gebhart/patrepeval huggingface dataset:
The IL-1 beta-converting enzyme (caspase-1) inhibits apoptosis of inflammatory neutrophils through activation of IL-1 beta. (1998)

IL-1 beta-converting enzyme (ICE), also known as caspase-1, subserves two dichotomous biologic roles. It processes newly synthesized pro-IL-1 beta to yield the active cytokine and, as the human homologue of the Caenorhabditis elegans gene product, ced-3, it also induces cellular apoptosis through the cleavage of key intracellular structural and regulatory proteins and through the catalytic activation of other caspase family members. We show here that two different proinflammatory stimuli, LPS and granulocyte-macrophage-CSF, up-regulate the expression of both ICE and IL-1 beta in human polymorphonuclear neutrophils, and that the ICE-dependent cleavage of pro-IL-1 beta results in delayed expression of the constitutive cell death program. The apoptotic delay can be blocked by inhibiting tyrosine kinases or NF-kappa B activation and by inhibiting protein synthesis. Since an antisense oligonucleotide for IL-1 beta, a blocking Ab to IL-1 beta, and preincubation with the IL-1R antagonist all prevent the delay in apoptosis, we conclude that IL-1 beta acts in an autocrine manner to inhibit granulocyte programmed cell death. We conclude that caspase-1 (ICE) subserves both pro- and antiapoptotic roles; the latter role is evident during inflammation as an inhibition of spontaneous neutrophil apoptosis through the processing of IL-1 beta. The ICE-dependent activation of IL-1 beta may represent a common autocrine pathway for the divergent stimuli that inhibit the constitutive expression of neutrophil programmed cell death during inflammation.
Learning user profiles for personalized information dissemination (2002)

Personalized information systems represent the recent effort of delivering information to users more effectively in the modern electronic age. This paper illustrates how a supervised adaptive resonance theory (ART) system, called fuzzy ARAM (adaptive resonance associative map), can be used to learn user profiles for personalized information dissemination. ARAM learning is online, fast, and incremental. Acquisition of new knowledge does not require re-training on previously learned cases. ARAM integrates both user-defined and system-learned knowledge in a single framework. Therefore inconsistency between the two knowledge sources will not arise. ARAM has been used to develop a personalized news system (PIN). Preliminary experiments have verified that PIN is able to provide personalized news by adapting to user's interests in an online manner and generalizing them to new information on-the-fly.
Production of poly(3-hydroxybutyrate) by fed-batch culture of filamentation-suppressed recombinant Escherichia coli (1997)

Recombinant Escherichia coli XL1-Blue harboring a high-copy-number plasmid containing the Alcaligenes eutrophus polyhydroxyalkanoate synthesis genes could efficiently synthesize poly(3-hydroxybutyrate) (PHB) in a complex medium containing yeast extract and tryptone but not in a defined medium. One of the reasons for the reduced PHB production in a defined medium was thought to be severe filamentation of cells in this medium. By overexpressing an essential cell division protein, FtsZ, in recombinant E. coli producing PHB, filamentation could be suppressed and PHB could be efficiently produced in a defined medium. A high PHB concentration of 149 g/liter, with high productivity of 3.4 g of PHB/liter/h, could be obtained by the pH-stat fed-batch culture of the filamentation-suppressed recombinant E. coli in a defined medium. It was also found that insufficient oxygen supply at a dissolved oxygen concentration (DOC) of 1 to 3% of air saturation during active PHB synthesis phase did not negatively affect PHB production. By growing cells to the concentration of 110 g/liter and then controlling the DOC in the range of 1 to 3% of air saturation, a PHB concentration of 157 g/liter and PHB productivity of 3.2 g of PHB/liter/h were obtained. For the scale-up studies, fed-batch culture was carried out in a 50-liter stirred tank fermentor, in which the DOC decreased to zero when cell concentration reached 50 g/liter. However, a relatively high PHB concentration of 101 g/liter and PHB productivity of 2.8 g of PHB/liter/h could still be obtained, which demonstrated the possibility of industrial production of PHB in a defined medium by employing the filamentation-suppressed recombinant E. coli.
MCP‐induced protein 1 suppresses TNFα‐induced VCAM‐1 expression in human endothelial cells (2010)

Endothelial inflammation plays a critical role in the development and progression of cardiovascular disease, albeit the mechanisms need to be fully elucidated. We here report that treatment of human umbilical vein endothelial cells (HUVECs) with tumor necrosis factor (TNF) alpha substantially increased the expression of MCP-induced protein 1 (MCPIP1). Overexpression of MCPIP1 protected ECs against TNFalpha-induced endothelial activation, as characterized by the attenuation in the expression of the adhesion molecule VCAM-1 and monocyte adherence to ECs. Conversely, small interfering RNA-mediated knock down of MCPIP1 increased the expression of VCAM-1 and monocytic adherence to ECs. These studies identified MCPIP1 as a feedback control of cytokines-induced endothelial inflammation.
Silver Doped with Acidic/Basic Polymers: Novel, Reactive Metallic Composites (2005)

Abstract We report the preparation and properties of metallopolymeric composites with acidic and basic properties. The composites are prepared via the recently developed method of entrapping organic molecules within metals. Specifically, we describe the entrapment of the polyacid Nafion or the polybase poly(vinylbenzyltrimethylammonium hydroxide) within silver. The resulting acidic or basic metallic composites decrease or increase, respectively, the pH of water through an ion‐exchange process. Furthermore, silver doped with Nafion can be employed as an acid catalyst, as shown for the pinacol–pinacolone rearrangement and for the dehydration of an alcohol. Characterization of these novel materials via microscopy and adsorption studies reveals a three‐level hierarchical structure: clusters of ≈ 10 μm in size built from ≈ 1 μm aggregates of ≈ 100 Å silver crystals. Thermogravimetric analysis of the entrapped polymers reveals a catalytic effect of the metal on this process. The two polymers are entrapped differently, and the differences are discussed. Applications ranging from ion‐exchange electrodes to bifunctional catalysts are envisaged.
Stimulation of neutrophils by tumor necrosis factor. (1986)

Human recombinant tumor necrosis factor (TNF) was shown to be a weak direct stimulus of the neutrophil respiratory burst and degranulation. The stimulation, as measured by iodination, H2O2 production, and lysozyme release, was considerably increased by the presence of unopsonized zymosan in the reaction mixture, an effect which was associated with the increased ingestion of the zymosan. TNF does not act as an opsonin but, rather, reacts with the neutrophil to increase its phagocytic activity. TNF-dependent phagocytosis, as measured indirectly by iodination, is inhibited by monoclonal antibodies (Mab) 60.1 and 60.3, which recognize different epitopes on the C3bi receptor/adherence-promoting surface glycoprotein of neutrophils. Other neutrophil stimulants, namely N-formyl-methionyl-leucyl-phenylalanine, the Ca2+ ionophore A23187, and phorbol myristic acetate, also increase iodination in the presence of zymosan; as with TNF, the effect of these stimulants is inhibited by Mab 60.1 and 60.3, whereas, in contrast to that of TNF, their stimulation of iodination is unaffected by an Mab directed against TNF. TNF may be a natural stimulant of neutrophils which promotes adherence to endothelial cells and to particles, leading to increased phagocytosis, respiratory burst activity, and degranulation.
CD1.1 Expression by Mouse Antigen-Presenting Cells and Marginal Zone B Cells (1998)

Mouse CD1.1 is an MHC class I-like, non-MHC-encoded, surface glycoprotein that can be recognized by T cells, in particular NK1.1+ T cells, a subset of alphabeta T cells with semiinvariant TCRs that promptly releases potent cytokines such as IL-4 and IFN-gamma upon stimulation. To gain insight into the function of CD1.1, a panel of nine mAbs was generated and used to biochemically characterize and monitor the surface expression of CD1.1 on different cell types. CD1.1 is a heavily glycosylated, beta2-microglobulin-associated surface protein. Its recognition by a panel of 12 V alpha14-positive and -negative CD1-specific alphabeta T cell hybridomas was blocked by two groups of mAbs that bound to adjacent clusters of epitopes, indicating that different alphabeta TCRs bind to the same region of CD1.1, presumably above the groove. Remarkably, CD1.1 was mainly expressed by dendritic cells, B cells, and macrophages, suggesting a function in Ag presentation to Th cells. Furthermore, the cell type that expressed the highest levels of CD1.1 was the splenic marginal zone B cell, a distinct subset of B cells that also expresses CD21 (the C3d receptor) and may be involved in natural responses to bacterial Ags. Altogether, the results support the idea that CD1.1 may function in recruiting a form of innate help from specialized cytokine producer alphabeta T cells to APCs, a role that might be important at the preadaptive phase of immune responses to some microbial pathogens.
Properties of sputter-deposited PbTiO3, Pb(Zr,Ti)O3, Pb2KNb5O15films (1985)

Abstract Polycrystalline and epitaxial films of PbTiO3, Pb(Zr, Ti)O3, and Pb2KNb5O15 in perovskite and tungsten-bronze phases have been fabricated on the glass, platinum and sapphire substrates by rf planar magnetron sputtering, using ceramic targets. The substrate temperature higher than 530°C is necessary to grow PbTiO3 films in the perovskite phase without post thermal annealing. Pb(Zr, Ti)O3 and Pb2KNb5O15 films in the pyrochlore phase grown at the substrate temperature lower than 500°C and 650°C, respectively change their phases to the perovskite and to the tungsten-bronze by post thermal annealing.
Structure and Function of MARTX Toxins and Other Large Repetitive RTX Proteins (2010)

The Repeats-in-Toxins (RTX) family of proteins classically consists of cytolysins and hemolysins. Over the past decade, genome sequencing revealed the existence of very large members of this family. These are all repetitive proteins ranging in size from 200 to 900 kDa that function as toxins or adhesins. Many are exported by Type I secretion. One major new subfamily is the large repetitive RTX adhesins and biofilm-associated proteins. These are characterized by 80- to 300-amino-acid repeats ordered in tandem, although the sequence and number of the repeats vary by protein. The second major new subfamily is the multifunctional-autoprocessing RTX toxins, which are associated with cytotoxicity and pathogenesis. These proteins are in turn distantly related to Yersinia hypothetical RTX proteins that may autoprocess by a similar mechanism. This review discusses current knowledge regarding the structure and function of these new subfamilies of RTX proteins.
Proteomic approaches for serum biomarker discovery in cancer. (2007)

Monitoring the protein expression pattern in tumour cells by proteomics technologies offers opportunities to discover potentially new biomarkers for the early detection and diagnosis of cancer. Different proteomic tools such as 2D-PAGE, 2D-DIGE, SELDI-ToF-MS technology, protein arrays, ICAT, iTRAQ and MudPIT have been used for differential analysis of various biological samples, including cell lysates, cell secretome (conditioned medium), serum, plasma, tumour tissue and nipple aspirate fluid, to better understand the molecular basis of cancer pathogenesis and the validation and characterisation of disease-associated proteins. In recent years, there has been a large increase in cancer-related publications dealing with new biomarker discovery for cancer, therefore, in this review we have focused on the contribution of proteomics technologies in serum and conditioned medium-based oncology research particularly for lung, breast, melanoma and pancreatic cancer.
Multiple modes intra-prediction in intra coding (2004)

Intra-prediction is a widely used technique in intra coding. In H.264, nine directional prediction modes are used, and in AVS (audio-video coding standard of China), six modes are used. The paper proposes a multiple mode, intra-prediction scheme to achieve a better balance between prediction precision and side information cost. Three kinds of additional modes are introduced to increase prediction precision from different aspects. A significant performance gain can be achieved using this multiple mode intra-prediction, with little complexity increase.
A field-funneling effect on the collection of alpha-particle-generated carriers in silicon devices (1981)

We studied the transient characteristics of charge collection from alpha-particle tracks in silicon devices. We have run computer calculations using the finite element method, in parallel with experimental work. When an alpha particle penetrates a pn-junction, the generated carriers drastically distort the junction field. After the alpha particle penetration, the field, which was originally limited to the depletion region, extends far down into the bulk silicon along the length of the alpha-particle track and funnels a large number of carriers into the struck junction. After a few nanoseconds, the field recovers to its position in the normal depletion layer, and, if the track is long enough, a residue of carriers is left to be transported by diffusion. The extent of this field funneling is a function of substrate concentration, bias voltage, and the alpha-particle energy.
Managing Enterprise IT Systems Using Online Communities (2011)

Effective design and implementation of any IT Optimization process relies on critical technical and business insights about IT environment. The essential information, which relates to hardware and software assets, is often in collective possession of the infrastructure and application specialists. In this paper, we describe the Knowledge Harvesting & Information Synthesis System (KHISS), which engages enterprise online communities to capture the information required for IT optimization activities. We describe our experience in deploying KHISS principles to manage enterprise IT infrastructure and application portfolio, as a first step in on-Cloud migration -- a large business transformation activity. We discuss the challenges in attracting and maintaining enterprise online communities, as well as in assuring the quality of knowledge collected through this collaborative mechanism to guide the strategic decisions about enterprise IT environment.
Evaluation of Alamar colorimetric broth microdilution susceptibility testing method for staphylococci and enterococci (1996)

We compared the results of the Alamar broth microdilution susceptibility testing method with the results of the National Committee for Clinical Laboratory Standards reference broth microdilution method for 119 gram-positive organisms. The strains were tested for their susceptibilities to 20 antimicrobial agents. Only appropriate antimicrobial agents were evaluated for each species of bacteria. Absolute categorical agreement between the reference method and the test method was 91.5% for enterococci, 99.8% for oxacillin-susceptible staphylococci, and 97.4% for oxacillin-resistant staphylococci. Essential agreement (percent complete agreement plus percent minor errors) was > 99% for all organisms tested. The results for enterococci showed no very major errors, one major error with ofloxacin, and numerous minor errors with the quinolones. However, all except one of the minor errors were within +/- 1 log2 dilution of the reference result. For staphylococci, only 2 very major errors (one each with chloramphenicol and oxacillin), 1 major error (chloramphenicol), and 15 minor errors (multiple drugs) were observed. The Alamar colorimetric system was easy to use and the results were easy to read. It appears to be an acceptable method for antimicrobial susceptibility testing of staphylococci and enterococci.
Monocytes, neutrophils, and platelets cooperate to initiate and propagate venous thrombosis in mice in vivo (2012)

Deep vein thrombosis (DVT) is a major cause of cardiovascular death. The sequence of events that promote DVT remains obscure, largely as a result of the lack of an appropriate rodent model. We describe a novel mouse model of DVT which reproduces a frequent trigger and resembles the time course, histological features, and clinical presentation of DVT in humans. We demonstrate by intravital two-photon and epifluorescence microscopy that blood monocytes and neutrophils crawling along and adhering to the venous endothelium provide the initiating stimulus for DVT development. Using conditional mutants and bone marrow chimeras, we show that intravascular activation of the extrinsic pathway of coagulation via tissue factor (TF) derived from myeloid leukocytes causes the extensive intraluminal fibrin formation characteristic of DVT. We demonstrate that thrombus-resident neutrophils are indispensable for subsequent DVT propagation by binding factor XII (FXII) and by supporting its activation through the release of neutrophil extracellular traps (NETs). Correspondingly, neutropenia, genetic ablation of FXII, or disintegration of NETs each confers protection against DVT amplification. Platelets associate with innate immune cells via glycoprotein Ibα and contribute to DVT progression by promoting leukocyte recruitment and stimulating neutrophil-dependent coagulation. Hence, we identified a cross talk between monocytes, neutrophils, and platelets responsible for the initiation and amplification of DVT and for inducing its unique clinical features.
Reversible Biotinylation Phosphoramidite for 5‘-End-Labeling, Phosphorylation, and Affinity Purification of Synthetic Oligonucleotides (2002)

A fluoride/amine-cleavable phosphoramidite designed for biotinylation, phosphorylation, and affinity purification of synthetic oligonucleotides was synthesized and coupled efficiently to the 5'-end of DNA on a solid-phase automatic synthesizer. The two hydroxyl groups of diethyl bis(hydroxymethyl)malonate were used to link biotin and the 5'-end of DNA together through a diisopropylsilyl acetal functionality and a phosphate ester group, respectively. The DNA was cleaved from solid support and fully deprotected by treating with a mixture of MeNH(2) ( approximately 40%) and NH(4)OH ( approximately 29%) (1:1, v/v, 65 degrees C, 30 min), and the linkage between biotin and DNA was found completely stable under these conditions. The biotinylated full-length DNA was efficiently attached to NeutrAvidin coated microspheres and failure sequences and other impurities were simply removed by washing with buffer and water. The microspheres were then treated with HF/pyridine/THF (rt, 1 h) and MeNH(2) ( approximately 40%, rt, 15 min) sequentially to yield high quality full-length 5'-end phosphorylated unmodified DNA as revealed by HPLC analysis. It is anticipated that this method will find applications in areas that require efficient isolation of 5'-end phosphorylated DNA from a complex mixture.
Probucol prevents the progression of atherosclerosis in Watanabe heritable hyperlipidemic rabbit, an animal model for familial hypercholesterolemia. (1987)

In this study, we questioned whether in vivo probucol could prevent the progression of atherosclerosis in homozygous Watanabe heritable hyperlipidemic (WHHL) rabbits, an animal model for familial hypercholesterolemia. At 2 months of age, eight WHHL rabbits were divided into two groups. Group A (n = 4) was fed standard rabbit chow for 6 months. Group B (n = 4) was fed standard rabbit chow containing 1% probucol for 6 months. At the end of the experiments, average plasma concentrations of cholesterol were 704 +/- 121 mg/dl in group A and 584 +/- 61 mg/dl in group B, respectively. The percentage of surface area of total thoracic aorta with visible plaques in group A versus group B was 54.2% +/- 18.8% versus 7.0% +/- 6.3%, respectively. What was noteworthy was that the percentage of plaque in the descending thoracic aorta was almost negligible (0.2% +/- 0.2%) in group B rabbits compared to that in group A rabbits (41.1% +/- 20.2%). Low density lipoproteins (LDL) isolated from WHHL rabbits under treatment with probucol (group B) were shown to be highly resistant to oxidative modification by cupric ion and to be minimally recognized by macrophages. On the contrary, LDL from group A rabbits incubated with cupric ion showed a 7.4-fold increase in peroxides (thiobarbituric acid-reactive substances) and a 4.3-fold increase in the synthesis of cholesteryl ester in macrophages compared to those of LDL from group B rabbits. Thus, probucol could definitely prevent the progression of atherosclerosis in homozygous WHHL rabbits in vivo by limiting oxidative LDL modification and foam cell transformation of macrophages.
Narrow‐Bandgap Diketo‐Pyrrolo‐Pyrrole Polymer Solar Cells: The Effect of Processing on the Performance (2008)

Solar cells based on a new conjugated donor polymer with alternating quaterthiophene and diketo pyrrolo-pyrrole units in combination with C60 and C70 PCBM acceptors afford high external quantum efficiencies over a broad spectral range into the near-infrared. The cells provide power conversion efficiencies of up to 4.0% under simulated AM1.5G solar light conditions.
Colocalization of Intracellular Osteopontin With CD44 Is Associated With Migration, Cell Fusion, and Resorption in Osteoclasts (2002)

Although osteopontin (OPN) is recognized generally as a secreted protein, an intracellular form of osteopontin (iOPN), associated with the CD44 complex, has been identified in migrating fibroblastic cells. Because both OPN and CD44 are expressed at high levels in osteoclasts, we have used double immunofluorescence analysis and confocal microscopy to determine whether colocalization of these proteins has functional significance in the formation and activity of osteoclasts. Analysis of rat bone marrow-derived osteoclasts revealed strong surface staining for CD44 and beta1- and beta3-integrins, whereas little or no staining for OPN or bone sialoprotein (BSP) was observed in nonpermeabilized cells. In permeabilized perfusion osteoclasts and multinucleated osteoclasts, staining for OPN and CD44 was prominent in cell processes, including filopodia and pseudopodia. Confocal microscopy revealed a high degree of colocalization of OPN with CD44 in motile osteoclasts. In cells treated with cycloheximide (CHX), perinuclear staining for OPN and BSP was lost, but iOPN staining was retained within cell processes. In osteoclasts generated from the OPN-null and CD44-null mice, cell spreading and protrusion of pseudopodia were reduced and cell fusion was impaired. Moreover, osteoclast motility and resorptive activity were significantly compromised. Although the area resorbed by OPN-null osteoclasts could be rescued partially by exogenous OPN, the resorption depth was not affected. These studies have identified an intracellular form of OPN, colocalizing with CD44 in cell processes, that appears to function in the formation and activity of osteoclasts.
A randomised, double-blind, parallel-group study of the safety and efficacy of subcutaneous tocilizumab versus intravenous tocilizumab in combination with traditional disease-modifying antirheumatic drugs in patients with moderate to severe rheumatoid arthritis (SUMMACTA study) (2013)

Tocilizumab-SC 162 mg weekly demonstrated comparable efficacy to tocilizumab-IV 8 mg/kg. The safety profile of tocilizumab-SC is consistent with the known and well-established safety profile of tocilizumab-IV, with the exception of a higher incidence of ISR, which were more common with tocilizumab-SC administration.