gebhart/patrepeval huggingface dataset:
Morphine Induces Gene Expression of CCR5 in Human CEM x174 Lymphocytes (2000)

All HIV-1 strains studied to date use CCR5, CXCR4, or both receptors to enter cells. Simian immunodeficiency virus (SIV) infection of non-human primates has served as a useful model for understanding AIDS pathogenesis in humans. Research on several genetically divergent SIV isolates has revealed that SIV uses CCR5, and not CXCR4, for entry. CEM x174, a human lymphoid cell line, has been routinely used to cultivate and maintain various SIV strains. However, questions have arisen about how CEM x174, which reportedly was unable to express detectable amounts of CCR5 transcripts, efficiently supports the growth of SIV. In searching for an answer, we resorted to a sensitive competitive reverse transcriptase-polymerase chain reaction procedure in an attempt to detect as well as quantify the amount of CCR5 expression. Here we present our findings, which indicate that CEM x174 indeed expresses CCR5 and that the amount of CCR5 is increased in cells pretreated with morphine. These results correlate well with our previous observations that morphine treatment causes CEM x174 cells to be more susceptible to SIV infection. Similar morphine effect was not observed on CEM x174 cells infected with simian retroviruses, which do not depend on CCR5 for entry. These findings suggest a plausible mechanism whereby opiate drug users render themselves more susceptible to HIV infection, thereby explaining the vast prevalence of HIV infection among endemic drug use populations.
The kinetics of baboon fibrinogen adsorption to polymers: In vitro and in vivo studies (1986)

Fibrinogen adsorption on polymers from blood may mediate or potentiate thrombosis because of its involvement in both the intrinsic clotting system and the formation of platelet aggregates. While the kinetics of fibrinogen adsorption from plasma in vitro have previously been found to be very different on polar and nonpolar surfaces [T. A Horbett, "The kinetics of adsorption of plasma proteins to a series of hydrophilic-hydrophobic copolymers," ACS Org. Coat. Plas. Chem. 40, 642-646 (1979)] the significance of this difference with respect to thrombogenesis in vivo has not been clarified. In this study, the kinetics of deposition of baboon 125I fibrinogen from plasma in vitro or from blood in vivo on a series of polymers was measured. The polymers chosen for this study had previously been found to have a large range in surface polarity and reactivity in the in vivo baboon shunt model. The kinetics of fibrinogen adsorption in vitro were observed to be of three types, depending on the polymer: high initial adsorption decreasing to a lower steady state value; constant throughout the time course; low initial adsorption rising steadily to a plateau value. In vivo, fibrinogen deposition kinetics were of two types: low, constant deposition throughout the time course, independent of heparinization; low deposition initially followed by a second phase of greatly increased deposition (probably as fibrin) which was prevented or greatly decreased by heparinizing the animals. Polymers for which fibrinogen adsorption increased to a plateau in vitro were found to have a heparin inhibitable second phase of enhanced in vivo fibrinogen deposition. These polymers also have been found in previous studies to enhance the rate of platelet destruction when used as in vivo shunts on baboons. Conversely, most polymers with high initial in vitro fibrinogen adsorption followed by a decrease had low fibrinogen deposition behavior in vivo and were also minimally destructive of platelets. The adsorption kinetics of fibrinogen to polymers from blood in vivo and in vitro and the consumption of platelets in vivo induced by the polymers all vary with polymer polarity. More polar polymers had in vitro fibrinogen kinetics characterized by a rise to a plateau, in vivo fibrinogen deposition characterized by a second stage of great increase inhibitable by heparin, and enhanced platelet consumption. The correlation of three separate indicators of surface thrombogenicity with surface polarity suggests that more polar materials may be more thrombogenic because of an influence on the way in which fibrinogen interacts with these surfaces.
How to perform the most accurate possible phase measurements (2009)

We present the theory of how to achieve phase measurements with the minimum possible variance in ways that are readily implementable with current experimental techniques. Measurements whose statistics have high-frequency fringes, such as those obtained from maximally path-entangled $(|N,0⟩+|0,N⟩)/\sqrt{2}$ (``NOON'') states, have commensurately high information yield (as quantified by the Fisher information). However, this information is also highly ambiguous because it does not distinguish between phases at the same point on different fringes. We provide schemes to eliminate this phase ambiguity in a highly efficient way, providing phase estimates with uncertainty that is within a small constant factor of the Heisenberg limit, the minimum allowed by the laws of quantum mechanics. These techniques apply to NOON state and multipass interferometry, as well as phase measurements in quantum computing. We have reported the experimental implementation of some of these schemes with multipass interferometry elsewhere. Here, we present the theoretical foundation and also present some additional experimental results. There are three key innovations to the theory in this paper. First, we examine the intrinsic phase properties of the sequence of states (in multiple time modes) via the equivalent two-mode state. Second, we identify the key feature of the equivalent state that enables the optimal scaling of the intrinsic phase uncertainty to be obtained. This enables us to identify appropriate combinations of states to use. The remaining difficulty is that the ideal phase measurements to achieve this intrinsic phase uncertainty are often not physically realizable. The third innovation is to solve this problem by using realizable measurements that closely approximate the optimal measurements, enabling the optimal scaling to be preserved. We consider both adaptive and nonadaptive measurement schemes.
Contrasting effects of glucocorticoids on the capacity of T cells to produce the growth factors interleukin 2 and interleukin 4 (1989)

The molecular mechanisms which govern the biosynthesis and secretion of the various T cell-derived lymphokines are poorly understood at this time, in spite of their tremendous importance to the control of the mammalian immune system. Here we provide compelling evidence that production of the murine T cell growth factors interleukin (IL) 2 and IL4 are differentially regulated by glucocorticoid (GCS) hormones. Under conditions where IL2 production is reduced by GCS hormones, IL4 production is increased. In vivo, this effect on T cell production of growth factors is manifest at low GCS concentrations that are well within physiologic ranges. In vitro, splenocytes isolated from antigen-stimulated donors, as well as antigen-specific cloned T cell lines, undergo alterations in their capacity to secrete T cell growth factors when stimulated with antigens in the presence of GCS. Responses normally dominated by IL2 are dramatically shifted to a condition where IL4 represents the major species of T cell growth factor produced. Similar changes in the pattern of T cell growth factor production are observed following short pulses with low-dose GCS in vitro, and the steroid-induced depression in IL2 production can be reversed and/or inhibited by treatment with the potent steroid antagonist RU486. Our results imply that GCS hormones, presumably through their capacity to activate a specified family of ligand-dependent transcriptional regulatory proteins (steroid hormone receptors), function to control the pattern of lymphokines produced by activated T cells. Steroid-mediated regulation of lymphokine gene expression could serve to dictate the types of immune effector mechanisms which can be initiated subsequent to antigen exposure.
Human Retroviruses and Aids - 1999 (1999)

a review or sequence monograph, it is not so conceived. Instead, the literature from which the database is derived has simply been summarized and some elementary computational analyses have been performed upon the data. Interpretation and commentary have been avoided insofar as possible so that the reader can form his or her own judgments concerning the complex information. In addition to the general descriptions below of the parts of the compendium, the user should read the individual introductions for each part.
Generation of Cytomegalovirus pp65-Specific T Cells from Seronegative Donors. (2007)

Abstract Cytomegalovirus (CMV) can cause significant disease in allogeneic stem cell transplant (SCT) recipients. Adoptive transfer of donor derived CMV-specific cytotoxic T lymphocytes (CTL) is currently used for prophylaxis and treatment of CMV infections in allogeneic transplant recipients, but this is only available for patients whose donors are CMV seropositive. We developed a method to prime and expand CMVpp65-specific T cells from the peripheral blood mononuclear cells (PBMC) of CMV seronegative donors. Monocyte-derived dendritic cells isolated from four CMV seronegative donors were pulsed with CMVpp65 peptides for two hours prior to T cell stimulation. CMVpp65 peptides consisted of 15 mers with an 11 amino acid overlap. T cells obtained from CMV seronegative donors were primed every seven days for three weeks using CMVpp65 peptide pulsed dendritic cells. Interleukin-7 and interleukin-12 were initially added to the T cell cultures to promote CTL differentiation. After ten days, interleukin-2 together with interleukin-7 and interleukin-12 were added at three day intervals. Intracellular cytokine staining (ICS) and 51Cr-release assays were used to measure the activity and specificity of CMVpp65 primed CMV seronegative donor T cells seven to ten days after the last stimulation. A four color ICS analysis revealed that CMVpp65-specific IFN-γ-producing CD4+ (Th1) T cells were expanded from two of the four seronegative donors; one of these two donors had CMVpp65-specific killing as measured by 51Cr-release assay, the other displayed non-specific killing. One of the other two donors exhibited CMVpp65 killing but lacked IFN-γ production. PBMC isolated from a CMV seronegative donor three weeks post CMV vaccination also exhibited CMV-specific killing after only one week in vitro stimulation, with no CMV specificity pre-vaccination. In conclusion CMV-specific effector cells can be expanded from some CMV seronegative donors using CMVpp65 peptide pulsed dendritic cells, interleukin-2, interleukin-7, and interlukin-12. These cells may have the potential to be used in adoptive cell therapy to prevent or treat CMV infections in SCT recipients from CMV seronegative donors. An alternative strategy for patients with persistent CMV infection may be to use CTL derived from a vaccinated donor. Analysis of CMVpp65-specific T cells from additional seronegative donors is in progress to further optimize ex vivo expansion.
In vivo administration of lymphocyte-specific monoclonal antibodies in nonhuman primates. IV. Cytotoxic effect of an anti-T11-gelonin immunotoxin. (1988)

The cytotoxic effect of a lymphocyte-specific immunotoxin formed by disulfide conjugation of an anti-T11 monoclonal antibody with the ribosome-inactivating protein gelonin was assessed in vitro on peripheral blood T cells and in vivo on splenic and lymph node T cells of macaque monkeys. This immunotoxin was cytotoxic to proliferating peripheral blood T cells in vitro as measured by both direct and indirect assays. Two sequential intravenous infusions into macaque monkeys achieved plasma concentrations of immunotoxin far in excess of those shown to be cytotoxic for cultured T cells and coated all T cells in lymph nodes and spleen with intact immunotoxin for four days. However, the cytotoxic effect of the immunotoxin on T cells in vivo was considerably less than that predicted by the in vitro studies. Further experiments suggested that the state of activation of the targeted T cell population in vivo, or the appearance of anti-immunotoxin antibodies, which occurred in all infused monkeys, might attenuate immunotoxin-mediated cell killing in vivo. These studies illustrate the significant differences between the action of immunotoxin conjugates in vitro, and those seen when these conjugates are utilized as therapeutic agents in vivo.
Cellular Chemosensitivity Assays: An Overview (2011)

Data on cell viability have long been obtained from in vitro cytotoxicity assays. Today, there is a focus on markers of cell death, and the MTT cell survival assay is widely used for measuring cytotoxic potential of a compound. However, a comprehensive evaluation of cytotoxicity requires additional assays which -measure short and long-term cytotoxicity. Assays which measure the cytostatic effects of compounds are not less important, particularly for newer anticancer agents. This overview discusses the advantages and disadvantages of different non-clonogenic assays for measuring short and medium-term cytotoxicity. It also discusses clonogenic assays, which accurately measure long-term cytostatic effects of drugs and toxic agents. For certain compounds and cell types, the advent of high throughput, multiparameter, cytotoxicity assays, and gene expression assays have made it possible to predict cytotoxic potency in vivo.
Opposing Effects of Protein Kinase Cα and Protein Kinase Cϵ on Collagen Expression by Human Lung Fibroblasts Are Mediated via MEK/ERK and Caveolin-1 Signaling (2005)

The roles of MEK, ERK, the epsilon and alpha isoforms of protein kinase C (PKC), and caveolin-1 in regulating collagen expression were studied in normal lung fibroblasts. Knocking down caveolin-1 gave particularly striking results. A 70% decrease caused a 5-fold increase in MEK/ERK activation and collagen expression. The combined data reveal a branched signaling pathway. In its central portion MEK activates ERK, leading to increased collagen expression. Two branches converge on MEK/ERK. In one, increased PKCepsilon leads to MEK/ERK activation. In another, increased PKCalpha induces caveolin-1 expression, which in turn inhibits MEK/ERK activation and collagen expression. Lung fibroblasts from scleroderma patients with pulmonary fibrosis showed altered signaling. Consistent with their overexpression of collagen, scleroderma lung fibroblasts contain more activated MEK/ERK and less caveolin-1 than normal lung fibroblasts. Because cutaneous fibrosis is the hallmark of scleroderma, we also studied dermal fibroblasts. As in lung, there was more activated MEK/ERK in cells from scleroderma patients than in control cells, and MEK inhibition decreased collagen expression. However, the distinctive levels of PKCepsilon, PKCalpha, and caveolin-1 in lung and dermal fibroblasts from scleroderma patients and control subjects indicate that the links between these signaling proteins and MEK/ERK must function differently in the four cell types. Finally, we confirmed the relevance of these signaling cascades in vivo. The combined results demonstrate that a branched signaling pathway involving MEK, ERK, PKCepsilon, PKCalpha, and caveolin-1 regulates collagen expression in normal lung tissue and is perturbed during fibrosis.
Two NOD Idd‐associated intervals contribute synergistically to the development of autoimmune exocrinopathy (Sjögren's syndrome) on a healthy murine background (2002)

Genes located within the 2 chromosomal intervals Idd3 and Idd5 appear necessary and sufficient for manifestation of AEC. We propose that this murine model of SS-like disease be designated C57BL/6.NOD-Aec1Aec2. Identification of specific genes within the Aec1 and Aec2 genetic regions should help elucidate the mechanism(s) underlying SS-like disease.
Effect of encapsulation of mefenamic acid with cationic Eudragit E on its bioavailability and gastric ulcerogenic activity in rabbits (1987)

Encapsulation of mefenamic acid (MFA), a potent non-steroidal anti-inflammatory drug with cationic acrylic resin, Eudragit E, was carried out using a fluidized-bed granulator (Glatt AG). Three drug:polymer ratios were prepared using 50 ml of 1, 2.5 and 5 per cent w/v aqueous suspension of Eudragit to coat 100 mg powdered drug. The bioavailability of the coated and uncoated drug was studied using four groups of animals, each consisting of six male rabbits (2-2.5 kg). Investigations were performed using the rabbits to examine the effects of prolonged administration of the coated and the uncoated MFA with Eudragit E(1 and 5 per cent) in a dose of 100 mg filled in hard gelatin capsules. One capsule was given daily for 30 days. Plasma levels of MFA with Eudragit E were significantly higher than those of drug only. Meanwhile, 5 per cent w/v polymer coating afforded higher drug availability than 2.5 per cent w/v which induced a higher level than 1 per cent w/v. Chronic gastric ulcers with different severities were found in the internal mucosa of all animals. In addition, there were multiple erosions in the glandular mucosa of stomachs of rabbits receiving MFA within the treatment period. IN the control group the gastric photograph was normal in every instance. Despite the extensive morphological damage at the end of treatment, the observed changes in the stomach of rabbits given coated drug is less deleterious than that treated with uncoated drug. The results of this study indicate that the coating of MFA with cationic Eudragit E increases its bioavailability and decreases the probability of ulceration.(ABSTRACT TRUNCATED AT 250 WORDS)
Cell-free replication of the human papillomavirus DNA with homologous viral E1 and E2 proteins and human cell extracts. (1994)

We have established the first homologous cell-free DNA replication system for a papillomavirus. The replication of the human papillomavirus type 11 (HPV-11) origin was achieved by using human 293 cell extracts supplemented with the HPV-11 E1 and E2 proteins purified from insect cells infected with recombinant baculoviruses. Efficient replication depends on the HPV-11 origin, the HPV-11 E1 and E2 proteins, as well as human DNA polymerase alpha, delta, replication protein A, topoisomerase I, and topoisomerase II. High concentrations of E1 protein also promoted a low level of origin-independent replication which was suppressed by the addition of the E2 protein, whereas E2 protein stimulated origin-dependent replication. We also show that an intact E2 protein binding site was absolutely necessary for origin activity, as a strong HPV-11 origin was rendered inactive when one half-site of each of the three E2 binding sites was mutated. In contrast, there was only a relatively small reduction in this mutant origin activity when the cell extracts were supplemented with the bovine papillomavirus type 1 (BPV-1) proteins. These results suggest that the HPV-11 E2 protein plays a primary role in HPV origin recognition. Furthermore, unlike transient replication in which HPV-11 and BPV-1 viral proteins promote efficient replication of homologous and heterologous origins, efficient cell-free replication took place only with the homologous combinations.
Wireless operations for 13.56-MHz band RFID tag using amorphous oxide TFTs (2011)

This paper presents an RFID chip for 13.56-MHz band communication fabricated on a glass substrate by using amorphous In-Ga-Zn-O thin-film transistors. Low driving-voltage logic circuits were achieved with a small Vth, a high field effect mobility of 15cm2/Vs and “active load” inverters that had small consumption currents. The RFID tag was successively driven by 13.56-MHz wireless input.
Sphingomyelin metabolites inhibit sphingomyelin synthase and CTP:phosphocholine cytidylyltransferase (2001)

Tissue injury in inflammation involves the release of several cytokines that activate sphingomyelinases and generate ceramide. In the lung, the impaired metabolism of surfactant phosphatidylcholine (PC) accompanies this acute and chronic injury. These effects are long-lived and extend beyond the time frame over which tumor necrosis factor (TNF)-alpha and interleukin-1beta are elevated. In this paper, we demonstrate that in H441 lung cells these two processes, cytokine-induced metabolism of sphingomyelin and the inhibition of PC metabolism, are directly interrelated. First, metabolites of sphingomyelin hydrolysis themselves inhibit key enzymes necessary for restoring homeostasis between sphingomyelin and its metabolites. Ceramide stimulates sphingomyelinases as effectively as TNF-alpha, thereby amplifying the sphingomyelinase activation, and TNF-alpha, ceramide, and sphingosine all inhibit PC:ceramide phosphocholine transferase (sphingomyelin synthase), the enzyme that restores homeostasis between sphingomyelin and ceramide pools. Second, ceramide inhibits PC synthesis, probably because of its effects on CTP:phosphocholine cytidylyltransferase, the rate-limiting enzymatic step in de novo PC synthesis. The data presented here suggest that TNF-alpha may be an inhibitor of phospholipid metabolism in inflammatory tissue injury. These actions may be amplified because of the ability of metabolites of sphingomyelin to inhibit the pathways that should restore the normal ceramide-sphingomyelin homeostasis.
Reproducing the bifidogenic effect of human milk in formula‐fed infants: Why and how? (2005)

Awareness of the key role of the intestinal microflora in the generation of the immunophysiological regulation and in the defence against pathogenic agents has attracted our interest in ways of manipulating the microbiota to improve health. Dietary modulation of the intestinal microflora is today one of the main topics of interest in the nutritional sciences. Performing this modulation in the neonatal or early infancy period, when immunological programming takes place, is a relatively new concept. Fructo-oligosaccharides (FOS) and galacto-oligosaccharides (GOS) are prebiotics whose bifidogenic activity has been proven in adults. However, only recently have they been combined in infant formulas to reproduce the prebiotic effect of human milk oligosaccharides. In two consecutive trials, it has been demonstrated that supplementation of infant formulas with a mixture of GOS and FOS modified the fecal flora of term and preterm infants, stimulating the growth of Bifidobacteria. In the trial with term infants, the bifidogenic effect of the prebiotic mixture was dose dependent and there was also a significant increase in the number of Lactobacilli in the supplemented group. These findings offer a promising horizon for the early prevention of allergy and infections in infants.
A Physically-Based Model for Urban Fire Spread (2003)

An attempt is made to develop a physically-based model for simulating urban fire spread. In the model, urban fire is regarded as an ensemble of multiple building fires. The model consists of two sub-models, i.e. the model to predict the building fire behavior under the exposure of heating from other building fires and the model to predict the thermal environment caused by building fires. The building fire model is based on single zone method, applying control volumes to compartments in a building. When the external heating, whether it is from the same building or from other buildings, exceeds the critical heat flux, the fire load in the compartment ignites and burns. For the thermal environment model, thermal radiation and fire-induced plume are considered as the factors of building-to-building fire spread. The model is applied to a fictitious urban district where 49 multi-room buildings are arrayed in a simple configuration.