gebhart/patrepeval huggingface dataset:
Molecular Mechanics Potential for Silica and Zeolite Catalysts Based on ab Initio Calculations. 2. Aluminosilicates (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMolecular Mechanics Potential for Silica and Zeolite Catalysts Based on ab Initio Calculations. 2. AluminosilicatesJoerg-R. Hill and Joachim SauerCite this: J. Phys. Chem. 1995, 99, 23, 9536–9550Publication Date (Print):June 1, 1995Publication History Published online1 May 2002Published inissue 1 June 1995https://pubs.acs.org/doi/10.1021/j100023a036https://doi.org/10.1021/j100023a036research-articleACS PublicationsRequest reuse permissionsArticle Views1088Altmetric-Citations181LEARN 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 options Get e-Alerts
Controlled growth of core–shell Si–SiOxand amorphous SiO2nanowires directly from NiO/Si (2004)

A simple, direct synthesis method is used to grow core-shell Si-SiOx and amorphous SiO2 nanowires by heating a NiO-catalyzed silicon substrate. The morphology of the nanowires was controlled by carbothermal reduction Of WO3, which provides a reductive environment to synthesize crystalline Si nanowires covered with a SiOx sheath at the growth temperature of 1000-1100degreesC. Only amorphous SiO2 nanowires were produced when the substrate was annealed without using WO3/C. Transmission electron microscopy shows that the Si core is 20-50 nm in diameter and the SiOx shell layer is 40-60 nm thick. After hydrofluoric acid (HF) treatment of core-shell Si-SiOx the single-crystalline silicon nanowires (SiNWs) were obtained in large quantities. The HF-treated SiNWs were 20-50 nm in diameter. The main crystal growth direction of the SiNWs was [I I I]. The nanowires grown were highly pure (no metal catalyst contamination) and very long (hundreds of micrometres). A solid-liquid-solid (SLS) mechanism is proposed for the growth of both core-shell Si-SiOx and amorphous SiO2 nanowires.
Stress analysis of optical fibers by a finite element method (1981)

Stress-induced birefringence in single-mode optical fibers having arbitrary shape of core has been investigated using a finite element method. The calculated modal birefringence due to the thermal stress and/or stress caused by external forces in noncircular core fibers is compared with the values obtained by measurement of polarization properties, showing good agreement.
Malonyl-CoA, fuel sensing, and insulin resistance (1999)

Malonyl-CoA is an allosteric inhibitor of carnitine palmitoyltransferase (CPT) I, the enzyme that controls the transfer of long-chain fatty acyl (LCFA)-CoAs into the mitochondria where they are oxidized. In rat skeletal muscle, the formation of malonyl-CoA is regulated acutely (in minutes) by changes in the activity of the beta-isoform of acetyl-CoA carboxylase (ACCbeta). This can occur by at least two mechanisms: one involving cytosolic citrate, an allosteric activator of ACCbeta and a precursor of its substrate cytosolic acetyl-CoA, and the other involving changes in ACCbeta phosphorylation. Increases in cytosolic citrate leading to an increase in the concentration of malonyl-CoA occur when muscle is presented with insulin and glucose, or when it is made inactive by denervation, in keeping with a diminished need for fatty acid oxidation in these situations. Conversely, during exercise, when the need of the muscle cell for fatty acid oxidation is increased, decreases in the ATP/AMP and/or creatine phosphate-to-creatine ratios activate an isoform of an AMP-activated protein kinase (AMPK), which phosphorylates ACCbeta and inhibits both its basal activity and activation by citrate. The central role of cytosolic citrate links this malonyl-CoA regulatory mechanism to the glucose-fatty acid cycle concept of Randle et al. (P. J. Randle, P. B. Garland. C. N. Hales, and E. A. Newsholme. Lancet 1: 785-789, 1963) and to a mechanism by which glucose might autoregulate its own use. A similar citrate-mediated malonyl-CoA regulatory mechanism appears to exist in other tissues, including the pancreatic beta-cell, the heart, and probably the central nervous system. It is our hypothesis that by altering the cytosolic concentrations of LCFA-CoA and diacylglycerol, and secondarily the activity of one or more protein kinase C isoforms, changes in malonyl-CoA provide a link between fuel metabolism and signal transduction in these cells. It is also our hypothesis that dysregulation of the malonyl-CoA regulatory mechanism, if it leads to sustained increases in the concentrations of malonyl-CoA and cytosolic LCFA-CoA, could play a key role in the pathogenesis of insulin resistance in muscle. That it may contribute to abnormalities associated with the insulin resistance syndrome in other tissues and the development of obesity has also been suggested. Studies are clearly needed to test these hypotheses and to explore the notion that exercise and some pharmacological agents that increase insulin sensitivity act via effects on malonyl-CoA and/or cytosolic LCFA-CoA.
Effect of Antibiotic Treatment on Establishment and Elimination of Intestinal Colonization by KPC-Producing Klebsiella pneumoniae in Mice (2011)

An understanding of the impact of antibiotics on the intestinal reservoir of KPC carbapenemase-producing Klebsiella pneumoniae (KPC-Kp) is important to prevent its emergence. We used a mouse model to examine the effect of antibiotic treatment on the establishment and elimination of intestinal colonization with KPC-Kp. Mice (10 per group) received subcutaneous antibiotics daily for 8 days. On day 3 of treatment, 10(3) CFU of KPC-Kp was given orogastrically, and concentrations of KPC-Kp in stool were monitored. Additional experiments assessed the effects of antibiotic treatment on concentrations of total anaerobes and Bacteroides spp. in stool and the efficacy of orogastric gentamicin and polymyxin E in suppressing KPC-Kp colonization. Of four antibiotics with minimal activity against the KPC-Kp test strain (MIC ≥ 16 μg/ml), those that suppressed total anaerobes and bacteroides (i.e., clindamycin and piperacillin-tazobactam) promoted colonization by KPC-Kp (P < 0.001), whereas agents that did not suppress total anaerobes or bacteroides (i.e., ciprofloxacin and cefepime) did not (P = 0.35). Of two agents with moderate activity against the KPC-Kp test strain, ertapenem (MIC, 4 μg/ml) did not promote colonization by KPC-Kp, whereas tigecycline (MIC, 3 μg/ml) did (P < 0.001), despite not reducing levels of total anaerobes or bacteroides. Orogastric treatment with gentamicin and polymyxin E suppressed KPC-Kp to undetectable levels in the majority of mice. These data suggest that antibiotics that disturb the intestinal anaerobic microflora and lack significant activity against KPC-Kp promote colonization by this organism. The administration of nonabsorbed oral antibiotics may be an effective strategy to suppress colonization with KPC-Kp.
Chemical Derivatization of Peptide Carboxyl Groups for Highly Efficient Electron Transfer Dissociation (2013)

The carboxyl groups of tryptic peptides were derivatized with a tertiary or quaternary amine labeling reagent to generate more highly charged peptide ions that fragment efficiently by electron transfer dissociation (ETD). All peptide carboxyl groups-aspartic and glutamic acid side-chains as well as C-termini-were derivatized with an average reaction efficiency of 99 %. This nearly complete labeling avoids making complex peptide mixtures even more complex because of partially-labeled products, and it allows the use of static modifications during database searching. Alkyl tertiary amines were found to be the optimal labeling reagent among the four types tested. Charge states are substantially higher for derivatized peptides: a modified tryptic digest of bovine serum albumin (BSA) generates ~90% of its precursor ions with z > 2, compared with less than 40 % for the unmodified sample. The increased charge density of modified peptide ions yields highly efficient ETD fragmentation, leading to many additional peptide identifications and higher sequence coverage (e.g., 70 % for modified versus only 43 % for unmodified BSA). The utility of this labeling strategy was demonstrated on a tryptic digest of ribosomal proteins isolated from yeast cells. Peptide derivatization of this sample produced an increase in the number of identified proteins, a >50 % increase in the sequence coverage of these proteins, and a doubling of the number of peptide spectral matches. This carboxyl derivatization strategy greatly improves proteome coverage obtained from ETD-MS/MS of tryptic digests, and we anticipate that it will also enhance identification and localization of post-translational modifications.
The Synthesis of Ribonuclease A (1971)

A protected linear polypeptide of 124 amino acid residues with the sequence of bovine pancreatic ribonuclease A was synthesized by the solid phase method. The polypeptide was removed from the solid support and purified, and the four disulfide bonds were closed by air oxidation of the reduced form. The synthetic enzyme was fractionated by gel filtration and ion exchange chromatography, and the material that eluted at the same position as natural reduced-reoxidized RNase A was isolated. The product was further purified by incubation with trypsin and removal of the enzymically degraded components. A fractional precipitation with (NH4)2·SO4 gave a purified synthetic RNase A with a specific activity of 78%. The synthetic RNase A was indistinguishable from natural bovine pancreatic RNase A by gel filtration on Sephadex G-75, by chromatography on carboxymethylcellulose, and by electrophoresis. Amino acid analyses, peptide maps of tryptic digests, and the Michaelis constant agreed well with those of the natural enzyme. The synthetic enzyme showed the high substrate specificity to be expected of RNase A. It was highly active against yeast RNA and 2', 3'-cyclic cytidine phosphate and was completely inactive toward DNA, 2', 3'-cyclic guanosine phosphate, and the dinucleotides 5'-(3'-guanylyl)-cytidylic acid and 5'-(3'-adenylyl)-adenylic acid. During the synthesis, samples were removed after 99 and 104 residues had been coupled and the corresponding polypeptides, des-(21-25)S-protein and S-protein, were isolated. They were then reduced and reoxidized in the presence of natural or synthetic S-peptide to give RNase S and des-(21-25)RNase S. The specific activities of the two products were approximately equal, thus indicating that the five NH2-terminal residues of S-protein are not required for the protein to oxidize and fold in the presence of S-peptide to give an active enzyme.
Synthesis of a Broad Array of Highly Functionalized, Enantiomerically Pure Cyclohexanecarboxylic Acid Derivatives by Microbial Dihydroxylation of Benzoic Acid and Subsequent Oxidative and Rearrangement Reactions (2001)

[reaction: see text]. We have found that the 1,2-dihydroxylation of benzoic acid with Alcaligenes eutrophus strain B9, first reported in 1971 by Reiner and Hegeman, is readily adapted for the preparation of tens to hundreds of grams of (1S,2R)-1,2-dihydroxycyclohexa-3,5-diene-1-carboxylic acid of >95% ee. This unique substrate undergoes many specific oxidative and rearrangement processes. Among these are transformations of unanticipated chemical novelty and many products that have not been previously described.
Studies of IFN-Induced Transcriptional Activation Uncover the Jak-Stat Pathway (1998)

Sharing the Milstein Award with George R. Stark and Ian M. Kerr in the fall of 1997 brought this invitation to record personal reflections on our experiments concerning the mechanisms of action of interferon. Our work and that of the Kerr and Stark laboratories uncovered the Jak-Stat pathway through which signals from cell surface receptors reach genes in the cell nucleus. This review concentrates on that to which I can speak most reliably, that is, experiments done by my young colleagues at Rockefeller University.
Inhibition of Cytotoxicity of Lymphocytes by Concanavalin A in vitro (1970)

Human lymphocytes treated with the plant protein concanavalin A are stimulated to transform into blasts, without developing cytotoxicity for chicken erythrocytes. Prior treatment of lymphocytes with concanavalin A potentiated phytohemagglutinin-induced blast transformation and DNA synthesis but completely inhibited phytohemagglutinin-induced cytotoxicity. Inhibiton was not due to suppression of the mixed lymphocyte-erythrocyte aggregation normally caused by phytohemagglutinin. Inhibition of cytotoxicity was reversible when concanavalin A was removed from the lymphocytes by treatment with methyl-alpha-D-manno-pyranoside after 1 hour but not after 20 hours. The results indicate that blast transformation and cytotoxicity are separate expressions of lymphocyte stimulation.
Bifunctional Small Molecules Are Biomimetic Catalysts for Silica Synthesis at Neutral pH (2004)

Silicatein is an enzyme isolated from the biosilica produced by the marine demosponge, Tethya aurantia. Once isolated from the sponge, silicatein can be used in vitro to catalyze the hydrolysis and direct polycondensation of a wide variety of alkoxide, ionic, and organometallic precursors to the corresponding chalcogens at standard temperature and pressure and neutral pH. On the basis of these results, an array of small molecules that mimic the unique physiochemical environment found in the enzyme active site was investigated for catalytic activity in the formation of silica from silicon alkoxides at neutral pH. The most successful of these biomimetic catalysts (cysteamine) was used to encapsulate firefly luciferase, green and blue fluorescent proteins (GFP, BFP), and Escherichia coli cells expressing GFP in silica matrixes. The benign conditions required for the catalysis of synthesis of these silica composites does not impair the activities of the encapsulated enzyme, fluorescent proteins, or live cells as shown by fluorescence measurements. In conjunction with microcontact printing, this biomimetically catalyzed encapsulation method has been used to produce patterned functional arrays of silica nanoparticulate composite materials.
Functional and Biochemical Characterization of Escherichia coli Sugar Efflux Transporters (1999)

A family of bacterial transporters, the SET (sugar efflux transporter) family, has been recently reported (Liu, J. Y., Miller, P. F., Gosink, M., and Olson, E. R. (1999) Mol. Microbiol. 31, 1845-1851). In this study, the biochemical and cell biological properties of the three Escherichia coli members (SetA, SetB, and SetC) of the family are characterized. We show that both SetA and SetB can transport lactose and glucose. In addition, SetA has broad substrate specificity, with preferences for glucosides or galactosides with alkyl or aryl substituents. Consistent with the observed in vitro substrate specificities, strains that hyperexpress SetA or SetB are desensitized to lactose analogues as measured by induction of the lac operon. In addition, strains that hyperexpress SetA are resistant to the growth inhibitory sugar analogue o-nitrophenyl-beta-D-thiogalactoside. Strains disrupted for any one or all of the set genes are viable and show no defects in lactose utilization nor increased sensitivity to inducers of the lac operon and nonmetabolizable sugar analogues. The data suggest that the set genes are either poorly expressed under normal laboratory growth conditions or are redundant with other cellular gene products.
Dual Methylation Pathways in Lignin Biosynthesis (1998)

Caffeoyl-coenzyme A (CoA) O-methyltransferase (CCoAOMT) has been proposed to be involved in an alternative methylation pathway of lignin biosynthesis. However, no direct evidence has been available to confirm that CCoAOMT is essential for lignin biosynthesis. To understand further the methylation steps in lignin biosynthesis, we used an antisense approach to alter O-methyltransferase (OMT) gene expression and investigated the consequences of this alteration. We generated transgenic tobacco plants with a substantial reduction in CCoAOMT as well as plants with a simultaneous reduction in both CCoAOMT and caffeic acid O-methyltransferase (CAOMT). Lignin analysis showed that the reduction in CCoAOMT alone resulted in a dramatic decrease in lignin content. The reduction in CCoAOMT also led to a dramatic alteration in lignin composition. Both guaiacyl lignin and syringyl lignin were reduced in the transgenic plants. However, guaiacyl lignin was preferentially reduced, which resulted in an increase in the S/G (syringl/guaiacyl) ratio. We have also analyzed lignin content and composition in transgenic plants having a simultaneous reduction in both CCoAOMT and CAOMT. The reduction in both OMTs resulted in a further decrease in total lignin content. This is in sharp contrast to the effect that resulted from the reduction in CAOMT alone, which only decreased the syringl lignin unit without a reduction in overall lignin content. These results unequivocally demonstrate that methylation reactions in lignin biosynthesis are catalyzed by both CCoAOMT and CAOMT.
TSG-6 Protein Binding to Glycosaminoglycans (2005)

TSG-6 protein, up-regulated in inflammatory lesions and in the ovary during ovulation, shows anti-inflammatory activity and plays an essential role in female fertility. Studies in murine models of acute inflammation and experimental arthritis demonstrated that TSG-6 has a strong anti-inflammatory and chondroprotective effect. TSG-6 protein is composed of the N-terminal link module that binds hyaluronan and a C-terminal CUB domain, present in a variety of proteins. Interactions between the isolated link module and hyaluronan have been studied extensively, but little is known about the binding of full-length TSG-6 protein to hyaluronan and other glycosaminoglycans. We show that TSG-6 protein and hyaluronan, in a temperature-dependent fashion, form a stable complex that is resistant to dissociating agents. The formation of such stable complexes may underlie the activities of TSG-6 protein in inflammation and fertility, e.g. the TSG-6-dependent cross-linking of hyaluronan in the cumulus cell-oocyte complex during ovulation. Because adhesion to hyaluronan is involved in cell trafficking in inflammatory processes, we also studied the effect of TSG-6 on cell adhesion. TSG-6 binding to immobilized hyaluronan did not interfere with subsequent adhesion of lymphoid cells. In addition to immobilized hyaluronan, full-length TSG-6 also binds free hyaluronan and all chondroitin sulfate isoforms under physiological conditions. These interactions may contribute to the localization of TSG-6 in cartilage and to its chondroprotective and anti-inflammatory effects in models of arthritis.
Network Tomography: Recent Developments (2004)

Today’s Internet is a massive, distributed network which continues to explode in size as e-commerce and related activities grow. The heterogeneous and largely unregulated structure of the Internet renders tasks such as dynamic routing, optimized service provision, service level verification and detection of anomalous/malicious behavior extremely challenging. The problem is compounded by the fact that one cannot rely on the cooperation of individual servers and routers to aid in the collection of network traffic measurements vital for these tasks. In many ways, network monitoring and inference problems bear a strong resemblance to other “inverse problems” in which key aspects of a system are not directly observable. Familiar signal processing or statistical problems such as tomographic image reconstruction and phylogenetic tree identification have interesting connections to those arising in networking. This article introduces network tomography, a new field which we believe will benefit greatly from the wealth of statistical theory and algorithms. It focuses especially on recent developments in the field including the application of pseudo-likelihood methods and tree estimation formulations.
Composite scintillators as detectors for fast neutrons and gamma-radiation detection in the border monitoring (2009)

A composite scintillator is non-toxic and nonflammable solid solution, which contains the grains of organic molecular single crystal introduced into a polymer matrix. Composite scintillators were designed as detectors of fast neutrons and gamma radiation. We present ¿/¿ discrimination properties of four composite scintillators: two of them are based on p-terphenyl and two other-on stilbene. The results obtained with a stilbene single crystal and a liquid scintillator (BC 501A) are shown as a comparison. First conclusion of this work is that composite scintillators can be an attractive offer for the border monitoring.
Whole-Cell versus Total RNA Extraction for Analysis of Microbial Community Structure with 16S rRNA-Targeted Oligonucleotide Probes in Salt Marsh Sediments (2000)

rRNA-targeted oligonucleotide probes have become powerful tools for describing microbial communities, but their use in sediments remains difficult. Here we describe a simple technique involving homogenization, detergents, and dispersants that allows the quantitative extraction of cells from formalin-preserved salt marsh sediments. Resulting cell extracts are amenable to membrane blotting and hybridization protocols. Using this procedure, the efficiency of cell extraction was high (95.7% +/- 3.7% [mean +/- standard deviation]) relative to direct DAPI (4',6'-diamidino-2-phenylindole) epifluorescence cell counts for a variety of salt marsh sediments. To test the hypothesis that cells were extracted without phylogenetic bias, the relative abundance (depth distribution) of five major divisions of the gram-negative mesophilic sulfate-reducing delta proteobacteria were determined in sediments maintained in a tidal mesocosm system. A suite of six 16S rRNA-targeted oligonucleotide probes were utilized. The apparent structure of sulfate-reducing bacteria communities determined from whole-cell and RNA extracts were consistent with each other (r(2) = 0.60), indicating that the whole-cell extraction and RNA extraction hybridization approaches for describing sediment microbial communities are equally robust. However, the variability associated with both methods was high and appeared to be a result of the natural heterogeneity of sediment microbial communities and methodological artifacts. The relative distribution of sulfate-reducing bacteria was similar to that observed in natural marsh systems, providing preliminary evidence that the mesocosm systems accurately simulate native marsh systems.
A Knockout of a Transgenic Mouse — Animal Models of Sickle Cell Anemia (1998)

Animal models of sickle cell anemia can be used to improve understanding of the pathophysiology of the disease, aid in the development of antisickling drugs, and test the feasibility of gene therapy. The basis of these interesting models is transgenic technology, in which foreign genes are introduced into the germ line of a mouse. With this method it is possible to create mice that carry the mutant sickle, or βS, gene and a normal human α-globin gene. In such animals, the human βS and α-globin genes code for sickle hemoglobin (α2βS 2), but . . .