gebhart/patrepeval huggingface dataset:
Detection of Constitutionally Equivalent Sites from a Connection Table (1996)

A simple and efficient algorithm for the perception of constitutionally equivalent atoms in a target molecule is reported. The algorithm consists of three steps with input data from a connection table. Our algorithm was tested on a number of typical complex structures. Results show that, with this algorithm, detection of topologically equivalent sites can be performed rapidly, and a solution (which up to now seems to be complete) can be obtained. Performance and computation time are also discussed.
Object databases for SGML document management (2002)

We have investigated the use of an object database as a platform for storing and retrieving Standard Generalized Markup Language (SGML) documents. Qualitative studies convinced us that object databases are a perfect fit for supporting SGML document management. Unfortunately, quantitative benchmark results showed that the particular object database management system (ODBMS) product we used was not capable of supporting large scale SGML applications due to certain defects in its system architecture. The most critical defect was a weak support for location-independent persistent object identifiers. We strongly believe however, ODBMSs in general are perfect platforms and continue the experiment using another ODBMS product. We explain why and how an ODBMS fits well with SGML document management applications, describe how the benchmark experiment was performed and what were the results, and finally present a list of features as a recommendation to those interested in developing or using an ODBMS in support for SGML document management.
Synthesis of copolyimides based on room temperature ionic liquid diamines (2010)

Abstract Block copolyimides based on aromatic dianhydrides and diamines copolymerized with diamino room temperature ionic liquid (RTIL) monomers were synthesized over a range of compositions. Specifically, two diamino RTILs, 1,3‐di(3‐aminopropyl) imidazolium bis[(trifluoromethyl)sulfonyl] imide ([DAPIM] [NTf 2 ]) and 1,12‐di[3‐(3‐aminopropyl) imidazolium] dodecane bis[(trifluoromethyl) sulfonyl] imide ([C 12 (DAPIM) 2 ] [NTf 2 ] 2 ) were synthesized using a Boc protection method. The two RTILs were reacted with 2,2‐bis(3,4‐carboxylphenyl) hexafluoropropane dianhydride (6FDA) to produce 6FDA‐RTILs oligomers that formed the RTIL component for the block copolyimides. The oligomers were reacted with 6FDA and m‐phenylenediamine (MDA) at oligomer concentration from 6.5 to 25.8 mol % to form block copolyimides. Increasing the concentration of the 6FDA‐RTIL oligomer in the block copolyimides resulted in a decrease in the thermal degradation temperature, glass transition temperature and an increase in the density. The gas permeability of the RTIL based block copolyimide decreased but the ideal permeability selectivity for CO 2 /CH 4 gas pair increased relative to the pure 6FDA‐MDA. © 2010 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 48: 4036–4046, 2010
Polyvalent Antigens Stabilize B Cell Antigen Receptor Surface Signaling Microdomains (2003)

The B cell Ag receptor (BCR) can distinguish subtle differences in Ag structure and trigger differential responses. In this study, we analyzed the effects of Ag valency on the signaling and Ag-targeting functions of the BCR. Although both paucivalent and polyvalent Ags induced the redistribution of the surface BCR into polarized caps, polyvalent Ag-induced BCR caps persisted. Ganglioside G(M1), a lipid raft marker, and tyrosine-phosphorylated proteins, but not CD45 and transferrin receptor, were concentrated in BCR caps, suggesting BCR caps as surface-signaling microdomains. Prolonged BCR caps were concomitant with an increase in the level and duration of protein tyrosine phosphorylation and a reduction in BCR internalization and movement to late endosomes/lysosomes. Thus, Ag valency influences B cell responses by modulating the stability of BCR-signaling microdomains and BCR trafficking.
Correlation of collagen organization with polarization sensitive imaging of in vitro cartilage: implications for osteoarthritis. (2001)

This in vitro study suggests PSOCT changes in cartilage are due to the state of collagen organization. The combination of high resolution structural imaging and birefringence detection make OCT a potentially powerful technology for early assessment of OA.
Monoclonal antibodies to thromboxane synthase from porcine lung. Production and application to development of a tandem immunoradiometric assay. (1986)

Two hybridoma cell lines secreting antibodies against thromboxane synthase of porcine lung were produced. Clone TS1 secretes IgG2a antibody of lower affinity, while clone TS2 secretes IgG1 antibody of higher affinity. Both antibodies (when bound to rabbit anti-mouse IgG-Staphylococcus aureus complex) can immunoprecipitate thromboxane synthase from crude enzyme preparations in an active form suggesting that binding was not directed at the active site. Each antibody showed a distinctive pattern of cross-reactivity with thromboxane synthase from different porcine tissues. Neither of the antibodies cross-reacted with the enzyme from tissues of other species tested, indicating the heterogeneous nature of the enzyme among species. Competitive binding assay revealed that TS1 and TS2 recognized different determinants on the enzyme. The fact that two antibodies bind to separate epitopes on the same enzyme allows the development of a sensitive tandem immunoradiometric assay. The assay, based on binding of 125I-TS2 to thromboxane synthase immobilized on TS1-S. aureus complex, was linear with 7.5 approximately 75 ng of purified lung thromboxane synthase as standards and applicable to enzyme preparations regardless of their purity. The concentration of immunoreactive thromboxane synthase in porcine tissues as determined by this assay followed the order of platelet greater than colon greater than duodenum greater than lung greater than kidney greater than stomach. The fact that gastrointestinal tract is enriched with thromboxane synthase suggests that thromboxane may have significant physiological roles to be recognized in these organs.
Wireless Integrated Network Sensors (WINS): Principles and Practice (2003)

Wireless Integrated Network Sensors (WINS) provide distributed network and Internet access to sensors, controls, and processors that are deeply embedded in equipment, facilities, and the environment. The WINS network is a new monitoring and control capability for applications in transportation,
Troybodies and Pepbodies (2002)

All antibodies (Abs) with effector function are produced in mammalian cells, whereas bacterial production is restricted to smaller targeting fragments (scFv and Fab) without effector functions. In this project, we isolated different peptides that bind one of several Ab effector molecules. We have developed bacterial expression vectors for direct cloning of these peptides as fusions to scFv and Fab, and have obtained targeting fragments that also have the ability to bind Ab effector molecules. Some of these fusions (pepbodies) may also initiate Ab effector functions. We have also genetically inserted T-cell epitopes into Abs with specificity for antigen-presenting cell (APC) surface molecules to target the Ab-T-cell epitope fusions (Troybodies) to APCs. The approach is to exchange loops in Ig constant domains with single copies of well-defined T-cell epitopes. We have shown that a number of such T-cell epitopes are loaded on to MHC class II on APCs and are presented to specific T-cells. An increase in T-cell activation of up to four orders of magnitude is achieved compared with synthetic peptide. Our current goal is to identify all the loops in all Ig constant domains that may be loaded with T-cell epitopes to produce a multi-vaccine.
Extracellular Cysteines of CCR5 Are Required for Chemokine Binding, but Dispensable for HIV-1 Coreceptor Activity (1999)

CCR5 is the major coreceptor for macrophage-tropic human immunodeficiency virus type I (HIV-1). For most G-protein-coupled receptors that have been tested so far, the disulfide bonds linking together the extracellular loops (ECL) are required for maintaining the structural integrity necessary for ligand binding and receptor activation. A natural mutation affecting Cys20, which is thought to form a disulfide bond with Cys269, has been described in various human populations, although the consequences of this mutation for CCR5 function are not known. Using site-directed mutagenesis, we mutated the four extracellular cysteines of CCR5 singly or in combination to investigate their role in maintaining the structural conformation of the receptor, its ligand binding and signal transduction properties, and its ability to function as a viral coreceptor. Alanine substitution of any single Cys residue reduced surface expression levels by 40-70%. However, mutation of Cys101 or Cys178, predicted to link ECL1 and ECL2 of the receptor, abolished recognition of CCR5 by a panel of conformation sensitive anti-CCR5 antibodies. The effects of the mutations on receptor expression and conformation were partially temperature-sensitive, with partial restoration of receptor expression and conformation achieved by incubating cells at 32 degrees C. All cysteine mutants were unable to bind detectable levels of MIP-1beta, and did not respond functionally to CCR5 agonists. Surprisingly, all cysteine mutants did support infection by R5 strains of HIV, though at reduced levels. These results indicate that both disulfide bonds of CCR5 are necessary for maintaining the structural integrity of the receptor necessary for ligand binding and signaling. Env binding and the mechanisms of HIV entry appear much less sensitive to alterations of CCR5 conformation.
Advances in mass spectrometry-based clinical biomarker discovery (2016)

The greatest unmet needs in biomarker discovery are those discoveries that lead to the development of clinical diagnostic tests. These clinical diagnostic tests can provide early intervention when a patient would present otherwise healthy (e.g., cancer or cardiovascular disease) and aid clinical decision making with improved clinical outcomes. The past two decades have seen significant technological improvements in the analytical capabilities of mass spectrometers. Mass spectrometers are unique in that they can directly analyze any biological molecule susceptible to ionization. The biological studies of human metabolites and proteins using contemporary mass spectrometry technology (metabolomics and proteomics, respectively) has been ongoing for over a decade. Some of these studies have resulted in exciting insights into human biology. However, relatively few biomarkers have been translated into clinical tests. This review will discuss some key technological developments that have occurred over this time with an emphasis on technologies that will create new avenues for biomarker discovery.
LPA Receptors: Subtypes and Biological Actions (2010)

Lysophosphatidic acid (LPA) is a small, ubiquitous phospholipid that acts as an extracellular signaling molecule by binding to and activating at least five known G protein-coupled receptors (GPCRs): LPA(1)-LPA(5). They are encoded by distinct genes named LPAR1-LPAR5 in humans and Lpar1-Lpar5 in mice. The biological roles of LPA are diverse and include developmental, physiological, and pathophysiological effects. This diversity is mediated by broad and overlapping expression patterns and multiple downstream signaling pathways activated by cognate LPA receptors. Studies using cloned receptors and genetic knockout mice have been instrumental in uncovering the significance of this signaling system, notably involving basic cellular processes as well as multiple organ systems such as the nervous system. This has further provided valuable proof-of-concept data to support LPA receptors and LPA metabolic enzymes as targets for the treatment of medically important diseases that include neuropsychiatric disorders, neuropathic pain, infertility, cardiovascular disease, inflammation, fibrosis, and cancer.
The steroid receptor superfamily: mechanisms of diversity (1991)

The steroid receptor superfamily of ligand-dependent transcription factors is characterized by marked conservation of both structure and function between the various receptors. Despite their well-documented extensive similarities, these receptors respond to a diverse range of ligands, which results in an even more impressive diversity of function. A variety of strategies is used at each point in the pathway from ligand binding to gene expression to achieve this diversity. The nature of the ligand is important as are the tissue-specific patterns of receptor gene expression, the presence of binding proteins, and the effects of cell- or tissue-specific ligand-modifying enzymes. Once bound to the receptor, the nature of which may vary as a result of either differential splicing or gene duplication yielding multiple isoforms, the activated receptor may form hetero- or homodimers. A complex interplay then occurs between the receptor dimer, other nuclear proteins, the response element, and the promoter complex to regulate gene expression. These elements may vary as a function of the cell type, other stimuli, and the context and sequence of the response element (or elements) in a given gene. By these mechanisms diversity may even be achieved for a given ligand, receptor subtype, gene, or cell. The observations may help to explain certain phenomena in hormone biology that are difficult to reconcile with the previous, simple, univariant model of steroid hormone action.
Molecular cloning and amino acid sequence of leukotriene A4 hydrolase. (1987)

A cDNA clone corresponding to leukotriene A4 hydrolase was isolated from a human lung lambda gt11 expression library by immunoscreening with a polyclonal antiserum. Several additional clones from human lung and placenta cDNA lambda g11 libraries were obtained by plaque hybridization with the 32P-labeled lung cDNA clone. One of these clones has an insert of 1910 base pairs that contains the complete protein-coding region. From the deduced primary structure, leukotriene A4 hydrolase is a 610 amino and protein with a calculated molecular weight of 69,140. No apparent homologies with microsomal epoxide hydrolases were found. RNA blot analysis indicated substantial amounts of a discrete mRNA of approximately equal to 2250 nucleotides in lung tissue and leukocytes.
Coherent Coupling of Molecular Excitons to Electronic Polarizations of Noble Metal Nanoparticles (2004)

We report the observation of coherent polarization coupling between the exciton of a molecular J-aggregate and the electronic polarization of noble metal nanoparticles. For Ag nanoparticles, coherent exciton coupling to the conduction band electrons leads to constructive interference and a long-lived exciton. For Au nanoparticles, the excitonic state interferes destructively with bound electron transition dipoles and the exciton lifetime is reduced by two orders of magnitude. Coherent polarization coupling in heterostructured nanomaterials may strongly impact the functionality of future nanoelectronic and nanooptical materials.
Mechanisms of spontaneous current generation in an inhomogeneousd-wave superconductor (2001)

A boundary between two d-wave superconductors or an s-wave and a d-wave superconductor generally breaks time-reversal symmetry and can generate spontaneous currents due to proximity effect. On the other hand, surfaces and interfaces in d-wave superconductors can produce localized current-carrying states by supporting the $\mathcal{T}$-breaking combination of dominant and subdominant order parameters. We investigate spontaneous currents in the presence of both mechanisms and show that at low temperatures, counterintuitively, the subdominant coupling decreases the amplitude of the spontaneous current due to the proximity effect. Superscreening of spontaneous currents is demonstrated to be present in any ideal $d\ensuremath{-}d$ (but not $s\ensuremath{-}d)$ junction and surface with ${d+id}^{\ensuremath{'}}$ order parameter symmetry. We show that this superscreening is the result of contributions from the local magnetic moment of the condensate to the spontaneous current.
Electronic Structure of Cubic GaN with Self-Energy Corrections (1994)

We present the results of a calculation for the bulk electronic structure of gallium nitride in the zincblende phase. We determine the equilibrium lattice constant, the cohesive energy and the bulk modulus in the Density Functional approach within the Local Density Approximation (DFT-LDA). The one-particle eigenvalues of the DFT Kohn-Sham equation do in principle not agree with the experimental band structure. Therefore, we calculate the quasi-particle energies by including self-energy corrections to the DFT-LDA exchange correlation potential, with the GW approximation for the electron self-energy. We use norm-conserving pseudopotentials and a large plane-wave basis set (100 Ry cut-off) for a converged calculation in the DFT-LDA. The LDA band gap turns out to be very sensitive to the crystal volume. We find that GW corrections to the LDA band gap are significant. A detailed comparison with other DFT-LDA results and approximate GW calculations and with existing experimental data is given.
Adaptive and Scalable Optimizations for High Performance SR-IOV (2012)

High performance networking interfaces, such as 10-Gigabit Ethernet (10GE), are now widely deployed in commercial Cloud computing environments. Virtualization is a standard technique for these environments, one of whose key challenges is to achieve highly efficient and scalable I/O virtualization. Single Root I/O Virtualization (SR-IOV) eliminates the overhead of redundant data copies and the virtual network switch through direct I/O, but needs more work on performance and scalability. In this paper, we first study the defects of SR-IOV with 10GE networking and find two major challenges. Due to multiplexing of traffic from different virtual machines, SR-IOV may generate redundant interrupts unexpectedly and thus result in high CPU overhead. SR-IOV also suffers from single-threaded NAPI which prevents it from fully utilizing multi-core machines. Then we propose two optimizations for enhancing the SR-IOV performance. The first uses adaptive interrupt rate control (AIRC) to reduce CPU overhead caused by excessive interrupts. The second is a multi-threaded network driver (MTND) which allows SR-IOV to make full use of multi-core resources. We implement these optimizations and carry out a detailed performance evaluation. The results show that AIRC can reduce CPU overhead by up to 143% and MTND can improve SR-IOV performance by up to 38%.
Decreased Pigment Epithelium-Derived Factor Is Associated with Metastatic Phenotype in Human and Rat Prostate Tumors (2004)

Pigment epithelium-derived factor, a potent angiogenesis inhibitor in the eye, is also expressed in the prostate. Prostate size and angiogenesis is increased in pigment epithelium-derived factor knockout mice, and pigment epithelium-derived factor is down-regulated in some prostate cancers. To investigate whether pigment epithelium-derived factor expression correlates with tumor progression, we examined 5 Dunning rat prostate sublines with different growth rates, differentiation, androgen dependence, vascular density, and metastatic ability and 26 human prostate cancers of Gleason score 8-10 obtained from patients at transurethral resection selected to represent two groups, with and without metastases at diagnosis. By Western blot, real-time quantitative reverse transcription-PCR, and immunostaining, pigment epithelium-derived factor was detected in highly differentiated, nonmetastatic, androgen-sensitive Dunning tumors and in the anaplastic, androgen insensitive but nonmetastatic Dunning tumors. In contrast, the metastatic Dunning tumor sublines showed very low pigment epithelium-derived factor expression levels. In human cancer tissues, by immunohistochemistry and real-time quantitative reverse transcription-PCR, patients without metastases at diagnosis had higher tumor pigment epithelium-derived factor levels than tumors from patients with metastases at diagnosis. In both the rat model and in the human tumors, the proliferation index and vascular count, as determined by Ki-67 staining and endoglin and/or factor VIII-related antigen staining, inversely correlated with pigment epithelium-derived factor mRNA levels. These observations indicate that loss of pigment epithelium-derived factor expression could be associated with the progression toward a metastatic phenotype in prostate cancer.
Lck SH3 Domain Function Is Required for T-Cell Receptor Signals Regulating Thymocyte Development (2006)

Thymocyte development is shaped by signals from the T-cell antigen receptor. The strength of receptor signaling determines developmental progression as well as deletion of self-reactive T cells. Receptor stimulation of the extracellular signal-regulated kinase (ERK) pathway plays an important regulatory role during thymocyte development. However, it is unclear how differences in receptor signaling are translated into distinctive activation of the ERK pathway. We have investigated the potential role of the Lck tyrosine kinase in regulating intracellular signaling during thymocyte development. While Lck is known to be critical for initial T-cell receptor signaling events, it may have an independent role in regulating intracellular signaling through the function of its SH3 domain. To determine whether such a regulatory mechanism functions during thymocyte development, we generated mice in which the normal lck allele is replaced with an lck SH3 domain mutant. Analysis of these mice revealed that both early thymocyte development and maturation of CD4(+) and CD8(+) lineages is impaired. Investigation of thymocyte responses to antigen receptor stimulation showed a significant reduction in proliferation and ERK pathway activation, although initial signaling events were intact. These findings indicate that Lck SH3 domain function may provide a means to independently couple receptor signaling to regulation of the ERK pathway during thymocyte development.
Superoxide Dismutase/Catalase Mimetics Are Neuroprotective against Selective Paraquat-mediated Dopaminergic Neuron Death in the Substantial Nigra (2005)

Exposure of mice to the herbicide paraquat has been demonstrated to result in the selective loss of dopaminergic neurons of the substantia nigra, pars compacta (SNpc) akin to what is observed in Parkinson disease (PD). In this study, we investigate the efficacy of two synthetic superoxide dismutase/catalase mimetics (EUK-134 and EUK-189) in protecting against paraquat-induced dopaminergic cell death in both the rat dopaminergic cell line 1RB3AN27 (N27) and primary mesencephalic cultures in vitro and in adult mice in vivo. Our data demonstrate that pretreatment with either EUK-134 or EUK-189 significantly attenuates paraquat-induced neurotoxicity in vitro in a concentration-dependent manner. Furthermore, systemic administration of EUK-189 decreases paraquat-mediated SNpc dopaminergic neuronal cell death in vivo. These findings support a role for oxidative stress in paraquat-induced neurotoxicity and suggest novel therapeutic approaches for neurodegenerative disorders associated with oxidative stress such as PD.