gebhart/patrepeval huggingface dataset:
Steady-State and Pre-Steady-State Kinetic Evaluation of Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) 3CLpro Cysteine Protease:  Development of an Ion-Pair Model for Catalysis (2008)

Severe acute respiratory syndrome (SARS) was a worldwide epidemic caused by a coronavirus that has a cysteine protease (3CLpro) essential to its life cycle. Steady-state and pre-steady-state kinetic methods were used with highly active 3CLpro to characterize the reaction mechanism. We show that 3CLpro has mechanistic features common and disparate to the archetypical proteases papain and chymotrypsin. The kinetic mechanism for 3CLpro-mediated ester hydrolysis, including the individual rate constants, is consistent with a simple double displacement mechanism. The pre-steady-state burst rate was independent of ester substrate concentration indicating a high commitment to catalysis. When homologous peptidic amide and ester substrates were compared, a series of interesting observations emerged. Despite a 2000-fold difference in nonenzymatic reactivity, highly related amide and ester substrates were found to have similar kinetic parameters in both the steady-state and pre-steady-state. Steady-state solvent isotope effect (SIE) studies showed an inverse SIE for the amide but not ester substrates. Evaluation of the SIE in the pre-steady-state revealed normal SIEs for both amide and ester burst rates. Proton inventory (PI) studies on amide peptide hydrolysis were consistent with two proton-transfer reactions in the transition state while the ester data was consistent with a single proton-transfer reaction. Finally, the pH-inactivation profile of 3CLpro with iodoacetamide is indicative of an ion-pair mechanism. Taken together, the data are consistent with a 3CLpro mechanism that utilizes an "electrostatic" trigger to initiate the acylation reaction, a cysteine-histidine catalytic dyad ion pair, an enzyme-facilitated release of P1, and a general base-catalyzed deacylation reaction.
Pathological changes associated with white striping in broiler breast muscles (2013)

White striping is a condition in broiler chickens characterized grossly by the occurrence of white striations, seen parallel to the direction of muscle fibers, on broiler breast fillets and thighs. Based on visual evaluation of the intensity of white striping, breast fillets can be categorized into normal (NORM), moderate (MOD), and severe (SEV) categories. This study was undertaken to evaluate the details of changes in histology as well as proximate composition occurring in the fillets with respect to the 3 degrees of white striping. In experiment 1, representative breast fillets for each degree of white striping (n = 20) were collected from 45-d-old broilers, approximately 2 h postmortem. From each fillet, 2 skeletal muscle samples were obtained and fixed in 10% neutral buffered formalin. To identify and differentiate the histological changes, slides were prepared and stained using hematoxylin and eosin, Masson's Trichrome, and Oil Red O stains. In experiment 2, samples with 3 degrees of white striping were collected from 57-d-old birds for conducting proximate analysis. Major histopathological changes observed in the MOD and SEV samples consisted of loss of cross striations, variability in fiber size, floccular/vacuolar degeneration and lysis of fibers, mild mineralization, occasional regeneration (nuclear rowing and multinucleated cells), mononuclear cell infiltration, lipidosis, and interstitial inflammation and fibrosis. Microscopic lesions were visually scored for degeneration and necrosis, fibrosis, and lipidosis. The scale used to score the samples ranged from 0 (normal) to 3 (severe). There was an increase (P < 0.05) in mean scores for degenerative or necrotic lesions, fibrosis, and lipidosis as the degree of white striping increased from NORM to SEV. The results from the histopathological study were supported by the findings from proximate analysis confirming that the fat and protein contents of muscle increased (P < 0.05) and decreased (P < 0.05), respectively, as the degree of white striping increased. In conclusion, the histopathological changes occurring in white striping indicate a degenerative myopathy that could be associated with increased growth rate in birds.
Patterned alignment of liquid crystals (2004)

In this study the &mu;-rubbing technique is used to micro-pattern polyimide alignment layers using a metallic sphere at different loads. Optical and atomic force microscopy shows that the width of the patterns ranges from 12-40 &mu;m and depth ranges from 2-14 nm. Our primary finding is that &mu;-rubbing induces planar alignment in polyimides. We performed &mu;-rubbing on pre-rubbed polyimide perpendicular to the rubbing direction. It is found that &mu;-rubbing erases the alignment properties of the pre-rubbing procedure. Liquid crystal cells were constructed using the pre-rubbed polyimide substrates with &mu;-rubbed patterns on one side and a homogeneously rubbed polyimide layer on the other side. Therefore the pre-rubbed polyimide layers are crossed and consequently a twisted nematic alignment is observed outside the micro-patterns. Within the micro-patterns, the directions of the pre-rubbing and &mu;-rubbing are parallel, a planar alignment observed. In another configuration, liquid crystal cells were made with pre-rubbed polyimide substrates having micro-patterns on both sides to give grid pattern with planar and twisted nematic configuration. Studies were extended to determine the pretilt of the micro patterned area.
Surface Organization and Nanopatterning of Collagen by Dip Pen Nanolithography (2002)

The degree of fluidity or crystallinity in these spherulites varies with the amino acid sequence of the collagen
Demonstration of 300 Gbps Error-Free Transmission of WDM Data Stream in Silicon Photonic Wires (2007)

We present the first experimental demonstration of error-free (bit error rates < 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-12</sup> ) transmission of a 300-Gbps WDM data stream through a 2-cm-long silicon photonic wire using 24 C-band channels, each modulated at 12.5 Gbps.
Invading the Yeast Nucleus: a Nuclear Localization Signal at the C Terminus of Ty1 Integrase Is Required for Transposition In Vivo (1998)

Retrotransposon Ty1 faces a formidable cell barrier during transposition--the yeast nuclear membrane which remains intact throughout the cell cycle. We investigated the mechanism by which transposition intermediates are transported from the cytoplasm (the presumed site of Ty1 DNA synthesis) to the nucleus, where they are integrated into the genome. Ty1 integrase has a nuclear localization signal (NLS) at its C terminus. Both full-length integrase and a C-terminal fragment localize to the nucleus. C-terminal deletion mutants in Ty1 integrase were used to map the putative NLS to the last 74 amino acid residues of integrase. Mutations in basic segments within this region decreased retrotransposition at least 50-fold in vivo. Furthermore, these mutant integrase proteins failed to localize to the nucleus. Production of virus-like particles, reverse transcriptase activity, and complete in vitro Ty1 integration resembled wild-type levels, consistent with failure of the mutant integrases to enter the nucleus.
Induction of Interleukin-8 Synthesis Integrates Effects on Transcription and mRNA Degradation from at Least Three Different Cytokine- or Stress-Activated Signal Transduction Pathways (1999)

A hallmark of inflammation is the burst-like formation of certain proteins, initiated by cellular stress and proinflammatory cytokines like interleukin 1 (IL-1) and tumor necrosis factor, stimuli which simultaneously activate different mitogen-activated protein (MAP) kinases and NF-kappaB. Cooperation of these signaling pathways to induce formation of IL-8, a prototype chemokine which causes leukocyte migration and activation, was investigated by expressing active and inactive forms of protein kinases. Constitutively active MAP kinase kinase 7 (MKK7), an activator of the stress-activated protein kinase/c-Jun N-terminal kinase (SAPK/JNK) pathway, induced IL-8 synthesis and transcription from a minimal IL-8 promoter. Furthermore, MKK7 synergized in both effects with NF-kappaB-inducing kinase (NIK). Activation of the IL-8 promoter by either of the kinases required functional NF-kappaB and AP-1 sites. While NIK and MKK7 did not affect degradation of IL-8 mRNA, an active form of MKK6, which selectively activates p38 MAP kinase, induced marked stabilization of the transcript and further increased IL-8 protein formation induced by NIK plus MKK7. Consistently, the MAP kinase kinase kinase MEKK1, which can activate NF-kappaB, SAPK/JNK, and p38 MAP kinases, most potently induced IL-8 formation. These results provide evidence that maximal IL-8 gene expression requires the coordinate action of at least three different signal transduction pathways which cooperate to induce mRNA synthesis and suppress mRNA degradation.
Diffeomorphic Demons Using ITK's Finite Difference Solver Hierarchy (2008)

This article provides an implementation of our non-parametric diffeomorphic image registration algorithm generalizing Thirion’s demons algorithm. Within the Insight Toolkit (ITK), the demons algorithm is implemented as part of the finite difference solver framework. We show that this framework can be extended to handle diffeomorphic transformations. The source code is composed of a set of reusable ITK filters and classes. In addition to an overview of our implementation, we provide a small example program that allows the user to compare the different variants of the demons algorithm.
Economic evaluation of a cognitive radio based solution for increasing capacity of LTE networks (2013)

This paper presents an economic evaluation of a cognitive radio based solution using TV white space frequencies to increase the capacity of LTE networks. The evaluation is performed from the viewpoint of a mobile operator who is facing capacity problems in its LTE network and wants to assess if using cognitive radio can be a competitive solution. The assessment is done by comparing the costs of implementing the cognitive radio solution to the costs of acquiring a licence for a block of spectrum where both options provide the same capacity increase.
Triazole phosphonates. Electrophilic substitution of 1‐substituted‐1H‐1,2,4‐triazoles via lithiated triazole intermediates (1986)

Abstract The metalation chemistry of several 1‐substituted‐1 H ‐1,2,4‐triazoles has been investigated. When various alkyl groups were incorporated in the 1‐position, lithiation proceeded exclusively at C‐5. The 1‐trityl‐, 1‐methyl‐, and 1‐benzyl‐5‐lithio‐1,2,4‐triazoles were stable at −78° and reacted cleanly with a variety of electrophiles. The 1‐benzyl and 1‐methyl derivatives were synthetically more versatile and could be successfully utilized to prepare several examples of the previously unknown 1,2,4‐triazol‐5‐yl phosphonates.
Chemically Induced Conductance Switching in Carbon Nanotube Circuits (2006)

The chemical reactivity of carbon nanotubes in H2SO4 is investigated using individual, single-walled carbon nanotubes (SWNTs) incorporated into electronic devices. Exploiting the device conductance as a sensitive indicator of chemical reactions, discrete oxidation and reduction events can be clearly observed. During oxidation, a SWNT opens circuits to a nanometer-scale tunnel junction with residual conduction similar to Frenkel-Poole charge emission. When electrochemically reduced, a SWNT returns to its original conductance. This redox cycle can be repeated many times, suggesting a novel chemical method of reversibly switching SWNT conductivity.
Surface structures of hybrid aligned liquid crystal network coatings containing reverse tilt domain (2019)

Controlled shape changes of polymerized liquid crystalline coatings is often achieved via prepatterning the molecular orientation of liquid crystal (LC) monomers at the stage of preparation. In this work, using the so-called hybrid alignment of the LC, we produce surface structures of positive Gaussian curvature of coatings without complex techniques such as photoalignment. A mixture of LC monomers coated onto a glass plate with planar alignment of the director is exposed to air, which promotes vertical alignment. The competing planar and homeotropic boundary conditions result in a) thickness dependent director and b) spontaneous formation of spindle-like regions, limited by disclination loops, that are called the reverse tilt domains (RTDs). The disclination separates different director configurations inside and outside the RTD. The RTDs produce relatively big protrusions (100 − 600 nm) of the LC network coating. Actuation of the coating by heat increases the amplitude of RTD protrusions.
Supplementary Figure 5 from Cisplatin Selects for Multidrug-Resistant CD133<sup>+</sup> Cells in Lung Adenocarcinoma by Activating Notch Signaling (2023)

&lt;p&gt;PDF file - 255K, The role of ABC transporters in cisplatin-induced multi-drug resistance to paclitaxol in H460 and H661 cell lines&lt;/p&gt;
Ethnobotany, Phytochemistry and Pharmacology of Uncaria (Rubiaceae) (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
Coherent Excitation-Selective Spectroscopy in Planar Metamaterials (2014)

We demonstrated that the electric and magnetic resonances of metamaterials can be separately switches off and on by positioning the metamaterials along a standing wave, while both resonances are present in travelling-wave spectra.
Regulation of ovarian progestin production by epidermal growth factor in cultured rat granulosa cells. (1982)

The modulation of ovarian steroidogenesis by epidermal growth factor (EGF) was investigated in cultured rat granulosa cells. Granulosa cells, obtained from ovaries of immature, hypophysectomized, estrogen-treated rats, were incubated for 2 days with EGF, follicle-stimulating hormone (FSH), or EGF plus FSH. Treatment with EGF did not affect estrogen production, but stimulated progestin (i.e. progesterone and 20 alpha-hydroxy-pregn-4-en-3-one) production in a dose-dependent manner. Stimulation of progestin production by EGF appears to be the result of an increase in pregnenolone biosynthesis as well as increases in the activities of 20 alpha-hydroxysteroid dehydrogenase and 3 beta-hydroxysteroid dehydrogenase/isomerase. Treatment with FSH increased both estrogen and progestin production by cultured granulosa cells. When cells were treated concomitantly with EGF, FSH-stimulated estrogen production was inhibited, while progestin production was further enhanced. The EGF enhancement of FSH-stimulated progestin production appears to be the result of synergistic increases in pregnenolone biosynthesis and 20 alpha-hydroxysteroid dehydrogenase activity, resulting in substantial increases in 20 alpha-hydroxypregn-4-en-3-one but not progesterone production. The effects of EGF were shown to be time-dependent. The concept of a direct action of EGF on rat granulosa cells is reinforced by the demonstration of high affinity (Kd approximately 3 X 10(-10) M), low capacity (approximately 5,000 sites/cell) EGF binding sites in these cells. Thus, EGF interacts with specific granulosa cell receptors to stimulate progestin but to inhibit estrogen biosynthesis.
Corrosion Fatigue of 316L Stainless Steel, Co-Cr-Mo Alloy, and ELI Ti-6Al-4V (1979)

The purpose of this paper is to compare corrosion-fatigue properties of selected implant alloys and to discuss the corrosion fatigue-life in terms of the corrosion behavior and the metal microstructure. The tests were conducted in fully reversed torsion in flowing Hank's solution at a temperature of 37°C and a pH of 7.4. Specimens were subjected to fatigue at shear strains ranging from 0.006 to 0.018 and at a frequency of 1 Hz. Surfaces of the 0.5-cm-diameter specimens were prepared by mechanically polishing through a 0.05 alumina powder and following this with steam sterilization. During the tests, the specimen electrode potentials versus time were monitored on a strip chart recorder. The potential-time curves for the metals studied show the establishment of a steady rest potential which does not change until the fatigue motion has been applied. The potential then goes in the negative direction. The rate of this decline in potential appears to-be related to the metal microstructure as well as to the alloy composition. This electronegativity of the potential-time curves indicated the formation of cracks in the oxide film. These curves were more electronegative with increased shear strain, and the curves were different for the different metals tested. Fatigue results of these tests show that the ELI Ti-6Al-4V has the longest fatigue life under these conditions. The fatigue strength of the Ti-6Al-4V can be increased many times by changing the microstructure through heat treating and quenching. The Type 316L stainless steel had the next longest fatigue life. The cast Co-Cr-Mo alloy had the shortest fatigue life and also showed more scatter in the results. Other workers have shown that further heat treating and processing improves the fatigue resistance of this material too.
An agile and scalable manufacturing model to support 5G growth (2020)

The increasing number of RF, microwave and analog-intensive-mixed-signal IC applications had led, over the two last decades, to the emergence of engineered substrate technologies that have helped to increase the adoption of the specialty foundry model for the semiconductor supply chain. In this paper we will review engineered substrate technologies with a special focus on 5G and its use case scenarios. We will also discuss how using 100% standard toolset and agile rampup techniques, engineered substrates could be manufactured to meet the stringent time-to-market and yield requirements of a semiconductor market in constant evolution
Pyrene as a fluorescent probe for monitoring polymerization rates (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticlePyrene as a fluorescent probe for monitoring polymerization ratesO. Valdes-Aguilera, C. P. Pathak, and D. C. NeckersCite this: Macromolecules 1990, 23, 2, 689–692Publication Date (Print):January 1, 1990Publication History Published online1 May 2002Published inissue 1 January 1990https://pubs.acs.org/doi/10.1021/ma00204a055https://doi.org/10.1021/ma00204a055research-articleACS PublicationsRequest reuse permissionsArticle Views350Altmetric-Citations56LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
High performance semitransparent phosphorescent white organic light emitting diodes with bi-directional and symmetrical illumination (2013)

A semitransparent white organic light-emitting diode (WOLED) is produced based on a blue phosphorescence from iridium(III)[bis(4,6-difuorophenyl)-pyridinato-N,C2] picolinate and an orange phosphorescence from bis(2-(9,9-diethyl-9H-fluoren-2-yl)-1-phenyl-1H-benzoimidazol-N,C3) iridium(acetylacetonate). In this work, a hole-transporting layer of N,N′-diphenyl-N,N′-bis(1-naphthylphenyl)-1,1′-biphenyl-4,4′-diamine (NPB) and an electron-transporting layer of 3,5,3″,5″-tetra-3-pyridyl-[1,1′;3′,1″] terphenyl (B3PyPB) were used. B3PyPB has high electron mobility and a high triplet energy level. The use of B3PyPB helps to reduce the triplet quenching and also to confine the charge recombination in the emissive region of a single-host two-color WOLED. A bi-layer Ag (10 nm)/MoO3 (2.5 nm)-modified indium tin oxide anode and a cathode of Al (1.5 nm)/Ag (15 nm)/NPB (50 nm) were employed. The semitransparent WOLEDs thus developed have perfect symmetrical, bi-directional illumination characteristics, and the weak angular dependent EL emission spectra, which are beneficial for application in planar diffused lighting.
Effect of Domain Boundary on Carrier Transport of Calamitic Liquid Crystalline Photoconductive Materials (2000)

Abstract Smectic mesophases in the calamitic liquid crystalline materials such as 2-phenylnaphthalene derivatives exhibit fast ambipolar carrier transport, whose mobility is up to 10−2 cm2/Vs. For these mesophases, we have investigated the effect of defects in the bulk and at the domain boundary on these carrier transport by measuring transient photocurrents in thick cells up to 120 μm in thickness and in the cells of different domain sizes of 10–100s μm. It was found that non-dispersive carrier transports was observed for all the cells and the carrier transport was affected neither by cell thickness nor by domain sizes. Thus, it was concluded that there are few deep defects in the bulk and that the domain boundary is electrically inactive in these mesophases, demonstrating their high potential for practical application to large-area electronic devices.
Guest-host effect of dyes in polymer dispersed liquid crystals (2002)

The guest-host [GH) effect of a tetracyanoquinodimethane (TCNQ) dye in nematic liquid crystals (LC) and polymer dispersed liquid crystals (PDLC) has been studied and compared with commercial azo and anthraquinone dyes. The adduct (MORPIP) is a conjugated molecule with a high dipole moment of 15 Debyes. E7 LC doped with MORPIP was found to give a dichroic ratio of 2.34 and an order parameter of 0.31; these values are lower than for the other dichroic dyes, typically 0.6 - 0.78. However, MORPIP showed a useful property When doped in LC and PDLC samples. The rise time of E7 was decreased by 21% when doped with 0.3 wt% MORPIP. It was suggested that MORPIP increased the dielectric anisotropy of E7 and hence reduced the rise time. Nevertheless, no change in dielectric anisotropy was observed. This observation favours a model in which the dipolar dopant reorients rapidly in the applied field and drives the reorientation of the surrounding LC The effects of the dyes incorporated in PDLGs were also studied, in order to explore their suitability for use in a colour reflective display. Dichroic PDLQ were made using the photo-initiated phase separation method. 0.37 wt7o MORPIP doped PDLCs showed a 45% faster response to an applied electric field than that of the undoped PDLCs. However, the contrast ratio of the dichroic PDLCs was not sufficiently high for display use due to insufficient scattering and dye trapping. Two new fabrication methods were developed to overcome this problem One method involved the preparation of a network type PDLC into which a doped LC was dispersed. Another method involved the preparation of voids by removing the LC from the PDLC In both methods, subsequent re-filling of the doped LC into the pre-made polymer matrix improved the contrast ratio and reduced the decay time of the dichroic PDLC