gebhart/patrepeval huggingface dataset:
Impaired (S)-warfarin metabolism catalysed by the R144C allelic variant of CYP2C9 (1994)

Rettie, Allan E.; Wienkers, Larry C.; Gonzalez, Frank J.; Trager, William F.; Korzekwa, Kenneth R. Author Information
Negative resist profiles in 248 nm photolithography: experiment, modelling and simulation (1998)

We consider the effects both of exposure energy dose and of developer temperature on the developed negative resist profiles. The spin-formatted resist film tends to have macromolecules oriented parallel to the substrate surface. The orientation of the resist macromolecules introduces an anisotropic component to the etch rate: higher in the direction parallel to the substrate surface and lower in the perpendicular one. We performed a series of experiments for 400 nm pitch periodic and isolated lines on Shipley SNR-248 negative resist coated Si wafers using a stepper and a deep UV source at 248 nm. We obtained scanning electron micrographs for various developer temperatures and exposure doses. The variation of the lateral etch rate manifested itself in sidewall profile slopes. We used Dill's ABC parameter model to model and quantify the exposure, and cellular automata to model the resist cross-linking during post-exposure bake and the resist etching. Simulation using an algorithm based on this model validated the experimental results.
Aldol and Knoevenagel condensations catalysed by modified Mg–Al hydrotalcite: a solid base as catalyst useful in synthetic organic chemistry (1998)

Aldol and Knoevenagel condensations were performed with suitably activated Mg–Al hydrotalcite as catalyst in quantitative yields in the liquid phase under mild reaction conditions at a faster rate for the first time.
Role of Magnesium Chelatase Activity in the Early Steps of the Tetrapyrrole Biosynthetic Pathway (2000)

Magnesium-protoporphyrin IX chelatase (Mg-chelatase) is located at the branchpoint of tetrapyrrole biosynthesis, at which point protoporphyrin IX is distributed for the synthesis of chlorophyll and heme. We investigated the regulatory contribution of Mg-chelatase to the flow of metabolites. In plants, the enzyme complex consists of three subunits, designated CHL D, CHL I, and CHL H. Transgenic tobacco (Nicotiana tabacum) plants expressing antisense RNA for the Mg-chelatase subunit CHL H were analyzed to elucidate further the role of Mg-chelatase in the distribution of protoporphyrin IX into the branched tetrapyrrolic pathway. The transgenic plants displayed a reduced growth rate and chlorophyll deficiency. Both phenotypical properties were correlated with lower Mg-chelatase activity. Unexpectedly, less protoporphyrin IX and heme accumulated, and a decrease in 5-aminolevulinate (ALA)-synthesizing capacity and ALA dehydratase activity paralleled the progressive reduction in Mg-chelatase activity in the transformants compared with control plants. The reduced activities of the early enzymatic steps corresponded with lower levels of transcripts encoding glutamyl-tRNA reductase and ALA-dehydratase. The decreased expression and activities of early enzymes in the pathway could be explained by a feedback-controlled mechanism in response to lower Mg-chelatase activity. We discuss intercompartmental signaling that synchronizes the activities of the first steps in tetrapyrrolic metabolism with the late steps for the synthesis of end products.
Antibody Catalysis of the Oxidation of Water (2001)

Recently we reported that antibodies can generate hydrogen peroxide (H2O2) from singlet molecular oxygen (1O2*). We now show that this process is catalytic, and we identify the electron source for a quasi-unlimited generation of H2O2. Antibodies produce up to 500 mole equivalents of H2O2 from 1O2*, without a reduction in rate, and we have excluded metals or Cl- as the electron source. On the basis of isotope incorporation experiments and kinetic data, we propose that antibodies use H2O as an electron source, facilitating its addition to 1O2* to form H2O3 as the first intermediate in a reaction cascade that eventually leads to H2O2. X-ray crystallographic studies with xenon point to putative conserved oxygen binding sites within the antibody fold where this chemistry could be initiated. Our findings suggest a protective function of immunoglobulins against 1O2* and raise the question of whether the need to detoxify 1O2* has played a decisive role in the evolution of the immunoglobulin fold.
Longitudinal Changes in Leukocyte Telomere Length and Mortality in Humans (2013)

This study establishes that certain lifestyle factors influence LTL dynamics. However, it questions the applicability of LTL dynamics as a predictor of mortality. We suggest cautiousness when assessing actual LTL attrition due to the need for high-quality DNA and the phenomena of regression to the mean.
Antitumor effect and structure-activity relationship of asterriquinone analogs. (1982)

Asterriquinone (ARQ), a metabolic product from Aspergillus terreus IFO 6123, showed an inhibitory effect on some transplantable animal tumors, Ehrlich carcinoma, ascites hepatoma AH13 and mouse P388 leukemia, but had little or no effect on Yoshida sarcoma, ascites hepatoma AH109A and mouse L1210 leukemia. ARQ also inhibited the growth of HeLa cells in monolayer culture. Although metabolic products from Aspergillus terreus var. africanus IFO 8835 were almost ineffective against Ehrlich carcinoma, some chemically modified ARQ-like compounds were found to have potent inhibitory activity against the growth of the carcinoma in mice. The presence of free hydroxyl groups in the benzoquinone moiety and the number and position of tert-, iso-pentenyl, or both pentyl groups seem to be important in relation to the antitumor activity.
Automating System Configuration of Distributed Machine Learning (2019)

The performance of distributed machine learning systems is dependent on their system configuration. However, configuring the system for optimal performance is challenging and time consuming even for experts due to the diverse runtime factors such as workloads or the system environment. We present cost-based optimization to automatically find a good system configuration for parameter server (PS) machine learning (ML) frameworks. We design and implement Cruise that applies the optimization technique to tune distributed PS ML execution automatically. Evaluation results on three ML applications verify that Cruise automates the system configuration of the applications to achieve good performance with minor reconfiguration costs.
Human variation databases (2010)

More than 100 000 human genetic variations have been described in various genes that are associated with a wide variety of diseases. Such data provides invaluable information for both clinical medicine and basic science. A number of locus-specific databases have been developed to exploit this huge amount of data. However, the scope, format and content of these databases differ strongly and as no standard for variation databases has yet been adopted, the way data is presented varies enormously. This review aims to give an overview of current resources for human variation data in public and commercial resources.
Use of non-negative matrix factorization for language model adaptation in a lecture transcription task (2002)

Introduces the non-negative matrix factorization for language model adaptation. This approach is an alternative to latent semantic analysis based language modeling using singular value decomposition with several benefits. A new method, which does not require an explicit document segmentation of the training corpus is presented as well. This method resulted in a perplexity reduction of 16% on a database of biology lecture transcriptions.
Selection in vitro (1979)

Abstract The Qβ-polymerase-Qβ-RNA system is reviewed and the evolution of resistance to inhibitors is discussed. It is suggested that this system provides a useful model of the evolution of haploid genomes under natural selection. Consequences for theories of the origins of life are discussed.
The Role of Tissue Factor Pathway Inhibitor-2 in Cancer Biology (2007)

Tissue factor pathway inhibitor-2 (TFPI-2), a member of the Kunitz-type serine proteinase inhibitor family, is a structural homologue of tissue factor pathway inhibitor (TFPI). The expression of TFPI-2 in tumors is inversely related to an increasing degree of malignancy, which may suggest a role for TFPI-2 in the maintenance of tumor stability and inhibition of the growth of neoplasms. TFPI-2 inhibits the tissue factor/factor VIIa (TF/VIIa) complex and a wide variety of serine proteinases including plasmin, plasma kallikrein, factor XIa, trypsin, and chymotrypsin. Aberrant methylation of TFPI-2 promoter cytosine-phosphorothioate-guanine (CpG) islands in human cancers and cancer cell lines was widely documented to be responsible for diminished expression of mRNA encoding TFPI-2 and decreased or inhibited synthesis of TFPI-2 protein during cancer progression. Furthermore, an aberrantly spliced variant of TFPI-2 mRNA (designated asTFPI-2) was detected, which represents an untranslated form of TFPI-2. The levels of asTFPI-2 were very low or undetectable in normal cells but markedly upregulated in neoplastic tissue. TFPI-2 functions in the maintenance of the stability of the tumor environment and inhibits invasiveness and growth of neoplasms, as well as metastases formation. TFPI-2 has also been shown to induce apoptosis and inhibit angiogenesis, which may contribute significantly to tumor growth inhibition. Restoration of TFPI-2 expression in tumor tissue inhibits invasion, tumor growth, and metastasis, which creates a novel possibility of cancer patient treatment. However, more information is still needed to define the precise role of TFPI-2 in human tumor biology.
The Nonuniform Transmission Line as a Broadband Termination (1958)

The problem of obtaining a broadband microwave termination is considered from the point of view of nonuniform transmission line theory. Attention is restricted to lines in which only the distributed shunt admittance may be varied. An optimization argument is presented which leads to the consideration of a line in which the fractional increase in admittance per wavelength in the line is constant. The nonuniform transmission line equations are solved exactly for this case, and the results are expressed in terms of readily interpretable elementary functions. It is shown that a fixed geometrical length of line can lead to an arbitrarily large effective length without destroying the match at the input. The introduction of a small loss term makes the line almost totally absorbing regardless of its termination. The line has a long-wavelength cutoff given by 4Π times the actual length of the line. If the line is short-circuited at its far end, a return loss of greater than 11.4 db is obtained at all frequencies above twice the cutoff frequency. The effect of certain practical limitations on the performance of this line is also discussed.
Cyclophanes. 14. Synthesis, structure assignment, and conformational properties of [2.2](2,5)oxazolo- and thiazolophanes (1982)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCyclophanes. 14. Synthesis, structure assignment, and conformational properties of [2.2](2,5)oxazolo- and thiazolophanesSabir H. Mashraqui and Philip M. KeehnCite this: J. Am. Chem. Soc. 1982, 104, 16, 4461–4465Publication Date (Print):August 1, 1982Publication History Published online1 May 2002Published inissue 1 August 1982https://pubs.acs.org/doi/10.1021/ja00380a022https://doi.org/10.1021/ja00380a022research-articleACS PublicationsRequest reuse permissionsArticle Views674Altmetric-Citations18LEARN 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 optionsGet e-Alertsclose Get e-Alerts
Mesenchymal Stromal Cells Improve Survival During Sepsis in the Absence of Heme Oxygenase-1: The Importance of Neutrophils (2012)

The use of mesenchymal stromal cells (MSCs) for treatment of bacterial infections, including systemic processes like sepsis, is an evolving field of investigation. This study was designed to investigate the potential use of MSCs, harvested from compact bone, and their interactions with the innate immune system, during polymicrobial sepsis induced by cecal ligation and puncture (CLP). We also wanted to elucidate the role of endogenous heme oxygenase (HO)-1 in MSCs during a systemic bacterial infection. MSCs harvested from the bones of HO-1 deficient (-/-) and wild-type (+/+) mice improved the survival of HO-1(-/-) and HO-1(+/+) recipient mice when administered after the onset of polymicrobial sepsis induced by CLP, compared with the administration of fibroblast control cells. The MSCs, originating from compact bone in mice, enhanced the ability of neutrophils to phagocytize bacteria in vitro and in vivo and to promote bacterial clearance in the peritoneum and blood after CLP. Moreover, after depleting neutrophils in recipient mice, the beneficial effects of MSCs were entirely lost, demonstrating the importance of neutrophils for this MSC response. MSCs also decreased multiple organ injury in susceptible HO-1(-/-) mice, when administered after the onset of sepsis. Taken together, these data demonstrate that the beneficial effects of treatment with MSCs after the onset of polymicrobial sepsis is not dependent on endogenous HO-1 expression, and that neutrophils are crucial for this therapeutic response.
Synthesis of Carbon Nanotubes and Nanobelts through a Medial-Reduction Method (2003)

The method of medial-reduction has been developed for the synthesis of carbon nanotubes and nanobelts. In this process, Mg was used as reductant, and Na2CO3 and CCl4 were used as carbon sources, respectively. X-ray power diffraction (XRD) patterns were used to identify the designed reaction process and carbon structure. Scanning electron microscopy studies showed that as-synthesized products were composed of a large number of carbon nanotubes with diameters of 60−200 nm. Transmission electron microscopy investigations indicated that both types of carbon nanotubes could be observed. Furthermore, carbon nanobelts were found to be coexistent in the as-prepared products. High-resolution transmission electron micrography images showed that as-synthesized carbon materials consisted of graphite layers, whose interlayer spacing was about 0.34 nm. The experimental results indicated that the spiral growth mechanism might be operative during the formation of carbon nanotubes.
Transport of a fluorescent macromolecule via endosomes to the vacuole in Saccharomyces cerevisiae. (1987)

Fluorescein isothiocyanate-conjugated dextran (FITC-dextran) is internalized by endocytosis into the lysosome-like vacuoles of Saccharomyces cerevisiae (Makarow, M., 1985, EMBO (Eur. Mol. Biol. Organ.) J. 4:1861-1866). Here we show that under energy depletion conditions FITC-dextran accumulated in a cytoplasmic compartment, from which it could be chased to the vacuole when the energy block was removed. The internal pH of the intermediate compartment under energy depletion was determined by fluorometry to be 5.8. The pH could be raised by the lysosomotropic agent ammonium chloride, the protonophore carbonyl cyanide p-trifluoromethoxyphenyl-hydrazone (CCCP) and the ATPase inhibitors dicyclohexylcarbodiimide (DCCD) and sodium vanadate. The pH of the vacuole was found to be 6.5. It was raised by ammonium chloride, CCCP, and DCCD, but not with sodium vanadate. Efrapeptin had no effect on the internal pH of either compartment. By dissecting the endocytic pathway, two portions of the route leading to the vacuole could be studied separately. The internalization of FITC-dextran from the extracellular fluid to the intermediate compartment followed linear kinetics, was independent of energy, and occurred at temperatures of between 15 degrees and 37 degrees C. Transfer of the marker from the intermediate compartment to the vacuole required energy, took place at temperatures between 19 degrees and 37 degrees C, and had a half-time of 7 min at 37 degrees C. Transport of the marker from the exterior of the cell to the vacuole did not require acidic pH values in the intermediate compartment or the vacuole. We suggest that the cytoplasmic compartment revealed by FITC-dextran, under energy depletion, represents the equivalent of the endosomes of mammalian cells.
HOW MANY SPECIES OF ALGAE ARE THERE? (2012)

Algae have been estimated to include anything from 30,000 to more than 1 million species. An attempt is made here to arrive at a more accurate estimate using species numbers in phyla and classes included in the on-line taxonomic database AlgaeBase (http://www.algaebase.org). Despite uncertainties regarding what organisms should be included as algae and what a species is in the context of the various algal phyla and classes, a conservative approach results in an estimate of 72,500 algal species, names for 44,000 of which have probably been published, and 33,248 names have been processed by AlgaeBase to date (June 2012). Some published estimates of diatom numbers are of over 200,000 species, which would result in four to five diatom species for every other algal species. Concern is expressed at the decline and potential extinction of taxonomists worldwide capable of improving and completing the necessary systematic studies.
Stimulation of human naive and memory T helper cells with bacterial superantigen. Naive CD4+45RA+ T cells require a costimulatory signal mediated through the LFA-1/ICAM-1 pathway (1992)

The role of the accessory molecule ICAM-1 in activation of subpopulations of human T cells was examined using the bacterial superantigen staphylococcal enterotoxin A (SEA) as a MHC class II and TCR-dependent polyclonal T cell activator. Human T cells responded with different sensitivity to SEA when presented on mouse accessory cells expressing a human transfected MHC class II gene product. Mouse L cells cotransfected with both MHC class II (DR2A or DR7) and ICAM-1-stimulated T cells at 100-fold lower concentrations of SEA as compared to the single transfected cells. mAb reacting with the CD11a, CD18, or ICAM-1 molecules efficiently inhibited T cell activation with the cotransfected HLA-DR2A/ICAM-1 cell but did not influence T cell activation with the HLA-DR2A single transfected cell. Analysis of the ICAM-1 requirement on CD4+ memory (CD4+45RO+) and naive (CD4+45RA+) T cells revealed that CD4+45RA+ naive Th cells were hyporesponsive to SEA-induced activation with the HLA-DR2A single transfectant. However, cotransfection of ICAM-1 enabled these cells to respond to low doses of SEA implicating that they are more dependent on accessory molecules than the CD4+45RO+ cells. rICAM-1 immobilized on a plastic surface, was able to strongly costimulate SEA-induced T cell activation with the HLA-DR2A single transfectant, suggesting that costimulatory signals mediated to the T cells through LFA-1 can be delivered physically separated from the TCR signal. CD4+45RO+ memory and CD4+45RA+ naive Th cells apparently differ in their capacities to be activated by SEA bound to HLA-DR. Although the TCR molecule densities are similar in these two subsets, costimulation with ICAM-1 is required for activation of the CD4+45RA+, but not the CD4+45RO+ T cell subset at 1 to 10,000 ng/ml concentrations of SEA. This observation indicates different activation thresholds of naive and memory Th cells when triggering the TCR over a wide dose interval of superantigen.
The Association or Otherwise of the Functional Somatic Syndromes (2007)

Phenomenological commonalities support a close relationship between the FSS, although differences remain in other domains. Whether the FSS may best be considered the same or different will depend on the pragmatics of diagnosis.
Pictures are not taken in a vacuum - an overview of exploiting context for semantic scene content understanding (2006)

Considerable research has been devoted to the problem of multimedia indexing and retrieval in the past decade. However, limited by state-of-the-art in image understanding, the majority of the existing content-based image retrieval (CBIR) systems have taken a relatively low-level approach and fallen short of higher-level interpretation and knowledge. Recent research has begun to focus on bridging the semantic and conceptual gap that exists between man and computer by integrating knowledge-based techniques, human perception, scene content understanding, psychology, and linguistics. In this article, we provide an overview of exploiting context for semantic scene content and understanding.
Linearity improvement in RF power amplifier system using integrated Auxiliary Envelope Tracking system (2011)

A new technique called Auxiliary Envelope Tracking (AET) is proposed, which demonstrates substantial improvement in linearity of RF power amplifiers. A small amplitude envelope-tracking voltage is superimposed on the fixed DC bias of a specially designed 25W GaN HEMT Class AB RF power amplifier (RFPA). A large improvement in third-order intermodulation (IM3) distortion has been observed while maintaining low fifth-order intermodulation (IM5). The overall drain efficiency of the RFPA is also observed to improve, even when the power consumption of the envelope tracking generator is included. The AET concept uses a simple and easily integrated system that consists of an RFPA, a diplexer and an envelope amplifier.
Isolation, crystallization and preliminary X-ray analysis of a methanol-induced corrinoid protein fromMoorella thermoacetica (2005)

A corrinoid protein was induced and overexpressed in methanol-grown cells of the thermophilic anaerobic bacterium Moorella thermoacetica. The protein was purified from cytosolic extracts. After screening for crystallization conditions and optimization, crystals were obtained that diffracted strongly on a rotating-anode X-ray source. A diffraction data set was collected and processed including reflections to 1.9 A resolution. Reflections were indexed in a primitive orthorhombic cell with unit-cell parameters a = 55.69, b = 62.74, c = 34.54 A. N-terminal amino-acid sequencing indicates that the crystals contain a C-terminal fragment of the protein.
Spontaneous Clearance of Chronic Hepatitis C Virus Infection Is Associated With Appearance of Neutralizing Antibodies and Reversal of T-Cell Exhaustion (2012)

T-cell exhaustion is reversible at least in the first 2 years of chronic HCV infection, and this reversion in conjunction with neutralizing antibodies may clear HCV. These findings are relevant for immunotherapy of chronic infections.
52.1: Invited Paper: Electrophosphorescent Organic Light Emitting Devices (2002)

Abstract We discuss recent results in ultrahigh efficiency electrophosphorescent organic light emitting devices. In particular, we consider electrophosphorescent devices emitting in the red, green and blue spectral regions, and the relationship between efficiency and energy transfer. Both small molecular weight and polymer OLEDs are discussed. Furthermore, very high brightness, white emitting electrophosphorescent OLEDs will be described.