gebhart/patrepeval huggingface dataset:
Getting Down to Earth: The Renaissance of Catalysis with Abundant Metals (2015)

ADVERTISEMENT RETURN TO ISSUEEditorialNEXTGetting Down to Earth: The Renaissance of Catalysis with Abundant MetalsPaul Chirik and Robert MorrisView Author Information Princeton University University of TorontoCite this: Acc. Chem. Res. 2015, 48, 9, 2495Publication Date (Web):September 15, 2015Publication History Published online15 September 2015Published inissue 15 September 2015https://pubs.acs.org/doi/10.1021/acs.accounts.5b00385https://doi.org/10.1021/acs.accounts.5b00385editorialACS PublicationsCopyright © 2015 American Chemical Society. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views8805Altmetric-Citations313LEARN 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 PDF (125 KB) Get e-AlertscloseSUBJECTS:Catalysis,Catalysts,Iron,Ligands,Metals Get e-Alerts
Selective Modulators of PPAR-γActivity: Molecular Aspects Related to Obesity and Side-Effects (2007)

Peroxisome proliferator-activated receptor gamma (PPAR-gamma) is a key regulator of lipid metabolism and energy balance implicated in the development of insulin resistance and obesity. The identification of putative natural and synthetic ligands and activators of PPAR-gamma has helped to unravel the molecular basis of its function, including molecular details regarding ligand binding, conformational changes of the receptor, and cofactor binding, leading to the emergence of the concept of selective PPAR-gamma modulators (SPPARgammaMs). SPPARgammaMs bind in distinct manners to the ligand-binding pocket of PPAR-gamma, leading to alternative receptor conformations, differential cofactor recruitment/displacement, differential gene expression, and ultimately differential biological responses. Based on this concept, new and improved antidiabetic agents for the treatment of diabetes are in development. This review summarizes the current knowledge on the mechanism of action and biological effects of recently characterized SPPARgammaMs, including metaglidasen/halofenate, PA-082, and the angiotensin receptor antagonists, recently characterized as a new class of SPPARgammaMs.
Abbott TDx monoclonal antibody assay evaluated for measuring cyclosporine in whole blood (1990)

Abstract We report here the evaluation of the Abbott TDx assay with a monoclonal antibody for selectively quantifying cyclosporine (CsA) in whole blood. Over the clinically relevant concentration ranges, results with this assay demonstrated within- and between-run CVs of less than 2.5% and 5%, respectively; sensitivity of 25 micrograms/L; good analytical recovery (100.3%); and linearity with whole-blood specimens. The percentage cross-reactivity of the major CsA metabolites varied from 15.3% for AM9 (M-1), 8.2% for AM1 (M-17), and 3.7% for AM4N (M-21), to less than 3% for the other metabolites tested. Results with the TDx assay (y) correlated well with those by the Sandimmune selective RIA (x; Sandoz) with blood specimens from 44 renal-transplant recipients (n = 44, x= 187.3, y = 198.9, y = 5.49 + 1.03x, r = 0.987). The TDx values were on average 24% higher than those by HPLC (x') with the same patients' specimens (n = 44, x' = 159.9, y = 198.9, y = 15.9 + 1.14x', r = 0.967). We conclude that the Abbott TDx monoclonal antibody assay provides a rapid, precise, and accurate means for quantifying CsA in whole blood.
IKK-i, a novel lipopolysaccharide-inducible kinase that is related to IκB kinases (1999)

Using the suppression subtractive hybridization technique, we isolated a novel kinase, IKK-i, whose message is drastically induced by lipopolysaccharide (LPS) in the mouse macrophage cell line RAW264. 7. The predicted protein contains the kinase domain in its N-terminus, which shares 30% identity to that of IKK-alpha or IKK-beta. The C-terminal portion contains a leucine zipper and a potential helix-loop-helix domain, as in the case of IKK-alpha and IKK-beta. IKK-i is expressed mainly in immune cells, and is induced in response to proinflammatory cytokines such as tumor necrosis factor-alpha, IL-1 and IL-6, in addition to LPS. Overexpression of wild-type IKK-i phosphorylated serine residues Ser32 and Ser36 of IkappaB-alpha (preferentially Ser36), and significantly stimulated NF-kappaB activation. These results suggest that IKK-i is an inducible IkappaB kinase which may play a special role in the immune response.
Direct writing of fibre Bragg gratings by femtosecond laser (2004)

Direct, point-by-point inscription of fibre Bragg gratings by infrared femtosecond laser is reported for the first time. Gratings of first to third order have been produced in non-photosensitised, standard telecommunication fibre and dispersion shifted fibre.
Improving the Density of Jammed Disordered Packings Using Ellipsoids (2004)

Packing problems, such as how densely objects can fill a volume, are among the most ancient and persistent problems in mathematics and science. For equal spheres, it has only recently been proved that the face-centered cubic lattice has the highest possible packing fraction phi=pi/18 approximately 0.74. It is also well known that certain random (amorphous) jammed packings have phi approximately 0.64. Here, we show experimentally and with a new simulation algorithm that ellipsoids can randomly pack more densely-up to phi= 0.68 to 0.71 for spheroids with an aspect ratio close to that of M&M's Candies-and even approach phi approximately 0.74 for ellipsoids with other aspect ratios. We suggest that the higher density is directly related to the higher number of degrees of freedom per particle and thus the larger number of particle contacts required to mechanically stabilize the packing. We measured the number of contacts per particle Z approximately 10 for our spheroids, as compared to Z approximately 6 for spheres. Our results have implications for a broad range of scientific disciplines, including the properties of granular media and ceramics, glass formation, and discrete geometry.
Targeting signal and subcellular compartments involved in the intracellular trafficking of HLA-DMB (1996)

Evidence suggests that peptide loading onto MHC class II molecules occurs in a specialized late endocytic compartment (MIIC) where HLA-DM predominantly resides and in which MHC class II transiently accumulates before transport to the cell surface. We examined the targeting signals and compartments involved in the intracellular trafficking of human HLA-DM by expressing hybrid molecules comprising the cytoplasmic domain of DMB and luminal and transmembrane domains of CD8 in HeLa cells. A tyrosine-based tetrapeptide motif present in the cytoplasmic domain of DMB targeted hybrid molecules to intracellular vesicles. Mutation of the tyrosine residue to alanine resulted in redistribution of hybrid molecules to the cell surface. Correct intracellular targeting of HLA-DM was crucial for normal function in B cells. Immunoelectron microscopy on ultrathin cryosections showed that CD8-DMB molecules accumulated in late endocytic compartments sharing characteristics with lysosomes, like MHC class II compartments in APCs. Thus far, the exit of DMB from the Golgi complex has not been elucidated. Interestingly, we found that although the mannose 6-phosphate receptor and CD8-DMB contain similar tyrosine signals, no co-localization was observed in the trans-Golgi network, suggesting that these proteins are differentially sorted at this site. Co-transfection of CD8-DMB, HLA-DR alpha, HLA-DR beta, and an invariant chain revealed that HLA-DR molecules accumulated together with CD8-DMB in these lysosomal compartments. The similarity of these lysosomal-like compartments in wild-type and transfected cells suggests that they are part of the normal endocytic pathway in non-APCs.
Photoreceptor characteristics in congenic strains of RCS rats. (1981)

Three congenic Royal College of Surgeons (RCS) strains of rats have been developed: the RCS-p+ strain, which is a black-eyed dystrophic strain; the pink-eyed RCS-rdy+ strain, which is wild-type (+/+) at the retinal dystrophy (rdy) genetic locus and serves as the control for the inbred, pink-eyed RCS strain; and the black-eyed RCS-rdy+p+ strain, which is +/+ at the rdy locus and serves as the control for the black-eyed RCS-p+ line. Several cytologic features of the photoreceptors were examined in the two control strains, including percentage of cone cells, rod outer segment lengths in different hemispheres of the eye and in different lighting conditions, rate of rod outer segment renewal, and the cyclic pattern of rod outer segment disc shedding. In the pink-eyed RCS-rdy+ strain these features were the same as those in previously described albino rat strains. Most of these features have not been described previously in fully pigmented rats. In the black-eyed RCS-rdy+p+ strain, rod outer segments in the superior eye hemisphere were about 50% longer than those in the inferior hemisphere. The rate of rod outer segment disc synthesis was the same in both hemispheres. Consequently, rod outer segment renewal time depended on outer segment length. This ranged from 9 to 10 days in the inferior hemisphere to 14.6 days in the superior hemisphere.
Bacterial lipopolysaccharide stimulates the production of cytokines and the expression of costimulatory molecules by human peripheral blood dendritic cells: evidence for a soluble CD14-dependent pathway (1997)

To investigate the responses of dendritic cells (DC) during Gram-negative infections, we analyzed the effects of graded doses of LPS on the cytokine profile, phenotype, and allostimulatory potential of human DC generated by culturing plastic-adherent PBMC in presence of IL-4 and granulocyte-macrophage-CSF. First, we found that LPS stimulates the production of high levels of TNF-alpha, IL-6, IL-8, IL-12 by DC and up-regulates their expression of HLA-DR, B7-1, B7-2, and CD40. The effects of LPS were dose dependent, with a significant stimulatory effect already observed at a concentration of 0.1 ng/ml and a plateau being reached at 10 ng/ml. These phenotypic changes correlated with increased allostimulatory properties of LPS-activated DC because DC treated with LPS were significantly more efficient than untreated DC in eliciting IL-2 and IFN-gamma synthesis by alloreactive T cells and stimulating their proliferation. Experiments using neutralizing anti-IL-12 mAb indicated that LPS-induced IL-12 is responsible for the increased production of IFN-gamma but not for the increased proliferation during MLR. Finally, we observed that the DC responses to low levels of LPS (1 ng/ml) were dramatically inhibited by a blocking anti-CD14 mAb, although DC do not express CD14 molecules on their membrane. Experiments using serum depleted of soluble CD14 (sCD14) and sCD14 either purified from human serum or in recombinant form further established that DC respond to LPS via a soluble CD14-dependent pathway.
A Phase I and Pharmacodynamic Study of Fludarabine, Carboplatin, and Topotecan in Patients With Relapsed, Refractory, or High-Risk Acute Leukemia (2004)

Fludarabine, carboplatin, topotecan regimen is a promising treatment based on potential pharmacodynamic interactions, which merits additional study in poor prognosis, acute leukemia patients.
Defects in m-face GaN films grown by halide vapor phase epitaxy on LiAlO2 (2003)

Free-standing wafers (50 mm diameter) of GaN were grown by halide vapor phase epitaxy on lattice-matched γ-LiAlO2. We report a transmission electron microscopy study of defects and defect densities in these wafers. The growth direction is [101_0]. Stacking faults in the basal plane are seen when viewing the specimen in the [12_10] direction with an average spacing of less than 100 nm. Convergent beam electron diffraction measurements show no switch in the polarity and thus the faults are proposed to be ABABACAC changes in the stacking. Threading dislocations are found to have a correlated arrangement with a density of 3×108 cm−2 when viewing the [12_10] direction and widely varying (depending upon location) when viewing in the [0001] direction. These dislocations act as “seeds” for postgrowth surface features that directly exhibit the correlated nature of these threading dislocations.
Hematopoietic differentiation of human embryonic stem cells progresses through sequential hematoendothelial, primitive, and definitive stages resembling human yolk sac development (2005)

We elucidate the cellular and molecular kinetics of the stepwise differentiation of human embryonic stem cells (hESCs) to primitive and definitive erythromyelopoiesis from human embryoid bodies (hEBs) in serum-free clonogenic assays. Hematopoiesis initiates from CD45 hEB cells with emergence of semiadherent mesodermal-hematoendothelial (MHE) colonies that can generate endothelium and form organized, yolk sac-like structures that secondarily generate multipotent primitive hematopoietic stem progenitor cells (HSPCs), erythroblasts, and CD13+CD45+ macrophages. A first wave of hematopoiesis follows MHE colony emergence and is predominated by primitive erythropoiesis characterized by a brilliant red hemoglobinization, CD71/CD325a (glycophorin A) expression, and exclusively embryonic/fetal hemoglobin expression. A second wave of definitive-type erythroid burst-forming units (BFU-e's), erythroid colony-forming units (CFU-e's), granulocyte-macrophage colony-forming cells (GM-CFCs), and multilineage CFCs follows next from hEB progenitors. These stages of hematopoiesis proceed spontaneously from hEB-derived cells without requirement for supplemental growth factors during hEB differentiation. Gene expression analysis of differentiating hEBs revealed that initiation of hematopoiesis correlated with increased levels of SCL/TAL1, GATA1, GATA2, CD34, CD31, and the homeobox gene-regulating factor CDX4 These data indicate that hematopoietic differentiation of hESCs models the earliest events of embryonic and definitive hematopoiesis in a manner resembling human yolk sac development, thus providing a valuable tool for dissecting the earliest events in human HSPC genesis.
Amino-terminally Modified RANTES Analogues Demonstrate Differential Effects on RANTES Receptors (1999)

Modification of the amino terminus of regulated on activated normal T-cell expressed (RANTES) has been shown to have a significant effect on biological activity and produces proteins with antagonist properties. Two amino-terminally modified RANTES proteins, Met-RANTES and aminooxypentane-RANTES (AOP-RANTES), exhibit differential inhibitory properties on both monocyte and eosinophil chemotaxis. We have investigated their binding properties as well as their ability to activate the RANTES receptors CCR1, CCR3, and CCR5 in cell lines overexpressing these receptors. We show that Met-RANTES has weak activity in eliciting a calcium response in Chinese hamster ovary cells expressing CCR1, CCR3, and CCR5, whereas AOP-RANTES has full agonist activity on CCR5 but is less effective on CCR3 and CCR1. Their ability to induce chemotaxis of the murine pre-B lymphoma cell line, L1.2, transfected with the same receptors, consolidates these results. Monocytes have detectable mRNA for CCR1, CCR2, CCR3, CCR4, and CCR5, and they respond to the ligands for these receptors in chemotaxis but not always in calcium mobilization. AOP-RANTES does not induce calcium mobilization in circulating monocytes but is able to do so as these cells acquire the macrophage phenotype, which coincides with a concomitant up-regulation of CCR5. We have also tested the ability of both modified proteins to induce chemotaxis of freshly isolated monocytes and eosinophils. Cells from most donors do not respond, but occasionally cells from a particular donor do respond, particularly to AOP-RANTES. We therefore hypothesize that the occasional activity of AOP-RANTES to induce leukocyte chemotaxis is due to donor to donor variation of receptor expression.
Dynamics of charge transport and recombination in ZnO nanorod array dye-sensitized solar cells (2006)

Intensity modulated photovoltage and photocurrent spectroscopies reveal that photoanodes based on nanorod arrays exhibit dramatically faster electron transport while retaining similar electron lifetimes (recombination times) compared to standard photoanodes assembled from colloidal nanoparticles.
Crystal structures of Escherichia coli and Lactobacillus casei dihydrofolate reductase refined at 1.7 A resolution. I. General features and binding of methotrexate. (1982)

X-ray data have been extended to 1.7 A for a binary complex of Escherichia coli dihydrofolate reductase with methotrexate and a ternary complex of Lactobacillus casei dihydrofolate reductase with methotrexate and NADPH. Models for both structures have been refined to R factors of 0.15 and include parameters for fixed and liquid solvent. The two species of dihydrofolate reductase resemble one another even more closely than was thought to be the case prior to refinement. Several new structural features have also been discovered. Among them are a cis peptide linking Gly-97 and Gly-98 (L. Casei numbering) in both species, an alpha helix involving residues 43 through 50 in the E. coli enzyme, and the existence of what may be a specific hydration site on exposed alpha helices. Refinement has led to a revised description of the details of methotrexate binding. We now see that a fixed water molecule mediates the interaction between methotrexate's 2-amino group and Thr-116 (L. casei numbering) and that the inhibitor's 4-amino group makes two hydrogen bonds with the enzyme (instead of one). Other revisions are also discussed. A hypothetical model for substrate binding is proposed in which the pteridine ring is turned upside down while all protein and solvent atoms remain fixed. Asp-26 in this model is hydrogen bonded to the substrate's 2-amino group and to N3.
Completing the job interface design (1992)

HyperNews, a user-interface management system that lets a user separate application and interface design to link a new interface to an old application with very little programming, is described. Much of a HyperNews interface can be designed without writing any code at all. With direct manipulation, a user can design a graphical user interface simply by creating, moving, and resizing objects on the screen. Experimentation with different interface styles is possible with less effort in HyperNews compared to specification languages and tool kits, and immediate feedback can result in extremely fast development. The ways HyperNews provides communication capabilities among all HyperNews objects (such as control objects, cards, backgrounds, and stacks) and links interfaces to internal applications, which were developed within HyperNews, to external applications, or to existing applications developed without HyperNews are discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Ripple (˜200-Hz) Oscillations in Temporal Structures (2000)

Spontaneous network oscillations near 200 Hz have been described in the hippocampus and parahippocampal regions of rodents and humans. During the last decade the characteristics and the mechanisms behind these field "ripples" have been studied extensively, mainly in rodents. They occur during rest or slow-wave sleep and provide a very fast, short-lasting (approximately 50 msec) rhythmic and synchronous activation of specific projection cells and interneurons. Ripples are frequently triggered by a massive synaptic activation from the hippocampal CA3 subfield, which is called a sharp wave. Recent evidence suggests that ripples have a specific task in memory processing-namely, that they convey information stored in the hippocampus to the cortex where it can be preserved permanently. Network mechanisms involved in ripple oscillations may be relevant for understanding pathologic synchronization processes in temporal lobe epilepsy.
An evaluation of the role of internal energy and translational energy in the endothermic proton transfer reaction of N2H+ with Kr (1984)

The Innsbruck SIDT (selected ion drift tube), now modified to include an octupole guided beam region, has been utilized to investigate the title reaction using both virbationally excited and ground state N2H+. Rate constants measured for three distinguishable proton transfers at a field strength of 40 Td are 1.1×10−9, 2.7×10−10, and 1.3×10−11 cm3 s−1. These are assigned to the exothermic proton transfer reaction N2H+ (X,v=2)+Kr→KrH++N2 and the endothermic reactions of N2H+ (X,v=1) and N2H+ (X,v=0), respectively. This assignment is supported by studies of the kinetic energy dependence of the rate coefficients and the collisonal relaxation of excited N2H+ ions with N2. The latter process is characterized by a large rate coefficient kr=3×10−10 cm3 s−1 approximately one-third the collision rate coefficient.
Cytokine Dialysis: An Ex Vivo Study (2002)

To test the hypothesis that dialysis using a new large pore membrane would achieve effective cytokine removal, blood from six volunteers was incubated with endotoxin (1 mg) and then circulated through a closed circuit with a polyamide membrane (nominal cut-off: 100 kDa). Hemodialysis was conducted at 1 or 9 L/hr of dialysate flow at the start of circulation and after 2 and 4 hours. The peak dialysate/plasma concentration ratios were 0.92 for interleukin (IL)-1beta, 0.67 for IL-6, 0.94 for IL-8, 0.33 for tumor necrosis factor (TNF)-a, and 0.11 for albumin. The dialysate/plasma ratios for all cytokines and albumin were decreased with increased dialysate flow from 1 to 9 L/hr (p < 0.05). Clearances for IL-1beta, IL-6, and IL-8, however, were significantly improved with increased dialysate flow (p < 0.01). There was no increase in TNF-a clearance (not significant) and a decrease in albumin clearance (p < 0.01). The peak clearance at 9 L/hr was 33 ml/min for IL-1beta, 19 for IL-6, 51 for IL-8, 11 for TNF-alpha, and 1.2 for albumin. No adsorption of cytokines was observed. We conclude that cytokine dialysis is achievable through a membrane with a high cut-off point with negligible albumin loss. These findings support the technical feasibility of this new approach to blood purification in sepsis.
ChimeraScan: a tool for identifying chimeric transcription in sequencing data (2011)

Supplementary data are available at Bioinformatics online.