gebhart/patrepeval huggingface dataset:
O-antigen seroepidemiology of Klebsiella clinical isolates and implications for immunoprophylaxis of Klebsiella infections (1997)

To provide a database for the development of an O-antigen-polysaccharide-containing vaccine against Klebsiella spp., we examined the O-antigen seroepidemiology of 378 Klebsiella clinical isolates collected prospectively in two university centers. Strains were typed by competitive enzyme-linked immunosorbent assay with rabbit antisera specific for serogroups O1 to O12 and monoclonal antibodies (MAbs) specific for serogroups O1, O2ab, O2ac, and the genus-specific core antigen. The numbers of isolates (percentages) of individual O serogroups were as follows: 148 (39.2) for serogroup O1, 40 (10.6) for serogroup O2ab, 4 (1.1) for serogroup O2ac, 89 (23.6) for serogroup O3, 2 (0.5) for serogroup O4, 32 (8.5) for serogroup O5, none for serogroups O7, O9, and O12, and 21 (5.6) for serogroup O11. Forty-two (11.1) of the strains were non-O-typeable. O-serogroup distributions were virtually identical between isolates from invasive infections and those from noninvasive infections or colonizations. A vaccine containing the O-specific polysaccharides of serogroups O1, O2ab, O3, and O5 would cover 82% of clinically occurring O-antigen specificities. Three hundred thirty-eight of 378 isolates (89.4%) reacted with the genus-specific MAb V/9-5, which recognizes an epitope of the outer core region of Klebsiella lipopolysaccharide. Antibodies directed against this epitope may represent a further alternative for O-antigen-targeted immunoprophylaxis of Klebsiella infections. These data support further experimental investigations on the protective potential of O-antigen-based vaccines and/or hyperimmune globulins in Klebsiella infection.
Functional Diversification During Evolution of the Murine α1-Proteinase Inhibitor Family: Role of the Hypervariable Reactive Center Loop (2002)

Alpha(1)-proteinase inhibitor (alpha(1)-PI) is a member of the serpin superfamily of serine proteinase inhibitors that are involved in the regulation of a number of proteolytic processes. Alpha(1)-PI, like most serpins, functions by covalent binding to, and inhibition of, target proteinases. The interaction between alpha(1)-PI and its target is directed by the so-called reactive center loop (RCL), an approximately 20 residue domain that extends out from the body of the alpha(1)-PI polypeptide and determines the inhibitor's specificity. Mice express at least seven closely related alpha(1)-PI isoforms, encoded by a family of genes clustered at the Spi1 locus on chromosome 12. The amino acid sequence of the RCL region is hypervariable among alpha(1)-PIs, a phenomenon that has been attributed to high rates of evolution driven by positive Darwinian selection. This suggests that the various isoforms are functionally diverse. To test this notion, we have compared the proteinase specificities of individual alpha(1)-PIs from each of the two mouse species. As predicted from the positive Darwinian selection hypothesis, the various alpha(1)-PIs differ in their ability to form covalent complexes with serine proteinases, such as elastase, trypsin, chymotrypsin, and cathepsin G. In addition, they differ in their binding ability to proteinases in crude snake venoms. Importantly, the RCL region of the alpha(1)-PI polypeptide is the primary determinant of isoform-specific differences in proteinase recognition, indicating that hypervariability within this region drives the functional diversification of alpha(1)-PIs during evolution. The possible physiological benefits of alpha(1)-PI diversity are discussed.
A graph-based framework for multiparadigmatic visual access to databases (1996)

Describes an approach for multiparadigmatic visual access integration of different interaction paradigms. The user is provided with an adaptive interface augmented by a user model, supporting different visual representations of both data and queries. The visual representations are characterized on the basis of the chosen visual formalisms, namely forms, diagrams and icons. To access different databases, a unified data model called the "graph model" is used as a common underlying formalism to which databases, expressed in the most popular data models, can be mapped. Graph model databases are queried through the adaptive interface. The semantics of the query operations is formally defined in terms of graphical primitives. Such a formal approach permits us to define the concept of an "atomic query", which is the minimal portion of a query that can be transferred from one interaction paradigm to another and processed by the system. Since certain interaction modalities and visual representations are more suitable for certain user classes, the system can suggest to the user the most appropriate interaction modality as well as the visual representation, according to the user model. Some results on user model construction are presented.
Characteristics of the time-optimal control of flexible structures with damping (1994)

The time-optimal control of flexible structures with damping is considered. We formulate the general time-optimal control problem for single-axis flexible structures, and an analytical result is given for a lower bound on the number of control switches for the one-bending-mode case. Numerical solutions and simulations are presented to show several interesting trends of the time-optimal control switch times as the frequencies and dampings of the flexible modes are varied.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment (2012)

This inferred functional metagenomic information provides the first insights into community-wide microbial processes and pathways that underpin IBD pathogenesis.
Mutual diffusion in octamethylcyclotetrasiloxane mixtures (1968)

Diffusion coefficients for the systems octamethylcyclotetrasiloxane + benzene and octamethylcyclotetrasiloxane + carbon tetrachloride at 18, 25, 35 and 45° have been measured by the Goüy interferometric method. Viscosities of these systems are also presented. The results are compared with some theoretical predictions.
ChemInform Abstract: A SYNTHESIS OF 8‐METHOXYCARBONYLOCT‐1‐YL O‐α‐D‐GALACTOPYRANOSYL‐(1 → 3)‐O‐β‐D‐GALACTOPYRANOSYL‐(1 → 4)‐2‐ACETAMIDO‐2‐DEOXY‐β‐D‐GLUCOPYRANOSIDE (1985)

Abstract Das Thiogalaktosid (Ia) wird über die Stufen (Ib) und (Ic) in die selektiv blockierte Verbindung (II) übergeführt, deren Glykosylierung mit dem Bromid (III) das Disaccharid (IVa) liefert.
Metastable polymers of the nitrogen oxides. 1. Open chain nitric oxide analogs of polythiazyl: a MNDO/AM1 study (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMetastable polymers of the nitrogen oxides. 1. Open chain nitric oxide analogs of polythiazyl: a MNDO/AM1 studyWalter H. JonesCite this: J. Phys. Chem. 1991, 95, 6, 2588–2595Publication Date (Print):March 1, 1991Publication History Published online1 May 2002Published inissue 1 March 1991https://pubs.acs.org/doi/10.1021/j100159a088https://doi.org/10.1021/j100159a088research-articleACS PublicationsRequest reuse permissionsArticle Views70Altmetric-Citations7LEARN 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
Atrazine Chlorohydrolase from Pseudomonas Sp. Strain ADP Is a Metalloenzyme (2002)

Atrazine chlorohydrolase (AtzA) from Pseudomonas sp. ADP initiates the metabolism of the herbicide atrazine by catalyzing a hydrolytic dechlorination reaction to produce hydroxyatrazine. Sequence analysis revealed AtzA to be homologous to metalloenzymes within the amidohydrolase protein superfamily. AtzA activity was experimentally shown to depend on an enzyme-bound, divalent transition-metal ion. Loss of activity obtained by incubating AtzA with the chelator 1,10-phenanthroline or oxalic acid was reversible upon addition of Fe(II), Mn(II), or Co(II) salts. Experimental evidence suggests a 1:1 metal to subunit stoichiometry, with the native metal being Fe(II). Our data show that the inhibitory effects of metals such as Zn(II) and Cu(II) are not the result of displacing the active site metal. Taken together, these data indicate that AtzA is a functional metalloenzyme, making this the first report, to our knowledge, of a metal-dependent dechlorinating enzyme that proceeds via a hydrolytic mechanism.
Investigation of the Solid Electrolyte Interphase Formed by Fluoroethylene Carbonate on Si Electrodes (2011)

The solid electrolyte interphase (SEI) formed by a fluoroethylene carbonate (FEC)-based electrolyte on a Si electrode was investigated using X-ray photoelectron spectroscopy (XPS) and time of flight–secondary ion mass spectrometry (ToF-SIMS). The FEC-derived SEI consists of lithium fluoride and a polyene-compound, which are originated from free fluoride and the acetylene unit due to the preferential reaction of FEC, and is very thin. Oxidation of the Si electrode of the EC-based cell was confirmed, although it did not proceed to a significant extent. The FEC-derived SEI protects against not only the decomposition of the FEC-based electrolyte, but also oxidation of the Si electrode. The FEC-derived SEI acts as a passivation film for the Si electrode, which results in the improvement of the cycling performance.
Catalytic disassembly of an organosolv lignin via hydrogen transfer from supercritical methanol (2010)

A novel approach to disassembling biomass-derived lignin into processible units is described. This transformation is achieved in supercritical methanol, using a Cu-doped porous metal oxide as the catalyst, at a relatively mild temperature (300 °C). Hydrogen transfer from methanol to an organosolv lignin results in the complete hydrogenolysis of phenyl ether bonds, coupled with the hydrogenation of aromatic rings. The product is a complex mixture composed principally of monomeric substituted cyclohexyl derivatives with greatly reduced oxygen content and negligible aromatics. Notably, no char formation was observed. We also describe operational indices based on the 1H NMR spectra that facilitate holistic evaluation of the product distribution in this and other biomass transformations.
Calcium-dependent Human Serum Homocysteine Thiolactone Hydrolase (2000)

Homocysteine thiolactone is formed in all cell types studied thus far as a result of editing reactions of some aminoacyl-tRNA synthetases. Because inadvertent reactions of thiolactone with proteins are potentially harmful, the ability to detoxify homocysteine thiolactone is essential for biological integrity. This work shows that a single specific enzyme, present in mammalian but not in avian sera, hydrolyzes thiolactone to homocysteine. Human serum thiolactonase, a 45-kDa protein component of high density lipoprotein, requires calcium for activity and stability and is inhibited by isoleucine and penicillamine. Substrate specificity studies suggest that homocysteine thiolactone is a likely natural substrate of this enzyme. However, thiolactonase also hydrolyzes non-natural substrates, such as phenyl acetate, p-nitrophenyl acetate, and the organophospate paraoxon. N-terminal amino acid sequence of pure thiolactonase is identical with that of human paraoxonase. These and other data indicate that paraoxonase, an organophosphate-detoxifying enzyme whose natural substrate and function remained unknown up to now, is in fact homocysteine thiolactonase. By detoxifying homocysteine thiolactone, the thiolactonase/paraoxonase would protect proteins against homocysteinylation, a potential contributing factor to atherosclerosis.
Chapter 3: Pig islet product manufacturing and release testing (2009)

This chapter provides recommendations on pig islet product manufacturing and release testing to scientific and corporate programs interested in future clinical studies using xenogeneic porcine pancreatic islet cell products for the treatment of type 1 diabetes.To facilitate control of manufacturing as well as reproducibility and consistency of product lots, the manufacturing process, and the manufacturing facility must be in compliance with current Good Manufacturing Practices regulations. Data must be provided to demonstrate that islet products can be consistently prepared that would meet basic lot release requirements. To facilitate product safety: (i) materials used in the manufacturing process, including the pig pancreas, must be free of adventitious agents; (ii) islets must be manufactured using aseptic processing; and (iii) final product must undergo tests for sterility, mycoplasma (if cultured) and endotoxin. Safety specifications for pig islet product release include a negative Gram stain and an endotoxin content of <5.0 EU/kg recipient body weight. Product post-release assessments must include sterility cultures on the final product. Because results for sterility are available only retrospectively, a plan of action must be in place for patient notification and treatment in case the sterility culture results are positive for contamination. Product characterization information must address important aspects of lot release testing such as identity/purity (cell composition), quantity [islet equivalents (IE), cell number] and potency (insulin secretory capacity, oxygen consumption rate corrected for DNA or transplant bioassay in immunoincompetent diabetic mice). This information is also critical to demonstrate manufacturing control and product consistency across multiple islet preparations (lots). Providing islet products containing an islet mass sufficient to restore euglycemia in trial participants (>or=10 000 IE/kg) requires pooling of islets from multiple donor pancreata (two to four from adult donors and seven to 10 from neonatal donors). Demonstration of product consistency across products from individual pancreata would warrant release testing to be performed on a sample of the pooled product. As product development and clinical trials advance, the increasingly more detailed specifications of potency assays on adult porcine islet products are expected to be predictive of post-transplant glycemic control. The immaturity of fetal and neonatal porcine islet tissue precludes the use of in vitro insulin secretion as a potency test as part of lot release testing; another measure of potency appropriate to fetal and neonatal cells will need to be developed for product release testing and evaluation of aliquots of these products in mouse transplant bioassays should be performed to provide meaningful post-release information.
Methyl cellulose gel obstructed bone formation by GBR: an experimental study in rats (2005)

Local application of a methyl cellulose gel obstructed bone formation under Teflon capsules placed adjacent to uninjured cortical bone in the mandibular ramus of rats. These data suggest that another material should be utilized to deliver growth factors under Teflon membranes for guided bone regeneration.
Structures of histone methyltransferase SET7/9 in complexes with adenosylmethionine derivatives (2013)

SET7/9 is a protein lysine methyltransferase that methylates histone H3 and nonhistone proteins such as p53, TAF10 and oestrogen receptor α. In previous work, novel inhibitors of SET7/9 that are amine analogues of the coenzyme S-(5'-adenosyl)-L-methionine (AdoMet) have been developed. Here, crystal structures of SET7/9 are reported in complexes with two AdoMet analogues, designated DAAM-3 and AAM-1, in which an n-hexylaminoethyl group or an n-hexyl group is attached to the N atom that replaces the S atom of AdoMet, respectively. In both structures, the inhibitors bind to the coenzyme-binding site and their additional alkyl chain binds in the lysine-access channel. The N atom in the azaalkyl chain of DAAM-3 is located at almost the same position as the N-methyl C atom of the methylated lysine side chain in the substrate-peptide complex structures and stabilizes complex formation by hydrogen bonding to the substrate-binding site residues of SET7/9. On the other hand, the alkyl chain of AAM-1, which is a weaker inhibitor than DAAM-3, binds in the lysine-access channel only through hydrophobic and van der Waals interactions. Unexpectedly, the substrate-binding site of SET7/9 complexed with AAM-1 specifically interacts with the artificial N-terminal sequence of an adjacent symmetry-related molecule, presumably stabilizing the alkyl chain of AAM-1.
A Conserved Telomerase Motif within the Catalytic Domain of Telomerase Reverse Transcriptase Is Specifically Required for Repeat Addition Processivity (2003)

Telomerase is a ribonucleoprotein reverse transcriptase responsible for the maintenance of one strand of the telomere terminal repeats. The catalytic protein subunit of the telomerase complex, known as TERT, possesses a reverse transcriptase (RT) domain that mediates nucleotide addition. The RT domain of TERT is distinguishable from retroviral and retrotransposon RTs in having a sizable insertion between conserved motifs A and B', within the so-called fingers domain. Sequence analysis revealed the existence of conserved residues in this region, named IFD (insertion in fingers domain). Mutations of some of the conserved residues in Saccharomyces cerevisiae TERT (Est2p) abolished telomerase function in vivo, testifying to their importance. Significant effects of the mutations on telomerase activity in vitro were observed, with most of the mutants exhibiting a uniform reduction in activity regardless of primer sequence. Remarkably, one mutant manifested a primer-specific defect, being selectively impaired in extending primers that form short hybrids with telomerase RNA. This mutant also accumulated products that correspond to one complete round of repeat synthesis, implying an inability to effect the repositioning of the DNA product relative to the RNA template that is necessary for multiple repeat addition. Our results suggest that the ability to stabilize short RNA-DNA hybrids is crucial for telomerase function in vivo and that this ability is mediated in part by a more elaborate fingers domain structure.
Simple, rapid method for determination of propionic acid and other short-chain fatty acids in serum. (1978)

Abstract A semimicro method for measuring propionic and other short-chain fatty acids in serum is presented. The procedure requires as little as 200 microliter of serum. Data are provided for premature infants, children, adults, and patients with propionicacidemia.
Simple And Efficient Architecture Search for Convolutional Neural Networks (2017)

Neural networks have recently had a lot of success for many tasks. However, neural network architectures that perform well are still typically designed manually by experts in a cumbersome trial-and-error process. We propose a new method to automatically search for well-performing CNN architectures based on a simple hill climbing procedure whose operators apply network morphisms, followed by short optimization runs by cosine annealing. Surprisingly, this simple method yields competitive results, despite only requiring resources in the same order of magnitude as training a single network. E.g., on CIFAR-10, our method designs and trains networks with an error rate below 6% in only 12 hours on a single GPU; training for one day reduces this error further, to almost 5%.
Retroviral analysis of cardiac morphogenesis: discontinuous formation of coronary vessels. (1992)

Cellular progenitors of the coronary vasculature are believed to enter the chicken heart during epicardial morphogenesis between stages 17 and 27 (days 3-5) of egg incubation. To trace cells which give rise to the coronary arteries in vivo, we applied retroviral cell tagging procedures and analyzed clonal populations of vascular smooth muscle, endothelium, and connective tissue in the hearts of post-hatch chickens. Our data provide direct proof that (i) vascular smooth muscle progenitors begin to enter the heart at stage 17, substantially after the heart begins propulsive contractions; (ii) cardiac myocytes, vascular smooth muscle, perivascular fibroblasts, and coronary endothelial cells all derive from independent precursors when these cells migrate into the heart; (iii) endothelial cells of the coronary vessels have a different clonal origin than endothelial cells of the endocardium; (iv) coronary arteries form by the coalescence of discontinuous colonies (i.e., in situ vasculogenesis), each derived from a founder cell tagged at the time of retroviral injection (stages 17-18); and (v) coronary arteries contain discrete segments composed of "polyclones." These studies indicate the feasibility of gene targeting to coronary progenitors through the use of recombinant retroviruses.
A low-cost WDM source with an ASE injected Fabry-Perot semiconductor laser (2000)

We propose and demonstrate a novel wavelength-division-multiplexing (WDM) source employing an uncooled and unisolated Fabry-Perot semiconductor laser diode (F-P SLD). The output wavelength of F-P SLD is locked to the externally injected narrow-band amplified spontaneous emission (ASE). The measured side-mode suppression ratio of the wavelength-locked F-P SLD is larger than 29 dB, when the extinction ratio of the directly modulated light output is above 13 dB. We achieved error-free transmission of 155-Mb/s data over 120 km of nondispersion-shifted fiber. We also propose a cost-effective WDM passive optical network architecture based on the proposed light sources.