenosine is concentration dependent, with a 5% reduction in permeability with 10(-6) M adenosine, a 21% reduction with 10(-5) M adenosine, and a 37% reduction with 10(-4) M adenosine. The effects of adenosine are not blocked by the adenosine transport inhibitor dipyridamole. Permeability is significantly reduced by the A2-specific adenosine analogue 5'-(N-cyclopropyl)-carboxamidoadenosine but not by the A1-specific adenosine analogue N6-(L-2-phenylisopropyl)adenosine. In addition, the permeability decrease is blocked by the A2-receptor antagonist 8-phenyltheophylline (10(-5)M). We conclude that adenosine decreases the permeability of bovine fetal aortic endothelial monolayers via endothelial A2-purinoceptors.
Duplex RNA activated ATPases (DRAs) (2012)

Double-stranded RNAs are an important class of functional macromolecules in living systems. They are usually found as part of highly specialized intracellular machines that control diverse cellular events, ranging from virus replication, antiviral defense, RNA interference, to regulation of gene activities and genomic integrity. Within different intracellular machines, the RNA duplex is often found in association with specific RNA-dependent ATPases, including Dicer, RIG-I and DRH-3 proteins. These duplex RNA-activated ATPases represent an emerging group of motor proteins within the large and diverse super family 2 nucleic acid-dependent ATPases (which are historically defined as SF2 helicases). The duplex RNA-activated ATPases share characteristic molecular features for duplex RNA recognition, including motifs (e.g., motifs IIa and Vc) and an insertion domain (HEL2i), and they require double-strand RNA binding for their enzymatic activities. Proteins in this family undergo large conformational changes concomitant with RNA binding, ATP binding and ATP hydrolysis in order to achieve their functions, which include the release of signaling domains and the recruitment of partner proteins. The duplex RNA-activated ATPases represent a distinct and fascinating group of nanomechanical molecular motors that are essential for duplex RNA sensing and processing in diverse cellular pathways.
An ejection chain algorithm for the quadratic assignment problem (2009)

Abstract In this study, we present a new tabu search algorithm for the quadratic assignment problem (QAP) that utilizes an embedded neighborhood construction called an ejection chain. Our ejection chain approach provides a combinatorial leverage effect, where the size of the neighborhood grows multiplicatively while the effort of finding a best move in the neighborhood grows only additively. Our results illustrate that significant improvement in solution quality is obtained in comparison to the traditional swap neighborhood. We also develop two multistart tabu search algorithms utilizing the ejection chain approach in order to demonstrate the power of embedding this neighborhood construction within a more sophisticated heuristic framework. Comparisons to the best large neighborhood approaches from the literature are presented. © 2009 Wiley Periodicals, Inc. NETWORKS, 2010
Serum erythropoietin at diagnosis in low grade myelodysplastic syndrome correlates with both red cell zinc protoporphyrin and serum lactic dehydrogenase (LDH) and may reflect severity of ineffective erythropoiesis (2009)

The myelodysplastic syndromes (MDS) are a heterogenous group of clonal hematological disorders, characterised by ineffective hematopoiesis [1]. Anemia in low grade MDS [refractory anemia (RA), refr...
Pre–T Cell Receptor (Tcr) and Tcr-Controlled Checkpoints in T Cell Differentiation Are Set by Ikaros (1999)

T cell differentiation relies on pre-T cell receptor (TCR) and TCR signaling events that take place at successive steps of the pathway. Here, we show that two of these T cell differentiation checkpoints are regulated by Ikaros. In the absence of Ikaros, double negative thymocytes can differentiate to the double positive stage without expression of a pre-TCR complex. Subsequent events in T cell development mediated by TCR involving transition from the double positive to the single positive stage are also regulated by Ikaros. Nonetheless, in Ikaros-deficient thymocytes, the requirement of pre-TCR expression for expansion of immature thymocytes as they progress to the double positive stage is still maintained, and the T cell malignancies that invariably arise in the thymus of Ikaros-deficient mice are dependent on either pre-TCR or TCR signaling. We conclude that Ikaros regulates T cell differentiation, selection, and homeostasis by providing signaling thresholds for pre-TCR and TCR.
Nanostructured Monolayers on Carbon Substrates Prepared by Electrografting of Protected Aryldiazonium Salts (2013)

The electrogeneration of aryl radicals from protected diazonium salts combined with protection–deprotection steps was evaluated to design functional monolayers on carbon substrates with a well-controlled organization at the nanometric scale. The structure of the obtained monolayer is adjusted by varying the size of the protecting group that is introduced on the precursors (trimethylsilyl, triethylsilyl, and tri(isopropyl)silyl were tested in the present study). After deprotection, a robust ethynylaryl monolayer is obtained whatever the substituent that serves as a platform to attach other functional groups by a specific “click chemistry” coupling step. Electrochemical and structural analyses show that the organization of the attached monolayer is totally governed by the size of the protecting group that leaves a footprint after removal but maintains a total availability of the immobilized functional groups. Properties of the monolayer (charge transfer, permeation of molecules through the layer, density of functional groups) were examined in combination with the performances for postfunctionalization taken with an alkyl-ferrocene derivative as an example of the immobilized species.
<title>High-aspect-ratio resist for thick-film applications</title> (1995)

In recent years, increased activity in micromachining has driven the need for high aspect ratio thick films resist systems. This paper discusses a new epoxy based resist that can be used to achieve high aspect ratios (> 10:1) using UV lithography. The resulting negative resist system provides sharp, clean images in thick films (> 200 micrometers ). Because of the high aspect ratio and short exposure times, this material may be a viable candidate for producing the images required for micromachined parts. The resist images exhibit straight sidewalls and developed patterns, have excellent thermal stability, good adhesion, and chemical resistance. The high aspect ratio and high thermal stability make these epoxy resists suitable for other packaging applications such as plating stencils and optical wave guides.
Evolution of TPS20‐related terpene synthases influences chemical diversity in the glandular trichomes of the wild tomato relative <i>Solanum habrochaites</i> (2012)

A systematic screen of volatile terpene production in the glandular trichomes of 79 accessions of Solanum habrochaites was conducted and revealed the presence of 21 mono- and sesquiterpenes that exhibit a range of qualitative and quantitative variation. Hierarchical clustering identified distinct terpene phenotypic modules with shared patterns of terpene accumulation across accessions. Several terpene modules could be assigned to previously identified terpene synthase (TPS) activities that included members of the TPS-e/f subfamily that utilize the unusual cis-prenyl diphosphate substrates neryl diphosphate and 2z,6z-farnesyl diphosphate. DNA sequencing and in vitro enzyme activity analysis of TPS-e/f members from S. habrochaites identified three previously unassigned enzyme activities that utilize these cisoid substrates. These produce either the monoterpenes α-pinene and limonene, or the sesquiterpene 7-epizingiberene, with the in vitro analyses that recapitulated the trichome chemistry found in planta. Comparison of the distribution of S. habrochaites accessions with terpene content revealed a strong preference for the presence of particular TPS20 alleles at distinct geographic locations. This study reveals that the unusually high intra-specific variation of volatile terpene synthesis in glandular trichomes of S. habrochaites is due at least in part to evolution at the TPS20 locus.
Isolation and sequence of a cDNA clone that contains the entire coding region for chicken smooth-muscle alpha-tropomyosin. (1984)

We have constructed a cDNA-expression library of approximately 100,000 members from embryonic chicken smooth-muscle mRNA using the plasmid-expression vectors pUC8 and pUC9. Using an immunological screening procedure and 32P-labeled cDNA probes, we have identified and isolated clones encoding smooth-muscle tropomyosin. Plasmid pSMT-10 (approximately 1100 base pairs) was found to hybrid-select mRNA for smooth-muscle alpha-tropomyosin. DNA-sequence analysis revealed that pSMT-10 contained the entire coding region for alpha-tropomyosin and portions of the 5'- and 3'-untranslated regions. Comparison of the derived amino acid sequence of smooth-muscle alpha-tropomyosin with known skeletal-muscle (rabbit and chicken) and platelet (equine) sequences revealed extensive homology between the various proteins. The smooth-muscle tropomyosin shows the greatest sequence divergence from the skeletal-muscle tropomyosins at the COOH-terminal region. In contrast, the smooth-muscle tropomyosin is most homologous to the platelet tropomyosin at the COOH-terminal end. The relationship of the various tropomyosin sequences to function (e.g. interactions with troponin) are considered.
Voronoi diagrams for planar shapes (1995)

Although many algorithms compute Voronoi diagrams for polygons, few do so for shapes bounded by arbitrary closed curves. The paper presents an algorithm which does this. It also traces the diagrams directly from their differential properties.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Persantine and aspirin in coronary heart disease. The Persantine-Aspirin Reinfarction Study Research Group. (1980)

In the Persantine-Aspirin Reinfarction Study (PARIS) trial, 2026 persons who had recovered from myocardial infarction (MI) were randomized into three groups: Persantine plus aspirin (PR/A) (n = 810); aspirin alone (ASA) (n = 810); placebo (PLBO) (n = 406). The average length of follow-up study was 41 months. Results for the three specified primary end points were: total mortality 16% lower in PR/A and 18% lower in ASA compared with PLBO; coronary mortality 24% and 21% lower; incidence of nonfatal MI plus fatal coronary disease 25% and 24% lower. These differences were not satistically significant by the study criterion (Z greater than or equal to 2.6). By life-table analysis, the rates of coronary mortality and coronary incidence were about 50% lower in the PR/A group than in the PLBO group from 8-24 months, and for coronary incidence all Z values were greater than or equal to 2.6; ASA rates were about 30% lower than PLBO rates, and for coronary incidence, Z values were greater than or equal to 2.6 at two points. For these end points, from 8-20 months, PR/A rates were about 30% lower than ASA rates, but all Z values were less than 2.0 PR/A and ASA patients entering within 6 months of last MI showed the largest percentage reductions in mortality; only the difference between PR/A and PLBO groups for 3-year coronary mortality yielded a Z value of 2.6.
Synthesis, Structures, and Norbornene ROMP Behavior of <i>o</i>-Aryloxide-N-Heterocyclic Carbene <i>p</i>-Cymene Ruthenium Complexes (2012)

Treatment of the o-hydroxyaryl imidazolium proligands (2-OH-3,5-tBu2C6H2)(R)(C3H3N2)+Br– (R = iPr (1a), tBu (1b), Ph (1c), Mes (1d)) with 3 equiv of Ag2O afforded the corresponding silver complexes 2a–d. The subsequent metal-exchange reactions with [(p-cymene)RuCl2]2 at room temperature yielded the desired o-aryloxide-N-heterocyclic carbene p-cymene ruthenium complexes 3a–d in nearly quantitative yields. All the complexes were characterized by 1H and 13C NMR, high-resolution mass spectrometry (HRMS), and elemental analysis. The molecular structure of complex 3b was determined by single-crystal X-ray diffraction analysis. The ring-opening metathesis polymerization (ROMP) of norbornene (NBE) with 3a–d was studied. Among them, complex 3d showed high activity and efficiency toward ROMP of NBE at 85 °C without the need for any cocatalyst, and polymers with very high molecular weight (>106) and narrow molecular weight distributions were obtained. This complex can also catalyze the alternating copolymerization of NBE and cyclooctene (COE).
Čerenkov radiation emission and excited luminescence (CREL) sensitivity during external beam radiation therapy: Monte Carlo and tissue oxygenation phantom studies (2012)

Radiotherapy generates Čerenkov radiation emission in tissue, and spectral absorption features appearing in the emission spectrum can be used to quantify blood oxygen saturation (S(t)O(2)) from the known absorptions of hemoglobin. Additionally, the Čerenkov light can be used to excite oxygen-sensitive phosphorescence of probe PtG4, whose emission lifetime directly reports on tissue oxygen partial pressure (pO(2)). Thus, it is feasible to probe both hemoglobin S(t)O(2) and pO(2) using external radiation therapy beam to create as an internal light source in tumor tissue. In this study, the sensitivity and spatial origins of these two signals were examined. Emission was detected using a fiber-optic coupled intensifier-gated CCD camera interfaced to a spectrometer. The phosphorescence lifetimes were quantified and compared with S(t)O(2) changes previously measured. Monte Carlo simulations of the linear accelerator beam were used together with tracking of the optical signals, to predict the spatial distribution and zone sensitivity within the phantom. As the fiber-to-beam distance (FBD) varied from 0 to 30 mm, i.e. the distance from the fiber tip to the nearest side of the radiotherapy beam, the effective sampling depth for CR emission changed from 4 to 29 mm for the wavelengths in the range of 600-1000 nm. For the secondary emission (phosphorescence) the effective sampling depth was determined to be in the range of 9 to 19 mm. These results indicate that sampling of S(t)O(2) and pO(2) in tissue should be feasible during radiation therapy, and that the radiation beam and fiber sampling geometry can be set up to acquire signals that originate as deep as a few centimeters in the tissue.
Correction of the retinal dystrophy phenotype of the RCS rat by viral gene transfer of <i>Mertk</i> (2001)

The Royal College of Surgeons (RCS) rat is a widely studied animal model of retinal degeneration in which the inability of the retinal pigment epithelium (RPE) to phagocytize shed photoreceptor outer segments leads to a progressive loss of rod and cone photoreceptors. We recently used positional cloning to demonstrate that the gene Mertk likely corresponds to the retinal dystrophy (rdy) locus of the RCS rat. In the present study, we sought to determine whether gene transfer of Mertk to a RCS rat retina would result in correction of the RPE phagocytosis defect and preservation of photoreceptors. We used subretinal injection of a recombinant replication-deficient adenovirus encoding rat Mertk to deliver the gene to the eyes of young RCS rats. Electrophysiological assessment of animals 30 days after injection revealed an increased sensitivity of treated eyes to low-intensity light. Histologic and ultrastructural assessment demonstrated substantial sparing of photoreceptors, preservation of outer segment structure, and correction of the RPE phagocytosis defect in areas surrounding the injection site. Our results provide definitive evidence that mutation of Mertk underlies the RCS retinal dystrophy phenotype, and that the phenotype can be corrected by treatment of juvenile animals. To our knowledge, this is the first demonstration of complementation of both a functional cellular defect (phagocytosis) and a photoreceptor degeneration by gene transfer to the RPE. These results, together with the recent discovery of MERTK mutations in individuals with retinitis pigmentosa, emphasize the importance of the RCS rat as a model for gene therapy of diseases that arise from RPE dysfunction.