gebhart/patrepeval huggingface dataset:
Cytokine Expression and Tumorigenicity of Large Granular Lymphocytic Leukemia Cells From Mice Transgenic for the tax Gene of Human T-Cell Leukemia Virus Type I (1997)

The human T-cell leukemia virus type I (HTLV-I) regulatory protein, Tax, has been speculated to play a major role in HTLV-I leukemogenesis. Indeed, several studies have suggested that upregulation of various cellular oncogenes and cytokines by Tax may explain the pathogenesis observed in HTLV-I–infected individuals, as well as several Tax-transgenic animal models. We report here the analysis of cytokine expression in a Tax-transgenic animal model with large granular lymphocytic (LGL) leukemia. Two different transgenic mice showed identical expression of interleukin-1α (IL-1α), IL-1β, interferon γ (IFNγ), and granulocyte-macrophage colony-stimulating factor (GM-CSF ) in peripheral tail tumors. Interestingly, LGL cell lines derived from these same tumors expressed high levels of both IFNγ and GM-CSF, which correlated with the level of Tax expression. These same LGL cell lines also expressed high levels of lymphocyte function-associated antigen-1 (LFA-1) and intracellular adhesion molecule-1 (ICAM-1). Engraftment of these LGL cell lines into severe combined immunodeficient (SCID) mice led to the development of leukemia and lymphomas. Examination of these SCID mice showed that their pathology was nearly identical to that observed in the original Tax-transgenic mouse model. Both the Tax-transgenic and engrafted SCID mouse models allow for the analysis of cellular events that are required for tumor development associated with HTLV infection and suggest that Tax expression may be responsible for the upregulation of certain cytokines and adhesion molecules that affect the infiltrating capabilities of HTLV-I–infected cells.
Lipopolysaccharide: a tool and target in enterobacterial vaccine development (2008)

Lipopolysaccharide (LPS) is an essential component of Gram-negative bacteria. While mutants exhibiting truncated LPS molecules are usually over-attenuated, alternative approaches that affect the extent or timing of LPS expression, as well as its modification may establish the optimal balance for a live vaccine strain of sufficient attenuation and retained immunogenicity. On the other hand, a specific immune response to LPS molecules in itself is capable of conferring protective immunity to certain enterobacterial pathogens. Therefore, purified LPS derivatives could be used as parenteral vaccines. This review summarizes various LPS-based vaccination strategies, as well as approaches that utilize LPS mutants as whole-cell vaccines.
A wireless micro-sensor for simultaneous measurement of pH, temperature, and pressure (2001)

In response to a magnetic field impulse, magnetostrictive magnetoelastic sensors mechanically vibrate. These vibrations can be detected in several ways: optically from the amplitude modulation of a reflected laser beam, acoustically using a microphone or hydrophone, and by using a pickup coil to detect the magnetic flux emitted from the sensor. Earlier work has shown that the resonant frequency of a magnetoelastic sensor shifts in response to different environmental parameters, including temperature, pressure, fluid flow velocity and mass loading, with each parameter determined in an otherwise constant environment. To extend the utility of the sensor technology in this work we report on the fabrication and application of a miniaturized array of four magnetoelastic sensors that enable the simultaneous remote query measurement of pH, temperature, and pressure from a passive, wireless platform.
Activity of pp60c-src in 60 different cell lines derived from human tumors. (1994)

The activity of the protein tyrosine kinase pp60c-src was determined for each of the 60 human cell lines in the panel used by the National Cancer Institute for the random screening of potential anticancer drugs. The leukemia, lymphoma, melanoma, and small-cell lung cancer derived cell lines had low pp60c-src activity. Surprisingly, non-small-cell lung and ovarian cell lines had a median pp60c-src activity which was greater than that of the panel of cells representing colon cancer, which is most often associated with elevated pp60c-src activity. This data defines homologous cell lines which contain low and high pp60c-src activity which will aid attempts to understand the role of this enzyme in human cancer.
Use of Ecotilling as an efficient SNP discovery tool to survey genetic variation in wild populations of Populus trichocarpa (2006)

Abstract Ecotilling was used as a simple nucleotide polymorphism (SNP) discovery tool to examine DNA variation in natural populations of the western black cottonwood, Populus trichocarpa, and was found to be more efficient than sequencing for large-scale studies of genetic variation in this tree. A publicly available, live reference collection of P. trichocarpa from the University of British Columbia Botanical Garden was used in this study to survey variation in nine different genes among individuals from 41 different populations. A large amount of genetic variation was detected, but the level of variation appears to be less than in the related species, Populus tremula, based on reported statistics for that tree. Genes examined varied considerably in their level of variation, from PoptrTB1 which had a single SNP, to PoptrLFY which had more than 23 in the 1000-bp region examined. Overall nucleotide diversity, measured as (Total), was relatively low at 0.00184. Linkage disequilibrium, on the other hand, was higher than reported for some woody plant species, with mean r2 equal to 0.34. This study reveals the potential of Ecotilling as a rapid genotype discovery method to explore and utilize the large pool of genetic variation in tree species.
Development of a Destabilized Firefly Luciferase Enzyme for Measurement of Gene Expression (2000)

Firefly luciferase is used widely as a reporter enzyme for studies of gene regulation and expression. The recent development of new technologies that combine luciferase reporter technology and digital imaging microscopy has enabled multiple measurements of gene expression in the same living cell. Although this approach has already provided new insights about expression dynamics, its future utility is limited by the three- to four-hour half-life of firefly luciferase in mammalian cells. Because of this, rapid increases or decreases in gene expression may not be detected, owing to the accumulation of residual luciferase. Accordingly, the goal of the present study was to develop a luciferase reporter with a reduced functional half-life. This was accomplished by adding a synthetic fragment to the firefly luciferase-coding sequence that encoded the proteolytic "PEST" signal from mouse ornithine decarboxylase. When placed under the control of estrogen response elements and expressed in human breast cancer T-47D cells, the modified luciferase protein (LUCODC-DA) displayed a functional half-life of 0.84 h compared to 3.68 h for the wild-type enzyme. As anticipated, the overall rate of photonic emissions in cells expressing the destabilized luciferase was about sevenfold lower than that of their wild-type counterparts, presumably because of the reduction of steady-state luciferase accumulation. Even so, the photonic activity derived from LUCODC-DA was still sufficient to enable real-time measurements of gene expression in single living cells.
Modulation of Hematopoietic Stem Cell Homing and Engraftment by CD26 (2004)

Hematopoietic stem cell homing and engraftment are crucial to transplantation efficiency, and clinical engraftment is severely compromised when donor-cell numbers are limiting. The peptidase CD26 (DPPIV/dipeptidylpeptidase IV) removes dipeptides from the amino terminus of proteins. We present evidence that endogenous CD26 expression on donor cells negatively regulates homing and engraftment. By inhibition or deletion of CD26, it was possible to increase greatly the efficiency of transplantation. These results suggest that hematopoietic stem cell engraftment is not absolute, as previously suggested, and indicate that improvement of bone marrow transplant efficiency may be possible in the clinic.
Efficient computation of queries on feature streams (2011)

This article introduces the notion of virtual feature stream , a feature stream defined from a primary data stream, in which at any time only the features that are needed to compute the queries that are currently running in the system are computed. Virtual feature streams are, in general, impossible to determine a priori, but the paper introduces an algorithm that stops the computation of features as soon as it can be proved that they are no longer needed thus generating, albeit in a roundabout and more expensive than the ideal way, a feature stream that is less expensive than the complete one to compute and safe: the queries that accept the virtual feature stream are those (and only those) that would accept the original feature stream.
HIV Drug Resistance (2004)

Combinations of antiretroviral drugs have proven remarkably effective in controlling the progression of HIV disease and prolonging survival, but these benefits can be compromised by the development of drug resistance. About 50 percent of patients receiving antiretroviral therapy in the United States are estimated to harbor viruses that express resistance to at least one of the available antiretroviral drugs.
New directions in signaling for broadband ISDN (1989)

User networks signaling is considered. The evolution of signaling protocols is outlined, analyzing the forces producing changes in the past. Emerging broadband switching technologies and services are discussed, emphasizing capabilities that might be required. A conceptual model for representing integrated-services digital network (ISDN) calls is presented as the basis for structuring a more flexible signaling protocol to meet the needs for a broadband environment.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Association of cdk2 Kinase with the Transcription Factor E2F During S Phase (1992)

The transcription factor E2F controls the expression of several proliferation-related genes and is a target of the adenovirus E1A oncogene. In human cells, both cyclin A and the cdk2 protein kinase were found in complexes with E2F. Although the total amounts of cdk2 were constant in the cell cycle, binding to E2F was detected only when cells entered S phase, a time when the cdk2 kinase is activated. These data suggest that the interaction between cdk2 and E2F requires an active kinase that has cyclin A as a targeting component.
A System Supporting Flexible Distributed Real-Time Music Processing (2018)

Local-area networks offer a means to interconnect personal computers to achieve more processing, input, and output for music and multimedia performances. The distributed, realtime object system, Aura, offers a carefully designed architecture for distributed real-time processing. In contrast to streaming audio or MIDI-over-LAN systems, Aura offers a general real-time message system capable of transporting audio, MIDI, or any other data between objects, regardless of whether objects are located in the same process or on different machines. Measurements of audio synthesis and transmission to another computer demonstrate about 20ms of latency. Practical experience with protocols, system timing, scheduling, and synchronization are discussed.
Evaluation of interface potential barrier heights between ultrathin silicon oxides and silicon (1985)

Interface potential barrier heights for ultrathin silicon oxides (15– 44 Å) on silicon and effective electron masses in some of these oxides are evaluated. Evaluation is performed using a new technique of analyzing the charging characteristics of metal-nitride-oxide-semiconductor capacitors. Oxides thicker than 36 Å have the same potential barrier heights as those for thick oxides, assuming the effective electron mass of the oxides is the same. However, for oxides thinner than 31 Å, the potential barrier heights decrease and the effective electron masses increase as the oxide thickness decreases. These results suggest that oxides at least thicker than 36 Å can be applied to metal-oxide-semiconductor field-effect transistors as gate oxides.
Timing Analysis and Performance Improvement of MOS VLSI Designs (1987)

TV is a MOS VLSI switch-level timing verifier. It has built-in direction-finding through pass transistors to minimize the number of false paths found, and has knowledge of clocking disciplines to increase the usefulness of timing analysis for chips with several clock phases. TV can find several distinct critical paths at once by using a modified breadth-first search, so that the number of runs of the timing verifier is reduced over systems providing single or multiple equivalent paths. It can analyze circuits with 40.000 transistors in under 30 min of VAX 11/780 CPU time. The IA is TV's novel interactive timing advisor that provides incremental timing analysis. The IA can compute the effects of small design changes in circuits with 100 000 transistors using only seconds of CPU time. The IA Autopilot can propose and evaluate its own design changes.
Effects of Leflunomide on Hyaluronan Synthases (HAS): NF-κB-Independent Suppression of IL-1-Induced HAS1 Transcription by Leflunomide (2005)

Despite evidence that points to unfettered hyaluronic acid (HA) production as a culprit in the progression of rheumatic disorders, little is known about differences in regulation and biological functions of the three hyaluronan synthase (HAS) genes. Testing the effects of drugs with proven anti-inflammatory effects could help to clarify biological functions of these genes. In this study, we demonstrate that leflunomide suppresses HA release in fibroblast-like synoviocytes (FLS) in a dose-dependent manner. We further demonstrate that leflunomide suppresses HA synthase activity, as determined by (14)C-glucuronic acid incorporation assays. Additional experiments revealed that in FLS, leflunomide specifically blocked the induction of HAS1. HAS2 and HAS3, genes that are, in contrast to HAS1, constitutively expressed in FLS, are not significantly affected. Leflunomide can function as a NF-kappaB inhibitor. However, EMSA experiments demonstrate that at the concentrations used, leflunomide neither interferes with IL-1beta- nor with PMA-induced NF-kappaB translocation. Furthermore, reconstituting the pyrimidine synthase pathway did not lead to the restoration of IL-1beta-induced HAS1 activation. More importantly, two tyrosine kinase inhibitors mimicked the effect of leflunomide in that both blocked IL-1beta-induced HAS1 activation without affecting HAS2 or HAS3. These data point at HAS1 activation as the possible cause for unfettered HA production in rheumatoid arthritis and might explain, at least in part, the beneficial effects of leflunomide treatment. These findings also support the concept that IL-1beta-induced HAS1 activation depends on the activation of tyrosine kinases, and indicate that leflunomide blocks HA release by suppressing tyrosine kinases rather than through inhibition of NF-kappaB translocation.
Carotid Plaque Neovascularization and Hemorrhage Detected by MR Imaging are Associated with Recent Cerebrovascular Ischemic Events (2011)

Adventitial enhancement and IPH are independently associated with previous events and may provide important insight into stroke risk not achievable by stenosis.
Oscillatory Behavior of Double-Walled Nanotubes under Extension:  A Simple Nanoscale Damped Spring (2003)

Computer simulations of double-walled carbon nanotubes show that if the inner nanotube is pulled out part of the way and then released, then the inner tube exhibits damped oscillatory behavior at gigahertz frequencies. A simple mathematical model, formulated in terms of macroscopic ideas of friction, is shown to predict the observed behavior to a high degree of accuracy.
InGaAs / InAlAs quantum wells on wafer bonded InP / GaAs substrates (2005)

Metalorganic vapor phase epitaxial growth of InGaAs/InAlAs quantum well structures on wafer bonded and exfoliated InP films on GaAs substrates were assessed. The composite substrates were fabricated using silicon nitride intermediate layers and through hydrogen-implant induced exfoliation of an InP layer. The InP layer was subjected to a chemical mechanical polish step to produce an epi-ready sub-nm surface roughness prior to the epitaxial growth. Photoluminescence, x-ray rocking curve, and transmission electron microscopy results from the heterostructures grown on the InP/GaAs template wafers were comparable to measurements from structures grown on standard InP substrates, demonstrating that this type of composite substrate can withstand high temperature epitaxial growth processes.
Mechanism of the Interaction of β2-Glycoprotein I with Negatively Charged Phospholipid Membranes (2001)

In an attempt to understand the multifunctional involvement of beta(2)-glycoprotein I (beta(2)GPI) in autoimmune diseases, thrombosis, atherosclerosis, and inflammatory processes, substantial interest is focused on the interaction of beta(2)GPI with negatively charged ligands, in particular, with acidic phospholipids. In this study, unilamellar vesicles composed of cardiolipin were used as in vitro membrane system to test and further refine a model of interaction based on the crystal structure of beta(2)GPI. The data suggest that beta(2)GPI anchors to the membrane surface with its hydrophobic loop adjacent to the positively charged lysine rich region in domain V. Subsequently, beta(2)GPI penetrates the membrane interfacial headgroup region as indicated by a restriction of the lipid side chain mobility, but without formation of a nonbilayer lipid phase. A structural rearrangement of beta(2)GPI upon lipid binding was detected by microcalorimetry and may result in the exposure of cryptic epitopes located in the complement control protein domains. This lipid-dependent conformational change may induce oligomerization of beta(2)GPI and promote intermolecular associations. Thus, the aggregation tendency of beta(2)GPI may serve as the basis for the formation of a molecular link between cells but may also be an essential feature for binding of autoantibodies and hence determine the role of beta(2)GPI in autoimmune diseases.
Effect of Fatty Acid Oxidation Inhibition on Glucose Metabolism in Diabetic Rats (1993)

Inhibition of fatty acid (FA) oxidation has been shown previously to lower blood glucose levels acutely in diabetic rats. However, the longer term effects of FA oxidation inhibition have not been determined. This study examines the effect of inhibition of (FA) oxidation for 3 weeks on carbohydrate metabolism in rats rendered diabetic with streptozotocin (STZ). STZ treated rats (50 mg/kg) were randomized into 3 groups: a non-treated diabetic group and 2 groups treated with either 12.5 or 25 mg/kg/day Etomoxir (a specific carnitine palmitoyl transferase inhibitor) for 3 weeks. The 3 groups of rats had ad libitum access to a high fat diet (50% energy fat, 30% carbohydrate and 20% protein) throughout the study. After 3 weeks hepatic glucose production (HGP) was estimated using a constant infusion of (3H)-6-glucose in-vivo after an overnight fast. Inhibition of FA oxidation in diabetic rats resulted in a significant reduction in fasting glucose levels and hepatic glucose production. In addition, experiments with adipocytes isolated from diabetic rats treated with etomoxir demonstrated an increase in sensitivity and responsiveness to insulin of glucose utilization and pyruvate dehydrogenase (PDH) activity. It is important to note that these improvements in carbohydrate metabolism were not accompanied by increases in circulating FFA or triglyceride levels which were unchanged or lower after inhibition of FA oxidation.
Expression of Concern: The haptoglobin beta subunit sequesters HMGB1 toxicity in sterile and infectious inflammation (2017)

Haptoglobin β protein offers a novel therapeutic approach to fight against various inflammatory diseases caused by excessive HMGB1 release.
Involvement of neutrophils and natural killer cells in the anti-tumor activity of alemtuzumab in xenograft tumor models (2010)

Alemtuzumab is a recombinant humanized IgG1 monoclonal antibody directed against CD52, an antigen expressed on the surface of normal and malignant B and T lymphocytes. Alemtuzumab is approved for the treatment of B-cell chronic lymphocytic leukemia (B-CLL), but the exact mechanism by which the antibody depletes malignant lymphocytes in vivo is not clearly defined. To address this issue, the anti-tumor activity of alemtuzumab was studied in disseminated and subcutaneous xenograft tumor models. The density of CD52 target antigen on the surface of tumor cells appeared to correlate with the anti-tumor activity of alemtuzumab. Deglycosylation of alemtuzumab resulted in a loss of cytotoxicity in vitro and was found to abolish anti-tumor activity in vivo. Individual inactivation of effector mechanisms in tumor-bearing mice indicated that the protective activity of alemtuzumab in vivo was primarily dependent on ADCC mediated by neutrophils and to a lesser extent NK cells. Increasing the number of circulating neutrophils by treatment with G-CSF enhanced the anti-tumor activity of the antibody, thus providing further evidence for the involvement of neutrophils as effector cells in the activity of alemtuzumab.
Structural studies of the carbohydrate chains of human gamma-interferon (1986)

Human gamma-interferon (IFN-gamma) was prepared biotechnologically using Chinese hamster ovary cells. These cells were shown to be able to produce glycosylated IFN-gamma. Sugar analysis revealed the presence of Man, Gal, GlcNAc, NeuAc and Fuc residues in a molar ratio of 3.8:2.0:3.5:0.6:0.4 suggesting the occurrence of N-glycosidically linked N-acetyllactosamine type of carbohydrate chains. For structure determination of these chains, the glycoprotein was subjected to the hydrazinolysis procedure, yielding oligosaccharide-alditols. The latter compounds were analysed by 500-MHz 1H-NMR spectroscopy. The carbohydrate material was found to consist of biantennary structures, exhibiting microheterogeneity as to the terminal sialic acids and the core Fuc residue: (Formula: see text). As similar carbohydrates are present on several human secreted proteins, this glycosyl group is not expected to be immunogenic in man. It remains to be established to what extent the carbohydrate chains of this biotechnologically produced IFN-gamma are identical to those of naturally occurring human IFN-gamma.