gebhart/patrepeval huggingface dataset:
Post-transcriptional regulation of glutamyl-prolyl-tRNA synthetase in rat salivary gland. (1994)

Treatment of rats with isoproterenol resulted in elevated levels of prolyl- and glutamyl-tRNA synthetase activities in the parotid and submandibular glands. This increase in enzyme activity was accompanied by an increase in the bi-functional glutamyl-prolyl-tRNA synthetase and of a low molecular weight form of prolyl-tRNA synthetase. Isoproterenol also induced the synthesis of proline-rich glycoproteins in the parotid and submandibular glands. Withdrawal from the drug was accompanied by a decline in prolyl- and glutamyl-tRNA synthetase activities and by a decline in the levels of proline-rich glycoproteins in the salivary gland. During the time course of isoproterenol treatment, little change in the levels of mRNA encoding the bi-functional glutamyl-prolyl-tRNA synthetase was detected by Northern blot analysis. These results indicate that the synthesis of glutamyl-prolyl-tRNA synthetase is regulated at a post-transcriptional step and that the synthesis of this bifunctional protein may be linked to the utilization of proline and glutamic acid in protein synthesis.
Caching on the World Wide Web (1999)

With the recent explosion in usage of the World Wide Web, the problem of caching Web objects has gained considerable importance. Caching on the Web differs from traditional caching in several ways. The nonhomogeneity of the object sizes is probably the most important such difference. In this paper, we give an overview of caching policies designed specifically for Web objects and provide a new algorithm of our own. This new algorithm can be regarded as a generalization of the standard LRU algorithm. We examine the performance of this and other Web caching algorithms via event- and trace-driven simulation.
The Manufacture of NiTi Foams (2002)

Ongoing research is presented on processing of NiTi-based shape memory alloy (SMA) foams. The aim is to demonstrate a new class of materials that combine the advantages of light-weight metallic foams with the strain recovery and energy-dissipation capability of SMAs. There are a number of potential novel structural and biomedical applications that could be enabled by the unusual passive and active properties of such a material. This paper presents initial results on our attempt to fabricate functional prototype specimens using a polymeric foam precursor and a powder metallurgy process to produce NiTi foams with user-selected topology and relative density. It is shown that open-cell NiTi foams with relative density less than 5% can be produced with this technique. While definite martensitic transformational behavior has been achieved in the prototypes, the quality of the foams are found to be sensitive to the sintering temperature, the binder system employed, and the levels of interstitial contamination. Further work is needed before good superelastic and shape-memory properties can be demonstrated. Nevertheless, the current technique appears promising, since the method is capable of producing NiTi foam with a more regular structure and at a relative density nearly an order of magnitude less than other techniques currently used to produce porous NiTi.
Overlapping and distinct actions of the neurotrophins BDNF, NT-3, and NT-4/5 on cultured dopaminergic and GABAergic neurons of the ventral mesencephalon (1994)

The neurotrophins brain-derived neurotrophic factor (BDNF), neurotrophin-3 (NT-3), and neurotrophin-4/5 (NT-4/5) were compared for their effects in promoting the survival and/or regulation of expression of phenotypic markers of dopaminergic and GABAergic neurons in cultures derived from embryonic rat ventral mesencephalon. Dopaminergic neuron number and phenotypic expression were monitored by tyrosine hydroxylase (TH) immunocytochemistry, and measurement of high-affinity dopamine uptake activity and dopamine content, respectively. High-affinity GABA uptake, glutamic acid decarboxylase (GAD) activity, and endogenous GABA content were used to detect GABAergic neurons. Seven days of treatment with either BDNF or NT-3 resulted in dose-dependent increases in the number of TH-positive neurons, with maximal responses of 3-fold and 2.3-fold, respectively. Dopamine uptake activity and dopamine content were similarly increased. The effects of BDNF and NT-3 on dopamine uptake activity showed no additivity. NT-4/5 treatment elicited the greatest increase (7-fold) in the number of TH-positive neurons, as well as a 2.6-fold increase in dopamine content. In marked contrast to BDNF or NT-3, NT-4/5 had no effect on dopamine uptake capacity. BDNF, NT-3, or NT-4/5 also produced dose-dependent elevations of 2-3-fold in GABA uptake activity. These effects were not additive. GAD activity was increased by BDNF (1.8-fold) and NT-3 (threefold) treatment, but not by NT-4/5, whereas GABA content was increased to a similar extent by all three neurotrophins. NGF had no effect on any of the parameters measured in this study. Northern analyses indicated that the mRNAs encoding TrkB and TrkC, the functional high-affinity receptors for BDNF and NT-4/5, and NT-3, respectively, are expressed in the substantia nigra of adult rat brain, as well as in cultures of developing ventral mesencephalon. Taken together, our results indicate that BDNF and NT-3 have broadly similar effects in promoting the survival and differentiated phenotype of both dopaminergic and GABAergic neurons of the developing substantia nigra. Although BDNF and NT-4/5 are thought to act through the same high-affinity receptor, TrkB, it is evident that these two neurotrophins have distinct as well as overlapping actions toward mesencephalic dopaminergic or GABAergic neurons.
Characterization of the functional specificity of a cloned T-cell receptor heterodimer recognizing the MART-1 melanoma antigen. (1995)

T cells can play a central role in the immune response to cancer, with tumor-specific T-lymphocyte reactivity provided by the T-cell receptor (TCR) alpha and beta chain heterodimer. This study is the first report of the definitive identification and characterization of a functional tumor-associated, antigen-specific TCR by reconstitution in an alternate cell line. Jurkat T cells were transfected with the cDNAs encoding the full-length alpha and beta T-cell receptor chains from the HLA-A2 restricted, melanoma-reactive T-cell clone, clone 5. Expression of the transfected TCR was evaluated by immunofluorescence after down-modulation of the endogenous receptor with Jurkat T-cell receptor beta chain-specific mAb. Jurkat clone 5 TCR+ cells recognized MART-1 peptides presented by T2 cells in a pattern and sensitivity equivalent to native MART-1-reactive T-cells. Recognition of HLA-A2+ melanoma cell lines by the Jurkat clone 5 TCR+ cells, however, did not occur without the addition of exogenous MART-1 peptide. The cloning and expression of functional TCR genes which are capable of specifically recognizing MART-1 antigen provides reagents which could be used for the study of the mechanisms of T-cell/tumor antigen interactions and creates immortalized reagents which can facilitate studies requiring detection of the MART-1 antigen. The tumor reactivity provided by these genes could also have application in novel immunotherapeutic strategies for treating patients with melanoma, including redirection of tumor-infiltrating lymphocyte specificity and bone marrow stem cell therapy.
A Transcriptional Activator Protein Encoded by the x- lor Region of the Human T-Cell Leukemia Virus (1985)

Human T-cell leukemia viruses type I and II (HTLV-I and -II) exhibit several features characteristic of this retroviral family: the presence of an x-lor gene encoding a nuclear protein, transformation properties suggesting the involvement of a virus-associated trans-acting factor, and transcriptional trans-activation of the long terminal repeat (LTR) in infected cells. In the study described here the HTL x-lor products, in the absence of other viral proteins, were able to activate gene expression in trans directed by HTLV LTR. The regulation of the expression of particular genes in trans by HTLV x-lor products suggests that they play a role in viral replication and possibly in transformation of T lymphocytes.
Low pregnancy-associated plasma protein A level in the first trimester. (2014)

While the clinical meaning of a low PAPP-A level detected in the context of normal fetal aneuploidy screening remains under debate, pregnant patients with such results should be counseled that at present no strong evidence exists to justify an ongoing ultrasound surveillance program.
Low Power Digital Communication in Implantable Devices Using Volume Conduction of Biological Tissues (2006)

This work investigates the data communication problem of implantable devices using fundamental theories in communications. We utilize the volume conduction property of biological tissues to establish a digital communications link. Data obtained through animal experiments are used to analyze the time and frequency response of the volume conduction channel as well as to characterize the biological signals and noises present in the system. A low power bandwidth efficient channel-coded modulation scheme is proposed to conserve battery power and reduce the health risks associated.
Water-in-Carbon Dioxide Emulsions:  Formation and Stability (1999)

Stable water-in-carbon dioxide (W/C) emulsions, for either liquid or supercritical CO2 containing up to 70 vol % water, are formed with various molecular weight perfluoropolyether ammonium carboxylate surfactants. Water droplet sizes ranging from 3 to 10 μm were determined by optical microscopy. From conductivity measurements, an inversion to C/W emulsions results from a decrease in CO2 density or salinity at constant pressure, a decrease in surfactant molecular weight, or an increase in temperature. Emulsions become more stable with a change in any of these formulation variables away from the balanced state, which increases interfacial tensions and interfacial tension gradients, enhancing Marangoni−Gibbs stabilization. This type of stability is enhanced with an increase in the molecular weight of the surfactant tails, which increases the thickness of the stabilizing films between droplets. W/C emulsions formed with the 7500 molecular weight surfactant were stable for several days.
Phagocyte function : a guide for research and clinical evaluation (1998)

Partial table of contents: Cytometric Approaches to the Study of Receptors (J. Nolan, et al.). Early Events in Receptor-Mediated Neutrophil Signal Transduction (E. Simons). Actin Polymerization in Human Neutrophils (G. Omann). Oxygen and Nitrogen Reactive Metabolites and Phagocytic Cells (J. Robinson). Neutrophil-Endothelial Cell Interactions (W. Carter & J. Robinson). Alterations in the Nonspecific Immune Response Following Severe Traumatic Injury (G. Babcock). The Role of Monocytes/Macrophages in Wound Healing (D. Greenhalgh). Monocytes and Macrophages in Solid Organ Transplantation: Important Implications for the Future of Transplant Immunology (J. Valente, et al.). Index
Characterization of Dendritic Cells and Macrophages Generated by Directed Differentiation from Mouse Induced Pluripotent Stem Cells (2009)

Methods have been established to generate dendritic cells (DCs) from mouse and human embryonic stem (ES) cells. We designated them as ES-DCs and mouse models have demonstrated the induction of anti-cancer immunity and prevention of autoimmune disease by in vivo administration of genetically engineered ES-DCs. For the future clinical application of ES-DCs, the histoincompatibility between patients to be treated and available human ES cells and the ethical concerns associated with human ES cells may be serious obstacles. However, recently developed induced pluripotent stem (iPS) cell technology is expected to resolve these issues. This report describes the generation and characterization of DCs derived from mouse iPS cells. The iPS cell-derived DCs (iPS-DCs) possessed the characteristics of DCs including the capacity of T-cell-stimulation, antigen-processing and presentation and cytokine production. DNA microarray analyses revealed the upregulation of genes related to antigen-presenting functions during differentiation into iPS-DCs and similarity in gene expression profile in iPS-DCs and bone marrow cell-derived DCs. Genetically modified iPS-DCs expressing antigenic protein primed T-cells specific to the antigen in vivo and elicited efficient antigen-specific anti-tumor immunity. In addition, macrophages were generated from iPS cells (iPS-MP). iPS-MP were comparable with bone marrow cell-derived macrophages in the cell surface phenotype, functions, and gene expression profiles.
Charge-Reversal Amphiphiles for Gene Delivery (2004)

Delivering a missing gene or a functional substitute of a defective gene has the potential to revolutionize current medical care. Of the two gene delivery approaches, viral and synthetic vectors, synthetic cationic vectors possess several practical advantages but suffer from poor transfection efficiency. A new approach to gene delivery using charge-reversal amphiphiles is described. This synthetic vector transforms from a cationic to an anionic amphiphile intracellularly. This amphiphile performs two roles: first, it binds and then releases DNA, and second, as an anionic multicharged amphiphile, it destabilizes lipid bilayers. A charge-reversal amphiphile was synthesized and fully characterized, including the supramolecular complex it forms with DNA. Enhanced gene transfection was observed using these vectors compared to current cationic amphiphiles.
Enhancement of antibody response by mouse dendritic cells pulsed with tobacco mosaic virus or with rabbit antiidiotypic antibodies raised against a private rabbit idiotype. (1985)

The role of splenic lymphoid dendritic cells (DC) and macrophages (M phi) from mice in induction of immune responses in vivo has been investigated. Varying numbers of purified DC and M phi pulsed in vitro with tobacco mosaic virus (TMV) or with rabbit antiidiotypic antibodies (Ab2) directed against a private rabbit anti-TMV idiotype were injected back into syngeneic mice. In both systems, DC appeared to strongly enhance the primary and secondary responses to the virus. Optimal responses were obtained with 5 X 10(4) purified DC carrying TMV or rabbit Ab2. In contrast, M phi were less efficient by a factor of at least 100. These results show the potency of lymphoid DC as inducing cells in T-dependent antibody responses in vivo.
Mutations Defining the Operator-binding Sites of Bacteriophage Repressor (1983)

We have characterized about 50 different amino acid substitutions in the aminoterminal domain of lambda repressor. Sixteen of these substitutions alter external side chains of the repressor and cause a substantial reduction in the affinity of the mutant repressor for operator DNA. Seven of these mutant repressors were purified and were shown to be stably folded. The strong, external repressor mutations occur near the aminoterminal end of alpha helix 2, throughout alpha helix 3, and in the aminoterminal-arm region of the repressor. These results suggest that these regions of lambda repressor are close to operator DNA in the protein-DNA complex and thus that these regions comprise the DNA-binding sites of the repressor. Our genetic results support and are completely consistent with more-detailed models of the repressor-operator interaction based on model-building (Pabo and Lewis 1982; Lewis et al. this volume) and biochemical studies (Pabo et al. 1982).
Retrovirally induced CTL degranulation mediated by IL-15 expression and infection of mononuclear phagocytes in patients with HTLV-I–associated neurologic disease (2008)

CD8(+) T cells contribute to central nervous system inflammation in human T-cell lymphotropic virus type I (HTLV-I)-associated myelopathy/tropical spastic paraparesis (HAM/TSP). We analyzed CD8(+) T-cell dysfunction (degranulation and IFN-gamma production) and have demonstrated that CD8(+) T cells of patients with HAM/TSP (HAM/TSP patients) spontaneously degranulate and express IFN-gamma in ex vivo unstimulated culture. CD8(+) T cells of HTLV-I asymptomatic carriers and healthy donors did not. Spontaneous degranulation was detected in Tax11-19/HLA-A*201 tetramer(+) cells, but not in CMV pp65 tetramer(+) cells. Interestingly, degranulation and IFN-gamma production in CD8(+) T cells was induced by coculture with autologous CD14(+) cells, but not CD4(+) T cells, of HAM/TSP patients, which correlated with proviral DNA load in CD14(+) cells of infected patients. Moreover, the expression of IL-15, which induced degranulation and IFN-gamma production in infected patients, was enhanced on surface of CD14(+) cells in HAM/TSP patients. Blockade of MHC class I and IL-15 confirmed these results. Thus, CD8(+) T-cell dysregulation was mediated by both virus infection and enhanced IL-15 on CD14(+) cells in HAM/TSP patients. Despite lower viral expression than in CD4(+) T cells, HTLV-I-infected or -activated CD14(+) cells may be a heretofore important but under recognized reservoir particularly in HAM/TSP patients.
Experimental versus theoretical evidence for the rate‐limiting steps in uncatalyzed and H+‐ and HO−‐catalyzed hydrolysis of the amide bond (2009)

Abstract Recent theoretical studies of the alkaline hydrolysis of the amide bond have indicated that the nucleophilic attack of the hydroxide ion at the carbonyl carbon of the amide group is rate limiting. This is shown to be inconsistent with a large amount of experimental observations where the expulsion of the leaving group has been shown to be rate limiting. A kinetic approach has been described, which allows us to diagnose whether the pH‐independent/uncatalyzed hydrolysis of amides involves (a) both the uncatalyzed water reaction ( k w ) and H + ‐ ( k H ) and HO − ‐catalyzed ( k OH ) water reaction, (b) only the k w reaction, or (c) only the k + k OH reaction. The analysis described in this critical review does not favor the recent theoretical claims of the absence of the water reaction in the pH‐independent/uncatalyzed hydrolysis of formamide and urea. © 2009 Wiley Periodicals, Inc. Int J Chem Kinet 41: 599–611, 2009
Making alignments prettier (2000)

BoxShade takes sequence alignments and creates an output file in which the alignment is displayed with identical or similar residues shaded in two different tones of gray.
Age-Related Impairment in Executive Functioning: Updating, Inhibition, Shifting, and Access (2004)

Miyake, Friedman, Emerson, Witzki, Howerter and Wager (2000) have argued that the central executive is fractionated consisting of at least three separable component processes: updating, shifting, and inhibition. The Wisconsin Card Sort Test, random letter generation, Brooks spatial sequences, reading and computation span, word fluency, and a measure of dual task performance were administered to 95 individuals aged between 20 and 81, average age 41.89. The executive measures were factor analyzed, using the oblique rotation method, yielding four factors. The factor structure obtained was broadly consistent with Miyake et al's. However, an additional factor, the only one not to show a significant performance decline with age, was also obtained and was believed to reflect the efficiency of access to long-term memory.
Binding of SH2 Domains of Phospholipase Cγ1, GAP, and Src to Activated Growth Factor Receptors (1990)

Phospholipase C gamma 1 (PLC gamma 1) and p21ras guanosine triphosphatase (GTPase) activating protein (GAP) bind to and are phosphorylated by activated growth factor receptors. Both PLC gamma 1 and GAP contain two adjacent copies of the noncatalytic Src homology 2 (SH2) domain. The SH2 domains of PLC gamma 1 synthesized individually in bacteria formed high affinity complexes with the epidermal growth factor (EGF)- or platelet derived growth factor (PDGF)-receptors in cell lysates, and bound synergistically to activated receptors when expressed together as one bacterial protein. In vitro complex formation was dependent on prior growth factor stimulation and was competed by intracellular PLC gamma 1. Similar results were obtained for binding of GAP SH2 domains to the PDGF-receptor. The isolated SH2 domains of other signaling proteins, such as p60src and Crk, also bound activated PDGF-receptors in vitro. SH2 domains, therefore, provide a common mechanism by which enzymatically diverse regulatory proteins can physically associate with the same activated receptors and thereby couple growth factor stimulation to intracellular signal transduction pathways.
Inhibition of Daptomycin by Pulmonary Surfactant: In Vitro Modeling and Clinical Impact (2005)

The lipopeptide daptomycin has been approved for use in skin and skin-structure infections but has failed to meet statistical noninferiority criteria in a clinical trial for severe community-acquired pneumonia. Daptomycin exhibited an unusual pattern of activity in pulmonary animal models: efficacy in Staphylococcus aureus hematogenous pneumonia and inhalation anthrax but no activity against Streptococcus pneumoniae in simple bronchial-alveolar pneumonia. Daptomycin was shown to interact in vitro with pulmonary surfactant, resulting in inhibition of antibacterial activity. This effect was specific to daptomycin and consistent with its known mechanism of action. This represents the first example of organ-specific inhibition of an antibiotic.
Hepatitis C virus-associated hepatitis following treatment of HIV-infected patients with HIV protease inhibitors (1998)

Hepatitis in HCV-HIV-coinfected patients following treatment with potent antiretroviral therapy may reflect restoration of anti-HCV immune responses rather than increased HCV replication or a hepatotoxic effect of antiretroviral therapy.
Isolation and characterization of an epithelial-specific receptor tyrosine kinase from an ovarian cancer cell line. (1994)

A protein receptor tyrosine kinase (RTK 6) has been isolated from a complementary DNA library of SKOV-3, an epithelial ovarian cancer cell line, using a polymerase chain reaction (PCR)-mediated approach. The primary structure of the predicted amino acid sequence of the protein shows a novel NH2-terminal region which has homology to a factor VIII-like domain. The juxtamembrane region is proline and glycine rich and is the longest for any known receptor kinase. The COOH-terminal catalytic domain has all of the canonical sequence motifs of a receptor tyrosine kinase with homology to the TRK-2H protein (49%). A single transcript of 4.5 kilobases is expressed at low levels in heart, placenta, lung, liver, muscle, kidney, and pancreas, with high levels of expression in the brain. Ribonuclease protection assay showed a varying level of expression of message in a panel of eight ovarian cancer cell lines compared to placenta. In situ hybridization analysis demonstrated localization of mRNA in the epithelial cells of the ovary, kidney, small bowel, lung, thymus, and brain. There was a lower level of message in normal, benign, and borderline tumors of the ovary compared to malignant tumors of the ovary. Polyclonal antisera raised against a COOH-terminal synthetic peptide recognize a M(r) 140,000 protein in ovarian cancer cells, which autophosphorylates in an in vitro kinase assay.
Assisted querying using instant-response interfaces (2007)

We demonstrate a novel query interface that enables users to construct a rich search query without any prior knowledge of the underlying schema or data. The interface, which is in the form of a single text input box, interacts in real-time with the users as they type, guiding them through the query construction. We discuss the issues of schema and data complexity, result size estimation, and query validity; and provide novel approaches to solving these problems. We demonstrate our query interface on two popular applications; an enterprise-wide personnel search, and a biological information database.