gebhart/patrepeval huggingface dataset:
Purification and characterization of a haloalkane dehalogenase of a new substrate class from a gamma-hexachlorocyclohexane-degrading bacterium, Sphingomonas paucimobilis UT26 (1997)

The linB gene product (LinB), 1,3,4,6-tetrachloro-1,4-cyclohexadiene halidohydrolase, which is involved in the degradation of gamma-hexachlorocyclohexane in Sphingomonas paucimobilis UT26 (Y. Nagata, T. Nariya, R. Ohtomo, M. Fukuda, K. Yano, and M. Takagi, J. Bacteriol. 175:6403-6410, 1993), was overproduced in E. coli and purified to homogeneity. The molecular mass of LinB was deduced to be 30 kDa by gel filtration chromatography and 32 kDa by electrophoresis on sodium dodecyl sulfate-polyacrylamide gel, indicating that LiuB is a monomeric enzyme. The optimal pH for activity was 8.2. Not only monochloroalkanes (C3 to C10) but also dichloroalkanes, bromoalkanes, and chlorinated allphatic alcohols were good substrates for LinB, suggesting that LinB shares properties with another haloalkane dehalogenase, DhlA (S. Keuning, D.B. Janssen, and B. Witholt, J. Bacteriol. 163:635-639, 1985), which shows significant similarity to LinB in primary structure (D. B. Janssen, F. Pries, J. van der Ploeg, B. Kazemier, P. Terpstra, and B. Witholt, J. Bacteriol. 171:6791-6799, 1989) but not in substrate specificity. Principal component analysis of substrate activities of various haloalkane dehalogenases suggested that LinB probably constitutes a new substrate specificity class within this group of enzymes.
Orientation robust object detection in aerial images using deep convolutional neural network (2015)

Detecting objects in aerial images is challenged by variance of object colors, aspect ratios, cluttered backgrounds, and in particular, undetermined orientations. In this paper, we propose to use Deep Convolutional Neural Network (DCNN) features from combined layers to perform orientation robust aerial object detection. We explore the inherent characteristics of DC-NN as well as relate the extracted features to the principle of disentangling feature learning. An image segmentation based approach is used to localize ROIs of various aspect ratios, and ROIs are further classified into positives or negatives using an SVM classifier trained on DCNN features. With experiments on two datasets collected from Google Earth, we demonstrate that the proposed aerial object detection approach is simple but effective.
In vitro and in vivo evaluation of diclofenac sodium loaded album in microspheres (2000)

The use of polymeric carriers in formulations of therapeutic drug delivery systems has gained widespread application, due to their advantage of being biodegradable and biocompatible. Among the microparticulate systems, microspheres have a special importance since it is possible to target drugs and provide controlled release. Diclofenac sodium (DS), is a potent drug in the NSAID group having non-steroidal, anti-inflammatory properties, and is widely used in the treatment of rheumatoid arthritis, osteoarthritis and ankylosing spondylitis. In this present study, it was aimed to prepare microsphere formulations of DS using a natural biodegradable polymer as a carrier for intraarticular administration to extend the duration period of the dosage form in the knee joint. Microsphere formulations of DS which were prepared were evaluated in vitro for particle size, yield value, encapsulation efficiency, surface morphology, and in vitro drug release. Two appropriate formulations were selected for in vivo trials. For the in vivo studies, Technetium-99m labelled polyclonal human immunogammaglobulin (99mTc-HIG) was used as the radiopharmaceutical to demonstrate arthritic lesions by gamma scintigraphy. After the induction of arthritis in knee joints of rabbits, the radio-labelled microspheres loaded with DS were injected directly into the articular cavity and at specific time points gamma scintigrams were obtained to find the residence time of the microspheres in knee joints in order to determine the most suitable formulation.
Fate of DNA targeted to the liver by asialoglycoprotein receptor-mediated endocytosis in vivo. Prolonged persistence in cytoplasmic vesicles after partial hepatectomy (1993)

After intravenous injection, DNA complexed with asialoglycoprotein-polylysine conjugates is endocytosed by hepatocytes via asialoglycoprotein receptors and is expressed transiently. Long term persistence and expression occurs when partial hepatectomy is performed after gene delivery. To determine the intracellular location of the persisting DNA, we transferred a plasmid expressing bacterial chloramphenicol acetyltransferase into the liver of rats in vivo by asialoglycoprotein receptor-mediated endocytosis. The internalized DNA was measured by Southern blot. Twenty min after administration, 80-85% of the plasmid appeared in the liver, 80% of which was within hepatocytes (12,000-18,000 copies/hepatocyte). In sham-operated control rats, the transgene concentration decreased to 8-12 and 2-4% of the initial levels in 4 and 24 h, respectively, and became undetectable at 7 days. In rats subjected to 66% hepatectomy 20 min after DNA administration, 20, 9, and 7% of the plasmid in the residual liver persisted at 4 h, 24 h, and 7 days, respectively. Liver homogenates were fractionated by differential centrifugation and Percoll gradient centrifugation. In 66% hepatectomized rats, the plasmid persisted in an undegraded, transfection-competent form in plasma membrane/endosome-enriched fractions throughout the duration of the experiment (7 days), indicating that cytoplasmic vesicles are the main site of persistence of the endocytosed DNA.
Enhancing Road Maps by Parsing Aerial Images Around the World (2015)

In recent years, contextual models that exploit maps have been shown to be very effective for many recognition and localization tasks. In this paper we propose to exploit aerial images in order to enhance freely available world maps. Towards this goal, we make use of OpenStreetMap and formulate the problem as the one of inference in a Markov random field parameterized in terms of the location of the road-segment centerlines as well as their width. This parameterization enables very efficient inference and returns only topologically correct roads. In particular, we can segment all OSM roads in the whole world in a single day using a small cluster of 10 computers. Importantly, our approach generalizes very well, it can be trained using only 1.5 km <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> aerial imagery and produce very accurate results in any location across the globe. We demonstrate the effectiveness of our approach outperforming the state-of-the-art in two new benchmarks that we collect. We then show how our enhanced maps are beneficial for semantic segmentation of ground images.
The role of glutamate antagonists for the treatment of CNS injury. (1992)

Ischemic damage, chiefly of the focal type, and axonal disruption (diffuse axonal injury) are the major factors causing brain damage after human head injury. About one third of this damage may be delayed hours or days after the injury. Evidence from four animal models, each relevant to different aspects of human head injury, has shown that excitatory amino acid-induced changes are responsible for a proportion of the posttraumatic sequelae and that these effects can be blocked by EAA antagonists. This evidence is reviewed, and the implications for the conduct of human trials with EAA antagonists are discussed.
Kinetic study of the stability of the o-phthalaldehyde-spermine fluorophore formed by on-column derivatization (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTKinetic study of the stability of the o-phthalaldehyde-spermine fluorophore formed by on-column derivatizationKoichi. Saito, Masakazu. Horie, and Hiroyuki. NakazawaCite this: Anal. Chem. 1994, 66, 1, 134–138Publication Date (Print):January 1, 1994Publication History Published online1 May 2002Published inissue 1 January 1994https://doi.org/10.1021/ac00073a023RIGHTS & PERMISSIONSArticle Views121Altmetric-Citations13LEARN 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 InReddit PDF (528 KB) Get e-Alerts Get e-Alerts
Adult mouse epicardium modulates myocardial injury by secreting paracrine factors (2011)

The epicardium makes essential cellular and paracrine contributions to the growth of the fetal myocardium and the formation of the coronary vasculature. However, whether the epicardium has similar roles postnatally in the normal and injured heart remains enigmatic. Here, we have investigated this question using genetic fate-mapping approaches in mice. In uninjured postnatal heart, epicardial cells were quiescent. Myocardial infarction increased epicardial cell proliferation and stimulated formation of epicardium-derived cells (EPDCs), which remained in a thickened layer on the surface of the heart. EPDCs did not adopt cardiomyocyte or coronary EC fates, but rather differentiated into mesenchymal cells expressing fibroblast and smooth muscle cell markers. In vitro and in vivo assays demonstrated that EPDCs secreted paracrine factors that strongly promoted angiogenesis. In a myocardial infarction model, EPDC-conditioned medium reduced infarct size and improved heart function. Our findings indicate that epicardium modulates the cardiac injury response by conditioning the subepicardial environment, potentially offering a new therapeutic strategy for cardiac protection.
Inflammation Modifies the Effects of a Reduced-Fat Low-Cholesterol Diet on Lipids (2003)

In this study, the presence of increased CRP was associated with less total and LDL cholesterol reduction and a greater increase in triglycerides from a reduced-fat/low-cholesterol diet. These findings document an additional mechanism by which inflammation might increase cardiovascular disease risk.
Methods for saturation modelling of railway lines: the case of High-Speed Line Paris-Lyon (2014)

International audience
Genetic manipulation of<i>Kluyveromyces lactis</i>linear DNA plasmids: gene targeting and plasmid shuffles (1999)

Genetic manipulation of yeast linear DNA plasmids, particularly of k1 and k2 from the non-conventional dairy yeast Kluyveromyces lactis, has been advanced by the recent establishment of DNA transformation-mediated one-step gene disruption and allele replacement techniques. These methods provide the basis for a strategy for the functional analysis of plasmid genes and DNA elements. By use of double selection regimens, these single-gene procedures have been extended to effect disruption of individual genes on plasmid k2 and transplacement of a functional copy onto plasmid k1, resulting in the production of yeast strains with an altered plasmid composition. This cytoplasmic gene shuffle system facilitates the introduction of specifically modified alleles into k1 or k2 in order to study the function, expression (from UCS promoters) and regulation of cytoplasmic linear plasmid genes. Additionally, identification, characterization and localization of plasmid gene products of interest are made possible by shuffling GFP-, epitope- or affinity purification-tagged alleles between k2 and k1. The gene shuffle approach can also be used for vector development and heterologous protein expression in order to exploit the biotechnical potential of the K. lactis k1/k2 system in yeast cell factory research.
Photon Migration in a Two-layer Turbid Medium a Diffusion Analysis (1992)

Abstract We analyse the diffusion of photons in a two-layer turbid medium, paying specific attention to parameters suggested by the use of lasers for diagnostic purposes in a medical setting. The data produced by such experiments consists of an intensity profile measured on the surface of the medium, which is measured either as a function of time at a fixed distance from the input laser beam, or else as a function of distance keeping the measurement time fixed. In both cases we demonstrate that the presence of a second layer can be detected provided that physical properties of the two layers differ by a sufficient amount, and also show up in calculated values of such parameters as the mean travel time of a photon to the surface of the medium, and the distribution of the maximum depth reached by an arbitrary photon.
Programmable Hydrogels for Controlled Cell Catch and Release Using Hybridized Aptamers and Complementary Sequences (2012)

The ability to regulate cell-material interactions is important in various applications such as regenerative medicine and cell separation. This study successfully demonstrates that the binding states of cells on a hydrogel surface can be programmed by using hybridized aptamers and triggering complementary sequences (CSs). In the absence of the triggering CSs, the aptamers exhibit a stable, hybridized state in the hydrogel for cell-type-specific catch. In the presence of the triggering CSs, the aptamers are transformed into a new hybridized state that leads to the rapid dissociation of the aptamers from the hydrogel. As a result, the cells are released from the hydrogel. The entire procedure of cell catch and release during the transformation of the aptamers is biocompatible and does not involve any factor destructive to either the cells or the hydrogel. Thus, the programmable hydrogel is regenerable and can be applied to a new round of cell catch and release when needed.
Chlorpromazine amplifies macrophage-dependent IL-10 production in vivo. (1995)

Chlorpromazine (CPZ) has potent immunomodulatory effects in vivo; it induces humoral autoimmunity in up to 50% of patients, inhibits delayed-type hypersensitivity reactions, and suppresses lethal immune hyperactivation in animal models of septic shock. Here, we show that in an in vivo model of acute superantigen-driven immune activation, CPZ independently down-regulates the production of various T cell-derived lymphokines (IL-2, IFN-gamma, IL-4, TNF, and GM-CSF) and up-regulates the secretion of IL-10. Whereas only low, if any, serum IL-10 levels are detectable by ELISA after injection of CPZ, bacterial LPS, or staphylococcal enterotoxin B (SEB) alone, simultaneous administration of CPZ + LPS or CPZ + SEB causes a significant increase in IL-10 production in vivo. CPZ-mediated amplification of the SEB-driven CPZ secretion is accompanied by an enhanced IL-10 mRNA accumulation, as shown by PCR analysis and in situ hybridization. Determination of IL-10 production in mice lacking T cells, B cells, or phagocytes revealed that SEB + CPZ-induced IL-10 was produced by phagocytic cells, but not by lymphocytes, a finding that is in accord with the distribution of splenic cells transcribing the IL-10 gene in response to SEB + CPZ. Moreover, these data indicate that bacterial superantigen can directly stimulate tissue phagocytes, even in the virtual absence of T lymphocytes. The blockade of dopamine type 1 (D1) but not type 2 (D2) receptors abolishes the CPZ effect on IL-10 production. Inhibition of Th1 and Th2 lymphokine production by CPZ is not mediated by dopamine receptors and is independent of IL-10 up-regulation. These findings may explain the mechanism by which CPZ and related drugs enhance humoral autoimmune reactions, block cellular immune responses, and prevent lethal septic shock in vivo.
Expression of syndecan-1 inhibits cell invasion into type I collagen. (1994)

Before cells can invade the extracellular matrix, they must alter their expression of adhesion receptors. Syndecan-1 is a cell surface proteoglycan that binds cells to matrix and undergoes changes in expression during development, during differentiation of some cell types, and following malignant transformation in some tumors. To determine if changes in syndecan-1 expression influence cell invasion, we employed a model system in which human B lymphoid cells invade type I collagen gels. Examination of a panel of cell lines reveals that those lines not expressing syndecan-1 invade and migrate within collagen. In contrast, cell lines expressing syndecan-1 fail to invade. To directly assess the effect of syndecan-1 on invasion, ARH-77 cells, which do not express syndecan-1 and readily invade collagen, were transfected with a cDNA for syndecan-1. The syndecan-1-positive transfectants exhibit a drastically reduced ability to invade as compared to parental cells. This inhibition of invasion by syndecan-1 is reversed by preincubating gels with heparin or by growing cells in chlorate, an inhibitor of glycosaminoglycan sulfation. These results demonstrate that expression of syndecan-1 inhibits cell invasion into collagen and that loss of syndecan-1 expression may be necessary prior to the migration of normal or metastatic cells.
The role of purinergic signaling in depressive disorders. (2012)

The purinergic signaling system consists of transporters, enzymes and receptors responsible for the synthesis, release, action and extracellular inactivation of adenosine 5'-triphosphate (ATP) and its extracellular breakdown product adenosine. The actions of ATP are mediated ionotropic P2X and metabotropic P2Y receptor subfamilies, whilst the actions of adenosine are mediated by P1 adenosine receptors. Purinergic signaling pathways are widely expressed in the central nervous system (CNS) and participate in its normal and pathological functions. Among P2X receptors, the P2X7 receptor (P2rx7) has received considerable interest in both basic and clinical neuropsychiatric research because of its profound effects in animal CNS pathology and its potential involvement as a susceptibility gene in mood disorders. Although genetic findings were not always consistently replicated, several studies demonstrated that single nucleotide polymorphisms (SNPs) in the human P2X7 gene (P2RX7) show significant association with major depressive disorder and bipolar disorder. Animal studies revealed that the genetic knock-down or pharmacological antagonism leads to reduced depressive-like behavior, attenuated response in mania-model and alterations in stress reactivity. A potential mechanism of P2rx7 activation on mood related behavior is increased glutamate release, activation of extrasynaptic NMDA receptors and subsequent enduring changes in neuroplasticity. In addition, dysregulation of monoaminergic transmission and HPA axis reactivity could also contribute to the observed changes in behavior. Besides P2rx7, the inhibition of adenosine A1 and A2A receptors also mediate antidepressant-like effects in animal experiments. In conclusion, despite contradictions between existing data, these findings point to the therapeutic potential of the purinergic signaling system in mood disorders.
Synthesis of unsaturated lactones via palladium-catalyzed cyclization of alkenoic acids (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis of unsaturated lactones via palladium-catalyzed cyclization of alkenoic acidsRichard C. Larock and Timothy R. HightowerCite this: J. Org. Chem. 1993, 58, 20, 5298–5300Publication Date (Print):September 1, 1993Publication History Published online1 May 2002Published inissue 1 September 1993https://doi.org/10.1021/jo00072a004RIGHTS & PERMISSIONSArticle Views3398Altmetric-Citations177LEARN 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 InReddit PDF (302 KB) Get e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Fluorescent Chemosensor for Detection and Quantitation of Carbon Dioxide Gas (2010)

CO(2) sensing is of great societal implications, as CO(2) is a component of gas mixtures from many natural and anthropogenic processes with huge impacts on globe climate and human well-being. Herein we report a CO(2) assay scheme over a wide concentration range, utilizing a fluorogen with an aggregation-induced emission feature and a liquid with tunable polarity and viscosity. The CO(2) sensing process is specific, quantitative, and interferent tolerant.
Bioavailability, gastrointestinal transit, solubilization and faecal excretion of ursodeoxycholic acid in man (1985)

The bioavailability of ursodeoxycholic acid (UDCA), a cholesterolic gallstone dissolving agent, has been analysed in seven healthy human volunteers. After absorption of a capsule containing a 500 mg dose, the time course of plasma concentrations of the drug presented a double peak profile over a 240 min period. In order to explain this result, a second group of five subjects bearing a four-way jejunal catheter fitted with an occluding balloon, received an oral dose of 250, 500 or 750 mg of the drug. Simultaneous analyses of plasma UDCA concentrations and jejunal UDCA contents were carried out. UDCA is poorly soluble in the gastro-duodeno-jejunal contents of fasted subjects since 21-50% of the ingested doses were recovered in solid form. The profile of plasma concentration paralleled the amount of soluble UDCA present in intestinal lumen. When jejunal contents were infused below the balloon a second plasma peak appeared in cases corresponding to ingestion of higher doses of UDCA. In conclusion, pharmacological doses of UDCA are not readily soluble in the stomach and intestine of a healthy fasting man. In consequence, the bioavailability of the drug varies with its progressive solubilization in the gastrointestinal tract. The present results suggest that repeated daily doses of UDCA should improve its bioavailability in treated gallstone patients.
Properties of group III nitrides (1994)

Basic physical properties phase diagrams electrical properties band structure optical functions infra-red absorption and impurity energy levels photoluminescence and cathodoluminescence Raman and reflection spectra interfaces including heterojunctions.
Effect of Deoxyribozymes Targeting c-Jun on Solid Tumor Growth and Angiogenesis in Rodents (2004)

DNAzymes targeting c-Jun may have therapeutic potential as inhibitors of tumor angiogenesis and growth.