gebhart/patrepeval huggingface dataset:
Software fault isolation in wide area networks (1992)

The problem of real-time detection and isolation of errors in distributed software systems operating in a wide-area networked environment is considered. The approach presented combines the results of static software analysis with dynamic event-driven monitoring. Static software analysis is used to generate a model of the distributed system. The model describes all possible executions of the processes composing the distributed system. The event-driven monitoring algorithm upon detecting an erroneous event uses the model to isolate the distributed software process states causing the fault. Because this approach does not require the use of the network for fault isolation, it is ideal for use in the low-bandwidth, high-latency communications environments characterizing wide-area networks.
Integrated two-stage liquefaction. Quarterly technical progress report, October 1, 1980-December 31, 1980: parametric study (1981)

This program combines a research study on Catalytic Expanded Bed Hydroprocessing of coal extracts and the operation of an integrated Two-Stage Liquefaction process development unit. Equilibration of the recycle paste solvent was achieved early in this period. Three short contact time (SCT) runs wre made with equilibrium solvent. Conversions ranged from 88 to 95 percent at hydrogen consumptions of 0.41 to 2.40 percent of moisture, ash-free coal. Elemental balances strongly suggest that considerable hydrogen is being transferred from the solvent to the coal. The recycle solvent contained 23 to 48 percent 850/sup 0/F+. The LC-Fining bottoms constitute about 70 percent of the recycle solvent. The deasher recovered 71 to 80.5 percent of the extract from the SCT unit. Ash concentrations of less than 0.10 percent in the recovered extract were achieved. The first batch of LC-Fining catalyst was removed because of an operating upset. The catalyst had an accumulated life of 1336 pounds of 850/sup 0/F+ feed per pound of catalyst and it showed virtually no decline in conversion activity. Nitrogen concentrations in the distillate products were below 0.2 percent. Both the catalyst activity and the product quality are the highest obtained thus far in the hydrocracking of coal extracts.more » A new batch of catalyst was charged and the LC-Finer resumed operation. An overall yield structure was calculated, based on the results of this period. The distillate (C/sub 5/-850/sup 0/F) yield was 3.29 barrels per ton of moisture, ash-free coal at a hydrogen consumption of 4.78 percent based on MAF coal.« less
High-Frequency Transformation, by Electroporation, of Lactococcus lactis subsp. cremoris Grown with Glycine in Osmotically Stabilized Media (1989)

An efficient method for genetic transformation of lactococci by electroporation is presented. Highly competent lactococci for electrotransformation were obtained by growing cells in media containing high concentrations of glycine and 0.5 M sucrose as the osmotic stabilizers. These cells could be stored at -85 degrees C without loss of competence. With Lactococcus lactis subsp. cremoris BC101, a transformation frequency of 5.7 x 10 transformants per mug of pIL253 DNA was obtained, which represents 5% of the surviving cells. All the lactococcal strains tested could be transformed by the present method.
Peptide‐β2‐microglobulin‐major histocompatibility complex expressing cells are potent antigen‐presenting cells that can generate specific T cells (2007)

Adoptive T-cell therapy represents a promising therapeutic approach for the treatment of cancer. Successful adoptive immunotherapy depends on the ex vivo priming and expansion of antigen-specific T cells. However, the in vitro generation of adequate numbers of functional antigen-specific T cell remains a major obstacle. It is important to develop efficient and reproducible methods to generate high numbers of antigen-specific T cells for adoptive T-cell transfer. We have developed a new artificial antigen-presenting cell (aAPC) by transfection of major histocompatibility (MHC) class I negative Daudi cells with a peptide-beta2-microglobulin-MHC fusion construct (single-chain aAPC) ensuring presentation of the peptide-MHC complex of interest. Using this artificial antigen-presenting cell, we could generate up to 9.2 x 10(8) antigen-specific cytotoxic CD8(+) T cells from 10 ml blood. In vitro generated T cells lysed endogenously presented antigens. Direct comparison of the single-chain aAPC with autologous monocyte-derived dendritic cells demonstrated that these cells were equally efficient in stimulation of T cells. Finally, we were able to generate antigen-specific T cell lines from perpheral blood mononuclear cells of patients receiving cytotoxic chemotherapy. The use of single-chain aAPC represent a promising option for the generation of antigen-specific CD8(+) T cells, which could be used for adoptive T-cell therapy.
Dynamics of in silico leukocyte rolling, activation, and adhesion (2007)

The overlap in phenotypic attributes of our analogue with those of leukocytes in vitro confirm the considerable potential of our model for studying the key events that determine the behavioral outcome of individual leukocytes during rolling, activation, and adhesion. Our results provide an important foundation and framework for future in silico research into plausible causal links between well-documented, subcellular molecular level events and the variety of systemic phenotypic attributes that distinguish normal leukocyte adhesion from abnormal disease-associated adhesion.
Scientific and Social Issues of Human Immunodeficiency Virus Vaccine Development (1993)

Development of a preventive immunogen for human immunodeficiency virus (HIV) infection is a national priority. The complexities associated with HIV host-virus interactions, coupled with the rapid progression of the HIV epidemic worldwide, have necessitated lowering expectations for an HIV vaccine that is 100 percent effective and have raised important scientific and nonscientific issues regarding development and use of preventive and therapeutic HIV vaccines.
Isolation and characterization of a novel insecticidal crystal protein gene from Bacillus thuringiensis subsp. aizawai (1991)

Bacillus thuringiensis subsp. aizawai EG6346, a novel grain dust isolate, was analyzed by Southern blot hybridization for its insecticidal crystal protein (ICP) gene profile. Strain EG6346 lacks previously characterized cryIA ICP genes yet does possess novel cryI-related gene sequences. A recombinant genomic plasmid library was constructed for strain EG6346 in Escherichia coli. One recombinant plasmid, pEG640, isolated from the library contained a novel ICP gene on a 5.7-kb Sau3A insert. The sequence of this gene, designated cryIF, was related to, but distinct from, the published sequences for other cryI genes. A second novel cryI-related sequence was also located on pEG640, approximately 500 bp downstream from cryIF. Introduction of cryIF into a Cry- B. thuringiensis recipient strain via electroporation enabled sufficient production of CryIF protein for quantitative bioassay analyses of insecticidal specificity. The CryIF crystal protein was selectively toxic to a subset of lepidopteran insects tested, including the larvae of Ostrinia nubilalis and Spodoptera exigua.
Characterization of a new human B7-related protein: B7RP-1 is the ligand to the co-stimulatory protein ICOS (2000)

Optimal T cell activation requires the interactions of co-stimulatory molecules, such as those in the CD28 and B7 protein families. Recently, we described the co-stimulatory properties of the murine ligand to ICOS, which we designated as B7RP-1. Here, we report the co-stimulation of human T cells through the human B7RP-1 and ICOS interaction. This ligand-receptor pair interacts with a K:(D) approximately 33 nM and an off-rate with a t((1/2)) > 10 min. Interestingly, tumor necrosis factor (TNF)-alpha differentially regulates the expression of human B7RP-1 on B cells, monocytes and dendritic cells (DC). TNF-alpha enhances B7RP-1 expression on B cells and monocytes, while it inhibits it on DC. The human B7RP-1-Fc protein or cells that express membrane-bound B7RP-1 co-stimulate T cell proliferation in vitro. Specific cytokines, such as IFN-gamma and IL-10, are induced by B7RP-1 co-stimulation. Although IL-2 levels are not significantly increased, B7RP-1 co-stimulation is dependent on IL-2. These experiments define the human ortholog to murine B7RP-1 and characterize its interaction with human ICOS.
LPA1 Receptor Activation Promotes Renal Interstitial Fibrosis (2007)

Tubulointerstitial fibrosis in chronic renal disease is strongly associated with progressive loss of renal function. We studied the potential involvement of lysophosphatidic acid (LPA), a growth factor-like phospholipid, and its receptors LPA(1-4) in the development of tubulointerstitial fibrosis (TIF). Renal fibrosis was induced in mice by unilateral ureteral obstruction (UUO) for up to 8 d, and kidney explants were prepared from the distal poles to measure LPA release into conditioned media. After obstruction, the extracellular release of LPA increased approximately 3-fold. Real-time reverse transcription PCR (RT-PCR) analysis demonstrated significant upregulation in the expression of the LPA(1) receptor subtype, downregulation of LPA3, and no change of LPA2 or LPA4. TIF was significantly attenuated in LPA1 (-/-) mice compared to wild-type littermates, as measured by expression of collagen III, alpha-smooth muscle actin (alpha-SMA), and F4/80. Furthermore, treatment of wild-type mice with the LPA1 antagonist Ki16425 similarly reduced fibrosis and significantly attenuated renal expression of the profibrotic cytokines connective tissue growth factor (CTGF) and transforming growth factor beta (TGFbeta). In vitro, LPA induced a rapid, dose-dependent increase in CTGF expression that was inhibited by Ki16425. In conclusion, LPA, likely acting through LPA1, is involved in obstruction-induced TIF. Therefore, the LPA1 receptor might be a pharmaceutical target to treat renal fibrosis.
Electrophoretic distributions of human peripheral blood mononuclear white cells from normal subjects and from patients with acute lymphocytic leukemia. (1976)

The electrophoretic mobilities of mononuclear white cells from the peripheral blood of normal subjects and leukemic patients were measured. Analysis of both fresh and cryopreserved samples of each type showed that cryopreservation had no distinguishable effect on the electrophoretic distribution of either normal or leukemic cells. Mode mobilities (mobilities at which maximum intensities are observed) of cells from nine leukemic patients were 7-28% below the average mode mobility of normal cells. The standard deviation of the electrophoretic mobilities of normal cells was 2%. Normal cells had an asymmetric, often bimodal, electrophoretic distribution; leukemic cells consistently had a single symmetric distribution.
[Campylobacter pylori, gastritis and peptic ulcer]. (1987)

In the course of routine gastroduodenoscopic examination of 218 patients bioptic mucosal specimens were examined bacteriologically for the presence of Campylobacter (C.) pylori. The organism was isolated from 52 out of 53 patients (98%) with duodenal ulcer, 7 out of 9 with gastric ulcer (78%), 24 out of 31 with mucosal erosions (77%), 10 out of 10 with duodenitis (100%), 16 out of 16 with chronic active gastritis (100%) and from 40 out of 73 patients (55%) with inactive chronic gastritis. By contrast, all specimens from 26 patients with endoscopically and histologically normal mucosa were negative for this bacterium. The rate of elimination of C. pylori from mucosal specimens was investigated as a first step towards studying the influence of antibiotic therapy upon healing of gastric and duodenal ulcers. For this purpose 30 patients with duodenal ulcers were treated either with ranitidine alone (15) or together with bacampicillin (15), which was shown to be highly active in studies with ampicillin in vitro. After 4 weeks the organism was still found in specimens from all patients treated with ranitidine alone, but also in 12 out of 15 patients given combined therapy. This result demonstrates that systemic antimicrobial chemotherapy with bacampicillin is insufficient to eradicate C. pylori from the stomach and the duodenum.
The Cellular Target of Histatin 5 on Candida albicans Is the Energized Mitochondrion (1999)

Histatin 5 is a human basic salivary peptide with strong fungicidal properties in vitro. To elucidate the mechanism of action, the effect of histatin 5 on the viability of Candida albicans cells was studied in relation to its membrane perturbing properties. It was found that both the killing activity and the membrane perturbing activity, studied by the influx of a DNA-specific marker propidium iodide, were inhibited by high salt conditions and by metabolic inhibitors, like sodium azide. In addition, exposure to histatin 5 resulted in a loss of the mitochondrial transmembrane potential in situ, measured by the release of the potential-dependent distributional probe rhodamine 123. Localization studies using tetramethylrhodamine isothiocyanate-labeled histatin 5 or fluorescein isothiocyanate-labeled histatin 5 showed a granular intracellular distribution of the peptide, which co-localized with mitotracker orange, a permeant mitochondria-specific probe. Like the biological effects, uptake of labeled histatin 5 was inhibited by mitochondrial inhibitors and high salt conditions. Our data indicate that histatin 5 is internalized, and targets to the energized mitochondrion.
Identification and pharmacological characterization of the prostaglandin FP receptor and FP receptor variant complexes (2008)

Bimatoprost lacks effects on the FP receptor but may interact with the FP-altFP receptor heterodimer to induce alterations in second messenger signalling. Hence, FP-altFP complexes may represent the underlying basis of bimatoprost pharmacology.
Abstract 3158: Ex vivo expansion and activation of human lymphocytes with a selective activator of effector cells (2015)

Abstract RDB 1450 is an engineered fusion protein of circularly permuted IL-2 and IL-2Rα that is selective for the intermediate-affinity IL-2 receptor. The intermediate-affinity receptor is comprised of the IL-2 receptor beta chain (CD122) and common gamma chain (CD132) expressed on lymphocytes with effector function, whereas the high-affinity receptor, which additionally includes the alpha chain (CD25), is expressed primarily on immunosuppressive CD4+CD25+ regulatory T cells (Tregs). Ex vivo proliferation of subsets of human lymphocytes in response to RDB 1450 or rhIL-2 were evaluated. RDB 1450 supports the selective activation and expansion of effector lymphocytes based on higher observed memory CD8 T/Treg and NK/Treg ratios. Both RDB 1450 and IL-2 drive expansion of NK cells, however, a greater proportion of CD25+ NK cells are observed in response to RDB 1450. Furthermore, unlike IL-2, RDB 1450 does not effectively expand highly suppressive ICOS+ Tregs. The immunological profile resulting from the ex vivo treatment of human PBMCs with RDB 1450 supports its use as a novel immunotherapy for cancer. Citation Format: Jared E. Lopes, Jan L. Fisher, Heather C. Losey, Marc S. Ernstoff, Juan C. Alvarez. Ex vivo expansion and activation of human lymphocytes with a selective activator of effector cells. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3158. doi:10.1158/1538-7445.AM2015-3158
An Integrated Serial to Parallel Converter for Teletext Application (1979)

Teledata systems implemented as either television add-ons or new set features will require relatively complex integrated circuits. Consumer acceptance of these systems will be a sensitive function of their price. Thus, the various IC technologies must be evaluated with respect to achieving adequate performance at minimum cost. We have investigated the feasibility of N-channel MOS for teledata serial- to-parallel conversion.
Neutralization of West Nile virus by cross-linking of its surface proteins with Fab fragments of the human monoclonal antibody CR4354 (2010)

Many flaviviruses are significant human pathogens, with the humoral immune response playing an essential role in restricting infection and disease. CR4354, a human monoclonal antibody isolated from a patient, neutralizes West Nile virus (WNV) infection at a postattachment stage in the viral life-cycle. Here, we determined the structure of WNV complexed with Fab fragments of CR4354 using cryoelectron microscopy. The outer glycoprotein shell of a mature WNV particle is formed by 30 rafts of three homodimers of the viral surface protein E. CR4354 binds to a discontinuous epitope formed by protein segments from two neighboring E molecules, but does not cause any detectable structural disturbance on the viral surface. The epitope occurs at two independent positions within an icosahedral asymmetric unit, resulting in 120 binding sites on the viral surface. The cross-linking of the six E monomers within one raft by four CR4354 Fab fragments suggests that the antibody neutralizes WNV by blocking the pH-induced rearrangement of the E protein required for virus fusion with the endosomal membrane.
Immunotherapy with lymphokine-activated natural killer cells and recombinant interleukin-2: a feasibility trial in metastatic renal cell carcinoma. (1990)

Clinical immunotherapy trials have been performed recently where ex vivo interleukin-2 (IL-2)-activated peripheral blood mononuclear cells (i.e., the "LAK" cells) have been transfused in addition to IL-2 infusions. In such protocols, patients have received highly heterogeneous cell suspensions and the nature of the effector cells that may have contributed to tumor regression has remained unclear. In certain animal models, it has appeared that natural killer lymphocytes were the effector cell type responsible for tumor regression. To test whether NK cells could eventually be relevant for the treatment of human tumors, we have performed a feasibility trial where purified lymphokine-activated natural killer (LANAK) cells have been prepared and transfused to a limited series of renal cell carcinoma patients receiving IL-2 (continuous infusions at 3 x 10(6) U/m2/day). Natural killer lymphocytes (1-2 x 10(6] were purified from peripheral blood mononuclear cells and expanded during 4-5 weeks in the presence of IL-2 on microtiter plates containing feeder layers cells. In vitro, the resulting LANAK cell suspensions were 100 times (range of 2 to 10(3] more efficient against Daudi target cells than their autologous LAK counterparts. Twelve patients were included; 9 received the two planned courses of treatment with LANAK cells and IL-2. Overall toxicity was relatively moderate. Besides occasional chills, there were no apparent secondary effects due to cell infusions. The mean number of LANAK cells transfused per patients was 45.1 x 10(9), ranging from 7 to 125 x 10(9). The biodistribution of LANAK cells was similar to that reported previously for LAK cells with no preferential localization to tumor sites. We conclude from this study that using well-defined populations of effector lymphocytes is a feasible cellular therapy approach that may lead to improved understanding and efficacy of the novel immunotherapy methods.
Antibody cross-competition analysis of the human immunodeficiency virus type 1 gp120 exterior envelope glycoprotein (1996)

Forty-six monoclonal antibodies (MAbs) able to bind to the native, monomeric gp120 glycoprotein of the human immunodeficiency virus type 1 (HIV-1) LAI (HXBc2) strain were used to generate a competition matrix. The data suggest the existence of two faces of the gp120 glycoprotein. The binding sites for the viral receptor, CD4, and neutralizing MAbs appear to cluster on one face, which is presumably exposed on the assembled, oligomeric envelope glycoprotein complex. A second gp120 face, which is presumably inaccessible on the envelope glycoprotein complex, contains a number of epitopes for nonneutralizing antibodies. This analysis should be useful for understanding both the interaction of antibodies with the HIV-1 gp120 glycoprotein and neutralization of HIV-1.
Quantitative analysis of triglycerides using atmospheric pressure chemical ionization‐mass spectrometry (1996)

Atmospheric pressure chemical ionization-mass spectrometry (APCI-MS) was used for quantitative analysis of triglycerides (TG) separated by reverse-phase high-performance liquid chromatography. APCI-MS was used for analysis of mono-acid TG standards containing deuterated internal standard, of a synthetic mixture of heterogeneous TG, of randomized and normal soybean oils and of randomized and normal lard samples. Quantitation of the TG by four approaches based on APCI-MS were compared, and these were compared to quantitation obtained using liquid chromatography (LC) with flame-ionization detection (FID). The APCI-MS methods were based on (i) calibration curves from data for mono-acid TG standards, (ii) response factors obtained from a synthetic mixture of TG, (iii) response factors calculated from comparison of randomized samples to their statistically expected compositions, and (iv) response factors calculated from comparison of fatty acid (FA) compositions calculated from TG compositions to FA compositions obtained by calibrated gas chromatography (GC) with FID. Response factors derived from a synthetic mixture were not widely applicable to samples of disparate composition. The TG compositions obtained using APCI-MS data without application of response factors had average relative errors very similar to those obtained using LC-FID. Numerous TG species were identified using LC/APCI-MS which were undetected using LC-FID. Two quantitation methods, based on response factors calculated from randomized samples or on response factors calculated from FA compositions, both gave similar results for all samples. The TG compositions obtained using response factors calculated from FA compositions showed less average relative error than was obtained from LC-FID data, and were in good agreement with predicted compositions for the synthetic mixture and for randomized soybean oil and lard samples.
Plasma and Urinary Cytokine Homeostasis and Renal Dysfunction during Cardiac Surgery (2000)

Cardiac surgery using CPB leads to changes in plasma and urinary cytokine homeostasis that correlate with renal proximal tubular dysfunction. This dysfunction may be related to the renal filtration of proinflammatory mediators. Renal autoprotective mechanisms may involve the intrarenal generation of antiinflammatory cytokines.
Combined Vascular Endothelial Growth Factor Receptor and Epidermal Growth Factor Receptor (EGFR) Blockade Inhibits Tumor Growth in Xenograft Models of EGFR Inhibitor Resistance (2009)

These studies suggest that erlotinib resistance may be associated with a rise in both tumor cell and host stromal VEGF and that combined blockade of the VEGFR and EGFR pathways can abrogate primary or acquired resistance to EGFR TKIs. This approach merits further evaluation in NSCLC patients.