gebhart/patrepeval huggingface dataset:
Specialization of Function Among Aldehyde Dehydrogenases: The ALD2 and ALD3 Genes Are Required for β-Alanine Biosynthesis in Saccharomyces cerevisiae (2003)

Abstract The amino acid β-alanine is an intermediate in pantothenic acid (vitamin B5) and coenzyme A (CoA) biosynthesis. In contrast to bacteria, yeast derive the β-alanine required for pantothenic acid production via polyamine metabolism, mediated by the four SPE genes and by the FAD-dependent amine oxidase encoded by FMS1. Because amine oxidases generally produce aldehyde derivatives of amine compounds, we propose that an additional aldehyde-dehydrogenase-mediated step is required to make β-alanine from the precursor aldehyde, 3-aminopropanal. This study presents evidence that the closely related aldehyde dehydrogenase genes ALD2 and ALD3 are required for pantothenic acid biosynthesis via conversion of 3-aminopropanal to β-alanine in vivo. While deletion of the nuclear gene encoding the unrelated mitochondrial Ald5p resulted in an enhanced requirement for pantothenic acid pathway metabolites, we found no evidence to indicate that the Ald5p functions directly in the conversion of 3-aminopropanal to β-alanine. Thus, in Saccharomyces cerevisiae, ALD2 and ALD3 are specialized for β-alanine biosynthesis and are consequently involved in the cellular biosynthesis of coenzyme A.
Helical twisting power of chiral mono- and bis-aminoanthraquinones. Intramolecular and intermolecular chirality transfer in liquid-crystal phases (1995)

The helical twisting power (HTP) of mono- and bis-aminoanthraquinones with chiral substituents depends strongly on the position of substitution. It is shown that the Intramolecular chirality transfer yields, for each compound, several conformers which are different for the 1-cyclohexylethyl, 1-phenylethyl and 1-naphthalen-1-ylethyl substituents. Each conformer contributes differently to the HIP of a compound. Furthermore, the HIP of a bis-substituted compound is approximately the sum of the HIP values of the corresponding mono-substituted compounds if the orientation of the substituents with respect to the orientation axis (principal axis of the order tensor belonging to the largest eigenvalue) is the same in each case. This means that the contribution of a ‘chiral area’, induced around an asymmetric carbon atom by Intramolecular chirality transfer, to the HTP depends on its orientation with respect to the orientation axis. A variation of this orientation can cause even a change of sign of the HIP in spite of the fact that the dependence of the HIP on the order parameters, S* and D*, is small.
A Uniform Resource Name (URN) Namespace for Extensions to the Extensible Messaging and Presence Protocol (XMPP) (2007)

XSF).
Slo3, a Novel pH-sensitive K+ Channel from Mammalian Spermatocytes (1998)

Potassium channels have evolved to play specialized roles in both excitable and inexcitable tissues. Here we describe the cloning and expression of Slo3, a novel potassium channel abundantly expressed in mammalian spermatocytes. Slo3 represents a new and unique type of potassium channel regulated by both intracellular pH and membrane voltage. Reverse transcription-polymerase chain reaction, Northern analysis, and in situ hybridization show that Slo3 is primarily expressed in testis in both mouse and human. Because of its sensitivity to both pH and voltage, Slo3 could be involved in sperm capacitation and/or the acrosome reaction, essential steps in fertilization where changes in both intracellular pH and membrane potential are known to occur. The protein sequence of mSlo3 (the mouse Slo3 homologue) is similar to Slo1, the large conductance, calcium- and voltage-gated potassium channel. These results suggest that Slo channels comprise a multigene family, defined by a combination of sensitivity to voltage and a variety of intracellular factors. Northern analysis from human testis indicates that a Slo3 homologue is present in humans and conserved with regard to sequence, transcript size, and tissue distribution. Because of its high testis-specific expression, pharmacological agents that target human Slo3 channels may be useful in both the study of fertilization as well as in the control or enhancement of fertility.
Solid-Phase Synthesis of Thermolytic DNA Oligonucleotides Functionalized with a Single 4-Hydroxy-1-butyl or 4-Phosphato-/Thiophosphato-1-butyl Thiophosphate Protecting Group (2007)

Several thermolytic CpG-containing DNA oligonucleotides analogous to 1 have been synthesized to serve as potential immunotherapeutic oligonucleotide prodrug formulations for the treatment of infectious diseases in animal models. Specifically, the CpG motif (GACGTT) of each DNA oligonucleotide has been functionalized with either the thermolabile 4-hydroxy-1-butyl or the 4-phosphato-/thiophosphato-1-butyl thiophosphate protecting group. This functionalization was achieved through incorporation of activated deoxyribonucleoside phosphoramidite 8b into the oligonucleotide chain during solid-phase synthesis and, optionally, through subsequent phosphorylation effected by phosphoramidite 9. Complete conversion of CpG ODNs hbu1555, psb1555, and pob1555 to CpG ODN 1555 (homologous to 2) occurred under elevated temperature conditions, thereby validating the function of these diastereomeric oligonucleotides as prodrugs in vitro. Noteworthy is the significant increase in solubility of CpG ODN psb1555 and CpG pob1555 in water when compared to that of neutral CpG ODN fma1555 (homologous to 1).
Stable Amplification of the S-Adenosylmethionine Decarboxylase Gene in Chinese Hamster Ovary Cells (1995)

A Chinese hamster ovary cell subline (CHO/664) > 1000-fold resistant to the S-adenosylmethionine decarboxylase (AdoMetDC) inhibitor, CGP-48664 (4-(aminoiminomethyl)-2,3-dihydro-1H-inden-1-one diaminomethylenehydrazone), has been developed and characterized. The cells were also cross-resistant to the highly specific nucleoside analog inhibitor of AdoMetDC, MDL-73811. These unique cells stably overexpress AdoMetDC due to a 10-16-fold amplification of the AdoMetDC gene, which resulted in a similar increase in AdoMetDC transcript levels. In the presence of 100 microM CGP-48664, the CHO/664 cells displayed AdoMetDC activities similar to the parental line. Following removal of the inhibitor, AdoMetDC activity increased steadily over 20 days to 10-12 times that found in parental CHO cells. Decarboxylated (dc) AdoMet pools accumulated rapidly from < 5 pmol/10(6) cells to approximately 1000-1500 pmol/10(6) cells at 3 days due to diffusion away of intracellular inhibitor and to the depletion of putrescine and spermidine as aminopropyl acceptors in dcAdoMet-mediated synthase reactions. Polyamine pools shifted as putrescine, and spermidine pools were processed forward to spermine. During the period from 3 days to 20 days, dcAdoMet pools fell steadily and eventually stabilized at 100-200 pmol/10(6) cells. Providing excess putrescine at this time as an aminopropyl acceptor rapidly lowered dcAdoMet pools and led to a near normalization of polyamine pools, indicating that both dcAdoMet and putrescine are essential in maintaining steady-state polyamine pool profiles. As with cell line variants that overproduce ornithine decarboxylase, polyamine transport was found to be increased in CHO/664 cells due to an apparent inability of the system to down-regulate polyamine transport in response to polyamine excess. Given the unique metabolic disturbances seen in these cells, we anticipate that in addition to providing a useful system for evaluating the specificity of newly developed AdoMetDC inhibitors, they will undoubtedly prove valuable for investigating the various regulatory interrelationships involved in polyamine homeostasis and possibly other aspects of purine metabolism.
Integrated Portable Genetic Analysis Microsystem for Pathogen/Infectious Disease Detection (2004)

An integrated portable genetic analysis microsystem including PCR amplification and capillary electrophoretic (CE) analysis coupled with a compact instrument for electrical control and laser-excited fluorescence detection has been developed. The microdevice contains microfabricated heaters, temperature sensors, and membrane valves to provide controlled sample positioning and immobilization in 200-nL PCR chambers. The instrument incorporates a solid-state laser and confocal fluorescence detection optics, electronics for sensing and powering the PCR reactor, and high-voltage power supplies for conducting CE separations. The fluorescein-labeled PCR products are amplified and electrophoretically analyzed in a gel-filled microchannel in <10 min. We demonstrate the utility of this instrument by performing pathogen detection and genotyping directly from whole Escherichia coli and Staphylococcus aureus cells. The E. coli detection assay consists of a triplex PCR amplification targeting genes that encode 16S ribosomal RNA, the fliC flagellar antigen, and the sltI shigatoxin. Serial dilution demonstrates a limit of detection of 2-3 bacterial cells. The S. aureus assay uses a femA marker to identify cells as S. aureus and a mecA marker to probe for methicillin resistance. This integrated portable genomic analysis microsystem demonstrates the feasibility of performing rapid high-quality detection of pathogens and their antimicrobial drug resistance.
von Willebrand factor–mediated platelet adhesion is critical for deep vein thrombosis in mouse models (2010)

Deep vein thrombosis (DVT) and its complication, pulmonary embolism, are frequent causes of disability and mortality. Although blood flow disturbance is considered an important triggering factor, the mechanism of DVT initiation remains elusive. Here we show that 48-hour flow restriction in the inferior vena cava (IVC) results in the development of thrombi structurally similar to human deep vein thrombi. von Willebrand factor (VWF)-deficient mice were protected from thrombosis induced by complete (stasis) or partial (stenosis) flow restriction in the IVC. Mice with half normal VWF levels were also protected in the stenosis model. Besides promoting platelet adhesion, VWF carries Factor VIII. Repeated infusions of recombinant Factor VIII did not rescue thrombosis in VWF(-/-) mice, indicating that impaired coagulation was not the primary reason for the absence of DVT in VWF(-/-) mice. Infusion of GPG-290, a mutant glycoprotein Ibα-immunoglobulin chimera that specifically inhibits interaction of the VWF A1 domain with platelets, prevented thrombosis in wild-type mice. Intravital microscopy showed that platelet and leukocyte recruitment in the early stages of DVT was dramatically higher in wild-type than in VWF(-/-) IVC. Our results demonstrate a pathogenetic role for VWF-platelet interaction in flow disturbance-induced venous thrombosis.
Optical Wave Propagation In Discrete Waveguide Arrays (2005)

The propagation dynamics of light in optical waveguide arrays is characteristic of that encountered in discrete systems. As a result, it is possible to engineer the diffraction properties of such structures, which leads to the ability to control the flow of light in ways that are impossible in continuous media. In this work, a detailed theoretical investigation of both linear and nonlinear optical wave propagation in one- and two-dimensional waveguide lattices is presented. The ability to completely overcome the effects of discrete diffraction through the mutual trapping of two orthogonally polarized coherent beams interacting in Kerr nonlinear arrays of birefringent waveguides is discussed. The existence and stability of such highly localized vector discrete solitons is analyzed and compared to similar scenarios in a single birefringent waveguide. This mutual trapping is also shown to occur within the first few waveguides of a semi-infinite array leading to the existence of vector discrete surface waves. Interfaces between two detuned semi-infinite waveguide arrays or waveguide array heterojunctions and their possible applications are also considered. It is shown that the detuning between the two arrays shifts the dispersion relation of one array with respect to the other. Consequently, these systems provide spatial filtering functions that may prove useful in future all-optical networks. In addition by exploiting the unique diffraction properties of discrete arrays, diffraction compensation can be achieved in a way analogous to dispersion compensation in dispersion managed optical fiber systems. Finally, it is demonstrated that both the linear (diffraction) and nonlinear dynamics of two-dimensional waveguide arrays are significantly more complex and considerably more versatile than their one-dimensional counterparts. As is the case in one-dimensional arrays, the discrete diffraction properties of these two-dimensional lattices can be effectively altered depending on the propagation Bloch k-vector within the first Brillouin zone. In general, this diffraction behavior is anisotropic and as a result, allows the existence of a new class of discrete elliptic solitons in the nonlinear regime. Moreover, such arrays support two-dimensional vector soliton states, and their existence and stability are also thoroughly explored in this work.
Chemistry in hydrogen fluoride. 7. A novel synthesis of aryl trifluoromethyl ethers (1979)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTChemistry in hydrogen fluoride. 7. A novel synthesis of aryl trifluoromethyl ethersAndrew E. FeiringCite this: J. Org. Chem. 1979, 44, 16, 2907–2910Publication Date (Print):August 1, 1979Publication History Published online1 May 2002Published inissue 1 August 1979https://pubs.acs.org/doi/10.1021/jo01330a017https://doi.org/10.1021/jo01330a017research-articleACS PublicationsRequest reuse permissionsArticle Views1876Altmetric-Citations116LEARN 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
Mutagenic nucleotide incorporation and hindered translocation by a food carcinogen C8-dG adduct in Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4): modeling and dynamics studies (2006)

Bulky carcinogen-DNA adducts commonly cause replicative polymerases to stall, leading to a switch to bypass polymerases. We have investigated nucleotide incorporation opposite the major adduct of 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP) in the DinB family polymerase, Dpo4, using molecular modeling and molecular dynamics (MD) simulations. PhIP, the most prevalent heterocyclic aromatic amine formed by cooking of proteinaceous food, is mutagenic in mammalian cells and is implicated in mammary and colon tumors. Our results show that the dG-C8-PhIP adduct can be accommodated in the spacious major groove Dpo4 open pocket, with Dpo4 capable of incorporating dCTP, dTTP or dATP opposite the adduct reasonably well. However, the PhIP ring system on the minor groove side would seriously disturb the active site, regardless of the presence and identity of dNTP. Furthermore, the simulations indicate that dATP and dTTP are better incorporated in the damaged system than in their respective mismatched but unmodified controls, suggesting that the PhIP adduct enhances incorporation of these mismatches. Finally, bulky C8-dG adducts, situated in the major groove, are likely to impede translocation in this polymerase (Rechkoblit et al. (2006), PLoS Biol., 4, e11). However, N2-dG adducts, which can reside on the minor groove side, appear to cause less hindrance when in this position.
The preparation and characterization of [3H] histamine.2HCl at high specific activity1 (1987)

Abstract [ 3 H] Histamine.2HCl will continue to play a key role in establishing the neurotransmitter status of histamine.2HCl. To more consistently achieve high specific activity in the preparation of the radioligand and incorporate as much tritium into the stable side chain positions as possible, we explored the use of alternative tritiation precursors. Imidazole 4‐acetonitrile ( 5 ) and 2,5‐diiodoimidazole‐4‐acetonitrile ( 6 ) were catalytically reduced with tritium gas and the radiolabeling specificity of the resulting [ 3 H] histamine.2HCl produced was confirmed by 3 H NMR.
Temperature Dependence of Transistor Characteristics and Electronic Structure for Amorphous In–Ga–Zn-Oxide Thin Film Transistor (2010)

We fabricated an inverted-staggered amorphous In–Ga–Zn-oxide (a-IGZO) thin film transistor (TFT) and measured the temperature dependence of its characteristics. A threshold voltage ( V th ) shift between 120 and 180 °C was as large as 4 V. In an analysis with two-dimensional (2D) numerical simulation, we reproduced the measured result by assuming two types of donor-like states as carrier generation sources. Furthermore, by ab initio molecular dynamics (MD) simulation, we determined the electronic structures of three types of a-IGZO structures, namely, “stoichiometric a-IGZO”, “oxygen deficiency”, and “hydrogen doping”.
Idiopathic Pulmonary Fibrosis: Update on Genetic Discoveries (2011)

Idiopathic pulmonary fibrosis (IPF) is a progressive fibrotic disease of the lungs that increases in prevalence with advanced age. Recent evidence indicates that mutations in genes of two different biologic pathways lead to the common phenotype of familial pulmonary fibrosis (FPF) and sporadic IPF. Mutations in the genes encoding the lung surfactant proteins C and A2 (SFTPC and SFTPA2, respectively) cause increased endoplasmic reticulum stress in type II alveolar epithelial cells. Mutations in the genes encoding telomerase (TERT and TERC) cause IPF through shortening of telomere lengths and probable exhaustion of lung stem cells. All of the mutations are individually rare, but, collectively, TERT mutations are the most common genetic defect found in FPF. The overall penetrance of pulmonary fibrosis in TERT mutation carriers is 40% in subjects with a mean age of 51 years. Penetrance increases with advanced age, is greater in males than in females, and is positively associated with fibrogenic environmental exposures. Short telomere lengths are found in patients with FPF and sporadic IPF without mutations in telomerase, suggesting that the biologic pathway of telomerase dysfunction provides a biologic explanation for the age-related prevalence of IPF. The molecular data of two seemingly unrelated biologic pathways-alveolar epithelial endoplasmic reticulum stress and telomerase dysfunction-are beginning to elucidate the pathogenesis of IPF. These results have potentially predictive and therapeutic value.
Fabrication and Characterization of Glassy Carbon MEMS (1997)

This paper describes the fabrication of free-standing high-carbon microstructures by soft-lithographic techniques; these structures ranged in complexity from simple beams to complex, suspended deflectors. Microstructures of polymeric precursors (copolymers of furfuryl alcohol−phenol) to high-carbon solids were fabricated using poly(dimethylsiloxane) (PDMS) molds. Carbonization of these microstructures under argon resulted in mass loss (up to 45%) and shrinkage (up to 20% linearly); the density increased to reach a plateau value of ∼1.5 g/cm3 at ∼900 °C. Microstructures pyrolyzed at 900 °C were electrically conductive, with a conductivity of ∼10-2 Ω cm. Elementary microelectromechanical functions were demonstrated in these microstructures: electrostatic actuation induced deflection or vibrations of suspended structures. The measurement of the frequency of resonance of high-carbon cantilevered beams allowed the determination of Young's modulus for the solid: typical values were ∼15−20 GPa. The microelectromechanical properties of more complex structures (microresonators, light deflectors) were also determined. This paper demonstrates that high-carbon microstructures can be easily fabricated that have potential use as the active components of MEMS.
The induction of T cell unresponsiveness by rapidly modulating CD3. (1989)

The immunomodulatory effects of an IgM anti-CD3 mAb (38.1) were investigated. 38.1 was distinct from other anti-CD3 mAb, in that it was rapidly modulated from the cell surface in the absence of a secondary antibody. Although 38.1 induced an immediate increase in intracellular free calcium [Ca2+]i by highly purified T cells, it did not induce entry of the cells into the cell cycle in the absence of accessory cells (AC) or a protein kinase C-activating phorbol ester. Clearing of 38.1 from the surface of AC-depleted T cells, documented both by immunofluorescence and by functional activity, was rapid, with markedly reduced levels of initially bound mAb observed after a 1 to 2 h incubation at 37 degrees C and complete modulation noted after a 5-h incubation. Despite rapid modulation of 38.1, the T cells continued to express substantial amounts of surface CD3, suggesting there is a rapid rate of turnover of CD3 molecules on resting T cells. After modulation of 38.1 bound CD3, T cells were markedly inhibited in their capacity to respond to PHA. Inhibition could be overcome by culturing the cells with supplemental AC or IL-2. The inhibitory effects of 38.1 could be mimicked by briefly pulsing cells with the calcium ionophore, ionomycin, that had no effect on surface expression of CD3. 38.1- or ionomycin-pulsed cells were inhibited in their subsequent response to PHA even when exposures were carried out in the presence of EGTA to prevent increases in [Ca2+]i from extracellular sources. Inhibition could not be accounted for by an inability of the ionomycin-treated or 38.1-modulated T cells to increase [Ca2+]i in response to PHA. These studies demonstrate that a state of T cell nonresponsiveness can be induced by modulating CD3 with an anti-CD3 mAb in the absence of co-stimulatory signals. A brief increase in [Ca2+]i resulting from mobilization of internal calcium stores appears to be sufficient to induce this state of T cell nonresponsiveness.
Immunoglobulin VH genes are transcribed by T cells in association with a new 5' exon. (1988)

We previously detected mRNAs in a number of human T cell lines with a probe from within the Ig VH gene locus. We now show these mRNAs consist of Ig VH genes expressed in T cells. In one human T cell line, two RNA species have been studied and found to come from transcripts of unrearranged VH segments in which the leader exon, normally associated with VH transcripts in B cells, is replaced by a novel 5' exon (ET) not encoding a hydrophobic leader peptide. In genomic DNA, this new ET exon is adjacent to a pseudo-VH gene that has not been observed in mature mRNA. This implies that RNA splicing controls association of the new exon with the expressed VH segments. Hence, VH transcription does indeed occur in T cells, but is qualitatively different from that in B cells.