gebhart/patrepeval huggingface dataset:
An introduction to software agents (1997)

ion and delegation: Agents can be made extensible and composable in ways that common iconic interface objects cannot. Because we can &amp;quot;communicate&amp;quot; with them, they can share our goals, rather than simply process our commands. They can show us how to do things and tell us what went wrong (Miller and Neches 1987). . Flexibility and opportunism: Because they can be instructed at the level of 16 BRADSHAW goals and strategies, agents can find ways to &amp;quot;work around&amp;quot; unforeseen problems and exploit new opportunities as they help solve problems. . Task orientation: Agents can be designed to take the context of the person&amp;apos;s tasks and situation into account as they present information and take action. . Adaptivity: Agents can use learning algorithms to continually improve their behavior by noticing recurrent patterns of actions and events. Toward Agent-Enabled System Architectures In the future, assistant agents at the user interface and resource-managing agents behind the scenes will increas...
A mer-lux transcriptional fusion for real-time examination of in vivo gene expression kinetics and promoter response to altered superhelicity (1992)

We constructed mercury resistance operon-luciferase (mer-lux) transcriptional fusion plasmids to evaluate in vivo gene expression rates of the mer structural gene promoter (PTPCAD) of transposon Tn21. In vivo gene expression kinetics corresponded well with those previously determined in vitro, yielding an apparent K0.5 for Hg(II)-stimulated induction by MerR of 9.3 x 10(-8) M with the same ultrasensitive threshold effect seen in vitro. We also used the mer-lux fusions to elucidate subtle variations in promoter activity brought about by altered superhelicity. Binding of inducer [Hg(II)] to the transcriptional activator MerR is known to result in DNA distortion and transcriptional activation of the mer operon; it has recently been demonstrated that this distortion is a consequence of MerR-Hg(II)-induced local DNA unwinding to facilitate RNA polymerase open complex formation at PTPCAD. Since negative supercoiling results in DNA unwinding similar to this MerR activation, we hypothesized that a global increase in plasmid supercoiling would facilitate MerR-mediated activation and compromise MerR-mediated repression, while removal of plasmid supercoils would compromise MerR's ability to induce transcription and facilitate its ability to repress transcription. Indeed, we found that increased negative supercoiling results in increased gene expression rates and decreased supercoiling results in reduced gene expression rates for the induced, repressed, and derepressed conditions of PTPCAD. Thus, luciferase transcriptional fusions can detect subtle variations in initial rates of gene expression in a real-time, nondestructive assay.
Clinical Pharmacology and Pharmacokinetics of Oxcarbazepine (1994)

Oxcarbazepine (OCBZ) is a new antiepileptic drug (AED) structurally related to carbamazepine (CBZ) but differing in several important aspects, notably metabolism and induction of metabolic pathways. Consequently, OXCB has fewer drug-drug interactions compared with CBZ. Absorption of OCBZ is rapid and complete. In animals it is responsible for the pharmacological effect. In humans, however, the parent compound is rapidly and extensively metabolized to a monohydroxy derivative (MHD), which is responsible for the therapeutic effect. Exposure to the MHD increases dose proportionally, and steady state is achieved after only three or four doses in a twice-daily regimen. When given with food, systemic exposure to MHD increases by about 17%. MHD is eliminated with a half-life of about 8-10 h. About 27% of the dose is recovered in the urine as unchanged MHD and a further 49% as a glucuronide conjugate of MHD. Results suggest that the kinetics of OCBZ should not be affected by impaired liver function. Impaired kidney function does not affect the kinetics of MHD; the glucuronide conjugate will, however, accumulate in these patients. The conversion of OCBZ to MHD is catalyzed by reductase enzymes, which are not subject to induction. Furthermore, OCBZ itself does not appear to induce the cytochrome P-450 family in general, although it does induce the P-450 IIIA subfamily, which is responsible for the metabolism of estrogens and the dihydropyridine calcium-channel blockers (e.g., nifedipine, felodipine). In patients, linear and dose-proportional kinetics with no autoinduction of metabolism simplify OCBZ dosage adjustment.
76.1: High Aperture Ratio LCD Display using In‐Ga‐Zn‐Oxide TFTs without Storage Capacitor (2010)

Abstract By using oxide semiconductors, we succeeded in prototyping a 3.4‐inch QHD LCD panel whose aperture ratio is high and pixels do not include a storage capacitor. The aperture ratio is increased from 40 % to 59%, resulting in reduction of power consumption in a backlight unit.
Eradication of small cell lung cancer cells from human bone marrow with immunotoxins. (1993)

The potential of autologous bone marrow transplantation to improve the treatment results for patients with small cell lung cancer (SCLC) may be limited by the presence of tumor cells in the graft. We constructed immunotoxins (ITs) involving 4 monoclonal antibodies and Pseudomonas exotoxin A and investigated the cytotoxicity of the ITs to H-146 SCLC cells in the presence and absence of normal human bone marrow (BM) cells. The Pseudomonas exotoxin A conjugate with the MOC-1 antibody, which recognizes an NCAM antigen, was inactive, as tested in a reproducible soft agar assay. Conjugates involving the monoclonal antibodies MOC-31, NrLu10, and MLuC1 killed about 3.5 log tumor cells at 0.1 microgram/ml and > 5.0 log at 1 microgram/ml. In the absence of BM cells, the combination of the 3 ITs was not superior to each IT used individually. However, when H-146 cells were admixed to nucleated BM cells at the ratio of 1:10, > 5 log tumor cell kill was obtained at a concentration as low as 0.1 microgram/ml of each IT. Survival of normal BM progenitor cells was only moderately reduced by the IT treatment, even in experiments in which the 3 IT3s were used at 2.5 micrograms/ml each. Freezing and thawing of the BM, as required in a clinical setting, reduced the colony-forming unit, granulocyte-macrophage, and colony-forming unit, granulocyte-erythroid-macrophage-megakaryocyte, by 30-60% in both treated and untreated cultures. We conclude that the use of a mixture of the 3 ITs provides a safe, rapid, and effective method for eradicating SCLC cells from BM used for autologous bone marrow transplantation following high-dose chemotherapy.
Identification and Optimization of an Aminoalcohol-Carbazole Series with Antimalarial Properties (2013)

Recent observations on the emergence of artemisinin resistant parasites have highlighted the need for new antimalarial treatments. An HTS campaign led to the identification of the 1-(1-aminopropan-2-ol)carbazole analogues as potent hits against Plasmodium falciparum K1 strain. The SAR study and optimization of early ADME and physicochemical properties direct us to the selection of a late lead compound that shows good efficacy when orally administrated in the in vivo P. berghei mouse model.
PRMT 3, a Type I Protein Arginine N-Methyltransferase That Differs from PRMT1 in Its Oligomerization, Subcellular Localization, Substrate Specificity, and Regulation (1998)

Methylation is one of the many post-translational modifications that modulate protein function. Although asymmetric<i>N</i><sup>G</sup>,<i>N</i><sup>G</sup>-dimethylation of arginine residues in glycine-arginine-rich domains of eucaryotic proteins, catalyzed by type I protein arginine<i>N</i>-methyltransferases (PRMT), has been known for some time, members of this enzyme class have only recently been cloned. The first example of this type of enzyme, designated PRMT1, cloned because of its ability to interact with the mammalian TIS21 immediate-early protein, was then shown to have protein arginine methyltransferase activity. We have now isolated rat and human cDNA orthologues that encode proteins with substantial sequence similarity to PRMT1. A recombinant glutathione <i>S</i>-transferase (GST) fusion product of this new rat protein, named PRMT3, asymmetrically dimethylates arginine residues present both in the designed substrate GST-GAR and in substrate proteins present in hypomethylated extracts of a yeast<i>rmt1</i> mutant that lacks type I arginine methyltransferase activity; PRMT3 is thus a functional type I protein arginine<i>N</i>-methyltransferase. However, rat PRMT1 and PRMT3 glutathione <i>S</i>-transferase fusion proteins have distinct enzyme specificities for substrates present in both hypomethylated<i>rmt1</i> yeast extract and hypomethylated RAT1 embryo cell extract. TIS21 protein modulates the enzymatic activity of recombinant GST-PRMT1 fusion protein but not the activity of GST-PRMT3. Western blot analysis of gel filtration fractions suggests that PRMT3 is present as a monomer in RAT1 cell extracts. In contrast, PRMT1 is present in an oligomeric complex. Immunofluorescence analysis localized PRMT1 predominantly to the nucleus of RAT1 cells. In contrast, PRMT3 is predominantly cytoplasmic.
The human leukocyte antigen (HLA)-C-specific "activatory" or "inhibitory" natural killer cell receptors display highly homologous extracellular domains but differ in their transmembrane and intracytoplasmic portions. (1996)

Natural killer cells express clonally distributed receptors specific for major histocompatibility complex class I molecules. The human leukocyte antigen (HLA)-C-specific receptors have been molecularly identified and cloned. They exist not only as inhibitory (p58) but also as activatory (p50) receptors. Here we show that p50 and p58 are highly homologous in their extracellular regions formed by two Ig-like domains. In contrast, major differences exist in their transmembrane and cytoplasmic portions. Whereas p 58 displays a 76-84-amino acid cytoplasmic tail containing an unusual antigen receptor activation motif, p50 is characterized by a shorter 39-amino acid tail. In addition, whereas p58 has a nonpolar transmembrane portion, p50 contains the charged amino acid Lys. These data strongly suggest that receptors with identical HLA-C allele specificity can mediate functions of opposite sign owing to their different transmembrane/cytoplasmic portions.
Preparation of Monoclonal Antibodies Cross‐Reactive with Orthopoxviruses and Their Application for Direct Immunofluorescence Test (2005)

Variola virus (smallpox virus), vaccinia virus (VV), cowpox virus (CPV) and ectromelia virus (EV) belong to the genus Orthopoxvirus of the family Poxviridae. To establish the possible diagnosis for smallpox infection, monoclonal antibodies (MAbs) against VV and CPV were produced. The cross-reactivity of seven MAbs with cells infected with various strains of the orthopoxviruses (CPV, VV and EV) was confirmed by an immunofluorescence (IF) test and other immunological analyses. Four and three MAbs reacted with the common antigen of all poxviruses (probably NP antigen) and the antigen involved in neutralization, respectively. We developed the IF test using these MAbs. The direct IF test required only 45 min to perform. Smallpox infection is now eradicated, but it is important to prepare for the diagnosis of smallpox in an emergency. The direct IF assay using MAbs cross-reactive with orthopoxviruses is rapid, simple, specific, applicable for multiple samples, and will make it possible to screen for and detect orthopoxviruses that include variola virus with tissue impression smears from skin lesions in most laboratories or institutes.
CD146: biosynthesis and production of a soluble form in human cultured endothelial cells (1998)

We previously identified the S-Endo 1-associated antigen (CD146), an endothelial member of the immunoglobulin superfamily with a characteristic V-V-C2-C2-C2 Ig domain structure. In cultured human endothelial cells, we investigated its biosynthesis by immunoprecipitation and pulse-chase labeling. CD146 was synthesized as a 100 kDa precursor form, which was processed into a 120 kDa mature form. In the culture media of endothelial cells, we observed a CD146 soluble form that was about 10 kDa smaller than cell-associated CD146. In parallel with soluble forms of other members of the immunoglobulin superfamily, soluble CD146 could modulate and control the functions of the molecule.
Apoptosis and Proliferation Markers in Diffusely Infiltrating Astrocytomas (2006)

Caspases and inhibitor of apoptosis proteins (IAPs) are antagonizing key apoptosis regulators. Limited studies of a few IAPs indicated their roles in astrocytomas. However, the overall expression status and significance of apoptosis regulators in astrocytomas is not clear. We examined the expression profile of the caspases (CASP3, 6, 7, 8, 9, 10, and 14), APAF1, SMAC, BCL2, the IAPs (BIRC5/survivin, CIAP1, CIAP2, XIAP, and LIVIN), and the proliferation markers Ki67 and PHH3 in 78 diffusely infiltrating astrocytomas and 24 normal brain samples by immunohistochemistry. Western blotting for major caspases and IAPs and reverse transcription-polymerase chain reaction analyses for IAPs were performed on a subset of 27 fresh samples. Our data showed BIRC5 nuclear labeling index (BIRC5-N) was the apoptosis marker most significantly different in World Health Organization grade II to IV astrocytomas and most strongly associated with proliferative activity. Expression level of other apoptosis-related proteins was modest or low in astrocytomas and did not correlate significantly with tumor grade or proliferation. Apoptosis regulators and proliferation markers were not detected in astrocytes of normal brain by immunostaining. This expression profile suggested involvement of apoptosis regulators in astrocytoma tumorigenesis, but tumor progression was more closely associated with proliferative advantages of which BIRC5 nuclear expression appeared to be a manifestation.
Space-variant image restoration by coordinate transformations* (1974)

A method of image restoration for certain systems with space-variant point-spread functions is presented. The technique, called coordinate transformation restoration (CTR), is applicable to a large class of optical degradations, and operates by first transforming the degraded image by a geometrical distortion. Following this, space-invariant inverse filtering or estimation and another transformation are used to complete the process. The CTR technique makes restoration practical for a variety of incoherent systems with motion and aberration degradations by effectively reducing the system dimensionality.
Proposal for Creating a Spin-polarized p_x+ip_y State and Majorana Fermions (2009)

The spin polarized p_x + ip_y superconductor is known to support Majorana states but so far there has been no example. We propose a simple setup to create such a state by depositing a ferromagnetic metal on a non-centrosymmetric superconductor with strong spin-orbit coupling which contains a Rashba-type term.
Cloning and characterization of three genes (SUT1–3 ) encoding glucose transporters of the yeast Pichia stipitis (1999)

We have identified and characterized three genes, SUT1, SUT2 and SUT3, that encode glucose transporters of the yeast Pichia stipitis. When expressed in a Saccharomyces cerevisiae hxt null mutant strain that is unable to take up monosaccharides, all three proteins restored growth on glucose. Sequencing of the genes revealed open reading frames coding for 553 amino acids in the case of SUT1, and for 550 amino acids in the case of SUT2 and of SUT3. The derived protein sequences are closely related to one another, and show distinct sequence similarities to the S. cerevisiae hexose transporter family and to monosaccharide transporters of other organisms. The Sut2 and Sut3 proteins are nearly identical and differ only in one amino acid. Determination of substrate specificities and kinetic parameters of the individual Sut proteins expressed in a S. cerevisiae hxt1-7 mutant revealed Sut1, Sut2 and Sut3 as glucose transporters with K(m) values in the millimolar range. The proteins were also able to transport xylose and other monosaccharides, but with a considerably lower affinity. In P. stipitis, transcription of SUT1 was strongly induced by glucose and was independent of the oxygen supply. In contrast, SUT2 and SUT3 were only expressed under aerobic conditions, but independent of the carbon source. Cells disrupted for the SUT1 gene did not show any obvious growth phenotype, however low-affinity glucose uptake was lost. Further investigations suggest that the Sut proteins constitute a subfamily of glucose transporters in P. stipitis, and that other and probably unrelated proteins exist additionally mediating high-affinity glucose and xylose uptake.
Aneuploidy and Genetic Variation in the Arabidopsis thaliana Triploid Response (2005)

Abstract Polyploidy, the inheritance of more than two genome copies per cell, has played a major role in the evolution of higher plants. Little is known about the transition from diploidy to polyploidy but in some species, triploids are thought to function as intermediates in this transition. In contrast, in other species triploidy is viewed as a block. We investigated the responses of Arabidopsis thaliana to triploidy. The role of genetic variability was tested by comparing triploids generated from crosses between Col-0, a diploid, and either a natural autotetraploid (Wa-1) or an induced tetraploid of Col-0. In this study, we demonstrate that triploids of A. thaliana are fertile, producing a swarm of different aneuploids. Propagation of the progeny of a triploid for a few generations resulted in diploid and tetraploid cohorts. This demonstrated that, in A. thaliana, triploids can readily form tetraploids and function as bridges between euploid types. Genetic analysis of recombinant inbred lines produced from a triploid identified a locus on chromosome I exhibiting allelic bias in the tetraploid lines but not in the diploid lines. Thus, genetic variation was subject to selection contingent on the final ploidy and possibly acting during the protracted aneuploid phase.
The Systemic Inflammatory Response to Clostridium difficile Infection (2014)

A broad systemic inflammatory response occurs during CDI and severe cases appear to differ from non-severe infections.
Altered Kv3.3 channel gating in early‐onset spinocerebellar ataxia type 13 (2012)

Mutations in Kv3.3 cause spinocerebellar ataxia type 13 (SCA13). Depending on the causative mutation, SCA13 is either a neurodevelopmental disorder that is evident in infancy or a progressive neurodegenerative disease that emerges during adulthood. Previous studies did not clarify the relationship between these distinct clinical phenotypes and the effects of SCA13 mutations on Kv3.3 function. The F448L mutation alters channel gating and causes early-onset SCA13. R420H and R423H suppress Kv3 current amplitude by a dominant negative mechanism. However, R420H results in the adult form of the disease whereas R423H produces the early-onset, neurodevelopmental form with significant clinical overlap with F448L. Since individuals with SCA13 have one wild type and one mutant allele of the Kv3.3 gene, we analysed the properties of tetrameric channels formed by mixtures of wild type and mutant subunits. We report that one R420H subunit and at least one R423H subunit can co-assemble with the wild type protein to form active channels. The functional properties of channels containing R420H and wild type subunits strongly resemble those of wild type alone. In contrast, channels containing R423H and wild type subunits show significantly altered gating, including a hyperpolarized shift in the voltage dependence of activation, slower activation, and modestly slower deactivation. Notably, these effects resemble the modified gating seen in channels containing a mixture of F448L and wild type subunits, although the F448L subunit slows deactivation more dramatically than the R423H subunit. Our results suggest that the clinical severity of R423H reflects its dual dominant negative and dominant gain of function effects. However, as shown by R420H, reducing current amplitude without altering gating does not result in infant onset disease. Therefore, our data strongly suggest that changes in Kv3.3 gating contribute significantly to an early age of onset in SCA13.
hSK4/hIK1, a Calmodulin-binding KCa Channel in Human T Lymphocytes (1999)

Human T lymphocytes express a Ca2+-activated K+ current (IK), whose roles and regulation are poorly understood. We amplified hSK4 cDNA from human T lymphoblasts, and we showed that its biophysical and pharmacological properties when stably expressed in Chinese hamster ovary cells were essentially identical to the native IK current. In activated lymphoblasts, hSK4 mRNA increased 14.6-fold (Kv1.3 mRNA increased 1.3-fold), with functional consequences. Proliferation was inhibited when Kv1.3 and IK were blocked in naive T cells, but IK block alone inhibited re-stimulated lymphoblasts. IK and Kv1.3 were involved in volume regulation, but IK was more important, particularly in lymphoblasts. hSK4 lacks known Ca2+-binding sites; however, we mapped a Ca2+-dependent calmodulin (CaM)-binding site to the proximal C terminus (Ct1) of hSK4. Full-length hSK4 produced a highly negative membrane potential (Vm) in Chinese hamster ovary cells, whereas the channels did not function when either Ct1 or the distal C terminus was deleted (Vm approximately 0 mV). Native IK (but not expressed hSK4) current was inhibited by CaM and CaM kinase antagonists at physiological Vm values, suggesting modulation by an accessory molecule in native cells. Our results provide evidence for increased roles for IK/hSK4 in activated T cell functions; thus hSK4 may be a promising therapeutic target for disorders involving the secondary immune response.
Ligands for EPH-Related Receptor Tyrosine Kinases that Require Membrane Attachment or Clustering for Activity (1994)

The EPH-related transmembrane tyrosine kinases constitute the largest known family of receptor-like tyrosine kinases, with many members displaying specific patterns of expression in the developing and adult nervous system. A family of cell surface-bound ligands exhibiting distinct, but overlapping, specificities for these EPH-related kinases was identified. These ligands were unable to act as conventional soluble factors. However, they did function when presented in membrane-bound form, suggesting that they require direct cell-to-cell contact to activate their receptors. Membrane attachment may serve to facilitate ligand dimerization or aggregation, because antibody-mediated clustering activated previously inactive soluble forms of these ligands.