gebhart/patrepeval huggingface dataset:
Site-Saturation Mutagenesis of Tryptophan 116 of Saccharomyces pastorianus Old Yellow Enzyme Uncovers Stereocomplementary Variants (2009)

Site-saturation mutagenesis was used to generate all possible replacements for Trp 116 of Saccharomyces pastorianus (formerly Saccharomyces carlsbergensis ) old yellow enzyme (OYE). Our original hypothesisthat smaller amino acids at position 116 would allow better acceptance of bulky 3-alkyl-substituted 2-cyclohexenonesproved incorrect. Instead, Phe and Ile replacements favored the binding of some substrates in an opposite orientation, which yielded reversed stereochemical outcomes compared to that of the wild-type OYE. For example, W116I OYE reduced (R)- and (S)-carvone to enantiomeric products, rather than the diastereomers produced by the wild-type OYE. Deuterium labeling revealed that (S)-carvone reduction by the W116I OYE occurred by the same pathway as that by the wild type (net trans-addition of H(2)), proving that different substrate binding orientations were responsible for the divergent products. Trp 116 mutants also afforded different stereochemical outcomes for reductions of (R)-perillaldehyde and neral. Preliminary studies of an OYE family member whose native sequence contains Ile at position 116 ( Pichia stipitis OYE 2.6) revealed that this enzyme's stereoselectivity matched that of the wild-type S. pastorianus OYE, showing that the identity of the residue at position 116 does not solely determine the substrate binding orientation. Computational docking studies using an induced fit methodology successfully reproduced the majority of the experimental outcomes. These computational tools will allow preliminary in silico screening of additional residues to identify those most likely to control the substrate binding orientation and provide some guidance to future experimental studies.
Inhibition of murine plaque-forming cell responses <i>in vivo</i> by ribavirin. (1981)

Abstract The effects of ribavirin, a potent inhibitor of RNA and DNA virus replication, on the generation of primary plaque-forming cell (PFC) responses in vivo has been investigated. Intraperitoneal administration of ribavirin 1 day after immunization of C3H/HeJ mice with sheep erythrocytes (SRBC) suppressed splenic IgM and IgG PFC responses by 60 to 90%. Primary IgM PFC responses of C3HeB/FeJ mice to bacterial lipopolysaccharides (LPS), a T-independent antigen, were also inhibited to a similar extent. Inhibition of splenic PFC responses, without significant reduction in nucleated cell recoveries, was dose dependent between 0.5 and 4 mg ribavirin. Varying the time of treatment determined that optimal inhibitory activity occurred when ribavirin was administered simultaneously or 1 day after antigen. Kinetic analysis of PFC responses in ribavirin-treated mice revealed that suppression did not result from a delay in development since reduced numbers of PFC were found at all times after immunization. Ribavirin-treatment after primary sensitization in vivo also impaired the capacity of spleen cells to develop secondary PFC responses in vitro, indicating that ribavirin also inhibited memory cell generation.
Inherited Mutations within the Calcium‐Binding Sites of the Integrin α<sub>IIb</sub> Subunit (Platelet Glycoprotein IIb) (1996)

To examine the effects of naturally occurring inherited mutations on the ability of the integrin alpha-subunit, also termed glycoprotein IIb (GPIIb), to bind metal ions, we prepared small synthetic peptides that encompassed individual cation-binding domains, and recombinant GPIIb poly peptides that encompassed all four Ca(2+)-binding domains, and examined their interactions with divalent cations by means of Tb3+-luminescence spectroscopy. Replacement of the highly conserved Gly418 residue, located within the flanking region of the fourth Ca(2+)-binding domain of GPIIb, with a negatively charged Asp residue resulted in marked reduction in the ability to bind divalent cations. A variant form of GPIIb with a deletion of two amino acids at the -1 and X positions of the fourth Ca(2+)-binding domain of GPIIb also failed to bind metal ions in a normal manner. In contrast, a Glanzmann mutation at the -1 position of the first Ca(2+)-binding domain of GPIIb had no effect on divalent-cation-binding ability with either synthetic peptides or recombinant GPIIb polypeptides. These data support the hypothesis that the highly conserved Gly normally found 7-8 residues N-terminal to integrin metal-binding domains plays a critical role in the maintenance of the conformation or orientation of surrounding EF-hand structures so that they can effectively interact with and bind divalent cations. Furthermore, inherited mutations at or near the divalent-cation-binding domains of GPIIb do not necessarily exert their biochemical effects by disruption of cation binding, but can interfere with integrin biogenesis in a Ca(2+)-independent manner.
Photoreceptor apoptosis induced by a single systemic administration of N-methyl-N-nitrosourea in the rat retina. (1996)

Retinal degeneration was induced by a single intraperitoneal injection of N-methyl-N-nitrosourea in female Sprague-Dawley albino rats at 50 days of age by two dose regimens, which were observed sequentially at 24, 48, and 72 hours and 7, 21, and 35 days after the treatment. After a dose of 75 mg/kg, methylnitrosourea evoked progressive retinal degeneration in all treated rats whereas a dose of 50 mg/kg was less effective. The 75-mg/kg-treated rats showed selective destruction of the photoreceptor cells by an apoptotic mechanism, as confirmed morphologically and by the terminal dUTP nick end labeling method. Apoptosis had already started at 24 hours after the treatment and was completed by day 7. During the photoreceptor degeneration, proliferation of glial fibrillary acidic protein and vimentin-positive Müller cells as detected by proliferating cell nuclear antigen labeling appeared at 48 hours and was prominent 72 hours after the treatment, and macrophage infiltration within the retina as recognized by ED1 positivity was maximal 7 and 21 days after the treatment. Retinal degeneration was also induced in female Brown-Norway colored rats in a similar dose-dependent manner. Pigment epithelium was discontinuous above Bruch's membrane, and migration of the swollen pigment epithelium toward the inner nuclear layer was seen 7 days after the treatment. Therefore, as also confirmed electron microscopically, the most striking change was the destruction of photoreceptor cells by the apoptotic process, followed by Müller cell proliferation, pigment epithelium migration, and macrophage infiltration for cell debris phagocytosis, resulting in a thin remnant of retina with attenuated inner nuclear cells in direct contact with Bruch's membrane or with the pigment epithelium and/or with the Müller cells 35 days after the treatment.
New stool tests for colorectal cancer screening: A systematic review focusing on performance characteristics and practicalness (2005)

New stool tests may be promising tools for future colorectal cancer (CRC) screening. The aim of this review was to summarize current evidence of performance characteristics and practicalness in a population-based screening setting of recently developed stool tests. The MEDLINE database was searched for relevant articles published until July 2004. Studies were included if they comprised more than 10 cases and more than 10 controls. Details on study population, performance characteristics and stool collection procedure were taken into account. Overall, 29 studies, mostly retrospective, were included, investigating 17 different stool markers or marker combinations. Underlying study populations were very heterogeneous and mostly very small. Half of the studies reported sensitivity for adenomas in addition to sensitivity for CRC, and fewer than half reported sensitivity by tumor stage or location. Performance characteristics of stool tests varied to a large extent. For most DNA-based markers, specificity was about 95% or higher, but sensitivity was mostly low even for invasive CRC. More studies with larger sample sizes were done for protein-based markers, which typically had lower specificity. In most studies, stool samples were frozen within a rather short time period after defecation. While promising performance characteristics have been reported for some tests, more pervasive evidence from larger, prospectively designed studies, which also consider aspects of practicalness, e.g., the possibility of mailing the samples, is needed.
W'6Nv'5 Redox Reactions at the Interface of the Nanocrystalline TiO, Photoactive Electrode (1999)

Photocurrent of nanocrystalline TiO, thin films has been probed by using a steady-state photoconduction technique. A broad single peak (280-410 nm) photocurrent spectrum was observed for the TiO, thin films.. The photocurrent maximum at about 360 nm associates with the direct band gap of anatase TiO,. The electron-hole pair formation that occurs at the interface between semiconductor TiO, nanoparticles and a solution upon absorption of near W light leads to redox reactions of solution species (W/W+'). The mechanism of such photodriven processes are discussed along with the potential applications in photoelectrochemical cells and as particulate photochromic systems.
Delivering genes across the blood-brain barrier: LY6A, a novel cellular receptor for AAV-PHP.B capsids (2019)

The engineered AAV-PHP.B family of adeno-associated virus efficiently delivers genes throughout the mouse central nervous system. To guide their application across disease models, and to inspire the development of translational gene therapy vectors for targeting neurological diseases in humans, we sought to elucidate the host factors responsible for the CNS tropism of the AAV-PHP.B vectors. Leveraging CNS tropism differences across 13 mouse strains, we systematically determined a set of genetic variants that segregate with the permissivity phenotype, and rapidly identified LY6A as an essential receptor for the AAV-PHP.B vectors. Interfering with LY6A by CRISPR/Cas9-mediated Ly6a disruption or with blocking antibodies reduced transduction of mouse brain endothelial cells by AAV-PHP.eB, while ectopic expression of Ly6a increased AAV-PHP.eB transduction of HEK293T and CHO cells by 30-fold or more. Importantly, we demonstrate that this newly discovered mode of AAV binding and transduction can occur independently of other known AAV receptors. These findings illuminate the previously reported species- and strain-specific tropism characteristics of the AAV-PHP.B vectors and inform ongoing efforts to develop next-generation AAV vehicles for human CNS gene therapy.
Linear free energy relationships in the thiophen series. Part 2. The kinetics of the reactions of some 2-bromo-3-nitro-5-X-thiophens with substituted anilines in methanol (1981)

The rate constants for the reactions of 2-bromo-3-nitro-5-X-thiophens (X = H, Br, CONH2, CO2Me, Ac, SO2Me, CN, or NO2) with some substituted anilines YC6H4NH2(Y =p-OMe, p-Me, H, m-Cl, or p-CO2Me) have been measured in methanol at various temperatures. The sensitivity parameters, ρ(Y) and β(X), obtained from Hammett and Brönsted correlations are practically independent of the reactivity of the starting system. The relevance of these results to the reactivity–selectivity principle is discussed.
A Temperature-Responsive Antibody-Like Nanostructure (2010)

Antibodies play an essential role in various applications. However, antibodies exhibit considerable challenges in applications that require tunable binding capabilities and exposure to nonphysiological conditions such as chemical conjugation. This study is aimed to develop a novel antibody-like nanostructure with special features. The key components of the nanostructure are two DNA aptamers and a dendrimer. The aptamers are used to mimic the antigen-binding sites of an antibody; the dendrimer is used to provide a defined conjugation site for carrying molecules of interest. The results showed that the bivalent nanostructure exhibited a high binding affinity and specificity. Moreover, a temperature shift from 0 to 37 degrees C would trigger its rapid dissociation from the bound target cells, which is not possible in antibody-antigen complexes. Thus, an antibody-like nanostructure was successfully developed with novel features that natural antibodies do not possess.
Double bubbles sans toil and trouble (2015)

Simulating the delightful dynamics of soap films, bubbles, and foams has traditionally required the use of a fully three-dimensional many-phase Navier-Stokes solver, even though their visual appearance is completely dominated by the thin liquid surface. We depart from earlier work on soap bubbles and foams by noting that their dynamics are naturally described by a Lagrangian vortex sheet model in which circulation is the primary variable. This leads us to derive a novel circulation-preserving surface-only discretization of foam dynamics driven by surface tension on a non-manifold triangle mesh. We represent the surface using a mesh-based multimaterial surface tracker which supports complex bubble topology changes, and evolve the surface according to the ambient air flow induced by a scalar circulation field stored on the mesh. Surface tension forces give rise to a simple update rule for circulation, even at non-manifold Plateau borders, based on a discrete measure of signed scalar mean curvature. We further incorporate vertex constraints to enable the interaction of soap films with wires. The result is a method that is at once simple, robust, and efficient, yet able to capture an array of soap films behaviors including foam rearrangement, catenoid collapse, blowing bubbles, and double bubbles being pulled apart.
Effect of Murine Interferon Gamma on Murine Toxoplasmosis (1984)

Journal Article Effect of Murine Interferon Gamma on Murine Toxoplasmosis Get access Robert E. McCabe, Robert E. McCabe Search for other works by this author on: Oxford Academic PubMed Google Scholar Benjamin J. Luft, Benjamin J. Luft Search for other works by this author on: Oxford Academic PubMed Google Scholar Jack S. Remington Jack S. Remington Search for other works by this author on: Oxford Academic PubMed Google Scholar The Journal of Infectious Diseases, Volume 150, Issue 6, December 1984, Pages 961–962, https://doi.org/10.1093/infdis/150.6.961 Published: 01 December 1984 Article history Received: 14 May 1984 Revision received: 11 July 1984 Published: 01 December 1984
Detection of Interferon Regulatory Factor-1 in Lamina Propria Mononuclear Cells in Crohn's Disease (2000)

Increased expression of IRF-1 in lamina propria mononuclear cells from patients with Crohn's disease may be relevant to the pathogenesis of Crohn's disease.
Superconducting tunneling devices (1961)

THE IDEAL CAPACITOR shown in Figure 1 can consist of two parallel metal plates separated by a 10^-4cm wide vacuum region. No steady state current would be observable in such an arrangement. However, if the separation distance between the two plates could be reduced to, say 10^-7cm or 10Å, a rather large dc would flow in the circuit. The explanation for this phenomena is the quantum mechanical tunnel effect, which allows the electrons to flow across the vacuum region, even though classically this is energetically impossible. The general behavior of such a conduction mechanism is understood.
The XNOVAKTC Code (1990)

Abstract : A description of the one-dimensional two-phase with area change interior ballistic computer code XNOVAKTC (XKTC) is provided. XKTC has the tank gun and traveling charge features fully linked to the chemistry model. This version of the code has chemical kinetics, tank gun features (reactive sidewalls and boattail intrusion) and end burning traveling charge increments. Other extensions include the modeling of single perforated monolithic charges, charges bonded to the tube or the projectile, and a ballistic control tube. The XKTC code was applied to the simulation of traveling charges with finite reaction zones. It was concluded that a reaction zone of several calibers can be tolerated without significant loss of performance. Keywords: Interior ballistics; Two phase flow; Monolithic charge; Traveling charge; Control tube; Kinetics.
A general route to nanostructured bismuth chalcogenides (2005)

In this paper we describe a method for the synthesis of V/VI nanomaterials containing bismuth by a conventional “wet chemistry” technique. The reaction of bismuth acetate with the corresponding elemental chalcogen under reflux conditions in octylamine result in pure phases of the respective bismuth chalcogenide. A range of morphologies are reported which demonstrate a relationship between the crystal form and the morphology of the nanostructure.
Inhomogeneous critical current in nanowire superconducting single-photon detectors (2014)

A superconducting thin film with uniform properties is the key to realize nanowire superconducting single-photon detectors (SSPDs) with high performance and high yield. To investigate the uniformity of NbN films, we introduce and characterize simple detectors consisting of short nanowires with length ranging from 100 nm to 15 lm. Our nanowires, contrary to meander SSPDs, allow probing the homogeneity of NbN at the nanoscale. Experimental results, endorsed by a microscopic model, show the strongly inhomogeneous nature of NbN films on the sub-100 nm scale.
Spatial query processing in geographic database systems (2002)

In this paper, we propose a spatial query language, called GSQL, to handle complex spatial objects such as points, fines, rectangles, or polygons. To implement the spatial operators such as nearest, furthest, intersect, cover, adjacent to, end at, and distance, we present a two-phase query processing technique consisting of a filter phase and a refinement phase. The filter phase is based on spatial access methods. However, the filter phase does not exactly evaluate the query and yields a set of candidate objects which may fulfil the query condition. Therefore, the candidate objects have to be examined in the refinement phase. This phase applies complex algorithms used in the field of computational geometry to the original spatial objects and detects exactly those objects finally fulfilling the query condition.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
ABSTRACTS 11 <sup>th</sup> International Symposium on Chemistry and Biology of Pteridines and Folates (1997)

Neopterin, 6-( D-erythro-1 ,2,3-trihydroxypropyl)pterin, is the biochemical indicator for activity of cellular immune response, which is produced by responded macrophages by interferon-gamma. If there are diseases related with T-cell such as, tuberculosis' viral disease, AIDS, and cellular allograft rejection, lots of neopterin are produced in body and then extruded out. The chemical syn-Pteridines/ Vol. 8 / No. 2 11'" International Symposium on Chemistry and Biology of Pteridines and Folates/ Poster Presentations thesis of neopterin is produced by the oxidation of 5,6-dihydro-6-( 1 ,2,3-trihydroxypropyl)pteridine with O 2 which was yielded condensation of 5,6-diaminopyrimidine and phenylhydrazones of D-and L-arabinose under acidic condition.
Metal artifacts reduction for tomosynthesis (2014)

In tomosynthesis imaging, two kinds of metal artifacts will influence diagnosis: undershooting and ripple. In this paper we propose a novel metal artifact reduction (MAR) algorithm to reduce the both of these effects. First, the raw projection data are analyzed and metal areas are identified through segmentation. Then the metal areas are filled with an interpolated value based on the neighborhood background (non-segmented) pixels. The filled regions and metal regions are then reconstructed separately with Filtered Backprojection(FBP). Lastly, the two reconstruction results are combined together to get the final artifacts-free images. Phantom and clinical images are evaluated using qualitative and quantitative methods which demonstrate the algorithms effectiveness.
Bench-to-bedside review: The role of β-lactamases in antibiotic-resistant Gram-negative infections (2010)

Multidrug resistance has been increasing among Gram-negative bacteria and is strongly associated with the production of both chromosomal- and plasmid-encoded beta-lactamases, whose number now exceeds 890. Many of the newer enzymes exhibit broad-spectrum hydrolytic activity against most classes of beta-lactams. The most important plasmid-encoded beta-lactamases include (a) AmpC cephalosporinases produced in high quantities, (b) the expanding families of extended-spectrum beta-lactamases such as the CTX-M enzymes that can hydrolyze the advanced-spectrum cephalosporins and monobactams, and (c) carbapenemases from multiple molecular classes that are responsible for resistance to almost all beta-lactams, including the carbapenems. Important plasmid-encoded carbapenemases include (a) the KPC beta-lactamases originating in Klebsiella pneumoniae isolates and now appearing worldwide in pan-resistant Gram-negative pathogens and (b) metallo-beta-lactamases that are produced in organisms with other deleterious beta-lactamases, causing resistance to all beta-lactams except aztreonam. beta-Lactamase genes encoding these enzymes are often carried on plasmids that bear additional resistance determinants for other antibiotic classes. As a result, some infections caused by Gram-negative pathogens can now be treated with only a limited number, if any, antibiotics. Because multidrug resistance in Gram-negative bacteria is observed in both nosocomial and community isolates, eradication of these resistant strains is becoming more difficult.
Electrical characteristics of coplanar waveguide devices incorporating nonlinear dielectric thin films of SrTiO<sub>3</sub> and Sr<sub>0.5</sub>Ba<sub>0.5</sub>TiO<sub>3</sub> (1995)

Abstract We have studied voltage‐tunable (0–200 V) broadband (0.1–5.1 GHz) microwave properties at room temperature and the liquid nitrogen temperature of two coplanar waveguide devices made from a Au / Sr 0.5 Ba 0.5 TiO 3 bilayer and a YBa 2 Cu 3 O 7‐x / SrTiO 3 bilayer, respectively. The experimental results agree well with the predictions of simple quasistatic and quasi‐TEM models. © 1995 John Wiley & Sons, Inc.
Review of Injectable Materials for Soft Tissue Augmentation (2004)

Although a variety of injectable agents are available for soft tissue augmentation, no perfect filler material exists. The advantages and disadvantages of commonly used materials such as bovine collagen have been well documented. However, many newer injectables are still undergoing experimentation to determine their clinical efficacy and long-term safety. This article details recent scientific work to compare injectable materials from the following categories: xenografts (bovine collagen and hyaluronic acid derivatives), autografts (autologous fat, Isolagen, and Autologen), homografts (Dermalogen and Cymetra), and synthetic materials (fluid silicone and Artecoll).
<title>Comparative study on magnetic variable axis lenses using electrostatic and magnetic in-lens deflectors</title> (1999)

Variable axis lens (VAL) system for magnetic round lenses can be achieved by using electrostatic deflectors (ME-VAL) instead of magnetic deflectors (MM-VAL). The condition for the ME-VAL is obtained from the paraxial ray equation rather than from axial focusing field expansions. The study shows that the ME- VAL also reduces the off-axis aberrations significantly, though not as much as its MM-VAL counterpart. A ME-VAL has been proposed for a magnetic objective lens using octopole deflector electrodes, in which the VAL condition is slightly mismatched. The results shows that the ME-VAL is less sensitive to mismatches in the VAL fields than the MM-VAL counterpart in terms of off-axis aberrations, and comparable performance can be obtainable if the advantages of electrostatic deflection can be fully exploited.
Group Intuitionistic Fuzzy Topological Spaces (2015)

The notion of intuitionistic fuzzy set was introduced by K.T. Atanassov as a generalization of the notion of fuzzy set. Intuitionistic fuzzy topological spaces were introduced by D. Coker and studied by many eminent authors