gebhart/patrepeval huggingface dataset:
Preparation of a chiral building block based on 1,3-syn-diol using Pseudomonas fluorescens lipase and its application to the synthesis of a hunger modulator. (1989)

A novel, chiral building block (9) consisting of 1, 3-syn-diol was obtained by highly enantioselective hydrolysis of the meso-diacetate (8) with Pseudomonas fluorescens lipase (PFL), and (-)-9 was used to synthesize one of four possible stereoisomers of 2-hydroxy-4-hydroxymethyl-4-butanolide, which has hunger modulating activities.
Bacteroides fragilis subverts mucosal biology: from symbiont to colon carcinogenesis (2014)

The human body comprises fewer host cells than bacterial cells, most of which are obligate anaerobes residing in the gut. The symbiont Bacteroides fragilis constitutes a relatively small proportion (up to 1%-2%) of cultured fecal bacteria, but colonizes most humans. There are 2 classes of B. fragilis distinguished by their ability to secrete a zinc-dependent metalloprotease toxin, B. fragilis toxin (BFT). Strains that do not secrete BFT are nontoxigenic B. fragilis (NTBF), and those that do are called enterotoxigenic B. fragilis (ETBF). ETBF can induce clinical pathology, including inflammatory diarrhea, although asymptomatic colonization may be common. Intestinal inflammation is mediated by BFT, as yet the only known virulence factor of ETBF. Recent experimental evidence demonstrating that ETBF-driven colitis promotes colon tumorigenesis has generated interest in the potential contribution of ETBF to human colon carcinogenesis. Critical questions about the epidemiology of chronic, subclinical human colonization with ETBF and its impact on the biology of the colon need to be addressed.
Location of the antigenic determinants of conjugative F-like pili (1986)

The amino terminus of the pilin protein constitutes the major epitope of F-like conjugative pili studied to date (F, ColB2, R1-19, R100-1, and pED208). Anti-pED208 pilus antibodies were passed through a CNBr-Sepharose affinity column linked to bovine serum albumin which was conjugated to a synthetic peptide, AcP(1-12), containing the major epitope at the amino terminus of pED208 pilin. This allowed the separation of two classes of antibodies; one was specific for the amino terminus and bound to the column, while the other, which recognizes a second epitope on the pilus, did not bind to the column. In addition, antibodies were raised against two amino-terminal peptide-bovine serum albumin conjugates [AcP(1-8) and AcP(1-12)] to ensure a source of pure, high-titer antibodies directed against the amino terminus. The location of these antibodies on intact pili was assayed by immunoelectron microscopy with a protein A-gold technique. The amino terminus-specific antibodies did not bind to the sides of the pili but appeared to be associated with the pilus tip. In addition, these antibodies were found to bind to the vesicle-like structure at the base of the pilus. The anti-pilus antibodies not specific for the amino terminus (unbound immunoglobulin G) were found to bind to the sides of the pilus. Anti-F and anti-ColB2 pilus antibodies bound to the sides of F, ColB2, and R1-19 pili, which have only their secondary epitope in common. The carboxyl-terminal lysine of R1-19 pilin prevents the absorption of anti-F plus antiserum but not anti-ColB2 pilus antiserum to the sides of the pilus, presumably by interfering with the recognition of this secondary epitope.
Total Synthesis of Peribysin E Necessitates Revision of the Assignment of its Absolute Configuration (2007)

The right way round: Peribysin E, a naturally occurring adhesion inhibitor, has been synthesized and, as a result, its absolute configuration reassigned. The natural and nonnatural enantiomers can be reached starting from (R)- or (S)-carvone, respectively. A key step is the ring contraction of 1 to 2 (see scheme, TBS=tert-butyldimethylsilyl, TES=triethylsilyl). Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2007/z604308_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
New stable aryl-substituted acyclic imino-N-heterocyclic carbene: synthesis, characterisation and coordination to early transition metals (2011)

The synthesis of the bulky 1-(1-arylimino-2,2-dimethylpropyl)-3-(aryl)imidazolium salt from the corresponding imidazole and the activated imidoyl chloride is presented. The absence of acidic protons adjacent to the iminic carbon allowed for the first isolation of an imino-N-heterocyclic carbene of this ligand class. The free carbene was isolated, structurally characterised, and coordinated to titanium, zirconium, hafnium and chromium. The resulting metal halide complexes were fully characterised and were tested at room temperature and atmospheric pressure for their activity as ethylene polymerisation catalysts. The Zr(IV) complex was found to be the most active with a productivity of 140 kg PE mol M(-1) h(-1).
Prevention of tumors of the large intestine by celecoxib in mice. (2005)

Celecoxib (C), a COX-2 enzyme inhibitor, was administered at a 0.1% dose level in the diet of female Swiss Webster CFW outbred mice for life. The mice also received 1,2-dimethylhydrazine dihydrochloride (1,2-DMH) as 10 weekly subcutaneous injections at 20 microg/g body weight. The number of animals with large intestinal cancer and the total number of these cancers were 30 and 321 in the 1,2-DMH-treated group, while the corresponding figures in the C and 1,2-DMH-treated group were 29 and 156. This difference is statistically highly significant. The literature contains a limited number of publications concerning the cancer chemopreventive activity of C, particularly in mice. The present work, thus, provides additional proof in this field of interest.
Structural Features and Biologic Properties of Fragments Obtained by Limited Proteolysis of C3 (1976)

Limited proteolysis of the third component of human complement (C3) was performed by using trypsin and streptococcal proteinase and the digests were analyzed for biologic activity. Incubation of C3 with trypsin for 1 min yielded a peptide with smooth muscle-contracting activity but no chemotactic activity, whereas the digest obtained after 15 min of incubation had only chemotactic activity. The conversion of muscle contracting to chemotactic activity could be correlated with the time course of trypsin hydrolysis. Hydrolysis of C3 with streptococcal proteinase gave a digest demonstrating only chemotactic activity. Each digest was resolved on a Sephadex G-100 column and the fractions containing biologic activities were characterized. The amino acid composition of the trypsin fragments, despite having different biologic activities, was remarkably similar, although differences in NH2-terminal amino acids were demonstrable. The fragments obtained by digestion of C3 with the streptococcal proteinase had an amino acid composition different from the trypsin fragments and displayed marked heterogeneity of NH2-terminal residues. These results suggest that slight alterations in the primary structure of C3 fragments may yield significant changes in their biologic activities and that the structural requirements for chemotactic activity are not confined to a single peptide species.
The transmembrane protein tyrosine phosphatase α dephosphorylates the insulin receptor in intact cells (1997)

Protein tyrosine phosphatases (PTPs) are key regulators in a variety of signal transduction processes. However, substrates for most PTPs have not been determined. In a previous report, we demonstrated that in a transient expression system the intracellular phosphatases PTPs 1B and TC preferentially dephosphorylated the precursor form of several receptor tyrosine kinases. In this paper we show that the dephosphorylation of kinase precursors is a specific feature of PTPs 1B and TC that is not shared by two other intracellular PTPs, PTPH1 or SHP-1. By contrast, the receptor phosphatase PTP alpha preferentially dephosphorylated the beta-subunit of the insulin receptor localized on the cell surface. The insulin receptor was a better substrate for PTP alpha than for other receptor type PTPs. We conclude that the intracellular PTPs 1B and TC regulate the autophosphorylation of receptor tyrosine kinases during their posttranslational processing while receptor type PTPs regulate the mature, cell surface localized receptor tyrosine kinases.
Hypoxia-inducible Factor-1-mediated Regulation of Semaphorin 4D Affects Tumor Growth and Vascularity (2009)

Tumor progression and metastasis depend on the ability of cancer cells to initiate angiogenesis to ensure delivery of oxygen, nutrients, and growth factors to tumor cells and provide access to the systemic circulation. Hypoxia-inducible factor-1 (HIF-1) can activate expression of a broad range of genes that mediate many of the adaptive responses to decreased oxygen concentration, such as enhanced glucose uptake and formation of new blood vessels. Acting through Plexin-B1 on endothelial cells, Semaphorin 4D (Sema4D) has been shown to promote angiogenesis and enhance invasive growth and proliferation in some tumors. Here we show that the gene for Sema4D, the product of which is elevated in head and neck squamous cell carcinoma (HNSCC) cells, contains upstream hypoxia response elements (HRE) and is strongly induced in hypoxia in a HIF-1-dependent manner. Knocking down Sema4D expression with short hairpin (sh) RNA reduces in vitro endothelial cell migration and growth and vascularity of HNSCC xenografts expressing a degradation resistant HIF-1alpha subunit. We also demonstrate a correlation between HIF-1 activity and Sema4D expression in HNSCC specimens. These findings indicate that Sema4D is induced by hypoxia in a HIF-1-dependent manner and influences endothelial cell migration and tumor vascularity. Expression of Sema4D may be a strategy by which carcinomas promote angiogenesis and therefore could represent a therapeutic target for these malignancies.
Polycomb genes, miRNA, and their deregulation in B-cell malignancies (2015)

Posttranslational modifications of histone proteins represent a fundamental means to define distinctive epigenetic states and regulate gene expression during development and differentiation. Aberrations in various chromatin-modulation pathways are commonly used by tumors to initiate and maintain oncogenesis, including lymphomagenesis. Recently, increasing evidence has demonstrated that polycomb group (PcG) proteins, a subset of histone-modifying enzymes known to be crucial for B-cell maturation and differentiation, play a central role in malignant transformation of B cells. PcG hyperactivity in B-cell lymphomas is caused by overexpression or recurrent mutations of PcG genes and deregulation of microRNAs (miRNAs) or transcription factors such as c-MYC, which regulate PcG expression. Interplays of PcG and miRNA deregulations often establish a vicious signal-amplification loop in lymphoma associated with adverse clinical outcomes. Importantly, aberrant enzymatic activities associated with polycomb deregulation, notably those caused by EZH2 gain-of-function mutations, have provided a rationale for developing small-molecule inhibitors as novel therapies. In this review, we summarize our current understanding of PcG-mediated gene silencing, interplays of PcG with other epigenetic regulators such as miRNAs during B-cell differentiation and lymphomagenesis, and recent advancements in targeted strategies against PcG as promising therapeutics for B-cell malignancies.
Chemical genetic strategy for targeting protein kinases based on covalent complementarity (2011)

The conserved nature of the ATP-binding site of the > 500 human kinases renders the development of specific inhibitors a challenging task. A widely used chemical genetic strategy to overcome the specificity challenge exploits a large-to-small mutation of the gatekeeper residue (a conserved hydrophobic amino acid) and the use of a bulky inhibitor to achieve specificity via shape complementarity. However, in a number of cases, introduction of a glycine or alanine gatekeeper results in diminished kinase activity and ATP affinity. A new chemical genetic approach based on covalent complementarity between an engineered gatekeeper cysteine and an electrophilic inhibitor was developed to address these challenges. This strategy was evaluated with Src, a proto-oncogenic tyrosine kinase known to lose some enzymatic activity using the shape complementarity chemical genetic strategy. We found that Src with a cysteine gatekeeper recapitulates wild type activity and can be irreversibly inhibited both in vitro and in cells. A cocrystal structure of T338C c-Src with a vinylsulfonamide-derivatized pyrazolopyrimidine inhibitor was solved to elucidate the inhibitor binding mode. A panel of electrophilic inhibitors was analyzed against 307 kinases and MOK (MAPK/MAK/MRK overlapping kinase), one of only two human kinases known to have an endogenous cysteine gatekeeper. This analysis revealed remarkably few off-targets, making these compounds the most selective chemical genetic inhibitors reported to date. Protein engineering studies demonstrated that it is possible to increase inhibitor potency through secondary-site mutations. These results suggest that chemical genetic strategies based on covalent complementarity should be widely applicable to the study of protein kinases.
Digital Cinema Content Security and the DCI (2006)

This paper describes the content security system defined in the DCI digital cinema system specification. This specification is not a standard and is not a complete specification to which systems can be built. Rather it represents a sketch of how the major U.S. studios would like to see digital cinema systems develop. Many of the ideas in the specification will be implemented and others will be revised as the motion picture industry adopts and then transitions to digital cinema. As digital cinema systems are built and deployed, standards organizations such as SMPTE and ISO will further refine the functionality and interoperability requirements of various digital cinema components.
Low-cost and high-performance 1.3-/spl mu/m AlGaInAs-InP uncooled laser diodes (2006)

We utilize a self-terminated oxide polish (STOP) planarization technique to fabricate high-yield, high-performance, low-cost, and uncooled 1.3-μm ridge-waveguide AlGaInAs-InP laser diodes (LDs). The STOP technique is superior to the polyimide planarization, which suffers from high-temperature sustainability. The LDs fabricated by the STOP technique exhibit threshold currents of 8.5 and 30.5 mA, and light output powers of 25.9 and 4.8 mW at 100 mA for 20/spl deg/C and 110/spl deg/C, respectively. The characteristic temperatures (T <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0</sub> ) are 82.6 K from -30/spl deg/C to 80/spl deg/C and 55.9 K from 80/spl deg/C to 110/spl deg/C. Since the metal pad lies on a thick SiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> layer, the parasitic capacitance can be effectively lowered to 2 pF. The 3-dB modulation bandwidths of the LDs at 50 mA are 12.1 and 9.44 GHz at 20/spl deg/C and 90/spl deg/C, respectively.
<i>Paecilomyces variotii</i> central nervous system infection in a patient with cancer (2003)

Paecilomyces variotii was isolated from two subsequent cerebrospinal fluid (CSF) specimens of a cancer patient. Identification was confirmed through beta-tubulin and rDNA ITS sequencing. MICs were determined for seven antifungal agents; the isolate was found to be susceptible to amphotericin B (AMB), itraconazole (ITZ), ketaconazole (KTZ) and 5-fluorocytosine (5FC) but resistant to fluconazole (FLZ) and miconazole (MCZ). Despite antimycotic therapy, the infection proved to be fatal.
Micromotor dynamics in lubricating fluids (1994)

This paper presents results from step-transient measurements on salient-pole, side-drive, polysilicon micromotors operated in different viscosity silicone lubricating oils under different temperatures and excitation voltages. The step transient has been found to be overdamped, with the rise time decreasing with decreasing viscosity of the oil. The rise time, which is in the range of 1 to 20 msec, is around one to two orders of magnitude larger in oil than that in gaseous environments because of the larger viscous drag contribution. In oil, voltages as low as 12 V across 2.5 mu m rotor/stator gaps are sufficient to operate the micromotors. Micromotor speeds up to 12500 rpm are achieved with 110 V excitations across 1.5 mu m rotor/stator gaps. Based on the experimental findings, a model for micromotor dynamics in lubricating oils is examined in which the Coulomb frictional torque is neglected, since micromotor operation in oil is dominated by viscous drag.
Methine bases in the benzothiazole, benzoselenazole, and quinoline series, and geometry and conformational preferences of their acyl derivatives (1995)

Dimeric structures 2a–c are confirmed for the "methine bases" obtained from 2-methylbenzo-thiazolium and -selenazolium salts and aqueous sodium hydroxide, whereas monomeric structures 3 are confirmed for methine bases similarly derived from 2-methylquinolinium salts. The latter monomers dimerize slowly on standing. Monomeric methine bases 6–9, too hindered to dimerize, are described. 2-Acetonylidene-2,3-dihydro-3-methylbenzothiazole 10a and related compounds are assigned (Z) configurations on the basis of NOE difference spectra. Molecular mechanics calculations predict a slightly higher steric energy for the observed s-cis conformer of 10a than for the s-trans, indicating a stabilizing [Formula: see text] interaction in the s conformer that need only be a few kJ mol −1 in magnitude. For the quinolines 13a and b, the (E) configuration/s-cis conformation is favoured. The dielectric absorption method provides a rotational energy barrier of approximately 60 kJ mol −1 for acetyl group relaxation in 10a. Oxygen–sulfur exchange is observed in the conversion of 10a to 12a by thioacetic acid. Keywords: conformation, configuration, heterocyclic compounds, [Formula: see text] interaction.
Dynamic shifts in LFA-1 affinity regulate neutrophil rolling, arrest, and transmigration on inflamed endothelium (2005)

Polymorphonuclear leukocyte (PMN) recruitment to vascular endothelium during acute inflammation involves cooperation between selectins, G-proteins, and beta2-integrins. LFA-1 (CD11a/CD18) affinity correlates with specific adhesion functions because a shift from low to intermediate affinity supports rolling on ICAM-1, whereas high affinity is associated with shear-resistant leukocyte arrest. We imaged PMN adhesion on cytokine-inflamed endothelium in a parallel-plate flow chamber to define the dynamics of beta2-integrin function during recruitment and transmigration. After arrest on inflamed endothelium, high-affinity LFA-1 aligned along the uropod-pseudopod major axis, which was essential for efficient neutrophil polarization and subsequent transmigration. An allosteric small molecule inhibitor targeted to the I-domain stabilized LFA-1 in an intermediate-affinity conformation, which supported neutrophil rolling but inhibited cell polarization and abrogated transmigration. We conclude that a shift in LFA-1 from intermediate to high affinity during the transition from rolling to arrest provides the contact-mediated signaling and guidance necessary for PMN transmigration on inflamed endothelium.
A low-cost MCM implementation for 100-Hz TV up-conversion (2002)

A system-on-chip covering all 100 Hz TV digital signal processing functions has been implemented as a MCM in a P-MQFP-64 package. The design, architecture, test concept and special arrangement of two chips assembled together are presented. The yield improvement of the larger memory chip achieved by redundancy optimization has led to a profitable product with higher yield and lower costs than previous multi-package solutions. This development was based on state-of-the-art technology, using materials that were as standard as possible and included DFT (design for testability) right from the outset, i.e. sufficient flexibility to test every block of a multichip module. The time-to-market requirements were effectively satisfied by implementing the system as a MCM. The rough estimate made here shows that when it comes to implementing future high-performance on-chip systems with advanced logic and memory integration, the obvious choice is an emergent embedded DRAM technology.
Factors Affecting the Adoption of High Performance Work Systems in Foreign Subsidiaries: An Empirical Investigation in Hong Kong (2011)

High performance work systems (HPWS) have been increasingly used in multinational corporations (MNCs). Drawing upon institutional theory and alignment theory, we examine the determinants of the adoption of HPWS in foreign subsidiaries of MNCs. Our data were collected via a survey of HR directors/managers of MNCs operating in Hong Kong. The results of regression analysis show that the use of HPWS in foreign subsidiaries is related to headquarters' control, strategic HRM orientation, and adaptability of HRM, but not related to mimetic HRM orientation. We further find that strategic HRM orientation and adaptability of HRM has a significant interaction effect on the adoption of HPWS.
Object Tracking From Image Sequences Using Stereo Camera And Range Radar (1990)

The problem of estimating the position of and tracking an object undergoing 3-D translational and rotational motion using passive and active sensors is considered. The passive sensor used in this study is a stereo camera, whereas the active is a range radar. Three different estimation approaches are considered. The first involves estimation of the object position by direct registration of stereo images. In the second approach, the Extended Kalman Filter is used for estimation with measurements the stereo images. In the third approach, an integral filter based on stereo images and range radar measurements is used for tracking. The three different approaches are compared via simulation in the tracking of an object undergoing a 3-D motion with random translational and angular acceleration.
The Role of Sugar Residues in Molecular Recognition by Vancomycin (2001)

The sugar residues of the glycopeptide antibiotic vancomycin contribute to the cooperativity of ligand binding, thereby increasing ligand affinity and enhancing antimicrobial activity. To assess the structural basis for these effects, we determined a 0.98 A X-ray crystal structure of the vancomycin aglycon and compared it to structures of several intact vancomycin:ligand complexes. The crystal structure reveals that the aglycon binds acetate anions and forms back-to-back dimeric complexes in a manner similar to that of intact vancomycin. However, the four independent copies of the aglycon in each asymmetric unit of the crystal exhibit a high degree of conformational heterogeneity. These results suggest that the sugar residues, in addition to enlarging and strengthening the dimer interface, provide steric constraints that limit the vancomycin molecule to a relatively small number of productive conformations.
Practical code design for compute-and-forward (2011)

The Compute-and-Forward approach has been proven to be very beneficial for communication over Gaussian networks. While the theoretical results are promising, it is still not completely understood how to best apply this scheme in practice. The objective of this work is to provide a low complexity scheme suitable for Compute-and-Forward. The scheme is based on utilizing linear codes over ℤ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">q</sub> where q is not restricted to be prime and allows to achieve high transmission rates following Ungerboeck's set partitioning principle.