gebhart/patrepeval huggingface dataset:
An instance-based approach for identifying candidate ontology relations within a multi-agent system (2000)

. Discovering related concepts in a multi-agent system among agents with diverse ontologies is difficult using existing knowledge representation languages and approaches. We describe an approach for identifying candidate relations between expressive, diverse ontologies using concept cluster integration. We evaluate the feasibility of this approach using lightweight ontologies. These lightweight ontologies are constructed from the Magellan search Web site and consist of Web page categories, or concepts, and their corresponding instances. 1 INTRODUCTION In order to facilitate knowledge sharing between a group of interacting information agents (i.e. a multi-agent system), a common ontology should be shared. However, we recognize that often agents do not always commit a priori to a common, pre-defined global ontology. Our ongoing research investigates approaches for agents with diverse ontologies to share knowledge by automated learning methods and agent communication strategies [15]. Wh...
Determination of Carcinoembryonic Antigen in Human Sera by Integrated Bead-Bed Immunoasay in a Microchip for Cancer Diagnosis (2001)

A bead-bed immunoassay system was structured on a microchip and applied to determine carcinoembryonic antigen (CEA), which is a commonly used marker of colon cancer. Polystyrene beads precoated with anti-CEA antibody were introduced into a microchannel, and then a serum sample containing CEA, the first antibody, and the second antibody conjugated with colloidal gold were reacted successively. The resulting antigen-antibodies complex, fixed on the bead surface, was detected using a thermal lens microscope (TLM). A highly selective and sensitive determination of an ultratrace amount of CEA in human sera was made possible by a sandwich immunoassay system that needs three antibodies for an assay. A detection limit dozens of times lower than the conventional ELISA was achieved. Moreover, when serum samples for 13 patients were assayed with this system, there was a high correlation (r = 0.917) with the conventional ELISA. The integration reduced the time necessary for the antigen-antibody reaction to approximately 1%, thus shortening the overall analysis time from 45 h to 35 min. Moreover, troublesome operations required for conventional heterogeneous immunoassays could be much simplified. This microchip-based diagnosis system is the first microchip-based system that is practically useful for clinical diagnoses with short analysis time, high sensitivity, and easy procedures.
Transition Metal Catalysis in the Baeyer-Villiger Oxidation of Ketones (1998)

Environmentally friendly oxidizing agents such as hydrogen peroxide or dioxygen can be used today in catalytic versions of the almost one century old Baeyer-Villiger oxidation with transition metal complexes as catalysts. On the right is a sketch of a possible mechanism for this reaction with a platinum catalyst in homogeneous solution.
Biomimetic gradient hydrogels for tissue engineering (2010)

During tissue morphogenesis and homeostasis, cells experience various signals in their environments, including gradients of physical and chemical cues. Spatial and temporal gradients regulate various cell behaviours such as proliferation, migration, and differentiation during development, inflammation, wound healing, and cancer. One of the goals of functional tissue engineering is to create microenvironments that mimic the cellular and tissue complexity found in vivo by incorporating physical, chemical, temporal, and spatial gradients within engineered three-dimensional (3D) scaffolds. Hydrogels are ideal materials for 3D tissue scaffolds that mimic the extracellular matrix (ECM). Various techniques from material science, microscale engineering, and microfluidics are used to synthesise biomimetic hydrogels with encapsulated cells and tailored microenvironments. In particular, a host of methods exist to incorporate micrometer to centimetre scale chemical and physical gradients within hydrogels to mimic the cellular cues found in vivo. In this review, we draw on specific biological examples to motivate hydrogel gradients as tools for studying cell-material interactions. We provide a brief overview of techniques to generate gradient hydrogels and showcase their use to study particular cell behaviours in two-dimensional (2D) and 3D environments. We conclude by summarizing the current and future trends in gradient hydrogels and cell-material interactions in context with the long-term goals of tissue engineering.
Magnetic Resonance Imaging Measurements of the Response of Murine and Human Tumors to the Vascular-Targeting Agent ZD6126 (2004)

The contrast enhanced-MRI measured median IAUC is a useful end point for quantifying ZD6126 antivascular effects in human tumors.
Detection of characteristic phases using FFT's (1992)

Maximal-length linear recursive sequences (M-sequences) over GF(2) are used for a variety of purposes in communications, test, and other signals. An M-sequence contains a unique characteristic phase at which the sequence is invariant under a decimation by two. This point may be detected using an algorithm whose principal computation is the fast Fourier transform (FFT). This approach provides a method of detecting and synchronizing to the sequence, regardless of whether the sequence is at baseband or modulates a carrier, the relationship of sampling rate to bit rate, and whether the modulated sequence is regarded as a carrier which itself modulates a small-bandwidth, constant envelope signal. Moreover, the technique provides a method for obtaining the polynomial generator of the sequence if it is not already known.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Identification of Determinants for Inhibitor Binding within the RNA Active Site of Human Telomerase Using PNA Scanning (1997)

Telomerase is a ribonucleoprotein that participates in the maintenance of telomere length. Its activity is up-regulated in many tumor types, suggesting that it may be a novel target for chemotherapy. The RNA component of telomerase contains an active site that plays at least two roles&sbd;binding telomere ends and templating their replication [Greider, C. W., & Blackburn, E. H. (1989) Nature 337, 331-337]. The accessibility of RNA nucleotides for inhibitor binding cannot be assumed because of the potential for RNA secondary structure and RNA-protein interactions. Here we use high-affinity recognition by overlapping peptide nucleic acids (PNAs) [Nielsen, P. E., et al. (1991) Science 254, 1497-1500] to identify nucleotides within the RNA active site of telomerase that are determinants for inhibitor recognition. The IC50 for inhibition decreases from 30 microM to 10 nM as cytidines 50-52 (C50-52) at the boundary between the alignment and elongation domains are recognized by PNAs overlapping from the 5' direction. As C50-52 are uncovered in the 3' direction, IC50 increases from 10 nM to 300 nM. As cytidine 56 at the extreme 3' end of the active site is uncovered, IC50 values increase from 0.5 microM to 10 microM. This analysis demonstrates that C50-C52 and C56 are important for PNA recognition and are physically accessible for inhibitor binding. We use identification of these key determinants to minimize the size of PNA inhibitors, and knowledge of these determinants should facilitate design of other small molecules capable of targeting telomerase. The striking differences in IC50 values for inhibition of telomerase activity by related PNAs emphasize the potential of PNAs to be sensitive probes for mapping complex nucleic acids. We also find that PNA hybridization is sensitive to nearest-neighbor interactions, and that consecutive guanine bases within a PNA strand increase binding to complementary DNA and RNA sequences.
Protein Kinase A Signaling (2002)

Protein kinase A (PKA) signaling, in "classic" endocrine cell functioning, is known to mediate cAMP effects, generated through adenylate cyclase as a response to the activation of G protein-coupled receptors (GPCRs). This signaling system is highly versatile; its flexibility is supported by a number of adenylate cyclases, four PKA regulatory and three catalytic subunits, and several phosphodiesterases that close the negative feedback loop of cAMP generation, most molecules that are expressed in a tissue-specific manner. A central question, however, remains: how do the hundreds of GPCRs mediate their specific effects? Tissue specificity of the expression of the various components of the PKA system, albeit necessary, cannot be the only answer. It helps more to view PKA as a central hub that interacts with a variety of other signaling pathways in endocrine cells, not only mediating but also communicating cAMP effects to the mitogen-activated protein kinase (MAPK), protein kinase C and B (PKC and PKB/Akt, respectively). The net result of these complex interactions, evidence for which is reviewed in this chapter, is what we know as "cAMP effects." It is, perhaps, because of this complexity that investigations of PKA signaling in vivo and in vitro often give contradictory results and are difficult to interpret.
YAP1 and VGLL3, encoding two cofactors of TEAD transcription factors, are amplified and overexpressed in a subset of soft tissue sarcomas (2010)

In a series of 404 adult soft tissue sarcomas, analyzed by array-CGH, we have observed in approximately 10% of them a genomic amplification of either chromosome bands 11q22 or 3p12. These two amplicons likely target the YAP1 and VGLL3 genes, respectively. Both genes encode proteins that are cofactors of the TEAD family of transcription factors. Very good correlations between amplification and expression levels were observed. Welch test analyses of transcriptome data demonstrate that tumors with amplicons share a large set of upregulated and downregulated genes. Inhibition of YAP1 and VGLL3 in cell lines with these amplifications/overexpressions leads to similar phenotypes: decrease of proliferation rate, and to a lesser extent decrease of migration properties. These data, and the fact that these amplicons are observed either in de-differentiated liposarcomas or in undifferentiated pleomorphic sarcomas, suggest that these genetics events could be involved in oncogenesis and progression of soft tissue sarcomas.
Attenuation in Continuously Loaded Coaxial Cables (1958)

The formula for the attenuation of a coaxial line loaded continuously with magnetic materials involces, after a change of variables, only three parameters, even when the effect of dielectric losses is included. If the dimensions of the line have their optimum values, the, attenuation is a function of only two parameters. The relation is exhibited both graphically and analytically, in forms which can be applied to practical problems. A simple numerical example is given to illustrate the use of the formula.
Mitochondrial Protein Acylation and Intermediary Metabolism: Regulation by Sirtuins and Implications for Metabolic Disease (2012)

The sirtuins are a family of NAD(+)-dependent protein deacetylases that regulate cell survival, metabolism, and longevity. Three sirtuins, SIRT3-5, localize to mitochondria. Expression of SIRT3 is selectively activated during fasting and calorie restriction. SIRT3 regulates the acetylation level and enzymatic activity of key metabolic enzymes, such as acetyl-CoA synthetase, long-chain acyl-CoA dehydrogenase, and 3-hydroxy-3-methylglutaryl-CoA synthase 2, and enhances fat metabolism during fasting. SIRT5 exhibits demalonylase/desuccinylase activity, and lysine succinylation and malonylation are abundant mitochondrial protein modifications. No convincing enzymatic activity has been reported for SIRT4. Here, we review the emerging role of mitochondrial sirtuins as metabolic sensors that respond to changes in the energy status of the cell and modulate the activities of key metabolic enzymes via protein deacylation.
A Reagentless Signal-On Architecture for Electronic, Aptamer-Based Sensors via Target-Induced Strand Displacement (2005)

Thrombin binding stabilizes the alternative G-quadruplex conformation of the aptamer, liberating the methylene blue (MB)-tagged oligonucleotide to produce a flexible, single-stranded DNA element. This allows the MB tag to collide with the gold electrode surface, producing a readily detectable Faradaic current at thrombin concentrations as low as approximately 3 nM.
Biochemical characterization of the mammalian stress proteins and identification of two stress proteins as glucose- and Ca2+-ionophore-regulated proteins. (1983)

Biochemical properties of the heat shock or stress proteins of mammalian cells have been investigated using two-dimensional gel electrophoresis and immunological techniques. Of the major mammalian stress proteins (Mr = 72,000, 73,000, and 90,000) and minor stress proteins (Mr = 80,000, 100,000, and 110,000), the 80- and 90-kDa proteins were found to be phosphoproteins in all cell types examined. The 100-kDa protein was found to incorporate phosphate in only some cell types examined. In studies of the metabolic incorporation of mannose into the stress proteins, only the 100-kDa protein was found to be a glycoprotein. Two of the stress proteins, the 80- and 100-kDa species, were found to be identical with the proteins induced in cells grown in the absence of glucose (i.e. the "glucose-regulated proteins"). These same two proteins also were induced in cells treated with the calcium ionophore A23187. To begin examining the intracellular location of these multiregulated proteins, immunofluorescence microscopy studies were carried out using a monoclonal antibody against the 100-kDa stress protein. The antigen was localized primarily with the Golgi apparatus and less prominently with the plasma membrane and nucleus. Heat shock treatment resulted in an increased number of the cells exhibiting a nuclear location of 100 kDa.
Spectroscopic Methods and Analyses: NMR, Mass Spectrometry, and Metalloprotein Techniques (1993)

The three volumes in Methods in Molecular Biology covering Physical Methods of Analysis (vol. 1, Spectroscopic Methods and Analyses: NMR, Mass Spectrometry, and Metalloprotein Techniques; vol. 2, Optical Spectroscopy and Macroscopic Techniques; vol. 3, Cryst- lographic Methods and Techniques) differ from others in this series in several ways. Each volume covers a group of techniques for the char- terization of biological molecules and their interactions that involve the application of modern techniques of physical chemistry. These techniques by and large do not lend themselves to the "hands-on" approach and cannot usually be carried out by the molecular biologist alone, but most often require collaboration with a specialist. The biologist or biochemist contemplating such a collaboration may feel somewhat at a distance from the experimental work and further isolated by the use of the jargons of analytical and physical chemistry. Physical methods have been used in molecular biology from the earliest days, from simple applications of optical spectroscopy to the complexity of X-ray crystallography, and the full range of these me- ods will be covered over the three volumes. The methods dealt with in this first volume have largely developed from beginnings in small molecule chemistry to the point where they play a valuable role in the characterization of biological macromolecules
Janeway's Immunobiology (2016)

Part I An Introduction to Immunobiology and Innate Immunity 1. Basic Concepts in Immunology 2. Innate Immunity Part II The Recognition of Antigen 3. Antigen Recognition by B-cell and T-cell Receptors 4. The Generation of Lymphocyte Antigen Receptors 5. Antigen Presentation to T Lymphocytes Part III The Development of Mature Lymphocyte Receptor Repertoires 6. Signaling Through Immune System Receptors 7. The Development and Survival of Lymphocytes Part IV The Adaptive Immune Response 8. T Cell-Mediated Immunity 9. The Humoral Immune Response 10. Dynamics of Adaptive Immunity 11. The Mucosal Immune System Part V The Immune System in Health and Disease 12. Failures of Host Defense Mechanism 13. Allergy and Hypersensitivity 14. Autoimmunity and Transplantation 15. Manipulation of the Immune Response Part VI The Origins of Immune Responses 16. Evolution of the Immune System Appendix I Immunologists' Toolbox Appendix II CD Antigens Appendix III Cytokines and their Receptors Appendix IV Chemokines and their Receptors Appendix V Immunological Constants
Sox9, a novel pancreatic marker in Xenopus (2003)

The pancreas is a mixed exocrine and endocrine gland involved in the control of many homeostatic functions. During embryogenesis, the pancreas arises from dorsal and ventral evaginations of the foregut that will subsequently fuse into a single organ. The characterization of early genes expressed in the developing pancreas is critical to understand its specification and differentiation. Here we report the expression pattern of Sox9, a member of the Sox family of transcription factors, during development of the Xenopus pancreas and compare its expression to that of a well characterized pancreatic marker, Pdx1. By whole-mount in situ hybridization, Sox9 was first detected at stage 25 in the pancreatic anlagen--dorsally in the prospective foregut and ventrally on each side of the liver diverticulum. As development proceeds, Sox9 expression can be used to trace the development of the dorsal and ventral pancreatic buds and their repositioning associated with the dynamic movements of the gastrointestinal tract. Sox9 expression in the pancreatic rudiment was identical to that of Pdx1. However, while Pdx1 is expressed in both the pancreatic buds and the duodenum, Sox9 was restricted to ventral and dorsal pancreatic buds. Sox9 and Pdx1 are thus two of the earliest genes expressed in the presumptive pancreatic tissue.
Overexpression of metalloproteinase inhibitor in B16F10 cells does not affect extravasation but reduces tumor growth. (1994)

It is widely accepted that a major role of matrix metalloproteinases in the metastatic process is degradation of basement membrane during cancer cell invasion. We tested the hypothesis that the reduction in metastatic potential which has been demonstrated for B16F10 melanoma cells genetically engineered to overexpress tissue inhibitor of metalloproteinase-1 (TIMP-1) is caused by a decrease in their ability to extravasate. Using intravital videomicroscopy of chick embryo chorioallantoic membrane, we studied extravasation of B16F10 cells and B16F10 cells transfected to overexpress TIMP-1. More than 800 cells in 36 chick embryos were analyzed for each cell line during 72 h postinjection. TIMP-1 upregulation had no effect on the time course of extravasation, virtually all cells from both cell lines having extravasated by 36 h. We also studied the morphology of micrometastases at days 3 and 7. Lack of contact between cancer cells within micrometastases at day 3 and reduction in size and number of tumors at day 7 were observed for TIMP-1 overexpressor cells compared to B16F10. Our findings illustrate that the imbalance between TIMP and metalloproteinases created by overexpression of TIMP-1 in B16F10 cells reduces their metastatic ability in vivo by affecting tumor growth postextravasation.
Preeclampsia and Angiogenic Imbalance (2007)

Preeclampsia is a systemic syndrome of pregnancy that originates in the placenta and is characterized by widespread maternal endothelial dysfunction. Until recently, the molecular pathogenesis of preeclampsia was largely unknown, but recent work suggests a key role for altered expression of placental antiangiogenic factors. Soluble Flt1 and soluble endoglin, secreted by the placenta, are increased in the maternal circulation weeks before the onset of preeclampsia. These antiangiogenic factors produce systemic endothelial dysfunction, resulting in hypertension, proteinuria, and the other systemic manifestations of preeclampsia. The molecular basis for placental dysregulation of these pathogenic factors remains unknown, and the role of angiogenic proteins in early placental vascular development is just beginning to be explored. These discoveries have exciting clinical implications and are likely to transform the detection and treatment of preeclampsia in the future.
Determination of the inversion-layer thickness from capacitance measurements of metal-oxide-semiconductor field-effect transistors with ultrathin oxide layers (1988)

The capacitance of ultrathin-oxide (3.4--20.9 nm) large-area square metal-oxide-semiconductor field-effect-transistor devices has been measured at temperatures ranging from 4.2 to 300 K and for a wide range of gate voltages and substrate voltages. The contribution of the inversion layer to the capacitance is as large as 10%. The spatial extent of the lowest-lying inversion-layer subband wave function from the interface, the average inversion-layer thickness, can be determined from these measurements. The results are in semiquantitative agreement with calculations. The carriers are pushed toward the interface with an increase in the carrier density and/or the application of a negative substrate voltage. At elevated temperatures excitation of electrons to higher-lying subbands increases the average inversion-layer thickness and results in a decrease in the measured capacitance.
The Oxidative Inactivation of Tissue Inhibitor of Metalloproteinase-1 (TIMP-1) by Hypochlorous Acid (HOCl) is Suppressed by Anti-Rheumatic Drugs (1998)

Tissue inhibitors of metalloproteinases (TIMPs) prevent uncontrolled connective tissue destruction by limiting the activity of matrix metalloproteinases (MMPs). That TIMPs should be susceptible to oxidative inactivation is suggested by their complex tertiary structure which is dependent upon 6 disulphide bonds. We examined the oxidative inactivation of human recombinant TIMP-1 (hr TIMP-1) by HOCl and the inhibition of this process by anti-rheumatic agents. TIMP-1 was exposed to HOCl in the presence of a variety of disease modifying anti-rheumatic drugs. TIMP-1 activity was measured by its ability to inhibit BC1 collagenase activity as measured by a fluorimetric assay using the synthetic peptide substrate (DNP-Pro-Leu-Ala-Leu-Trp-Ala-Arg), best cleaved by MMP-1. The neutrophil derived oxidant HOCl, but not the derived oxidant N-chlorotaurine, can inactivate TIMP-1 at concentrations achieved at sites of inflammation. Anti-rheumatic drugs have the ability to protect hrTIMP-1 from inactivation by HOCl. For D-penicillamine, this effect occurs at plasma levels achieved with patients taking the drug but for other anti-rheumatic drugs tested this occurs at relatively high concentrations that are unlikely to be achieved in vivo, except possibly in a microenvironment. These results are in keeping with the concept that biologically derived oxidants can potentiate tissue damage by inactivating key but susceptible protein inhibitors such as TIMP-1 which form the major local defence against MMP induced tissue breakdown.
Dynamic Surface Activity of a Fully Synthetic Phospholipase-Resistant Lipid/Peptide Lung Surfactant (2007)

These results show that DEPN-8 and 1.5% Mini-B form an interactive binary molecular mixture with very high surface activity and the ability to resist degradation by phospholipases in inflammatory lung injury. These characteristics are promising for the development of related fully-synthetic lipid/peptide exogenous surfactants for treating diseases of surfactant deficiency or dysfunction.