gebhart/patrepeval huggingface dataset:
Exploitation of chemical predisposition in synthesis: an approach to the manzamenones (2002)

Full details of the syntheses of manzamenones A, C and F are reported, using an approach modelled on a plausible biogenetic theory. The key step of the approach is a “one-pot” conversion of the antileukemic cyclopentenone, untenone A, to manzamenone A which occurs in reasonable yield and which proceeds via a reaction sequence of dehydration, Diels–Alder dimerisation and retro-Dieckmann reaction. The synthetic approach has also been applied to the preparation of a number of shorter alkyl chain analogues of the natural products. Using a combination of NMR and X-ray crystallographic data for the shorter alkyl chain analogues of manzamenone A, it is suggested that the relative stereostructures of the majority of the manzamenones should be revised such that the acyl group at the C2 position lies on the α-face and that at the C5 position resides on the β-face.
Passively mode-locked, self-frequency doubled, diode-pumped Yb: YAl3(BO3)4 laser (2002)

The broad fluorescence of Ytterbium doped lasers allows tunability and/or subpicosecond pulse generation at wavelengths around 1040nm. Also, the small quantum defect (<0.1) and high quantum efficiency reduce the thermal load. The simple energy level scheme of the Yb ion minimizes undesirable effects such as upconversion, excitedstate absorption and concentration quenching and is particularly suited to intracavity frequency-doubled lasers. As a result there is a growing range of mode-locked Yb 3+ -doped lasers, including the 40mW, 90fs pulses from a Yb 3+ :Ca 4 GdO(BO 3 ) 3 laser 1 as well as the 200mW, 112fs pulses from a Yb 3+ :KGd(WO 4 ) 2 laser 2 . In particular, Yb:YAl 3 (BO 3 ) 4 (Yb: YAB) has a large second-order nonlinearity (d eff >1.4pm/V) and favorable laser properties making it well suited to visible subpicosecond pulse generation. CW and Q-switched Yb:YAB lasers3,4 have previously been demonstrated with 1.1W of green output.
Comparative Holographic Moire Interferometry: Separation Of Moire Fringes From The Carrier Interference Pattern (1989)

Comparative holographic moire interferometry (CHMI) permits defect detection by comparison of the mechanical responses of two macroscopically identical specimens at equal loading. In the present work a technique of moire fringe separation is suggested that is amenable to automatic readout. Two approaches are proposed and experimentally verified: phase shifting of the carrier interference pattern and auxiliary carrier fringe generation with subse-quent optical filtering. The phase shifting method is applicable to an additive moire scheme with two reference beams. Auxiliary carrier fringe generation can be used in both additive and multiplicative CHMI. The frequency constraints of the latter method due to the optical recording arrangement and mechanical responses of the tested specimen are analyzed.
A GASOMETRIC TECHNIQUE FOR EVALUATING KINETIC STABILITY AND APPARENT ACTIVATION ENERGIES OF MANGANESE OXIDE MINERALS (1994)

Reduction-dissolution kinetics and apparent activation energies (Ea) of reagent grade β-MnO2 (Fisher Scientific, Fair Lawn, NJ), β-MnO2 (Ward's Earth Science, Rochester, NY pyrolusite), and MnOOH (Ward's Earth Science, Rochester, NY manganite) were determined by continuous gasometric analysis employing an isothermal automanometric apparatus. This method was based on pseudo-first-order kinetics of oxygen gas (O2) evolution by reducing the Mn(IV) and/or Mn(III) to Mn(II). The manganese oxide reduction was carried out employing a solution mixture of 2.4% H2O2 and 9.7% concentrated H2SO4 on a volume basis. The pseudo-first-order constant (k) at 21°C was 0.66 min-1 for reagent grade β-MnO2, 1.68 min-1 for pyrolusite (β-MnO2), and 0.009 min-1 for manganite (MnOOH). The apparent activation Ea were determined to be 35.56 kJ/mol-1 for reagent grade β-MnO2, 29.95 kJ/mol-1 for pyrolusite (β-MnO2), and 44.75 kJ mol-1 for manganite (MnOOH). The most kinetically stable manganese oxide species of the three minerals tested was MnOOH (manganite).
Regulation of intron function: efficient splicing <i>in vivo</i> of a bacterial group II intron requires a functional promoter within the intron (2000)

Conjugative transfer of the Lactococcus lactis plasmid pRS01 requires splicing of a group II intron, Ll.ltrB, for accurate translation of the mRNA for the exon gene ltrB. The protein product of ltrB is a conjugative relaxase, essential for pRS01 transfer. Using a molecular technique for the identification of transcription initiation sites in bacteria, a functional promoter within Ll.ltrB was identified upstream from the gene for the intron-encoded protein (IEP) LtrA. LtrA is required for efficient splicing of Ll.ltrB in vivo. Mutation of the ltrA promoter dramatically reduced the steady-state level of ltrA mRNA, LtrA, intron splicing and conjugation in L. lactis. These effects could be relieved by expression in trans of the ltrA gene cloned under the control of an inducible promoter. These results suggest that the ltrA mRNAs are translated inefficiently. We hypothesize that this bacterial intron, in contrast to previously studied group II introns in eukaryotes, requires a promoter within the intron to regulate ltrA expression and to produce an adequate level of the protein in the cell for efficient splicing.
ChemInform Abstract: A Simple Method for the Preparation of Thioglycosides of N‐ Acetylneuraminic Acid. (1994)

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.
Structure of Human MTH1, a Nudix Family Hydrolase That Selectively Degrades Oxidized Purine Nucleoside Triphosphates (2004)

Oxygen radicals generated through normal cellular respiration processes can cause mutations in genomic and mitochondrial DNA. Human MTH1 hydrolyzes oxidized purine nucleoside triphosphates, such as 8-oxo-dGTP and 2-hydroxy-dATP, to monophosphates, thereby preventing the misincorporation of these oxidized nucleotides during replication. Here we present the solution structure of MTH1 solved by multidimensional heteronuclear NMR spectroscopy. The protein adopts a fold similar to that of Escherichia coli MutT, despite the low sequence similarity between these proteins outside the conserved Nudix motif. The substrate-binding pocket of MTH1, deduced from chemical shift perturbation experiments, is located at essentially the same position as in MutT; however, a pocket-forming helix is largely displaced in MTH1 (approximately 9 A) such that the shape of the pocket differs between the two proteins. Detailed analysis of the pocket-forming residues enabled us to identify Asn33 as one of the key residues in MTH1 for discriminating the oxidized form of purine, and mutation of this residue modifies the substrate specificity. We also show that MTH1 catalyzes hydrolysis of 8-oxo-dGTP through nucleophilic substitution of water at the beta-phosphate.
A case of traumatic diaphragmatic hernia manifesting itself half a year after injury (2008)

外傷性横隔膜ヘルニアは早期に診断・治療されることが多いが，我々は受傷後半年を経て診断された症例を経験した．症例は38歳男性．外傷による脳挫傷・下顎骨折・肋骨骨折の後，半年を経過して横隔膜ヘルニアを診断された．胸腔内の癒着が予想され胸腔鏡にて経胸的アプローチを採用したが，脱出臓器の腹腔内への整復が困難であったため，後側方開胸に変更した．癒着の有無や臓器の胸腔内脱出の程度の確認に，胸腔鏡が有用であり，癒着例や腹腔内還納の困難な症例に対し開胸に移行するのが理に適うと考えた．
Diversity, distribution and physiology of the aerobic phototrophic bacteria in the mixolimnion of a meromictic lake (2002)

The population of anoxygenic phototrophic bacteria in the aerobic zone of the meromictic Mahoney Lake was investigated using classical microbiological methods. This bacterial community was found to be very rich and diverse. Thirty-one new strains of the obligately aerobic phototrophic bacteria, and two new purple nonsulfur strains, were isolated in pure cultures and preliminarily characterized. The isolates contain a variety of carotenoids, bacteriochlorophyll a incorporated into pigment protein complexes, and are morphologically and physiologically diverse. These properties indicate a diversity of adaptations to the stratified environments of this meromictic lake. Phylogenetically all isolated strains belong to the alpha subclass of Proteobacteria.
Electrochemical Control of Calcium Carbonate Crystallization and Dissolution in Nanopipettes (2016)

Abstract Electrochemically controlled nanopipettes are becoming increasingly versatile tools for a diverse range of sequencing, sizing, and imaging applications. Herein, the use of nanopipettes to induce and quantitatively monitor crystallization and dissolution in real time is considered, using CaCO 3 in aqueous solution as an exemplar system. The bias between a quasi‐reference counter electrode in a nanopipette and one in a bulk solution is used to mix (or de‐mix) two different solutions by ion migration and drive either growth or dissolution, depending on the polarity. Furthermore, Raman spectroscopy can be applied simultaneously to identify polymorphs formed in the nanopipette. The technique is supported with a robust finite element method model that allows the extraction of time‐dependent saturation levels and mixing characteristics at the nanoscale. The technique shows great promise as a tool for rapidly screening growth additives and inhibitors, allowing eight different additives to be ranked in order of efficacy for crystal growth rate inhibition.
Development of Biaxially Textured YBa{sub 2}Cu{sub 3}O{sub 7} Coated Conductors in the U.S. (1999)

Two new processes have been under development since 1991 that promise a new, cost-effective way to manufacture flexible, high current density wires made from YBa{sub 2}Cu{sub 3}O{sub 7} (YBCO). The key is to prepare a textured substrate, or ''template,'' on which the YBCO may be deposited as a biaxially aligned thick film. Ion beam assisted deposition (IBAD) of yttria stabilized zirconia or magnesium oxide on alloy tapes enables a final superconducting layer with grain-to-grain, in-plane alignment to within 3-5 degrees. Similar results are achieved on rolling-assisted, biaxially textured substrates (RABiTS) using a variety of oxide layers on textured nickel tapes. The performance of research lengths of prototype wires in strong magnetic fields at 65 K already exceeds that of NbTi and Nb{sub 3}Sn in liquid helium. A scalable, ex-situ process for the YBCO coating has been demonstrated on both types of substrates. Consistent values of critical current density (J{sub c }) greater than 1 x 10{sup 6} A/cm{sup 2} are now obtained on RABiTS, and J{sub c}'s in excess of 2 x 10{sup 6} A/cm{sup 2} have been obtained on both substrates. A nonmagnetic variation of RABiTS (Ni-13% Cr) has also been shown to yield Jc greater than 1.5 x 10{sup 6} A/cm{sup 2} . Six private companies in the U.S. are scaling up YBCO coated conductors for power and physics applications.
Inorganic bottom ARC SiOxNy for interconnection levels on 0.18-μm technology (1998)

BARC technology, originally developed for gate level has now to be applied to interconnection one's. Requirements for dielectric interconnection levels are different from gate level. In the case of gate level ARC has to minimize reflectivity at resist/substrate interface due to notching and resist swing curve effects. Whereas ARC for interconnections has to minimize reflectivity variation at resist/substrate interface due to swing curve effect in the dielectric layer. For interconnections, ARC must be as absorbent as possible at stepper exposure wavelength, and two ways are foreseen: ARC layer with high k value at 248 nm, and ARC layer with high thickness. For a reflectivity variation minimum criteria, we can find a couple values (k, minimum thickness). Experiments give us for a reflectivity variation below 5% the following couples: (k equals 0.7, 1200 Angstrom thickness) and (k equals 1.1, 850 Angstrom). In this paper we describe different applications of SiOxNy for interconnection levels: via, contact and damascene line level. Improvements depending of the SiOxNy thickness are seen in CD dispersion. To conclude SiOxNy ARC can be used for interconnection levels, and its performances depends on ARC couple values (k, thickness).
Microbiota-Based Therapies for <i>Clostridium difficile</i> and Antibiotic-Resistant Enteric Infections (2017)

Bacterial pathogens are increasingly antibiotic resistant, and development of clinically effective antibiotics is lagging. Curing infections increasingly requires antimicrobials that are broader spectrum, more toxic, and more expensive, and mortality attributable to antibiotic-resistant pathogens is rising. The commensal microbiota, comprising microbes that colonize the mammalian gastrointestinal tract, can provide high levels of resistance to infection, and the contributions of specific bacterial species to resistance are being discovered and characterized. Microbiota-mediated mechanisms of colonization resistance and pathogen clearance include bactericidal activity, nutrient depletion, immune activation, and manipulation of the gut's chemical environment. Current research is focusing on development of microbiota-based therapies to reduce intestinal colonization with antibiotic-resistant pathogens, with the goal of reducing pathogen transmission and systemic dissemination.
Stark quantization in superlattices (1991)

The similarity and differences between real solids and superlattices for the localization induced by an electric field is discussed. In response to recent experimental results regarding the onset of negative differenial conductivity, the regimes of applicability of the Esaki-Tsu and Tsu-D\"ohler conditions are given.
Characterization and regulation of reductase kinase, a protein kinase that modulates the enzymic activity of 3-hydroxy-3-methylglutaryl-coenzyme A reductase (1979)

The activity of rat liver 3-hydroxy-3-methylglutaryl-coenzyme A reductase [HMG-CoA reductase; mevalonate:NADP(+) oxidoreductase (CoA-acylating), EC 1.1.1.34] can be modulated in vitro by a phosphorylation-dephosphorylation reaction sequence. A microsomal reductase kinase catalyzes the phosphorylation of HMG-CoA reductase and histones. Histone phosphorylation was enhanced 2- to 3-fold by cyclic AMP. Reductase kinase exists in interconvertible active and inactive forms. Incubation of reductase kinase with phosphoprotein phosphatase resulted in a time-dependent decrease in the ability of reductase kinase to catalyze the phosphorylation of histones and to inactivate HMG-CoA reductase. Incubation of phosphoprotein phosphatase-inactivated reductase kinase with [gamma-(32)P]ATP plus Mg(2+) and a partially purified protein kinase designated reductase kinase kinase resulted in parallel increases in protein-bound (32)P radioactivity and ability to inactivate HMG-CoA reductase. Incubation of (32)P-labeled reductase kinase with phosphoprotein phosphatase resulted in a time-dependent loss of protein-bound (32)P radioactivity and a decrease in the ability to inactivate HMG-CoA reductase. Polyacrylamide gel electrophoresis of purified reductase kinase incubated with reductase kinase kinase and [gamma-(32)P]ATP plus Mg(2+) revealed that the (32)P radioactivity and reductase kinase enzymic activity were located in a single electrophoretic position. Dephosphorylation of (32)P-labeled purified reductase kinase with phosphoprotein phosphatase was associated with significant loss of radioactivity and enzymic activity in the protein band ascribed to reductase kinase. These results provide evidence that the activity of reductase kinase, like HMG-CoA reductase, is modulated by a reversible phosphorylation-dephosphorylation reaction sequence.
The Role of m6A/m-RNA Methylation in Stress Response Regulation (2018)

N<sup>6</sup>-methyladenosine (m<sup>6</sup>A) and N<sup>6</sup>,2'-O-dimethyladenosine (m<sup>6</sup>Am) are abundant mRNA modifications that regulate transcript processing and translation. The role of both, here termed m<sup>6</sup>A/m, in the stress response in the adult brain in vivo is currently unknown. Here, we provide a detailed analysis of the stress epitranscriptome using m<sup>6</sup>A/m-seq, global and gene-specific m<sup>6</sup>A/m measurements. We show that stress exposure and glucocorticoids region and time specifically alter m<sup>6</sup>A/m and its regulatory network. We demonstrate that deletion of the methyltransferase Mettl3 or the demethylase Fto in adult neurons alters the m<sup>6</sup>A/m epitranscriptome, increases fear memory, and changes the transcriptome response to fear and synaptic plasticity. Moreover, we report that regulation of m<sup>6</sup>A/m is impaired in major depressive disorder patients following glucocorticoid stimulation. Our findings indicate that brain m<sup>6</sup>A/m represents a novel layer of complexity in gene expression regulation after stress and that dysregulation of the m<sup>6</sup>A/m response may contribute to the pathophysiology of stress-related psychiatric disorders.
Presence of hepatitis C virus (HCV) genomic RNA and viral replicative intermediates in bone marrow and peripheral blood mononuclear cells from HCV-infected patients (1994)

The cellular tropism of hepatitis C virus (HCV) was studied in vivo in samples from patients with persistent HCV infection. Plasma, liver, peripheral blood mononuclear cell (PBMC), and bone marrow cell (BMC) samples from 15 subjects positive for anti-HCV antibodies were tested for the presence of HCV RNA sequences by reverse transcription PCR. Virus-specific RNA sequences were found to be present in liver samples from all subjects (100%), in plasma samples from 13 of 15 patients (86.7%), in PBMC samples from 3 patients (20%), and in BMC samples from 9 (60%) of the 15 anti-HCV-positive patients enrolled in this study. The presence of the molecular intermediate of HCV replication (the negative-stranded HCV RNA) was evident in the two of the three PBMC and in five of the nine BMC HCV RNA-positive samples. Finally, we studied the nucleotide sequence of a large portion (-270 to -59) of the 5'untranslated region of HCV amplified from plasma samples of 12 of the 15 patients with and without HCV in BMCs; the degree of heterogeneity compared with the prototype HCV sequence was similar in both groups. The data principally indicate that HCV infection of PBMCs and BMCs is frequent in persistently infected patients, as shown by the occurrence of positive- and negative-stranded HCV RNA, thus suggesting the possibility of extrahepatic replication of HCV.
Effect of Change of Hepatic Drug-Metabolizing Activity on Plasma Concentrations of Major Metabolites of the New Sleep Inducer 450191-S, a 1H-1,2,4-Triazolyl Benzophenone Derivative (1987)

Plasma concentrations of the major metabolites of 450191-S, a new sleep inducer which is a 1H-1,2,4-triazolyI benzophenone derivative, were determined in rats. Under the HPLC conditions employed, several major metabolites were detected in plasma, and thus the plasma concentration-time profiles for these metabolites were checked in rats in various states. When the animals were pre-treated with high doses of 450191-S (200 or 600 mg/kg for 5 or 3 days, respectively) to induce hepatic drug-metabolizing enzymes, plasma concentrations of the metabolites after oral administration of a dose of 200 mg/kg of 450191-S decreased markedly depending on the induced enzyme activity. Pretreatment of rats with phénobarbital also caused decreased plasma levels of metabolites, which were almost the same as those in 450191 -S-pretreatment On the other hand, administration of beta-naphthoflavone to rats led to higher plasma levels of metabolites, and slower elimination compared with those in the control and 450191-S- or phenobarbital-pretreated rats. These results indicate that plasma levels of metabolites are regulated by the drug-metabolizing enzymes in the liver. It also suggests the participation of some specific forms of cytochrome P-450 In the biotransformation of 450191-S and its metabolites.
Vasoactive Intestinal Polypeptide: Measurement, Distribution and Putative Neurotransmitter Function (1979)

Vasoactive intestinal polypeptide (VIP) is a highly basic octacosapeptide isolated from porcine small intestine. <i>VIP </i>was originally considered to be a gut hormone, but radioimmunochemical and immunohistochemical studies have revealed that VIP has a widespread distribution localized in neurons. VIP-containing neurons are present in the central nervous system including the cerebral arteries, the digestive tract, the genitourinary tract and the adrenal glands. In the nerve terminals VIP is localized in synaptic vesicles. VIP fulfils a number of criteria to be a neurotransmitter both in central and peripheral nerves. Whilst the role of VIP in the central nervous system is unknown, it is likely that VIP is the mediator of gastrointestinal and pancreatic functions, which are controlled by non-cholinergic, non-adrenergic nerve fibres.
Immunoglobulin gene segment usage, location and immunogenicity in mutated and unmutated chronic lymphocytic leukaemia (2005)

The mutational status of the variable region of the immunoglobulin heavy chain gene (IgV(H)) is an important prognostic marker in B-cell chronic lymphocytic leukaemia (B-CLL), with mutated patients having improved outcome. To examine the impact of mutational status on V(H), D(H), and J(H) gene segment location and immunogenicity, we analysed 375 IgH sequences from 356 patients with B-CLL. Although V(H) and D(H) gene usage was different in mutated compared to unmutated patients, there was no impact of gene location on frequency of use or clinical outcome. Surprisingly, somatic mutations did not increase the immunogenicity of the Ig, as assessed by predicted binding affinity of Ig-derived peptides to major histocompatibility Class I and Class II molecules. Even excluding patients using V(H)1-69, cases using the V(H)1 gene family had a poor outcome. Both mutated and unmutated CLL patients demonstrated evidence of antigen selection. The worst outcome was seen in the subset of 14 unmutated patients with similar HCDR3 amino acid sequence using V(H)1-69, D(H)3-3 and J(H)6, suggesting an antigen-driven process modulating the clinical course.
ChemInform Abstract: Carbonylation of Alkynols Catalyzed by Pd(II)/2‐PyPPh<sub>2</sub> Dissolved in Organic Solvents and in Ionic Liquids: A Facile Entry to α‐Methylene γ‐ and δ‐Lactones. (2002)

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.
Recombination via flanking direct repeats is a major cause of large-scale deletions of human mitochondrial DNA (1990)

Large-scale deletions of mitochondrial DNA (mtDNA) have been described in patients with progressive external ophthalmoplegia (PEO) and ragged red fibers. We have determined the exact deletion breakpoint in 28 cases with PEO, including 12 patients already shown to harbor an identical deletion; the other patients had 16 different deletions. The deletions fell into two classes. In Class I (9 deletions; 71% of the patients), the deletion was flanked by perfect direct repeats, located (in normal mtDNA) at the edges of the deletion. In Class II (8 deletions; 29% of patients), the deletions were not flanked by any obviously unique repeat element, or they were flanked by repeat elements which were located imprecisely relative to the breakpoints. Computer analysis showed a correlation between the location of the deletion breakpoints and sequences in human mtDNA similar to the target sequence for Drosophila topoisomerase II. It is not known how these deletions originate, but both slipped mispairing and legitimate recombination could be mechanisms playing a major role in the generation of the large mtDNA deletions found in PEO.
Doppler US in Patients with Crohn Disease: Vessel Density in the Diseased Bowel Reflects Disease Activity (2000)

Vessel density in affected bowel loops, as estimated with Doppler US, and bowel wall thickness (>5 mm) reflect disease activity in patients with Crohn disease.