gebhart/patrepeval huggingface dataset:
Purification and partial sequence analysis of a 37-kDa protein that inhibits phospholipase A2 activity from rat peritoneal exudates. (1986)

We have purified from rat peritoneal exudates a 37-kDa protein that inhibits phospholipase A2 activity. It is the predominant phospholipase inhibitor protein in these preparations and also is detected in a wide variety of cell lines. Levels of expression range from 0 to 0.5% of total protein. In the peritoneal preparations, the inhibitor is partially proteolyzed into a series of lower mass forms, including species at 30, 24, and 15 kDa. These fragments all are immunoreactive with an antibody raised against the 37-kDa protein. The rat protein also is immunoreactive with an antibody developed against a 6-kDa phospholipase inhibitor protein from snake venom. The primary structure of more than half of the rat inhibitor has been deduced by protein microsequence analysis. These sequences are closely related to sequences from its human analogue, which we recently cloned and expressed (Wallner, B. P., Mattaliano, R. J., Hession, C., Cate, R. L., Tizard, R., Sinclair, L. K., Foeller, C., Chow, E. P., Browning, J. L., Ramachandran, K. L., and Pepinsky, R. B. (1986) Nature, in press), and thus we infer that the inhibitor is highly conserved evolutionarily. Properties of the molecule suggest that it is a member of a family of steroid-induced anti-inflammatory proteins collectively referred to as lipocortin.
Isolation of antigen-specific CD8+ T lymphocytes in vitro and in vivo (2013)

Meeting abstracts Depending on the mechanisms by which cancer develops and the strategies tumors use to escape the immune system, cancer therapies are more or less successful. A combination of different therapeutic agents, such as dendritic cell (DC) vaccines loaded with tumor antigens and adoptive
Mutational Analysis of a Plant Defensin from Radish (Raphanus sativus L.) Reveals Two Adjacent Sites Important for Antifungal Activity (1997)

Mutational analysis of Rs-AFP2, a radish antifungal peptide belonging to a family of peptides referred to as plant defensins, was performed using polymerase chain reaction-based site-directed mutagenesis and yeast as a system for heterologous expression. The strategy followed to select candidate amino acid residues for substitution was based on sequence comparison of Rs-AFP2 with other plant defensins exhibiting differential antifungal properties. Several mutations giving rise to peptide variants with reduced antifungal activity against Fusarium culmorum were identified. In parallel, an attempt was made to construct variants with enhanced antifungal activity by substituting single amino acids by arginine. Two arginine substitution variants were found to be more active than wild-type Rs-AFP2 in media with high ionic strength. Our data suggest that Rs-AFP2 possesses two adjacent sites that appear to be important for antifungal activity, namely the region around the type VI beta-turn connecting beta-strands 2 and 3, on the one hand, and the region formed by residues on the loop connecting beta-strand 1 and the alpha-helix and contiguous residues on the alpha-helix and beta-strand 3, on the other hand. When added to F. culmorum in a high ionic strength medium, Rs-AFP2 stimulated Ca2+ uptake by up to 20-fold. An arginine substitution variant with enhanced antifungal activity caused increased Ca2+ uptake by up to 50-fold, whereas a variant that was virtually devoid of antifungal activity did not stimulate Ca2+ uptake.
Towards highly reliable enterprise network services via inference of multi-level dependencies (2007)

Localizing the sources of performance problems in large enterprise networks is extremely challenging. Dependencies are numerous, complex and inherently multi-level, spanning hardware and software components across the network and the computing infrastructure. To exploit these dependencies for fast, accurate problem localization, we introduce an Inference Graph model, which is well-adapted to user-perceptible problems rooted in conditions giving rise to both partial service degradation and hard faults. Further, we introduce the Sherlock system to discover Inference Graphs in the operational enterprise, infer critical attributes, and then leverage the result to automatically detect and localize problems. To illuminate strengths and limitations of the approach, we provide results from a prototype deployment in a large enterprise network, as well as from testbed emulations and simulations. In particular, we find that taking into account multi-level structure leads to a 30% improvement in fault localization, as compared to two-level approaches.
Comment on " HST2 Mediates SIR2 -Independent Life-Span Extension by Calorie Restriction" (2006)

Calorie restriction (CR) increases life span in yeast independently of Sir2. Lamming et al. (Reports, 16 September 2005, p. 1861) recently proposed that Sir2-independent life-span extension by CR is mediated by the Sir2 paralogs Hst1 and Hst2. Contradictory to this, we find that CR greatly increases life span in cells lacking Sir2, Hst1, and Hst2, which suggests that CR is not mediated by Sir2, Hst2, or Hst1.
Impact of serum adiponectin and leptin levels in acute leukemia (2013)

Adipocytokines was stated to exert biological effect on tumor cells. Two adipokines, leptin and adiponectin in particular, have come to be recognized for their influence on tumor biology including leukemia. The prognostic effect of leptin and adiponectin concentrations in acute leukemia patients remains to be identified. This study was conducted on 80 acute leukemia patients: 35 acute myeloid leukemia (AML), 45 acute lymphoid leukemia (ALL), and 20 controls of matched age and sex. Leptin and adiponectin were assayed by enzyme-linked immunosorbent assay at diagnosis. Serum leptin levels were significantly higher in ALL patients, and significantly lower in AML patients when compared with normal controls (P = 0.01, P = 0.04 respectively). On the other hand, serum adiponectin levels were significantly lower in AML and ALL patients as compared with normal controls (P = 0.00 for both). No significant differences exist regarding body mass index between acute leukemia patients and normal controls (P > 0.05). Correlation studies revealed that there were significant negative correlations between serum adiponectin levels and bone marrow (BM) blast cells and serum lactic dehydrogenase (sLDH) in acute leukemia groups (r 0.542, P < 0.01, r 0.699, P < 0.001, respectively). Regarding serum leptin levels there were positive significant correlations with BM blast cells (r 0.74, P < 0.01), total WBC counts (r = 0.59, P < 0.05), sLDH (r 0.738, P < 0.01) in ALL group; and significant negative correlations with BM blast cells (r 0.542, P < 0.01) and sLDH in the AML group. Adipocytokines may represent a new non-invasive biomarker in acute leukemia patients. Estimation of adiponectin and leptin serum levels at acute leukemia diagnosis could also be considered as a prognostic marker, which will be used in acute leukemia stratification.
Gangliosides in normal human serum (1989)

The total content and pattern of gangliosides were determined in the unfractionated sera of 11 healthy human adults and in isolated lipoproteins. The total content of lipid-bound sialic acid was 10.5 +/- 3.2 nmol/ml serum. The ganglioside profile consisted of more than ten different components. The major ganglioside was GM3, followed by GD3, GD1a, GM2, GT1b, MG-3 (sialosyllactoneotetraosylceramide), GD1b and GQ1b. Traces of four additional gangliosides could not be quantified reliably. Ganglioside patterns did not vary in sera taken from healthy adults of different age and sex. Approximately 98% of human serum gangliosides were transported by serum lipoproteins, predominantly by LDL (66%), followed by HDL (25%) and VLDL (7%). The quantitative distribution of individual gangliosides in VLDL and LDL was almost the same as that in the unfractionated serum; some differences existed with the ganglioside profile in HDL.
Interleukin-1/Toll Receptor Family Members: Receptor Structure and Signal Transduction Pathways (2000)

Interleukin-1 (IL-1) is a central mediator of the inflammatory response. It plays a role in both systemic and local immune responses to invading microbes. There are two receptors (IL-1RI and IL-1RII) that mediate the cellular responses. These receptors belong to a family of receptors based on homologous receptor structure within the intracellular signaling domain. Other family members include the Drosophila protein Toll, the recently discovered mammalian Toll-like receptors (TLR), and the IL-18 receptor. Engagement of these receptors by their diverse ligands results in activation of very similar signal transduction cascades through use of common signaling intermediates. These signal transduction cascades lead to the activation of cellular responses that are known to regulate the innate immune response. Therefore, elucidating the function and redundancy of this receptor family is essential to the understanding of the innate immune response. This review examines each member of this receptor family and emphasizes similarities and potential differences in both receptor structure and signal transduction pathways to further the understanding of this complex receptor family.
Herbicide-Degrading α-Keto Acid-Dependent Enzyme TfdA:  Metal Coordination Environment and Mechanistic Insights (1999)

TfdA is a non-heme iron enzyme which catalyzes the first step in the oxidative degradation of the widely used herbicide (2, 4-dichlorophenoxy)acetate (2,4-D). Like other alpha-keto acid-dependent enzymes, TfdA utilizes a mononuclear Fe(II) center to activate O(2) and oxidize substrate concomitant with the oxidative decarboxylation of alpha-ketoglutarate (alpha-KG). Spectroscopic analyses of various Cu(II)-substituted and Fe(II)-reconstituted TfdA complexes via electron paramagnetic resonance (EPR), electron spin-echo envelope modulation (ESEEM), and UV-vis spectroscopies have greatly expanded our knowledge of the enzyme's active site. The metal center is coordinated to two histidine residues as indicated by the presence of a five-line pattern in the Cu(II) EPR signal, for which superhyperfine splitting is attributed to two equivalent nitrogen donor atoms from two imidazoles. Furthermore, a comparison of the ESEEM spectra obtained in H(2)O and D(2)O demonstrates that the metal maintains several solvent-accessible sites, a conclusion corroborated by the increase in multiplicity in the EPR superhyperfine splitting observed in the presence of imidazole. Addition of alpha-KG to the Cu-containing enzyme leads to displacement of an equatorial water on copper, as determined by ESEEM analysis. Subsequent addition of 2,4-D leads to the loss of a second water molecule, with retention of a third, axially bound water. In contrast to these results, in Fe(II)-reconstituted TfdA, the cosubstrate alpha-KG chelates to the metal via a C-1 carboxylate oxygen and the alpha-keto oxygen as revealed by characteristic absorption features in the optical spectrum of Fe-TfdA. This binding mode is maintained in the presence of substrate, although the addition of 2,4-D does alter the metal coordination environment, perhaps by creating an O(2)-binding site via solvent displacement. Indeed, loss of solvent to generate an open binding site upon the addition of substrate has also been suggested for the alpha-keto acid-dependent enzyme clavaminate synthase 2 [Zhou et al. (1998) J. Am. Chem. Soc. 120, 13539-13540]. Nitrosyl adducts of various Fe-TfdA complexes have also been investigated by optical and EPR spectroscopy. Of special interest is the tightly bound NO complex of Fe-TfdA.(alpha-KG).(2,4-D), which may represent an accurate model of the initial oxygen-bound species.
Nocturnal Hypoxemia: A Neglected Cardiovascular Risk Factor in End-Stage Renal Disease? (2002)

Its is well established that sleep apnea (SA) is a health problem of paramount importance because it disrupts sleep and quality of life and may induce serious neuroendocrine and cardiovascular complications. There is little doubt that chronic renal failure is an independent cause of SA. The hypothesis that SA may depend on the accumulation of endogenous opioids still remains to be tested. Cytokines, particularly TNF-alpha and IL-6 which are much elevated in end-stage renal disease (ESRD), may also be implicated in the pathogenesis of SA. Nocturnal hypoxemia is an independent predictor of cardiovascular events in ESRD and the prediction power of this parameter remains strong and substantially unmodified after statistical adjustment for established cardiovascular risk factors in the dialysis population. Left ventricular hypertrophy and dysautonomia appear to be most likely intermediate mechanisms mediating the adverse cardiovascular effects of SA in ESRD.
Grid FriendlyTM Device Model Development and Simulation (2009)

In late 2007, the Bonneville Power Administration (BPA) contracted Pacific Northwest National Laboratory (PNNL) to complete a research project titled Grid-Responsive Demand-Side Control Using Grid Friendly Appliance Technologies [Hammerstrom 2009, DeSteese and Hammerstrom 2009]. Cosponsors included Portland General Electric (PGE) and Puget Sound Energy (PSE). The project focused on applications of the Grid Friendly Appliance (GFA) controller, which is an autonomous controller that was designed to advise devices like appliances concerning valuable demand-side grid services that should be conducted. The controller bases its advice on observations it makes from the ac voltage signal. Electric tank water heaters were selected to be controlled by the GFA controller in this project. Two autonomous responses are addressed herein. First, an under-voltage-responsive water heater is able to recognize sudden reductions in feeder circuit voltage at each water heater and may curtail any electric load that is being consumed by the water heater. These under-voltage events are usually induced by nearby electrical faults. An under-voltage response is necessarily specified by the set of voltage thresholds at which the responsive water heaters would respond. The set of voltages at which the curtailment would be released must also be specified. Additionally, any delays prior to the water heater load becoming curtailed or again released must be specified. For example, a delay may be intentionally imposed prior to curtailing water heater loads to avoid responses during the fault itself. Much longer and randomized delays should be imposed prior to the release of curtailments in order to re-establish diversity of the water heater loads and soften what could otherwise be an abrupt reintroduction of a large aggregated electrical load into the already stressed grid region.
On the significance of self-similar fractal geometry in determining the multiband behavior of the Sierpinski gasket antenna (2002)

The relationship between the Sierpinski gasket's self-similar fractal gap structure and its multiband behavior is considered. It is demonstrated that the majority of the self-similar fractal gap structure can be eliminated from the Sierpinski gasket without significantly affecting its multiband behavior. The analysis presented here demonstrates that the multiband behavior of the Sierpinski gasket is primarily a function of the periodic placement of the four gaps located along the central vertical axis of the antenna.
Case 34-2006 (2006)

A 72-year-old woman awoke from sleep with nausea that worsened during a 24-hour period. Evaluation disclosed pulmonary infiltrates, an elevated granulocyte count, hypoxemia, and hypotension; antibiotics were administered. Blood drawn later showed elevated levels of cardiac enzymes, and an electrocardiogram showed ST-segment elevation. Hypoxemia and hypotension worsened. A diagnostic procedure was performed.
Purification of histidine tagged bacteriorhodopsin, pharaonis halorhodopsin and pharaonis sensory rhodopsin II functionally expressed in Escherichia coli (1999)

Bacteriorhodopsin (BR) from Halobacterium salinarum as well as halorhodopsin (pHR) and sensory rhodopsin II (pSRII) from Natronobacterium pharaonis were functionally expressed in E. coli using the method of Shimono et al. IFEBS Lett. (1997) 420, 54-56]. The histidine tagged proteins were purified with yields up to 1.0 mg/l cell culture and characterized by ESI mass spectrometry and their photocycle. The pSRII and pHR photocycles were indistinguishable from the wild type proteins. The BR photocycle was considerably prolonged. pSOII is located in the cytoplasmic membrane and the C-terminus is oriented towards the cytoplasm as determined by immunogold labelling.
Thermostable DNA polymerase from the archaebacterium Sulfolobus acidocaldarius (1989)

We have purified to near homogeneity a DNA polymerase from the thermoacidophilic archaebacterium Sulfolobus acidocaldarius. Sodium dodecyl sulfate gel electrophoresis of the purified enzyme revealed a polypeptide of 100 kDa. On the basis of a Stokes radius of 4.2 nm and a sedimentation coefficient of 6 S, the purified enzyme has an estimated molecular mass of 109 kDa. These results are consistent with the enzyme being a monomer of 100 kDa. In addition a polyclonal antiserum, obtained by injection of the electroeluted 100-kDa polypeptide into a rabbit, specifically neutralized the DNA-polymerase activity. The enzyme is sensitive to both N-ethylmaleimide and 2',3'-dideoxyribosylthymine triphosphate and resistant to aphidicolin. The purified DNA polymerase has neither exonuclease nor primase activities. In our in vitro conditions, the enzyme is thermostable up to 80 degrees C and is active between 55 degrees C and 85 degrees C in the presence of activated calf-thymus DNA.
TAKE YOUR HANDS OFF THAT CAR (1997)

This article describes the promise of hands-free computer-controlled vehicles to improve safety and reduce emissions, fuel consumption, and traffic congestion on the highway. It also suggests that the long- envisioned highways of the future are beginning to emerge
HSF1/hsp72 pathway as an endogenous anti‐inflammatory system (2001)

We investigated the occurrence and the role of HSF1 activation and inducible hsp72 expression in the carrageenin pleurisy in the rat. Molecular analysis performed on pleural cells collected from rat pleural cavity after carrageenin challenge revealed increased HSF1 activation and hsp72 expression. Moreover, local injection of a double-stranded oligodeoxynucleotide (ODN) containing the heat shock element sequence, acting as transcription factor decoy, exacerbated the inflammatory reaction. The exacerbation, induced by wild-type, but not by mutant ODN decoy, was associated to both inhibition of HSF1/DNA binding activity and reduction of hsp72 expression. In conclusion, this study shows that HSF1 activation and hsp72 expression both actually occur in acute inflammation and that the remission of the inflammatory reaction is tightly associated to the HSF1-dependent hsp72 expression, suggesting a a relevant role for the HSF1/hsp72 pathway as an endogenous anti-inflammatory system.
Identification of endo-beta-N-acetylglucosaminidase and N-acetylmuramyl-L-alanine amidase as cluster-dispersing enzymes in Staphylococcus aureus (1995)

Two proteins which are capable of dispersing cell clusters of Staphylococcus aureus have been purified from a S. aureus FDA209P culture supernatant. Both of them were found to have bacteriolytic activity. From the elution profile of column chromatography and Western blot (immunoblot) analysis, one of them was identified as a 51-kDa endo-beta-N-acetylglucosaminidase (GL). The other was a 62-kDa protein on the basis of sodium dodecyl sulfate gel electrophoresis. Analysis of the peptidoglycan fragments following treatment with the 62-kDa protein indicated that this protein is an N-acetylmuramyl-L-alanine amidase (AM). In vitro studies of cluster dispersion activities using S. aureus mutant strains Lyt66 or S. aureus Wood46 grown as clusters demonstrated that these two enzymes act synergistically to disperse clusters into single cells. Antiserum against the 51-kDa GL cross-reacted with the 62-kDa AM, and S. aureus FDA209P grown in the presence of anti-51-kDa-GL immunoglobulin G induced giant clusters. Clusters induced by anti-51-kDa GL and by Cibacron blue F3G-A were dispersed by coincubation with the 51-kDa GL and the 62-kDa AM. Western blot analysis demonstrated that the 51-kDa GL and the 62-kDa AM were missing in culture supernatants of S. aureus Lyt66, Wood46, and RUSAL2 (Tn551 autolysin-defective mutant), which grow in clusters. These results strongly suggest that the 51-kDa GL and 62-kDa AM are involved in cell separation of daughter cells after cell division.
Expression of heparan sulfate sulfotransferases in Kluyveromyces lactis and preparation of 3'-phosphoadenosine-5'-phosphosulfate (2011)

Heparan sulfate (HS) belongs to a major class of glycans that perform central physiological functions. Heparin is a specialized form of HS and is a clinically used anticoagulant drug. Heparin is a natural product isolated from pig intestine. There is a strong demand to replace natural heparin with a synthetic counterpart. Although a chemoenzymatic approach has been employed to prepare synthetic heparin, the scale of the synthesis is limited by the availability of sulfotransferases and the cofactor, 3'-phosphoadenosine-5'-phosphosulfate (PAPS). Here, we present a novel method to produce secreted forms of sulfotransferases in the yeast cells, Kluyveromyces lactis. Five sulfotransferases including N-sulfotransferase, 2-O-sulfotransferase, 3-O-sulfotransferase 1 and 6-O-sulfotransferases 1 and 3 were expressed using this method. Unlike bacterial-expressed sulfotransferases, the yeast proteins can be directly used to modify polysaccharides without laborious purification. The yeast-expressed sulfotransferases also tend to have higher specific activity and thermostability. Furthermore, we demonstrated the possibility for the gram-scale synthesis of PAPS from adenosine 5'-triphosphate at only 1/5000th of the price purchased from a commercial source. Our results pave the way to conduct the enzymatic synthesis of heparin in large quantities.
Nitric Oxide Delivery by Core/Shell Superparamagnetic Nanoparticle Vehicles with Enhanced Biocompatibility (2012)

We report the synthesis of Fe(3)O(4)/silica core/shell nanoparticles and their functionalization with S-nitrosothiols. These nanoparticles are of immense interest because of their nitric oxide (NO) release capabilities in human alveolar epithelial cells. Moreover, they act as large storage reservoirs of NO that can be targeted magnetically to the specific site with a sustainable release of NO for up to 50 h. Such nanoparticles provide an enhancement of the biocompatibility with released NO while allowing intracellular accumulation ascribed to their small size.
On the Incoherencies in Web Browser Access Control Policies (2010)

Web browsers' access control policies have evolved piecemeal in an ad-hoc fashion with the introduction of new browser features. This has resulted in numerous incoherencies. In this paper, we analyze three major access control flaws in today's browsers: (1) principal labeling is different for different resources, raising problems when resources interplay, (2) runtime changes to principal identities are handled inconsistently, and (3) browsers mismanage resources belonging to the user principal. We show that such mishandling of principals leads to many access control incoherencies, presenting hurdles for web developers to construct secure web applications. A unique contribution of this paper is to identify the compatibility cost of removing these unsafe browser features. To do this, we have built WebAnalyzer, a crawler-based framework for measuring real-world usage of browser features, and used it to study the top 100,000 popular web sites ranked by Alexa. Our methodology and results serve as a guideline for browser designers to balance security and backward compatibility.