gebhart/patrepeval huggingface dataset:
AppRAISE: application-level performance management in virtualized server environments (2009)

Managing application-level performance for multitier applications in virtualized server environments is challenging because the applications are distributed across multiple virtual machines, and workloads are dynamic in their intensity and transaction mix resulting in time-varying resource demands. In this paper, we present AppRAISE, a system that manages performance of multi-tier applications by dynamically resizing the virtual machines hosting the applications. We extend a traditional queuing model to represent application performance in virtualized server environments, where virtual machine capacity is dynamically tuned. Using this performance model, AppRAISE predicts the performance of the applications due to workload changes, and proactively resizes the virtual machines hosting the applications to meet performance thresholds. By integrating feedforward prediction and feedback reactive control, AppRAISE provides a robust and efficient performance management solution. We tested AppRAISE using Xen virtual machines and the RUBiS benchmark application. Our empirical results show that AppRAISE can effectively allocate CPU resources to application components of multiple applications to meet end-to-end mean response time targets in the presence of variable workloads, while maintaining reasonable trade-offs between application performance, resource efficiency, and transient behavior.
1,25-Dihydroxyvitamin D3 decreases expression of HLA class II molecules in a melanoma cell line. (1988)

An HLA class II-positive melanoma cell line, DU-Mel 17, was treated with three compounds known to induce differentiation in various cell lines. Neither retinoic acid nor dibutyryl cAMP altered levels of DR alpha mRNA, but 1,25-dihydroxyvitamin D3 (1,25(OH)2D3) significantly decreased the level of DR alpha mRNA 48 h after treatment. Optimal effect of the hormone on DR alpha mRNA was reached by 72 h. DU-Mel 17 cells were responsive to 1,25(OH)2D3 in a dose-dependent manner, and a reduction in DR alpha mRNA was seen at concentrations as low as 5 x 10(-13) M. The action of 1,25(OH)2D3 on DR alpha mRNA levels was dependent on protein synthesis as evidenced by inhibition of its effect upon addition of cycloheximide. Both DR and DQ protein levels on the surface of DU-Mel 17 were beginning to decline by 72 h after 1,25(OH)2D3 treatment, and by 96 h these proteins were decreased by 65%. 1,25(OH)2D3 was not capable of altering expression of class II molecules on three different class II-positive B lymphoblastoid cell lines, although one of these lines was shown to express the receptor for 1,25(OH)2D3. These findings are important because 1) there is no known physiologic regulator that actively down-regulates class II molecules that are present in and/or on cells, 2) levels of mRNA derived from a very limited number of genes are known to be altered by 1,25(OH)2D3, and 3) they support the contention that 1,25(OH)2D3 may alter the differentiation state of these cells and the activity of the normal counterpart of these cells in an immune response.
The role of nitric oxide in sepsis – an overview (1999)

Nitric oxide (NO) is normally produced in the endothelium by the constitutive isoform of the NO synthase. This physiological production of NO is important for blood pressure regulation and blood flow distribution. Several lines of evidence suggest that a hyperproduction of NO by the inducible form of NO synthase (iNOS) may contribute to the hypotension, cardiodepression and vascular hyporeactivity in septic shock. Lipopolysaccarides and cytokines, such as tumor necrosis factor, interleukin-1 and interferon-gamma, have been shown to induce iNOS in the endothelium, vascular smooth muscle cells, macrophages and different parenchymal cells. Treatment with inhibitors of NO synthesis has been shown to improve hemodynamic variables and survival in several animal models of septic shock. In human septic shock, inhibition of NO synthesis has been shown to alter hemodynamic variables in short-term studies, but it is uncertain whether this treatment has beneficial long-term effects. The aim of this review is to give an overview of the physiological role of NO and to discuss the role of NO in sepsis and the potential therapeutic implications of NO as a target in treatment of human septic shock. A main new aspect of this review is a critical discussion of previous reports measuring plasma nitrite/nitrate during septic shock and an evaluation of the validity of interpreting these data as evidence for a hyperproduction of NO. This review also emphasizes that many septic patients have preexisting endothelial dysfunction and lung diseases, which may contribute to adverse effects by systemic inhibition of NO synthesis. Another new aspect of the present review is a focus on the lack of direct evidence of iNOS expression in human septic shock.
Isolation of monoclonal antibodies specific for IL-4, IL-5, IL-6, and a new Th2-specific cytokine (IL-10), cytokine synthesis inhibitory factor, by using a solid phase radioimmunoadsorbent assay. (1990)

Hybridomas were produced from a rat that was immunized with partially purified proteins from supernatants of induced Th2 cells. These preparations were enriched for cytokine synthesis inhibitory factor (CSIF, IL-10). The mAb in the supernatants were screened by a solid phase radioimmunoadsorbent assay using 35S-methionine-labeled secreted proteins from a lectin-stimulated Th2 clone. A total of 18 anticytokine mAb were isolated, comprising 6 anti-CSIF, 1 anti-IL-4, 1 anti-IL-5, and 10 anti-IL-6 mAb. The anti-CSIF mAb were separable into three groups. mAb in groups A and B neutralized and depleted bioactivity, and bound to overlapping but nonidentical subpopulations of CSIF molecules. The 2 mAb in group C did not neutralize CSIF activity, and bound to CSIF molecules not recognized by mAb from groups A or B. A two-site sandwich ELISA for CSIF could be established with the group A antibody, SXC1, combined with any of the three group B antibodies. The sensitivity of this assay was equivalent to that of the CSIF bioassay. These antibodies have been used to show that CSIF is responsible for most or all of the ability of Th2 supernatants to inhibit cytokine synthesis by Th1 cells. In addition, the ELISA has been used to confirm that CSIF is produced by Th2 but not Th1 clones.
The Mechanism of Axl‐Mediated Ebola Virus Infection (2007)

We previously reported that expression of the receptor-type tyrosine kinase Axl, which regulates cell survival and activation, enhances both pseudotype and live Ebola virus (EBOV) infection. To clarify the mechanistic basis of this enhancement, we created a series of Axl mutants and identified amino acids/domains necessary for this function, by using a pseudotype virus carrying the EBOV glycoprotein (GP). Analyses of the Axl mutants showed the importance of extracellular and intracellular regions for Axl functions, including ligand binding and signal transduction, in EBOV GP-mediated infection. These data suggest that EBOV uses the physiological functions of Axl to enter cells.
Elevated level of some chemokines in plasma of gastric cancer patients (2017)

The accuracy of preoperative diagnosis in gastric cancer may include the monitoring of a wide range of chemokines in patients' plasma. Increased levels of chemokines may warn that the disease is more advanced than conventional diagnostic procedures suggest.
Singlet oxygen production by human eosinophils. (1988)

Human eosinophils, stimulated with phorbol myristate acetate, were found to produce 1268 nm chemiluminescence characteristic of singlet oxygen. Singlet oxygen generation required the presence of bromide ion. A bromide ion concentration of 100 microM, comparable to the total bromine content of whole blood, was sufficient for the eosinophils to generate measurable amounts of singlet oxygen. For the conditions used (10(7) cells/ml and 10 micrograms/ml phorbol myristate acetate), the duration of the singlet oxygen generation was brief, about 5 min, and the total yield of singlet oxygen was modest, 1.0 +/- 0.1 microM. The cells remained viable after the singlet oxygen production ceased. This is the first demonstration of singlet oxygen production from living cells. The singlet oxygen generated by eosinophils likely results from a peroxidase-catalyzed mechanism, since a purified eosinophil peroxidase-hydrogen peroxide-bromide system was also shown to produce singlet oxygen. The unique properties of eosinophil peroxidase are illustrated by the fact that at p2H 7.0 and with 100 microM bromide, eosinophil peroxidase generated 20 +/- 2% of the theoretical yield of singlet oxygen, whereas under identical conditions, myeloperoxidase and lactoperoxidase produced only 1.0 +/- 0.1% and -0.1 +/- 0.1%, respectively.
MicroRNA: A New Player in Breast Cancer Development (2007)

Breast cancer is the leading cause of death in women in North America. The etiology of breast cancer is complex, and genetic background and environmental factors are believed to contribute to the complexities. Over the past decades, a large body of literature has demonstrated that gene expression profile may be a useful tool to define the signature of cancer and predict the prognosis or response to treatment. Recently, microRNA (miRNA) expression profile calls a great attention to define various types of cancers. miRNAs are small non-coding RNAs that bind to the 3' untranslated region of target mRNAs and down-regulate their translation to protein or degrade the mRNAs. miRNAs play critical roles in many different cellular processes including metabolism, apoptosis, differentiation, and development. They are also linked to human diseases, including cancer. In this paper, we discuss the recent miRNA studies in breast cancer and provide a summary of the literatures focusing on miRNA signalling pathways and their potential involvement in breast cancer development.
Underground metabolism (1998)

All enzymes are able to use alternative substrates. When these are naturally occurring metabolites, an 'underground reaction' takes place. Examples are presented in which underground metabolism of this sort produces an observable phenotype. Although biological processes can be remarkably accurate, evolution has selected error rates far from perfect. It is suggested here that a certain level of metabolic inaccuracy, in addition to saving energy, may also confer an evolutionary advantage, for example by providing metabolic plasticity. Since underground reactions are unpredictable from DNA sequence data, caution is in order when interpreting correlations between genetic disorders and pathological syndromes.
All Three LDL Receptor Homology Regions of the LDL Receptor-Related Protein Bind Multiple Ligands (2003)

The three complete human LDL receptor homology regions of the LDL receptor-related protein (sLRP2, sLRP3, and sLRP4) have been expressed in Pichia pastoris SMD1168 with constitutive coexpression of the receptor-associated protein (RAP). Each sLRP was purified to homogeneity after deglycosylation using a combination of anion-exchange and size exclusion chromatography. Mass spectrometry and N-terminal sequencing confirmed the identity of each fragment at purified yields of several milligrams per liter. Despite the large number of disulfide linkages and glycosylation sites in each LDL receptor homology region (sLRP), all were shown to be competent for binding to several LRP1 ligands. Each sLRP also bound human RAP, which is thought to be a generalized receptor antagonist, in solution-binding experiments. As expected, sLRP2 bound the receptor-binding domain of alpha(2)-macroglobulin (residues 1304-1451). All three sLRPs bound human apolipoprotein-enriched beta very low density lipoprotein, the canonical ligand for this receptor. All three sLRPs also bound lactoferrin and thrombin-protease nexin 1 complexes. Only sLRP4 bound thrombin-antithrombin III complexes. The results show that binding-competent LDL receptor homology regions (sLRPs) can be produced in high yield in P. pastoris and readily purified. Each sLRP has binding sites for multiple ligands, but not all ligand binding could be competed by RAP.
Histone 3 Lysine 9 (H3K9) Methyltransferase Recruitment to the Interleukin-2 (IL-2) Promoter Is a Mechanism of Suppression of IL-2 Transcription by the Transforming Growth Factor-β-Smad Pathway (2011)

Suppression of IL-2 βproduction from T cells is an important process for the immune regulation by TGF-β. However, the mechanism by which this suppression occurs remains to be established. Here, we demonstrate that Smad2 and Smad3, two major TGF-β-downstream transcription factors, are redundantly essential for TGF-β-mediated suppression of IL-2 production in CD4(+) T cells using Smad2- and Smad3-deficient T cells. Both Smad2 and Smad3 were recruited into the proximal region of the IL-2 promoter in response to TGF-β. We then investigated the histone methylation status of the IL-2 promoter. Although both histone H3 lysine 9 (H3K9) and H3K27 trimethylation have been implicated in gene silencing, only H3K9 trimethylation was increased in the proximal region of the IL-2 promoter in a Smad2/3-dependent manner, whereas H3K27 trimethylation was not. The H3K9 methyltransferases Setdb1 and Suv39h1 bound to Smad3 and suppressed IL-2 promoter activity in collaboration with Smad3. Overexpression of Suv39h1 in 68-41 T cells strongly inhibited IL-2 production in response to T cell receptor stimulation irrespective of the presence or absence of TGF-β, whereas Setdb1 overexpression only slightly suppressed IL-2 production. Silencing of Suv39h1 by shRNA reverted the suppressive effect of TGF-β on IL-2 production. Furthermore, TGF-β induced Suv39h1 recruitment to the proximal region of the IL-2 promoter in wild type primary T cells; however, this was not observed in Smad2(-/-)Smad3(+/-) T cells. Thus, we propose that Smads recruit H3K9 methyltransferases Suv39h1 to the IL-2 promoter, thereby inducing suppressive histone methylation and inhibiting T cell receptor-mediated IL-2 transcription.
Transformation of Pd Nanocubes into Octahedra with Controlled Sizes by Maneuvering the Rates of Etching and Regrowth (2013)

Palladium octahedra with controlled edge lengths were obtained from Pd cubes of a single size. The success of this synthesis relies on a transformation involving oxidative etching and regrowth. Because the {100} side faces of the Pd nanocubes were capped by Br(-) ions, Pd atoms were removed from the corners during oxidative etching, and the resultant Pd(2+) ions could be reduced and deposited back onto the nanocubes, but preferentially on the {100} facets. We could control the ratio of the etching and regrowth rates (R(etching) and R(regrowth)) simply by varying the amount of HCl added to the reaction solution. With a large amount of HCl, etching dominated the process (R(etching) ≫ R(regrowth)), resulting in the formation of Pd octahedra with an edge length equal to 70% of that of the cubes. In contrast, with a small amount of HCl, all of the newly formed Pd(2+) ions could be quickly reduced and deposited back onto the Pd cubes. In this case, R(etching) ≈ R(regrowth), and the resultant Pd octahedra had roughly the same volume as the starting cubes, together with an edge length equal to 130% of that of the cubes. When the amount of HCl was between these two extremes, we obtained Pd octahedra with intermediate edge lengths. This work not only advances our understanding of oxidative etching in nanocrystal synthesis but also offers a powerful means for controlling the shape and size of metal nanocrystals simply by adjusting the rates of etching and regrowth.
Melanin and blood concentration in human skin studied by multiple regression analysis: experiments (2001)

Knowledge of the mechanism of human skin colour and measurement of melanin and blood concentration in human skin are needed in the medical and cosmetic fields. The absorbance spectrum from reflectance at the visible wavelength of human skin increases under several conditions such as a sunburn or scalding. The change of the absorbance spectrum from reflectance including the scattering effect does not correspond to the molar absorption spectrum of melanin and blood. The modified Beer-Lambert law is applied to the change in the absorbance spectrum from reflectance of human skin as the change in melanin and blood is assumed to be small. The concentration of melanin and blood was estimated from the absorbance spectrum reflectance of human skin using multiple regression analysis. Estimated concentrations were compared with the measured one in a phantom experiment and this method was applied to in vivo skin.
Wrapping Thick Membranes with Slipping Folds (2015)

A novel method of packaging finite-thickness membranes tightly and with high packaging efficiency is presented. This method allows the membrane to be packaged without extension and without plastic creasing. As such, initially flat membranes can be deployed to a flat state. Membrane thickness is accommodated by removing material along fold lines and exploiting the slipping deformation mechanism thus created. Also presented are methods for prestressing and deploying membranes packaged according to this technique. Initial tests demonstrate packaging efficiencies of 73% without plastic deformation. Experimental deployment tests of a meter-scale model showed controlled deployment with unfolding forces of less than 0.6 N.
Microbiological effect of photodynamic therapy (PDT) in healthy volunteers: a comparative study using methyl aminolaevulinate and hexyl aminolaevulinate cream (2007)

HAL-PDT and MAL-PDT transiently reduce density of Propionibacterium spp. density to a similar degree in normal healthy individuals. The transient reduction in Propionibacterium spp. suggests that the prolonged antiacne effect of PDT relies on factors independent of bacterial density. HAL-PDT appears to be better tolerated than MAL-PDT.
NMR Study of Redistribution Reactions in Blackglas™ and their Influence on Oxidative Stability (2008)

Previous work has shown that silicon oxycarbides, including Blackglas™, undergo bond redistribution with very minimal (< 1 percent) weight loss at temperatures above 800 °C. In this paper, the influence of pyrolysis temperature and time on these redistribution reactions, and the resultant effect on oxidative stability of Blackglas™ powders was studied. Tetrahedral bonding of C and O to Si was followed using 29Si nuclear magnetic resonance spectroscopy for both as pyrolyzed samples and samples oxidized at 600 °C. A statistical experimental design approach was employed to minimize experiments and allow for derivation of an empirical model to optimize pyrolysis parameters. Si-C bonding of the oxycarbide and oxidative stability were found to increase with increasing pyrolysis temperature over the temperature range of 900 to 1100 °C. Pyrolysis time over the range of 1 to 5 hours was not found to have a significant influence on the redistribution reactions. Based on the behavior of the matrix alone, pyrolysis at 1100 °C is recommended to optimize the 600 °C oxidative stability of Blackglas™ ceramics.
Intrathecal Octreotide for Relief of Intractable Nonmalignant Pain: 5-Year Experience with Two Cases (1996)

Somatostatin is distributed in the substantia gelatinosa in the dorsal horn of the spinal cord, and its application has been found to produce an inhibitory effect on nociceptive neurons. Although intraspinal administration of somatostatin-14 produces pain relief in patients with cancer and in postoperative patients, its short half-life limits its clinical usefulness. Octreotide, a synthetic analog of somatostatin, is more stable and not been associated with neurodegenerative changes when administered intrathecally in dogs. Intrathecal octreotide provides analgesia without adverse drug effects when administered chronically for cancer pain; however, treatment periods have been limited. This article describes the 5-year clinical course of two patients receiving intrathecal octreotide for severe, intractable nonmalignant pain. Included in this description are the results of blinded, randomized "N of 1" trials conducted in each of these patients.
Clinical utility of hyaluronic acid values in serum and bronchoalveolar lavage fluid as tumor marker for bronchogenic carcinoma (1995)

Various authors have proposed the use of hyaluronic acid (HA) as a tumor marker. In order to analyze its usefulness as a marker in bronchogenic carcinoma, the most common carcinoma in men, we determined the HA values in serum and bronchoalveolar lavage fluid (BAL). We performed prospective studies on two groups of patients: 81 diagnosed as having bronchial carcinoma and 34 with benign respiratory diseases. HA values were higher in patients with cancer than in those with benign diseases (serum: 79.8 ng/ml vs 63.7 ng/ml; BAL: 927 ng/mg vs 522 ng/mg). Also, the percentage of patients with levels exceeding the established cutoff was greater in the group with cancer than in the group with benign diseases (serum: 24.6 vs 17.6; BAL: 25.3 vs 3). Statistically significant differences in these percentages were found in BAL (p&lt;0.01). Patients with extended small cell carcinoma had higher HA values (p=0.04) than those with limited disease, and the percentage of patients with abnormal HA values was larger in the group with extended disease than in the group with limited disease (p=0.004). The serial determinations of HA values in serum reflected the clinical evolution after treatment in 73% of the small cell carcinomas. Most of the patients with benign diseases whose HA values exceeded the cutoff level suffered from acute infectious dis-eases. Once these cases were excluded, the specificity of HA value determination in the diagnosis of carcinoma was very high (serum 96%, BAL 100%). The determination of HA levels in serum or BAL did not have any prognostic value in this study. We conclude that the HA levels in serum and BAL could be of interest as a tumor marker, especially in patients with small cell carcinoma.
Levels of nerve growth factor in cerebrospinal fluid of chronic daily headache patients (2001)

Nerve growth factor (NGF) levels were determined in the CSF of patients with chronic daily headache (CDH) and correlated with levels of sensory neuropeptides. Patients with CDH showed higher NGF levels in the CSF compared with control subjects (p < 0.0001). Higher CSF levels of substance P (SP) (p < 0.002) and calcitonin-gene-related peptide (CGRP) (p < 0.0001) were also found. There was a significant positive correlation between NGF and both SP and CGRP values. These findings suggest that NGF is involved in the long-lasting sensitization and sustained activation of the trigeminal system in CDH.
The Role of Matrix Metalloproteinases in Wound Healing (2002)

The structure, classification, function, and regulation of matrix metalloproteinases in normal and abnormal wound healing is discussed. Results from key studies suggest that neutrophil-derived matrix metalloproteinase 8 (MMP-8) is the predominant collagenase present in normal healing wounds, and that overexpression and activation of this collagenase may be involved in the pathogenesis of nonhealing chronic leg ulcers. Excessive collagenolytic activity in these chronic wounds is possible because of the reduced levels of tissue inhibitor metalloproteinase 1 (TIMP-1). However, until recently, there have been no studies evaluating levels of matrix metalloproteinase or tissue inhibitors of metalloproteinase activity in chronic diabetic foot wounds. Improving basic knowledge and pharmaceutical intervention in this area ultimately may help clinicians identify and proactively intervene in an effort to prevent normal wounds from becoming chronic. This may prevent the high prevalence of morbidity associated with this significant health problem.