gebhart/patrepeval huggingface dataset:
Experimental and Theoretical Studies on Pyrolysis of O-Acetyl Derivatives of beta-phenylcinnamaldehyde and Benzaldehyde Oximes (2003)

Thermal behavior of β-phenylcinnamaldehyde and benzaldehyde oxime O-acetyl derivatives was studied experimentally and theoretically by the semi-empirical PM3 method. Intramolecular pericyclic mechanisms were proposed for the reactions of the E-isomers, intramolecular catalytic polar mechanism for elimination of acetic acid from the Z-isomers.
Kabuki make-up syndrome associated with congenital heart disease. (1994)

The Kabuki make-up syndrome, reported in 1981 by Niikawa et al. and Kuroki et al. independently, is also known as "Niikawa-Kuroki syndrome". Here we report two cases of this syndrome, both of them were boys, showing facial dysmorphism, hand abnormalities and congenital heart disease. The first case had developmental retardation noticed since 3 months old and frequent upper respiratory tract infections in the following years, and the cardiac echo revealed mitral regurgitation and tricuspid regurgitation. The second case had patent ductus arteriosus and ventricular septal defect diagnosed at 17 days old. He underwent corrective surgery for his heart problems, he also couldn't complete a sentence at two and half years old. It was estimated that the incidence of this syndrome was 1/32,000 in Japanese Children, and Chinese are similar to Japanese as yellow-skinned oriental, there should be more cases in our country, and a detailed cardiac study may be necessary for them.
Functional differences in the promoters of the interferon‐inducible (2′‐5′)A oligoadenylate synthetase and 6–16 genes in interferon‐resistant Daudi cells (1994)

A clone of interferon-alpha-resistant (IFNr) Daudi cells retained much greater transcriptional inducibility of the (2'-5') oligoadenylate synthetase than the 6-16 gene despite the fact that the response of both genes is mediated by highly similar interferon-stimulable DNA response elements (ISRE). The primary IFN-alpha activatable transcription factor E (ISGF3) and the additional IFN-alpha-inducible ISRE-binding complex M were greatly reduced in the IFNr cells. The defect in E was in the E alpha subunit. In electrophoretic mobility-shift assays the 6-16 and (2'-5') oligoadenylate synthetase ISRE competed approximately equivalently for E and M. Moreover although active in wild-type cells the (2'-5') oligoadenylate synthetase ISRE was no more capable of conferring inducibility on a reporter gene in the IFNr cells than was the 6-16 ISRE. The contrasting response of the endogenous (2'-5') oligoadenylate synthetase and 6-16 genes in the IFNr cells is, therefore, unlikely simply to reflect the slight difference in the sequence of their ISRE. Consistent with this, in addition to the ISRE, sequences 5' to the ISRE in the (2'-5') oligoadenylate synthetase promoter appeared necessary for good induction by IFN alpha in the IFNr cells. Subtle quantitative changes in the phenotype of the IFNr cells have, however, precluded a more precise definition of the DNA element(s) involved.
ChemInform Abstract: Novel Cyclization Chemistry Especially Suited for Biologically Derived, Unprotected Peptides. (1993)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
On Protein Denaturation in Aqueous−Organic Mixtures but Not in Pure Organic Solvents (1996)

FTIR spectroscopy was used to quantitatively assess the secondary structure of proteins in aqueous−organic mixtures ranging from pure water to a pure solvent. For every such solution/suspension, the α-helix content of the protein was independently calculated from the amide I and amide III spectral regions (which gave essentially identical results). In all cases studied (two unrelated enzymic proteinslysozyme and subtilisin; three dissimilar water-miscible solventsacetonitrile, tetrahydrofuran, and 1-propanol), the protein secondary structure was much more native-like in pure organic solvents than in most water−solvent mixtures, e.g., 60% (v/v) organic solvents. In fact, placing lyophilized (or crystalline) proteins in the anhydrous solvents tested had no appreciable effect on the α-helix content, whereas the latter declined markedly in the 60% (v/v) solvents. This behavior was found to be kinetically controlled, i.e., to be due to inherent restrictions on protein conformational mobility in anhydrous, in contrast to aqueous−organic, media.
Controlling flow in horizontal wells (1991)

Horizontal drilling technology has advanced dramatically over the past few years, and so has the number of horizontal gas and oil wells drilled, although the demand for advanced completion systems for these wells has been somewhat limited. Now however, flow control in horizontal completions is a rapidly emerging area of technology. Flow control technology is particularly important in the overall completion design to allow for production control, testing and downhole repairs. This article discusses the application of flow control techniques, equipment and hook-ups currently in use, and presents examples of horizontal wells where the technology has been applied.
Characterization of a Flavoprotein Oxidase from Opium Poppy Catalyzing the Final Steps in Sanguinarine and Papaverine Biosynthesis (2012)

Benzylisoquinoline alkaloids are a diverse class of plant specialized metabolites that includes the analgesic morphine, the antimicrobials sanguinarine and berberine, and the vasodilator papaverine. The two-electron oxidation of dihydrosanguinarine catalyzed by dihydrobenzophenanthridine oxidase (DBOX) is the final step in sanguinarine biosynthesis. The formation of the fully conjugated ring system in sanguinarine is similar to the four-electron oxidations of (S)-canadine to berberine and (S)-tetrahydropapaverine to papaverine. We report the isolation and functional characterization of an opium poppy (Papaver somniferum) cDNA encoding DBOX, a flavoprotein oxidase with homology to (S)-tetrahydroprotoberberine oxidase and the berberine bridge enzyme. A query of translated opium poppy stem transcriptome databases using berberine bridge enzyme yielded several candidate genes, including an (S)-tetrahydroprotoberberine oxidase-like sequence selected for heterologous expression in Pichia pastoris. The recombinant enzyme preferentially catalyzed the oxidation of dihydrosanguinarine to sanguinarine but also converted (RS)-tetrahydropapaverine to papaverine and several protoberberine alkaloids to oxidized forms, including (RS)-canadine to berberine. The K(m) values of 201 and 146 μm for dihydrosanguinarine and the protoberberine alkaloid (S)-scoulerine, respectively, suggested high concentrations of these substrates in the plant. Virus-induced gene silencing to reduce DBOX transcript levels resulted in a corresponding reduction in sanguinarine, dihydrosanguinarine, and papaverine accumulation in opium poppy roots in support of DBOX as a multifunctional oxidative enzyme in BIA metabolism.
Optimized Codon Usage and Chromophore Mutations Provide Enhanced Sensitivity with the Green Fluorescent Protein (1996)

The green fluorescent protein (GFP) from Aequorea victoria is a versatile reporter protein for monitoring gene expression and protein localization in a variety of cells and organisms. Despite many early successes using this reporter, wild type GFP is suboptimal for most applications due to low fluorescence intensity when excited by blue light (488 nm), a significant lag in the development of fluorescence after protein synthesis, complex photoisomerization of the GFP chromophore and poor expression in many higher eukaryotes. To improve upon these qualities, we have combined a mutant of GFP with a significantly larger extinction coefficient for excitation at 488 nm with a re-engineered GFP gene sequence containing codons preferentially found in highly expressed human proteins. The combination of improved fluorescence intensity and higher expression levels yield an enhanced GFP which provides greater sensitivity in most systems.
miR-200b and Cancer/Testis Antigen CAGE Form a Feedback Loop to Regulate the Invasion and Tumorigenic and Angiogenic Responses of a Cancer Cell Line to Microtubule-targeting Drugs (2013)

Cancer/testis antigen cancer-associated gene (CAGE) is known to be involved in various cellular processes, such as proliferation, cell motility, and anti-cancer drug resistance. However, the mechanism of the expression regulation of CAGE remains unknown. Target scan analysis predicted the binding of microRNA-200b (miR-200b) to CAGE promoter sequences. The expression of CAGE showed an inverse relationship with miR-200b in various cancer cell lines. miR-200b was shown to bind to the 3'-UTR of CAGE and to regulate the expression of CAGE at the transcriptional level. miR-200b also enhanced the sensitivities to microtubule-targeting drugs in vitro. miR-200b and CAGE showed opposite regulations on invasion potential and responses to microtubule-targeting drugs. Xenograft experiments showed that miR-200b had negative effects on the tumorigenic and metastatic potential of cancer cells. The effect of miR-200b on metastatic potential involved the expression regulation of CAGE by miR-200b. miR-200b decreased the tumorigenic potential of a cancer cell line resistant to microtubule-targeting drugs in a manner associated with the down-regulation of CAGE. ChIP assays showed the direct regulation of miR-200b by CAGE. CAGE enhanced the invasion potential of a cancer cell line stably expressing miR-200b. miR-200b exerted a negative regulation on tumor-induced angiogenesis. The down-regulation of CAGE led to the decreased expression of plasminogen activator inhibitor-1, a TGFβ-responsive protein involved in angiogenesis, and VEGF. CAGE mediated tumor-induced angiogenesis and was necessary for VEGF-promoted angiogenesis. Human recombinant CAGE protein displayed angiogenic potential. Thus, miR-200b and CAGE form a feedback regulatory loop and regulate the response to microtubule-targeting drugs, as well as the invasion, tumorigenic potential, and angiogenic potential.
Marker‐Assisted Selection as a Strategy for Increasing the Probability of Selecting Superior Genotypes (1998)

Marker‐assisted selection (MAS) has been shown, in theory, to produce greater selection gains than phenotypic selection for normally distributed quantitative traits. Theory is presented in this paper for estimating the probability of selecting one or more superior genotypes by MAS ( Pr MAS ). This paramater was used to estimate the cost efficiency of MAS relative to phenotypic selection ( E c ). Pr MAS and E c are functions of heritability ( h 2 ), heritability of a MAS index ( h 2 I ), the phenotypic selection threshold ( i ), the genotypic superiority threshold ( g ), and p = σ 2 M /σ 2 G , where σ 2 M is additive genetic variance associated with markers and 2 G is additive genetic variance, h 2 I increases as p increases. Heritability can be increased to 1.0 by increasing p to 1.0; however, estimated marker effects (p̂) and true quantitative trait locus effects (p) must be perfectly correlated to achieve this in practice. PrMAS increases throughout the range of p when i ≥ g, decreases as g increases, and increases as i increases for most p. The frequency of superior genotypes among selected progeny increases as selection intensity increases. Ec ranged from 1.0 to 16.7 for i and g from 1.282 to 2.326, h2 from 0.1 to 1.0, and p from 0.0 to 1.0; thus, a breeder using phenotypic selection must test 1.0 to 16.7 times more progeny than a breeder using MAS to be assured of selecting one or more superior genotypes. Ec increases as g or iincrease and h2 decreases and increases asp increases when i = g. Ec predicts that MAS substantially decreases the resources needed to accomplish a selectiOn goal for a low to moderate heritability trait when the selection goal and the selection intensity are high.
Superior Immunogenicity of Inactivated Whole Virus H5N1 Influenza Vaccine is Primarily Controlled by Toll-like Receptor Signalling (2008)

In the case of an influenza pandemic, the current global influenza vaccine production capacity will be unable to meet the demand for billions of vaccine doses. The ongoing threat of an H5N1 pandemic therefore urges the development of highly immunogenic, dose-sparing vaccine formulations. In unprimed individuals, inactivated whole virus (WIV) vaccines are more immunogenic and induce protective antibody responses at a lower antigen dose than other formulations like split virus (SV) or subunit (SU) vaccines. The reason for this discrepancy in immunogenicity is a long-standing enigma. Here, we show that stimulation of Toll-like receptors (TLRs) of the innate immune system, in particular stimulation of TLR7, by H5N1 WIV vaccine is the prime determinant of the greater magnitude and Th1 polarization of the WIV-induced immune response, as compared to SV- or SU-induced responses. This TLR dependency largely explains the relative loss of immunogenicity in SV and SU vaccines. The natural pathogen-associated molecular pattern (PAMP) recognized by TLR7 is viral genomic ssRNA. Processing of whole virus particles into SV or SU vaccines destroys the integrity of the viral particle and leaves the viral RNA prone to degradation or involves its active removal. Our results show for a classic vaccine that the acquired immune response evoked by vaccination can be enhanced and steered by the innate immune system, which is triggered by interaction of an intrinsic vaccine component with a pattern recognition receptor (PRR). The insights presented here may be used to further improve the immune-stimulatory and dose-sparing properties of classic influenza vaccine formulations such as WIV, and will facilitate the development of new, even more powerful vaccines to face the next influenza pandemic.
Usability analysis of 3D rotation techniques (1997)

Article Usability analysis of 3D rotation techniques Share on Authors: Ken Hinckley Microsoft Research, One Microsoft Way, Redmond, WA Microsoft Research, One Microsoft Way, Redmond, WAView Profile , Joe Tullio Department of Neurosurgery, University of Virginia Department of Neurosurgery, University of VirginiaView Profile , Randy Pausch Department of Computer Science, University of Virginia Department of Computer Science, University of VirginiaView Profile , Dennis Proffitt Department of Psychology, University of Virginia Department of Psychology, University of VirginiaView Profile , Neal Kassell Department of Neurosurgery, University of Virginia Department of Neurosurgery, University of VirginiaView Profile Authors Info & Claims UIST '97: Proceedings of the 10th annual ACM symposium on User interface software and technologyOctober 1997 Pages 1–10https://doi.org/10.1145/263407.263408Online:01 October 1997Publication History 115citation2,385DownloadsMetricsTotal Citations115Total Downloads2,385Last 12 Months93Last 6 weeks8 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
Transcription, Translation, and Function of Lubricin, a Boundary Lubricant, at the Ocular Surface (2013)

Our results show that lubricin is transcribed, translated, and expressed by ocular surface epithelia. Moreover, our findings demonstrate that lubricin presence significantly reduces friction between the cornea and conjunctiva and that lubricin deficiency may play a role in promoting corneal damage.
Inhibitors of histone deacetylase are potentially effective anticancer agents. (2001)

During the past decade, a number of HDAC[2][1] inhibitors have been identified that induce tumor cells in culture and in tumor-bearing animals to undergo growth arrest, differentiation, and/or apoptotic cell death [(1)][2] . Acetylation and deacetylation of histones, part of the core proteins of
Optical waveguides in SIMOX structures (1991)

Propagation characteristics determined experimentally and theoretically for planar optical waveguides formed in separation by implantation of oxygen (SIMOX) structures are discussed. All samples were found to support both TE and TM modes at both 1.15 mu m and 1.523 mu m with a lowest propagation loss of 8 dB/cm. This loss was measured at a wavelength of 1.15 mu m for the TE/sub 0/ mode of a planar waveguide with a 2.0- mu m-thick Si guiding layer.
Grafted Metallocalixarenes as Single-Site Surface Organometallic Catalysts (2004)

Metallocalixarenes were grafted onto silica using a surface organometallic approach and shown to be active and selective catalysts for epoxidation of alkenes using organic hydroperoxides. Calixarene-Ti(IV) precursors were anchored at surface densities from 0.1 to near-monolayer coverages (0.025-0.25 calixarene nm(-2)). Several spectroscopic methods independently detected calixarene-Ti(IV) connectivity before and after epoxidation catalysis. Kinetic analyses of cyclohexene epoxidation confirmed that the active sites were anchored on the silica surface and were significantly more active than their homogeneous analogues. The steric bulk and multidentate binding of the calixarenes led to structural stability and to single-site behavior during epoxidation catalysis. Rate constants were independent of surface density for cyclohexene epoxidation with tert-butyl hydroperoxide (11.1 +/- 0.3 M(-2) s(-1)) or cumene hydroperoxide (25 +/- 2 M(-2) s(-1)). The materials and methods reported here allow the assembly of robust surface organometallic structures in which the active sites behave as isolated species, even near saturation monolayer coverages. In turn, this makes possible the rational design and synthesis of a class of heterogeneous oxide catalysts with atomic-scale precision at the active site.
Characterization of Structure and Function of SECA Domains (2022)

SecA is a central component of the general secretion system that is essential for growth and virulence of bacteria. A series of fluorescein analogs were tested against ATPase activities of Escherichia coli SecA. Rose Bengal (RB) and Erythrosin B are potent inhibitors abolishing the activities of three forms of SecA ATPase with IC50 in ?M range. Both inhibit SecA intrinsic ATPase with two mechanisms depending on ATP concentrations, indicating they influence the two non-identical nucleotide binding sites differently. RB shows different inhibitory effects against three forms of SecA ATPase activities, suggesting that the inhibition is related to the conformation of SecA. RB with IC50 at sub-?M level is the most potent inhibitor of SecA ATPases and SecA-dependent protein translocation to date. The fluorescein analogs inhibit intrinsic ATPase of Bacillus subtilis SecA similarly, and also exhibit antibacterial effects in E. coli and B. subtilis. Our findings indicate the value of fluorescein analogs as probes for mechanistic studies of SecA and the potential development of new SecA-targeted antimicrobial agents. A series of SecA derivatives with truncated C-terminus within the first long ?-helix of the helix-bundle extending the ATPase catalytic domain of N68 was analyzed. These SecA variants interact with lipids, and those containing the C-terminal portion of the long ?-helix starting at residues #639 form the ring-like structure in liposomes, indicating the critical domains for forming the protein-conducting channel. The presence and length of the C-domain influence the response to RB of NBDII mutants and C-terminal truncates of SecA. Thus this region may interact with the inhibitors and is involved in the structure and regulation of SecA ATPase activity. B. subtilis SecA was analyzed for interspecies comparison. Despite sharing high homology, this SecA homolog cannot complement E. coli mutants with SecA defect. Phospholipids do not stimulate ATPase activities of B. subtilis SecA, but induce its conformational changes, leading to the lipid-specific domains and ring-like structures similar to E. coli SecA. These pore-ring structures may represent part of the protein-conducting channels. Therefore, the potential structural roles of SecA in the protein translocation machinery may be universal in both Gram-negative and Gram-positive bacteria.
Development and validation of promoter-probe vectors for the study of methane monooxygenase gene expression in Methylococcus capsulatus Bath (2009)

A series of integrative and versatile broad-host-range promoter-probe vectors carrying reporter genes encoding green fluorescent protein (GFP), catechol 2,3-dioxygenase (XylE) or beta-galactosidase (LacZ) were constructed for use in methanotrophs. These vectors facilitated the measurement of in vivo promoter activity in methanotrophs under defined growth conditions. They were tested by constructing transcriptional fusions between the soluble methane monooxygenase (sMMO) sigma(54) promoter or particulate methane monooxygenase (pMMO) sigma(70) promoter from Methylococcus capsulatus and the reporter genes. Reporter gene activity was measured under high- and low-copper growth conditions and the data obtained closely reflected transcriptional regulation of the sMMO or pMMO operon, thus demonstrating the suitability of these vectors for assessing promoter activity in methanotrophs. When beta-galactosidase expression was coupled with the fluorogenic substrate 4-methylumbelliferyl beta-D-glucuronide it yielded a sensitive and powerful screening system for detecting cells expressing this reporter gene. These data were substantiated with independent experiments using RT-PCR and RNA dot-blot analysis.
Update on Aplaviroc: An HIV Entry Inhibitor Targeting CCR5 (2005)

Aplaviroc (873140) is a novel spirodiketopiperazine CCR5 antagonist that binds specifically to human CCR5 and allosterically inhibits HIV entry. Aplaviroc has exhibited potent in vivo antiviral activity (1.66 log decrease in viral load at nadir) following 10 days of monotherapy. In vitro studies of antiviral activity demonstrate that aplaviroc is active against HIV isolates from a variety of clades as well as those resistant to current HIV therapies targeting RT, PR, and gp41. In vitro studies suggest prolonged CCR5 receptor occupancy (RO) by aplaviroc with an offset halflife of >100 hours. In vivo studies following short term aplaviroc administration using CCR5-specific mAb demonstrate substantial and prolonged CCR5 RO (>50%) by aplaviroc, when plasma drug levels were undetectable, observed for approximately 5 days.