gebhart/patrepeval huggingface dataset:
JQ1 reduces Epstein-Barr virus-associated lymphoproliferative disease in mice without sustained oncogene repression (2017)

Small molecule inhibitors of bromodomain and extra-terminal (BET) proteins are seeing increased investigation in clinical trials for treatment of hematological malignancies. These compounds also repress oncogene expression driven by the human Epstein-Barr virus (EBV) in cell culture. We therefore tested the efficacy of the prototypical BET inhibitor JQ1 against a mouse xenograft model of post-transplantation lymphoproliferative disorder. JQ1 potently inhibits growth of lymphoblastoid cell lines (LCLs) in culture at low nM concentrations. Growth of other cell lines with similar EBV type III latency transcription programs is comparably inhibited. JQ1 also slows tumor development of an LCL xenograft in immunocompromised mice, but oncogene repression is not observed in endpoint biopsies. We find reduction of EBV-associated lymphoproliferative disease in an animal model encouraging of further studies.
CD19: Lowering the Threshold for Antigen Receptor Stimulation of B Lymphocytes (1992)

Lymphocytes must proliferate and differentiate in response to low concentrations of a vast array of antigens. The requirements of broad specificity and sensitivity conflict because the former is met by low-affinity antigen receptors, which precludes achieving the latter with high-affinity receptors. Coligation of the membrane protein CD19 with the antigen receptor of B lymphocytes decreased the threshold for antigen receptor-dependent stimulation by two orders of magnitude. B lymphocytes proliferated when approximately 100 antigen receptors per cell, 0.03 percent of the total, were coligated with CD19. The B cell resolves its dilemma by having an accessory protein that enables activation when few antigen receptors are occupied.
Tuberculin-Active Carbohydrate That Induces Inhibition of Macrophage Migration but not Lymphocyte Transformation (1970)

A tuberculin carbohydrate fraction, GAE, in sensitized animals induced a delayed type of skin reactivity and inhibited the migration of macrophages but failed to stimulate lymphocyte transformation in vitro. Tuberculin protein-containing fractions were active in each test. These results show that in vitro lymphocyte transformation is not necessarily a corollary of delayed type hypersensitivity.
Desorption Electrospray Ionization: Proteomics Studies by a Method That Bridges ESI and MALDI (2008)

INTRODUCTIONDesorption electrospray ionization (DESI) is a desorption ionization (DI) method by nature, and, like matrix-assisted laser desorption/ionization (MALDI), it is used for the analysis of material present on a surface. DESI includes features reminiscent of electrospray ionization (ESI) in respect to both its instrumental and mechanistic aspects. However, the analyte in the DESI experiment is not in solution as in ESI. Instead, a microelectrospray ion source is used to produce charged droplets, ionic clusters, and/or gas-phase ions (depending on chosen experimental conditions), and these are directed at the sample surface. The sample is present in the ambient environment. An electrical potential of several kilovolts (kV) is applied to the spray solution, and pneumatic nebulization is used to assist in desolvation. Ionization of molecules present on the sample surface occurs upon the impact of the ESI-originated, charged particles with the surface. Surfaces include deposited samples on sample holder targets as well as surfaces of natural objects such as biological tissues or minerals.
Conditions for the Generation of Slip by Diffusion of Phosphorus into Silicon (1966)

On the basis of theoretical considerations it is shown that the critical surface-impurity concentration Nscrit for the generation of slip during diffusion, as well as the depth η0 to which dislocations will move, depend strongly on the impurity concentration profile. A weak dependence of Nscrit on crystal orientation has to be expected also. Nscrit has been calculated for phosphorus diffusing into silicon to be 4.11×1020 cm−3 with the reasonable assumption of a complementary error-function impurity profile. The experimental value is 2.0×1020 cm−3 &amp;lt;Nscrit &amp;lt;2.5×1020 cm−3. The theory has been used to explain details in slip patterns displayed on a {110} surface after etching the sample. Finally the markedly different appearance of slip patterns due to apparently small variations in diffusion parameters is demonstrated and discussed.
?-Phenylsulfonyl-N-arylacetamides (?-phenylsulfonylacetanilides):1H,13C and15N NMR spectral characterization (2000)

1H and 13C NMR chemical shift assignments for 11 α-phenylsulfonylacetanilides and 15N NMR chemical shifts for four representative congeners are reported. The 1H and 13C chemical shift assignments are based on DQF COSY and PFG 1H,13C HMQC/HMBC experiments. The 15N NMR chemical shifts were determined by PFG 1H,15N HMBC experiments. The correlation analyses with Hammett-type substituent constants gave a significant result with δ(C-1) in the aniline ring. Copyright © 2000 John Wiley & Sons, Ltd.
Cleavage of DNA without loss of genetic information by incorporation of a disaccharide nucleoside (2003)

A ribose residue inserted between the 3'-OH of one nucleotide and the 5'-phosphate group of the next nucleotide, functions as a site-specific cleavage site within DNA. This extra ribose does not interrupt helix formation and it protects duplex DNA against cleavage by restriction enzymes. Cleavage can be obtained with periodate and all ribose fragments can be removed with sodium hydroxide. As a result of this, an intact natural oligodeoxynucleotide is obtained after ligation reaction, which means that site-specific cleavage and recovering of intact DNA occurs without loss of genetic information.
Olfactory receptors are expressed in pancreatic β-cells and promote glucose-stimulated insulin secretion (2018)

Olfactory receptors (ORs) mediate olfactory chemo-sensation in OR neurons. Herein, we have demonstrated that the OR chemo-sensing machinery functions in pancreatic β-cells and modulates insulin secretion. First, we found several OR isoforms, including OLFR15 and OLFR821, to be expressed in pancreatic islets and a β-cell line, MIN6. Immunostaining revealed OLFR15 and OLFR821 to be uniformly expressed in pancreatic β-cells. In addition, mRNAs of Olfr15 and Olfr821 were detected in single MIN6 cells. These results indicate that multiple ORs are simultaneously expressed in individual β-cells. Octanoic acid, which is a medium-chain fatty acid contained in food and reportedly interacts with OLFR15, potentiated glucose-stimulated insulin secretion (GSIS), thereby improving glucose tolerance in vivo. GSIS potentiation by octanoic acid was confirmed in isolated pancreatic islets and MIN6 cells and was blocked by OLFR15 knockdown. While Gα <sub>olf</sub> expression was not detectable in β-cells, experiments using inhibitors and siRNA revealed that the pathway dependent on phospholipase C-inositol triphosphate, rather than cAMP-protein kinase A, mediates GSIS potentiation via OLFR15. These findings suggest that the OR system in pancreatic β-cells has a chemo-sensor function allowing recognition of environmental substances obtained from food, and potentiates insulin secretion in a cell-autonomous manner, thereby modulating systemic glucose metabolism.
Blockade of RAGE suppresses periodontitis-associated bone loss in diabetic mice (2000)

Diabetes is associated with increased prevalence, severity, and progression of periodontal disease. To test the hypothesis that activation of RAGE (Receptor for Advanced Glycation End products) contributes to the pathogenesis of diabetes-associated periodontitis, we treated diabetic mice, infected with the human periodontal pathogen Porphyromonas gingivalis, with soluble RAGE (sRAGE). sRAGE is the extracellular domain of the receptor, which binds ligand and blocks interaction with, and activation of, cell-surface RAGE. Blockade of RAGE diminished alveolar bone loss in a dose-dependent manner. Moreover, we noted decreased generation of the proinflammatory cytokines TNF-alpha and IL-6 in gingival tissue, as well as decreased levels of matrix metalloproteinases. Gingival AGEs were also reduced in mice treated with sRAGE, paralleling the observed suppression in alveolar bone loss. These findings link RAGE and exaggerated inflammatory responses to the pathogenesis of destructive periodontal disease in diabetes.
Enhanced brightness in organic light-emitting diodes using a carbon nanotube composite as an electron-transport layer (2001)

We have studied the effects of using a composite fabricated from carbon nanotubes and a host polymer, poly(m-phenylene-vinylene-co-2,5-dioctyloxy-p-phenylene-vinylene) (PmPV), as an electron-transport layer in organic light-emitting diodes. Double layer devices using this composite as an electron-transport layer, triple layer devices with a composite electron-transport layer, and poly(9-vinylcarbazole) as a hole-transport layer, as well as poly(2,5-dimethoxy-1,4phenylene-vinylene-2-methoxy- 5(2′-ethylhexyloxy)-1,4-phenylene-vinylene (M3EH-PPV) single layer devices were prepared. Current–voltage–luminance and electroluminescent spectral measurements were performed using six different nanotube powder to polymer mass ratios (0%, 2%, 4%, 8%, 16%, and 32%) for all device structures studied. dc transport and photoluminescence behavior of the polymer-nanotube composite were also investigated. Although a potential barrier is introduced at the M3EH-PPV/composite interface, a significant increase in efficiency was observed using the composite. The best efficiency was obtained for those devices with an electron-transport layer of mass ratio 8%. In addition, on doping with nanotubes, electron conductivity in the composite increased by over 4 orders of magnitude with little quenching of photoluminescence.
The Inhibiting Effect of Aqueous Azadirachta indica (Neem) Extract Upon Bacterial Properties Influencing in vitro Plaque Formation (1996)

The purpose of this investigation was to examine the inhibitory effects of aqueous extracts derived from the bark-containing sticks (Neem stick) of Azadirachta indica upon bacterial aggregation, growth, adhesion to hydroxyapatite, and production of insoluble glucan, which may affect in vitro plaque formation. Neem stick extracts were screened for minimal bacterial growth inhibition (MIC) against a panel of streptococci by means of a broth dilution assay. Initial bacterial attachment was quantified by the measurement of the adhesion of 3H-labeled Streptococcus sanguis to saliva-conditioned synthetic hydroxyapatite. The effect of the Neem stick extract upon insoluble glucan synthesis was measured by the uptake of radiolabeled glucose from 14C-sucrose. Aggregating activity of the Neem stick extracts upon a panel of streptococci was also examined. No inhibition of bacterial growth was observed among the streptococcal strains tested in the presence of < or = 320 micrograms/mL of the Neem stick extract. The pre-treatment of S. sanguis with the Neem stick extract or the gallotannin-enriched extract from Melaphis chinensis at 250 micrograms/mL resulted in a significant inhibition of the bacterial adhesion to saliva-conditioned hydroxyapatite. Pre-treatment of saliva-conditioned hydroxyapatite with the Neem stick or gallotannin-rich extract prior to exposure to bacteria yielded significant reductions in bacterial adhesion. The Neem stick extract and the gallotannin-enriched extract from Melaphis chinensis inhibited insoluble glucan synthesis. Incubation of oral streptococci with the Neem stick extract resulted in a microscopically observable bacteria aggregation. These data suggest that Neem stick extract can reduce the ability of some streptococci to colonize tooth surfaces.
An Introduction to Biodegradable Materials for Tissue Engineering Applications (2001)

Tissue generation by autogenous cell transplantation is one of the most promising treatment concepts being developed as it eliminates problems of donor site scarcity, immune rejection and pathogen transfer. Cultured cells are seeded onto a three-dimensional biocompatible scaffold that will slowly degrade and resorb as the soft and hard structures grow and assimilate in vitro and/or in vivo. The 3-D scaffold provides the necessary template for cells to proliferate and maintain their differentiated state. Ultimately, it defines the overall shape of the tissue-engineered transplant. The aim of this review is to describe and discuss the scaffold materials of natural and synthetic origin that are of specific interest to tissue engineers. This review is based on previous publications and our own experience in the use of biomaterials of natural and synthetic origin for tissue engineering applications. Biodegradable polymers which have been used for tissue engineering applications are mainly based on clinically established medical devices and implants. In the group of macromolecules of natural origin collagen, alginate, agarose, hyaluronic acid derivatives, chitosan, and fibrin glue have been used as scaffolds. Man-made polymers such as polyglycolide (PGA), polylactides (PLLA, PDLA), poly(caprolactone) (PCL), and poly(dioxanone) (PDS) have been studied as matrix material to guide the differentiation and proliferation of cells into the targeted functional premature and/or mature tissue. Appropriate selection of scaffold material with respect to the targeted tissue is essential. Today, biomaterials of choice remain to be those approved by the US Food and Drug Administration. In spite of that, novel biomaterials should be developed specifically designed for tissue engineering applications.
Clearance of pathological antibodies using biomimetic nanoparticles (2014)

Pathological antibodies have been demonstrated to play a key role in type II immune hypersensitivity reactions, resulting in the destruction of healthy tissues and leading to considerable morbidity for the patient. Unfortunately, current treatments present significant iatrogenic risk while still falling short for many patients in achieving clinical remission. In the present work, we explored the capability of target cell membrane-coated nanoparticles to abrogate the effect of pathological antibodies in an effort to minimize disease burden, without the need for drug-based immune suppression. Inspired by antibody-driven pathology, we used intact RBC membranes stabilized by biodegradable polymeric nanoparticle cores to serve as an alternative target for pathological antibodies in an antibody-induced anemia disease model. Through both in vitro and in vivo studies, we demonstrated efficacy of RBC membrane-cloaked nanoparticles to bind and neutralize anti-RBC polyclonal IgG effectively, and thus preserve circulating RBCs.
Human monocyte adherence to cultured vascular endothelium: monoclonal antibody-defined mechanisms. (1985)

We have evaluated the binding of human peripheral blood monocytes to cultured vascular endothelium as an in vitro model of monocyte interaction with the vessel wall. Monocytes were purified (91% +/- 4 SE esterase positive) by elutriation to avoid contact with surfaces before assay. Adherence of 51Cr-labeled monocytes after 45 min (36% +/- 11 SE) was significantly higher than that observed with autologous radiolabeled neutrophils (9% +/- 5 SE) and was greater on monolayers of human umbilical vein endothelium than on bovine aortic endothelium. Peripheral blood mononuclear cells treated with monoclonal antibody (MoAb) 60.3, a reagent that binds leukocyte membrane complex CDw18, implicated in multiple adherence-dependent functions, failed to adhere and flatten on artificial surfaces. Mononuclear cells treated with MoAb 60.3 simulated cells from a patient with recurrent infections whose phagocytes failed to react with MoAb 60.3 and failed to emigrate to extravascular sites in vivo. Incubation of monocytes with MoAb 60.3 inhibited (by 32 to 61%) monocyte adherence to endothelium in a dose-dependent manner for periods up to 24 hr, but had negligible effects on basal (unstimulated) neutrophil adherence. Basal monocyte adherence in the presence of MoAb 60.3 remained significantly greater than basal neutrophil adherence. Augmentation of phagocyte adherence to endothelial monolayers by autologous plasma or phorbol ester (PMA) was abrogated by incubation with MoAb 60.3. Studies with immunofluorescence flow cytometry indicated that PMA stimulation of monocytes resulted in a specific 40% increase in monocyte surface expression of the epitope recognized by MoAb 60.3. These in vitro findings, in conjunction with observations from two patients, support the hypothesis that monocyte adherence to endothelium and emigration to tissues is mediated by mechanisms both dependent upon and independent of the CDw18 complex and the epitope recognized by MoAb 60.3.
The Effect of Sulfur‐Based Reducing Agents and GAC Filtration on Chlorine Dioxide By‐products (1991)

Experiments were performed to determine the effect of granular activated carbon (GAC) filtration and sulfur‐based reducing agents on chlorite and chlorate ions in water. It is concluded that neither GAC filtration nor sulfur‐based reduction is a feasible means of removing chlorine dioxide by‐products.
Cooperative content distribution and traffic engineering in an ISP network (2009)

Traditionally, Internet Service Providers (ISPs) make profit by providing Internet connectivity, while content providers (CPs) play the more lucrative role of delivering content to users. As network connectivity is increasingly a commodity, ISPs have a strong incentive to offer content to their subscribers by deploying their own content distribution infrastructure. Providing content services in an ISP network presents new opportunities for coordination between traffic engineering (to select efficient routes for the traffic) and server selection (to match servers with subscribers). In this work, we develop a mathematical framework that considers three models with an increasing amount of cooperation between the ISP and the CP. We show that separating server selection and traffic engineering leads to sub-optimal equilibria, even when the CP is given accurate and timely information about the ISP's network in a partial cooperation. More surprisingly, extra visibility may result in a less efficient outcome and such performance degradation can be unbounded. Leveraging ideas from cooperative game theory, we propose an architecture based on the concept of Nash bargaining solution. Simulations on realistic backbone topologies are performed to quantify the performance differences among the three models. Our results apply both when a network provider attempts to provide content, and when separate ISP and CP entities wish to cooperate. This study is a step toward a systematic understanding of the interactions between those who provide and operate networks and those who generate and distribute content.
Epidermal Growth Factor-induced Phosphatidylinositol 3-Kinase Activation and DNA Synthesis (2000)

In previous work we showed that the phosphatidylinositol 3-kinase (PI3-kinase), not the mitogen-activated protein kinase, pathway is necessary and sufficient to account for insulin- and epidermal growth factor (EGF)-induced DNA synthesis in rat hepatocytes. Here, using a dominant-negative p85, we confirmed the key role of EGF-induced PI3-kinase activation and sought to identify the mechanism by which this is effected. Our results show that EGF activates PI3-kinase with a time course similar to that of the association of p85 with three principal phosphotyrosine proteins (i. e. PY180, PY105, and PY52). We demonstrated that each formed a distinct p85-associated complex. PY180 and PY52 each constituted about 10% of EGF-activated PI3-kinase, whereas PY105 was responsible for 80%. PY105 associated with Grb2 and SHP-2, and although it behaved like Gab1, none of the latter was detected in rat liver. We therefore cloned a cDNA from rat liver, which was found to be 95% homologous to the mouse Grb2-associated binder 2 (Gab2) cDNA sequence. Using a specific Gab2 antibody, we demonstrated its expression in and association with p85, SHP-2, and Grb2 upon EGF treatment of rat hepatocytes. Gab2 accounted for most if not all of the PY105 species, since immunoprecipitation of Gab2 with specific antibodies demonstrated parallel immunodepletion of Gab2 and PY105 from the residual supernatants. We also found that the PI3-kinase activity associated with Gab2 was totally abolished by dominant negative p85. Thus, Gab2 appears to be the principal EGF-induced PY protein recruiting and activating PI3-kinase and mitogenesis.
Synthesis of Biotin-Labelled Dexamethasone Derivatives. Novel Hormone-Affinity Probes (1983)

A new, general methodology for 'sandwich' affinity chromatography of steroid hormone receptors is proposed, the part purification of the human spleen tumor glucocorticoid receptor is quoted as an illustration. 9-Fluoro-16 alpha-methyl-11 beta, 17-dihydroxy-1,4-androstadiene-3-one-17 beta-carboxylic acid was coupled to biotin using pentamethylenediamine (BioDex 1) as a spacer. The bifunctional derivative binds to glucocorticoid receptors and avidin-Sepharose and efficiently protects the glucocorticoid receptor against inactivation when previously added during homogenisation. We have standardized the capacity and optimum conditions for elution of receptor-BioDex-1 complexes which are bound to avidin-Sepharose. Receptor purification of several thousand fold can be obtained with good yield.
Motion-driven sensing and biosensing using electrochemically propelled nanomotors (2011)

Electrochemically-propelled nanomotors offer considerable promise for developing new and novel bioanalytical and biosensing strategies based on the direct isolation of target biomolecules or changes in their movement in the presence of target analytes. For example, receptor-functionalized nanomotors offer direct and rapid target isolation from raw biological samples without preparatory and washing steps. Microtube engines functionalized with ss-DNA, aptamer or antibody receptors are particularly useful for the direct isolation of nucleic acids, proteins or cancer cells, respectively. A new nanomotor-based signal transduction involving measurement of speed and distance travelled by nanomotors, offers highly sensitive, rapid, simple and low cost detection of target biomarkers, and a new dimension of analytical information based on motion. The resulting distance signals can be easily visualized by optical microscope (without any sophisticated analytical instrument) to reveal the target presence and concentration. The attractive features of the new micromachine-based target isolation and signal transduction protocols reviewed in this article offer numerous potential applications in biomedical diagnostics, environmental monitoring, and forensic analysis.
Characteristics and expression of binding sites specific for ferritin H- chain on human cell lines (1988)

Purified recombinant human ferritin composed solely of H subunit was radiolabeled and incubated with proerythroleukemic K562 human cells. A specific binding was detected, and it could be displaced only by ferritins, natural or recombinant, containing large proportion of the H subunit. The specific ferritin H-chain binding was saturable, and cells showed 17,000 to 23,000 binding sites per cell. The affinity constant measured at 37 degrees C was of 3 x 10(8) M-1. Treatment with pronase eliminated the specific binding. The binding sites were expressed in a high number during the cellular exponential phase of growth and progressively decreased to disappear when cells reached the plateau phase. Treatment of the cells with desferrioxamine increased recombinant H-ferritin binding, while iron had little effect. K562 cells induced to differentiate by hemin failed to bind ferritin H. Ferritin H-chain binding capacity is present on various cell lines such as HL60, lung cancer, and hepatoma cells. Analysis of the binding sites by western blotting showed a peptide with apparent mol wt of about 100 kd.