gebhart/patrepeval huggingface dataset:
Comparative study of Cu(II) catalytic sites immobilized onto different polymeric supports (2003)

Abstract The catalysts with copper(II) ions stabilized onto different polymeric matrixes are prepared on either bulk (Cu/chitosan, Cu/polyethyleneimine‐polyacrylic acid (PPA), and Cu‐diiminate‐impregnated polystyrene, polyarylate, or polymethylmethacrylate) or composite supports (egg‐shell type Cu/chitosan/SiO 2 and Cu/PPA/SiO 2 ). The morphology of the samples and peculiarities of Cu(II) cationic sites are studied by SEM and ESR methods, and the catalyst activities are compared in oxidation of o ‐ and p ‐dihydroxybenzenes by air in water. The catalytic activity of Cu(II) centers is governed by the coordination of isolated copper ions: for the most active catalysts, i.e., Cu/chitosan and Cu/PPA, the symmetry of isolated Cu 2+ ‐sites approximates a coordinatively unsaturated square‐planar structure. At the same time, accessibility of active sites to water differs for different polymers, so the contribution of hydrophilicity to the reaction pattern cannot be excluded. Redox transformations of the active sites in the course of catalytic tests do not cause copper leaching from the polymer matrix. The binary composite systems with a film of low‐loaded hydrofilic Cu‐polymer supported on macroporous SiO 2 demonstrate substantially higher activity in oxidation of hydroquinone and 3,4‐dihydroxyphenylalanine, as compared with the bulk Cu/polymer samples. In turn, the specific activity of Cu/chitosan/SiO 2 exceeds significantly that of Cu/PPA/SiO 2 due to stabilization of a thinner and more uniform film of chitosan at the surface of silica.
A Practical Synthesis of 1,3-Oxazole (2000)

A short synthesis of oxazole (1,3-oxazole, 1) is described.1,3-Oxazole, also known simply as oxazole (1), is a low-boiling (69-70˚ C) member of the π-rich aromatic five-membered heterocycles with a characteristic 'pyridine-like' odor. 1 Oxazole is not found in nature in the free state, but the ring is usually encountered as 2,4-disubstituted oxazoles within the structures of complex biologically active natural products produced by certain bacteria and marine invertebrates.The latter include the exceedingly cytostatic agents, phorboxazoles A and B (IC 50 's ~10 -10 M), 2 and antifungal alkaloids, bengazoles. 3It has been shown that 2,4-disubstituted oxazoles are formally biosynthesized from acylserine precursors by enzyme catalyzed cyclodehydration-oxidation. 4 N O 1 1,3-oxazoleMost synthetic methods for generation of 2,4-disubstituted oxazoles are biomimetic variations on the latter sequence.We have described recently an alternative strategy to the synthesis of 2,4-disubstituted oxazole natural products that takes advantage of a directed two-step lithiation-electrophilic addition procedure by 'grafting' the substituents directly onto the parent heterocycle 1. 5 The utility of the grafting approach in synthesis of biologically active oxazole-containing natural products opens new vistas for substituted oxazole synthesis and has made 1 a timely commodity.Unfortunately, 1 is no longer commercially available and, because the literature syntheses of 1 are not trivial undertakings, a practical synthesis of 1 is now of contemporary interest.The classic Cornforth synthesis of 1 6 describes a five-step sequence beginning with glycine ethyl ester hydrochloride and O-isopropyl formimidate and proceeds through ethyl oxazole-4-carboxylate (2) to afford
Survey of Dogs From Vietnam for Antibodies to Visceralizing Leishmania spp (2009)

Cases of visceral leishmaniasis, one of the most neglected tropical diseases, are increasing globally. Dogs are considered an important reservoir host for visceral leishmaniasis in people. The first cases of human visceral leishmaniasis in Vietnam have recently been reported. Blood samples were collected from 41 dogs in rural Vietnam. Sera were examined for antibodies to visceralizing Leishmania spp. by canine immunochromatographic strip assays based on recombinant K39 antigen. Antibodies to Leishmania spp. were not detected in any of the dogs tested. Results from this study suggest that rural dogs are not likely to be involved in the emergence of human visceral leishmaniasis in Vietnam.
Bidirectional induction of the cognate receptor-ligand α4/VCAM-1 pair defines a novel mechanism of tumor intravasation (2000)

Engagement of cell surface adhesion receptors with extracellular constituents and with cellular counter-receptors is crucial for the extravasation of blood-borne neoplastic cells and their seeding at distant sites; however, the early events of tumor dissemination—ie, the intravasation step(s)—have been largely neglected. A role for the 4β7 integrin was hypothesized to explain the high leukemogenicity exhibited by one (NQ22) among several T-cell lymphomas studied. To clarify the mechanisms of early aggressivity, the behavior of highly and poorly leukemogenic cell lines were compared in vitro. Cocultivation of physically separated leukemic cells with resting endothelial cells resulted in the up-regulation of VCAM-1 expression. NQ22 cells expressed mRNA of different cytokines that up-regulate VCAM-1 and at higher levels than cells of a nonaggressive lymphoma, and they migrated more efficiently through an activated endothelial cell layer. With the use of neutralizing antibodies against interferon-γ, granulocyte macrophage colony-stimulating factor, and tumor necrosis factor (TNF)-, it was determined that TNF- is one of the soluble factors released by NQ22 cells involved in the up-regulation of VCAM-1. The finding that vascular cells within the early local growth were strongly positive for VCAM-1 indicated that NQ22 cells could activate endothelial cells also in vivo. Finally, cocultivation of preleukemic 4−NQ22 cells with TNF--activated endothelial cells induced the expression of 4 integrins on the former cells. Reciprocal up-regulation and engagement of 4/VCAM-1 pairs determined the sequential transmigration and intravasation steps, and similar mechanisms might affect the aggressivity of human T lymphoblastic lymphomas.
Unique peptidic agonists of a juvenile hormone receptor with species-specific effects on insect development and reproduction (2022)

Juvenile hormones (JHs) control insect metamorphosis and reproduction. JHs act through a receptor complex consisting of methoprene-tolerant (Met) and taiman (Tai) proteins to induce transcription of specific genes. Among chemically diverse synthetic JH mimics (juvenoids), some of which serve as insecticides, unique peptidic juvenoids stand out as being highly potent yet exquisitely selective to a specific family of true bugs. Their mode of action is unknown. Here we demonstrate that, like established JH receptor agonists, peptidic juvenoids act upon the JHR Met to halt metamorphosis in larvae of the linden bug, <i>Pyrrhocoris apterus</i>. Peptidic juvenoids induced ligand-dependent dimerization between Met and Tai proteins from <i>P. apterus</i> but, consistent with their selectivity, not from other insects. A cell-based split-luciferase system revealed that the Met-Tai complex assembled within minutes of agonist presence. To explore the potential of juvenoid peptides, we synthesized 120 new derivatives and tested them in Met-Tai interaction assays. While many substituents led to loss of activity, improved derivatives active at sub-nanomolar range outperformed hitherto existing peptidic and classical juvenoids including fenoxycarb. Their potency in inducing Met-Tai interaction corresponded with the capacity to block metamorphosis in <i>P. apterus</i> larvae and to stimulate oogenesis in reproductively arrested adult females. Molecular modeling demonstrated that the high potency correlates with high affinity. This is a result of malleability of the ligand-binding pocket of <i>P. apterus</i> Met that allows larger peptidic ligands to maximize their contact surface. Our data establish peptidic juvenoids as highly potent and species-selective novel JHR agonists.
Tracking the Evolution of MultipleIn VitroHepatitis C Virus Replicon Variants under Protease Inhibitor Selection Pressure by 454 Deep Sequencing (2010)

Resistance to hepatitis C virus (HCV) inhibitors targeting viral enzymes has been observed in in vitro replicon studies and during clinical trials. The factors determining the emergence of resistance and the changes in the viral quasispecies population under selective pressure are not fully understood. To assess the dynamics of variants emerging in vitro under various selective pressures with TMC380765, a potent macrocyclic HCV NS3/4A protease inhibitor, HCV genotype 1b replicon-containing cells were cultured in the presence of a low, high, or stepwise-increasing TMC380765 concentration(s). HCV replicon RNA from representative samples thus obtained was analyzed using (i) population, (ii) clonal, and (iii) 454 deep sequencing technologies. Depending on the concentration of TMC380765, distinct mutational patterns emerged. In particular, culturing with low concentrations resulted in the selection of low-level resistance mutations (F43S and A156G), whereas high concentrations resulted in the selection of high-level resistance mutations (A156V, D168V, and D168A). Clonal and 454 deep sequencing analysis of the replicon RNA allowed the identification of low-frequency preexisting mutations possibly contributing to the mutational pattern that emerged. Stepwise-increasing TMC380765 concentrations resulted in the emergence and disappearance of multiple replicon variants in response to the changing selection pressure. Moreover, two different codons for the wild-type amino acids were observed at certain NS3 positions within one population of replicons, which may contribute to the emerging mutational patterns. Deep sequencing technologies enabled the study of minority variants present in the HCV quasispecies population present at baseline and during antiviral drug pressure, giving new insights into the dynamics of resistance acquisition by HCV.
MicroRNAs and hepatitis C virus: Toward the end of miR-122 supremacy (2012)

The most common etiologic agents causing chronic hepatitis are hepatitis C and B viruses (HCV and HBV, respectively). Chronic infection caused by HCV is considered one of the major causative agents of liver cirrhosis and hepatocellular carcinoma worldwide. In combination with the increasing rate of new HCV infections, the lack of a current vaccine and/or an effective treatment for this virus continues to be a major public health challenge. The development of new treatments requires a better understanding of the virus and its interaction with the different components of the host cell. MicroRNAs (miRNAs) are small non-coding RNAs functioning as negative regulators of gene expression and represent an interesting lead to study HCV infection and to identify new therapeutic targets. Until now, microRNA-122 (miR-122) and its implication in HCV infection have been the focus of different published studies and reviews. Here we will review recent advances in the relationship between HCV infection and miRNAs, showing that some of them emerge in publications as challengers against the supremacy of miR-122.
Recombinant somatropin in treatment of growth hormone deficient children in Sweden and Finland. (1988)

A total of 23 previously untreated and 28 previously treated GH deficient children were included for at least 12 months in a trial of recombinant somatropin, 0.1 IU/kg/day given by subcutaneous injection. All the children increased their height velocity over the pretreatment values, to nearly 11 cm/year, corresponding to a significant increase in height of 1 SD score for chronological age. The increase in height SD score for bone age was also statistically significant. No adverse effects were recorded, though one child experienced local itching and redness at the injection site which did not recur after a short cessation of therapy. One child developed detectable antibodies to recombinant somatropin, but the binding capacity was low and no clinical symptoms or growth attenuation occurred. Recombinant somatropin was shown to be safe and effective during the first year of therapy in children with GH deficiency.
Comparative study on thermal robustness of GaN and AlGaN/GaN MOS devices with thin oxide interlayers (2019)

Abstract Similarities and differences in the design of the interfaces between gate dielectrics and GaN-based semiconductors were systematically investigated with a focus on the thermal stability of the interlayers. Although the excellent electrical properties of a SiO 2 /GaN interface with a thin Ga-oxide interlayer (SiO 2 /GaO x /GaN) were deteriorated by high-temperature treatment at around 1000 °C, the thin oxide on the AlGaN surface (SiO 2 /GaO x /AlGaN) exhibited superior thermal stability and interface quality even after treatment at 1000 °C. Physical characterizations showed that thermal decomposition of the thin GaO x layer on the GaN surface is promoted by oxygen transfer, which produces volatile products, leading to remarkable roughening of the GaN surface. In contrast, decomposition of the thin GaO x layer was suppressed on the AlGaN surface under the high temperatures, preserving a smooth oxide surface. The mechanisms behind both the improved and degraded electrical properties in these GaN-based MOS structures are discussed on the basis of these findings.
Advances in Mixed Precision Algorithms: 2021 Edition (2021)

Over the last year, the ECP xSDK-multiprecision effort has made tremendous progress in developing and deploying new mixed precision technology and customizing the algorithms for the hardware deployed in the ECP flagship supercomputers. The effort also has succeeded in creating a cross-laboratory community of scientists interested in mixed precision technology and now working together in deploying this technology for ECP applications. In this report, we highlight some of the most promising and impactful achievements of the last year. Among the highlights we present are: Mixed precision IR using a dense LU factorization and achieving a 1.8× speedup on Spock; results and strategies for mixed precision IR using a sparse LU factorization; a mixed precision eigenvalue solver; Mixed Precision GMRES-IR being deployed in Trilinos, and achieving a speedup of 1.4× over standard GMRES; compressed Basis (CB) GMRES being deployed in Ginkgo and achieving an average 1.4× speedup over standard GMRES; preparing hypre for mixed precision execution; mixed precision sparse approximate inverse preconditioners achieving an average speedup of 1.2×; and detailed description of the memory accessor separating the arithmetic precision from the memory precision, and enabling memory-bound low precision BLAS 1/2 operations to increase the accuracy by using high precision in the computations without degrading the performance. We emphasize that many of the highlights presented here have also been submitted to peer-reviewed journals or established conferences, and are under peer-review or have already been published.
Characterization of the Envelope Glycoproteins Associated with Infectious Hepatitis C Virus (2010)

Hepatitis C is caused by an enveloped virus whose entry is mediated by two glycoproteins, namely, E1 and E2, which have been shown to assemble as a noncovalent heterodimer. Despite extensive research in the field of such an important human pathogen, hepatitis C virus (HCV) glycoproteins have only been studied so far in heterologous expression systems, and their organization at the surfaces of infectious virions has not yet been described. Here, we characterized the envelope glycoproteins associated with cell-cultured infectious virions and compared them with their prebudding counterparts. Viral particles were analyzed by ultracentrifugation, and the envelope glycoproteins were characterized by coimmunoprecipitation and receptor pulldown assays. Furthermore, their oligomeric state was determined by sedimentation through sucrose gradients and by separation by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) under nonreducing conditions. In sucrose gradient analyses, HCV envelope glycoproteins were associated with fractions containing the most infectious viral particles. Importantly, besides maturation of some of their glycans, HCV envelope glycoproteins showed a dramatic change in their oligomeric state after incorporation into the viral particle. Indeed, virion-associated E1 and E2 envelope glycoproteins formed large covalent complexes stabilized by disulfide bridges, whereas the intracellular forms of these proteins assembled as noncovalent heterodimers. Furthermore, the virion-associated glycoprotein complexes were recognized by the large extracellular loop of CD81 as well as conformation-sensitive antibodies, indicating that these proteins are in a functional conformation. Overall, our study fills a gap in the description of HCV outer morphology and should guide further investigations into virus entry and assembly.
Asymmetric Optical Connections for Improved Network Efficiency (2013)

Links in an IP network are unidirectional but currently are routed over bidirectional optical circuits with identical A&#x2192;Z and Z&#x2192;A capacities. Potentially there could be savings if the two directions of an optical circuit could be treated independently. In this study of possible savings, we have quantified the asymmetry of traffic on a current large IP backbone. A theoretical greenfield network with similarly asymmetric traffic is modeled, and it is shown that the use of unidirectional circuits to satisfy traffic demands provides significant equipment savings. We consider this study of the benefits of this approach to be a first step in deciding whether it makes economic sense to tackle the hurdles that would face such a major change in network design and operations.
Enhanced Flux Pinning in MOD Second Generation HTS Wires by Silver- and Copper-Ion Irradiation (2007)

We have studied the effect of medium-energy ion irradiation on flux pinning in second-generation HTS wires. Irradiation with 74 MeV silver ions and 50 MeV copper ions have produced up to 60% enhancements in critical current. The field-angle dependence shows enhancements over a wide angle range, suggesting that the irradiation defects are point-like defects rather than continuous columns. Such isotropic enhancements are generally preferable over narrow-angle anisotropic effects for wire applications. Ion irradiation can then be used to create a model population of defects to study concentration dependences. We present transport, magnetization, and TEM results to probe the nature of the defects formed by this irradiation.
Mating dynamics in a nematode with three sexes and its evolutionary implications (2015)

Nematodes have diverse reproductive strategies, which make them ideal subjects for comparative studies to address how mating systems evolve. Here we present the sex ratios and mating dynamics of the free-living nematode Rhabditis sp. SB347, in which males, females and hermaphrodites co-exist. The three sexes are produced by both selfing and outcrossing, and females tend to appear early in a mother's progeny. Males prefer mating with females over hermaphrodites, which our results suggest is related to the female-specific production of the sex pheromones ascr#1 and ascr#9. We discuss the parallels between this system and that of parasitic nematodes that exhibit alternation between uniparental and biparental reproduction.
The Terry Fox Research Institute Canadian Prostate Cancer Biomarker Network: an analysis of a pan-Canadian multi-center cohort for biomarker validation (2018)

The CPCBN RP cohort is representative of real world PC disease observed in the Canadian population. The frequency of biochemical relapse and bone metastasis as events allows for a precise assessment of the prognostic value of biomarkers. This resource is available, in a step-wise manner, for researchers who intend to validate prognostic biomarkers in PC. Combining multiple biomarkers with clinical and pathologic parameters that are predictive of outcome will aid in clinical decision-making for patients treated for PC.
Monitoring beacon for early or hidden fungal development detection dedicated to heritage conservation (2016)

International audience
ODAM Expression Inhibits Human Breast Cancer Tumorigenesis (2011)

We have posited that Odontogenic Ameloblast Associated Protein (ODAM) serves as a novel prognostic biomarker in breast cancer and now have investigated its potential role in regulating tumor growth and metastasis. Human breast cancer MDA-MB-231 cells were transfected with a recombinant ODAM plasmid construct (or, as a control, the plasmid vector alone). ODAM expression increased adhesion and apoptosis of the transfected MDA-MB-231 cells and suppressed their growth rate, migratory activity, and capability to invade extracellular matrix-coated membranes. Implantation of such cells into mouse mammary fat pads resulted in significantly smaller tumors than occurred in animals that received control cells; furthermore, ODAM-expressing cells, when injected intravenously into mice, failed to metastasize, whereas the control-transfected counterparts produced extensive lung lesions. Our finding that induction of ODAM expression in human breast cancer cells markedly inhibited their neoplastic properties provides further evidence for the regulatory role of this molecule in tumorigenesis and, consequently, is of potential clinical import.
Spark-Induced Breakdown Spectroscopy-Based Monitor for Hazardous Airborne Biological Material (2006)

Spark-induced breakdown spectroscopy (SIBS) is a LIBS-like method of measuring the elemental composition of a sample excited with an electrically-generated plasma. Recently SIBS has been applied to monitoring hazardous airborne biological materials in ambient air.
Site-Specific Antibody Functionalization Using Tetrazine–Styrene Cycloaddition (2018)

Biologics, such as antibody-drug conjugates, are becoming mainstream therapeutics. Consequently, methods to functionalize biologics without disrupting their native properties are essential for identifying, characterizing, and translating candidate biologics from the bench to clinical practice. Here, we present a method for site-specific, carboxy-terminal modification of single-chain antibody fragments (scFvs). ScFvs displayed on the surface of yeast were isolated and functionalized by combining intein-mediated expressed protein ligation (EPL) with inverse electron-demand Diels-Alder (IEDDA) cycloaddition using a styrene-tetrazine pair. The high thiol concentration required to trigger EPL can hinder the subsequent chemoselective ligation reactions; therefore, the EPL reaction was used to append styrene to the scFv, limiting tetrazine exposure to damaging thiols. Subsequently, the styrene-functionalized scFv was reacted with tetrazine-conjugated compounds in an IEDDA cycloaddition to generate functionalized scFvs that retain their native binding activity. Rapid functionalization of yeast surface-derived scFv in a site-directed manner could find utility in many downstream laboratory and preclinical applications.
Institutions in Global Distributive Justice (2013)

The first systematic treatment of the role of institutions in cosmopolitan theories of distributive justiceDefining an institution as a public system of rules that sets out positions, rights and duties, Andras Miklos uses a philosophical argument to analyse the roles that social, economic and political institutions play in conditioning the justification, scope and content of principles of justice. He critically evaluates a number of positions about the role of institutions in generating requirements of distributive justice and considers their implications for the scope - global or otherwise - of justice. He then develops a new theory about the role political and economic institutions play in determining the content of requirements of distributive justice and, in a cosmopolitan argument against statist positions, shows how they can affect the scope of application of these requirements