gebhart/patrepeval huggingface dataset:
Accelerating Checkpoint Operation by Node-Level Write Aggregation on Multicore Systems (2009)

Clusters and applications continue to grow in size while their mean time between failure (MTBF) is getting smaller. Checkpoint/restart is becoming increasingly important for large scale parallel jobs. However, the performance of the checkpoint/restart mechanism does not scale well with increasing job size due to constraints within the file system. Furthermore, with the advent of multi-core architecture, the situation is aggravated due to larger number of processes running on the same node, trying to checkpoint simultaneously. This results in increased number of file writes at the time of checkpointing which leads to performance degradation. As a result, deployment of checkpoint/restart mechanisms for large scale parallel applications is limited. In this work, we explore the checkpoint/restart mechanism in MVAPICH2, which uses BLCR as the checkpointing library. Our profiling of the checkpoints for the NAS parallel benchmarks revealed a large number of small file writes interspersed with large writes. Based on these observation we propose to optimize checkpoint creation by classifying checkpoint file writes into small writes, medium writes and large writes based on their size of data to write, and use write aggregation to optimize the small and medium writes. At the aggregation threshold of 512 KB, the implementation of our design in BLCR shows improvements from 27% to 32% over the original BLCR in terms of time cost to checkpoint an MPI application.
Evidence for MAP kinase activation during mitotic division (1998)

MAP kinases have been implicated in the control of a broad spectrum of cellular events in many types of cells. In somatic cells, MAP kinase activation seems to be triggered after exit from a quiescent state (in G0 or G2) only and then inactivated by entry into a proliferative state. In oocytes of various species, a one-time activation of MAP kinase that is apparently not repeated during the succeeding mitotic cycles occurs after meiotic activation. However, several reports suggest that a myelin basic protein (MBP) kinase activity, unrelated to that of maturation promoting factor, can sometimes be detected during mitotic divisions in various types of cells and oocytes. We have reinvestigated this problem in order to determine the origin and the role of MBP kinase that is stimulated at time of mitosis in the fertilized eggs of the sea urchin Paracentrotus lividus. We used anti-ERK1 antibodies or substrates specific for different MAP kinases, and performed in-gel phosphorylation experiments. Our results suggest that an ERK1-like protein was responsible for part of the MBP kinase activity that is stimulated during the first mitotic divisions. Furthermore, we observed that wortmannin, an inhibitor of PI 3-kinase that arrests the fertilized sea urchin eggs at the prometaphase stage, inhibited the inactivation of MAP kinase normally observed when the eggs divide, suggesting a role for PI 3-kinase in the deactivation process of MAP kinase. We also discuss how the activities of MPF and MAP kinase may be interconnected to regulate the first mitotic divisions of the early sea urchin embryo.
Preservation of Mango Fruit (Mangifera indica, L.) Slices in Darfur (2012)

2 Abstract: Sun drying of 'Kitchiner', 'Alphonse' and 'Dibsha' mango (Mangifera indica, L.) cultivars grown in Darfur, Sudan was conducted to enhance durability, utilization of mango fruits and to reduce the cost of transportation and storage. Slices were soaked in cane-sugar, lime-juice and sodium chloride. Moisture content, pH, titratable acidity, total soluble solids and ascorbic acid were measured initially and every three months. After six months, sensory acceptance of dried slices was determined for the attributes of aroma, flavour, texture and overall acceptance using a hedonic scale. Sugar and lime-juice were found good soaking solutions. Treated slices retained 53-78% of their original ascorbic acid after six months of storage. Panel test showed that dried slices of 'Kitchiner' were the most acceptable. Cane treated samples gave higher scores than lime or salt treated samples based on colour, flavour, taste and texture and is suggested as preservative material for mango slices.
Antibodies to discontinuous or conformationally sensitive epitopes on the gp120 glycoprotein of human immunodeficiency virus type 1 are highly prevalent in sera of infected humans (1993)

We have used an indirect-capture enzyme-linked immunosorbent assay to quantitate the reactivity of sera from human immunodeficiency virus type 1 (HIV-1)-infected humans with native recombinant gp120 (HIV-1 IIIB or SF-2) or with the gp120 molecule (IIIB or SF-2) denatured by being boiled in the presence of dithiothreitol with or without sodium dodecyl sulfate. Denaturation of IIIB gp120 reduced the titers of sera from randomly selected donors by at least 100-fold, suggesting that the majority of cross-reactive anti-gp120 antibodies present are directed against discontinuous or otherwise conformationally sensitive epitopes. When SF-2 gp120 was used, four of eight serum samples reacted significantly with the denatured protein, albeit with ca. 3- to 50-fold reductions in titer. Only those sera reacting with denatured SF-2 gp120 bound significantly to solid-phase-adsorbed SF-2 V3 loop peptide, and none bound to IIIB V3 loop peptide. Almost all antibody binding to reduced SF-2 gp120 was blocked by preincubation with the SF-2 V3 loop peptide, as was about 50% of the binding to native SF-2 gp120. When sera from a laboratory worker or a chimpanzee infected with IIIB were tested, the pattern of reactivity was reversed, i.e., there was significant binding to reduced IIIB gp120, but not to reduced SF-2 gp120. Binding of these sera to reduced IIIB gp120 was 1 to 10% that to native IIIB gp120 and was substantially decreased by preincubation with IIIB (but not SF-2) V3 loop peptide. To analyze which discontinuous or conformational epitopes were predominant in HIV-1-positive sera, we prebound monoclonal antibodies (MAbs) to IIIB gp120 and then added alkaline phosphatase-labelled HIV-1-positive sera. MAbs (such as 15e) that recognize discontinuous epitopes and compete directly with CD4 reduced HIV-1-positive sera binding by about 50%, whereas neutralizing MAbs to the C4, V2, and V3 domains of gp120 were either not inhibitory or only weakly so. Thus, antibodies to the discontinuous CD4-binding site on gp120 are prevalent in HIV-1-positive sera, antibodies to linear epitopes are less common, most of the antibodies to linear epitopes are directed against the V3 region, and most cross-reactive antibodies are directed against discontinuous epitopes, including regions involved in CD4 binding.
Expression of epidermal growth factor receptor in human gastric and colonic carcinomas. (1988)

The expression of epidermal growth factor (EGF) receptor was examined immunohistochemically in a total of 122 gastric and 61 colonic carcinomas, out of which 16 gastric and 8 colonic carcinomas were also examined by 125I-labeled EGF binding analysis and Western blotting. The values of EGF binding were 12.68 +/- 1.98 (SE; n = 16) fmol/mg protein in gastric carcinomas and 5.72 +/- 2.15 (n = 8) fmol/mg protein in nonneoplastic gastric mucosa, the difference being significant (P less than 0.01). In the colonic tissue, the binding capacities in carcinomas and nonneoplastic mucosa were 13.29 +/- 4.17 (n = 8) and 10.68 +/- 0.41 (n = 3) fmol/mg protein, respectively. Scatchard analysis of 125I-labeled EGF binding indicated a single class of receptors in gastric and colonic carcinomas with an apparent Kd value of from 111 to 277 (n = 4) and from 87.4 to 341 fM (n = 5), respectively, except for one gastric carcinoma having two classes of receptors (Kd = 15.9 and 896 fM). In Western blotting using monoclonal anti-EGF receptor antibody, various levels of EGF receptor expression were detected in 12 (85.7%) of the 14 gastric carcinomas and in 7 (87.5%) of the 8 colonic carcinomas. Immunohistochemically, EGF receptor immunoreactivity was detected in one (3.8%) of the 26 early gastric carcinomas, while it was observed in 33 (34.4%) of the 96 advanced gastric carcinomas, the incidence between the two being significantly different (P less than 0.01). In the colonic carcinomas, 47 (77.1%) of the 61 cases showed positive immunoreactivity to EGF receptor, which did not differ by histological type.
The acrAB homolog of Haemophilus influenzae codes for a functional multidrug efflux pump (1997)

Disruption of gene HI0894 or HI0895 in Haemophilus influenzae Rd, homologs of Escherichia coli acrAB multidrug efflux genes, caused hypersusceptibility to erythromycin, rifampin, novobiocin, and dyes such as ethidium bromide and crystal violet and increased accumulation of radioactive erythromycin, showing that these genes are expressed and contribute to the baseline level resistance of this organism through active drug efflux. The gene disruption did not produce detectable changes in susceptibility to several other antibiotics, possibly because rapid influx of small antibiotic molecules through the large H. influenzae porin channels counterbalances their efflux.
Langerhans Cell Maturation and Contact Hypersensitivity Are Impaired in Aryl Hydrocarbon Receptor-Null Mice (2009)

Langerhans cells (LC) are professional APCs of the epidermis. Recently, it was suggested that they are tolerogenic and control adverse immune reactions, including against low molecular mass chemicals. The aryl hydrocarbon receptor (AhR), a ligand-activated transcription factor, is involved in low molecular mass chemical metabolism and cell differentiation. Growing evidence suggests a role for the AhR in the immune system, for example, by influencing dendritic cell and T cell differentiation. We found that the AhR and its repressor AhRR are expressed in LC of C57BL/6 mice. LC, unexpectedly, did not respond to a strong AhR agonist with induction of transcripts of xenobiotic metabolizing enzymes. To test for a physiological role of the AhR in LC, we investigated how AhR deficiency affects LC. We found that AhR-deficient LC were impaired in maturation; they remained smaller and less granular, did not up-regulate expression of costimulatory molecules CD40, CD80, and CD24a during in vitro maturation, and their phagocytic capacity was higher. Interestingly, the mRNA expression of tolerogenic Ido was severely decreased in AhR-deficient LC, and enzyme activity could not be induced in AhR-deficient bone marrow-derived dendritic cells. GM-CSF, needed for LC maturation, was secreted in significantly lower amounts by AhR-deficient epidermal cells. Congruent with this impaired maturity and capacity to mature, mice mounted significantly weaker contact hypersensitivity against FITC. Our data suggest that the AhR is involved in LC maturation, both cell autonomously and through bystander cells. At the same time, the AhR might be part of the risk strategy of LC against unwanted immune activation by potential skin allergens.
Investigation of the role of proline dehydrogenase in Arabidopsis thaliana (1999)

info:eu-repo/semantics/published
Synchronization methods for TDMA (1977)

A survey is given covering synchronization techniques for large-capacity time-division multiple-access (TDMA) systems using geosynchronous satellites. Five important classes are identified and compared. Also, several methods of initial acquisition are described. The fundamentals of multiple access and TDMA in particular are presented. Summary descriptions and comparisions of the TDMA systems developed to date are given for experimental, prototype, and operational systems. Some important related technologies are introduced. It is concluded that TDMA is in a maturing period.
Molecular inhibition of angiogenesis and metastatic potential in human squamous cell carcinomas after epidermal growth factor receptor blockade. (2002)

Tumor metastasis represents a complex multistep process that requires migration, invasion, and angiogenesis. In this study, we examined the impact of molecular blockade of the epidermal growth factor receptor on the invasive and metastatic capacity of human squamous cell carcinoma (SCC) of the head and neck using in vitro and in vivo model systems. Treatment with the anti-epidermal growth factor receptor antibody C225 attenuated the migration of SCC-1 tumor cells through a chemotaxis chamber in a dose-dependent manner. Incubation of SCC cells with 10-100 nM C225 for 4 h resulted in 40-60% inhibition of cell migration. Furthermore, in the presence of C225, the capacity of SCC-1 to invade across a layer of extracellular matrix (Matrigel) was significantly inhibited. Using an in vivo orthotopic floor-of-mouth xenograft model, locoregional tumor invasion of SCC-1 into muscle, vessel, bone, and perineural tissues was inhibited in C225-treated mice. This inhibition was additionally characterized by down-regulation in the expression of matrix metalloproteinase-9. These data suggest that inhibition of metastatic potential by C225 may be mediated via decreased migration and invasion of SCC cells. Regarding angiogenesis in vitro, we first studied human umbilical vascular endothelial cells, which established a capillary-like network structure (tube formation) in the presence of reconstituted Matrigel. Treatment with C225 reduced cell-to-cell interaction of human umbilical vascular endothelial cells, resulting in disruption of tube formation. The effect of C225 was additionally examined using an in vivo tumor xenograft neovascularization model of angiogenesis. Systemic treatment with C225 not only reduced tumor growth and the number of blood capillaries but also hindered the growth of established vessels toward the tumor. Taken together, these results provide evidence that C225 can suppress tumor-induced neovascularization and metastasis in SCC of the head and neck.
CD105 is important for angiogenesis: evidence and potential applications (2003)

Angiogenesis is the propelling force for tumor growth and metastasis, and antiangiogenic therapy represents one of the most promising modalities for cancer treatment. CD105 (endoglin) is a proliferation-associated and hypoxia-inducible protein abundantly expressed in angiogenic endothelial cells (EC). It is a receptor for transforming growth factor (TGF) -beta1 and -beta3 and modulates TGF-beta signaling by interacting with TGF-beta receptors I and/or II. Immunohistochemistry studies have revealed that CD105 is strongly expressed in blood vessels of tumor tissues. Intratumoral microvessel density (MVD) determined using antibodies to CD105 has been found to be an independent prognostic indicator, wherein increased MVD correlates with shorter survival. CD105 is able to be shed into the circulation, with elevated levels detected in patients with various types of cancer and positively correlated with tumor metastasis. Tangible evidence of its proangiogenic role comes from knockout studies in which CD105 null mice die in utero as a result of impaired angiogenesis in the yolk sac and heart defects. The potential usefulness of CD105 for tumor imaging has been evaluated in tumor-bearing mice and dogs that have shown the rapid accumulation of radiolabeled anti-CD105 monoclonal antibody in the tumors with a high tumor-to-background ratio. The anti-CD105 antibody conjugated with immunotoxins and immunoradioisotopes efficiently suppressed/abrogated tumor growth in murine models bearing breast and colon carcinoma without any significant systemic side effects. Immunoscintigraphy in patients with renal cell carcinomas has shown specific localization of 99Tcm-labeled CD105 mab in tumor endothelial cells. Thus, CD105 is a promising vascular target that can be used for tumor imaging, prognosis, and bears therapeutic potential in patients with solid tumors and other angiogenic diseases.
Pertussis Toxin and Extracytoplasmic Adenylate Cyclase as Virulence Factors of Bordetella pertussis (1984)

A wild-type strain of Bordetella pertussis and a series of transposon Tn5-induced mutants deficient in the production of various factors believed to play a role in pertussis (whooping cough) were tested for virulence in infant mice. The 50% lethal dose of the wild-type strain in these animals was 2 X 10(3) bacteria. A mutant deficient in the production of the filamentous hemagglutinin was almost as virulent as the wild type. Avirulent phase mutants (i.e., deficient in the production of all toxins), a pertussis-toxin mutant, and a double mutant deficient in both hemolysin and adenylate cyclase were severely impaired in the ability to cause pertussis. These data underscore the role of pertussis toxin in the disease and provide the first direct evidence that adenylate cyclase and hemolysin are important in the pathogenesis of the infection.
HO-1 expression in type II pneumocytes after transpulmonary gene delivery (2000)

Somatic cell gene transfer is a potentially useful strategy to alter lung function. However, achieving efficient transfer to the alveolar epithelium, especially in smaller animals, has not been demonstrated. In this study, the rat heme oxygenase-1 (HO-1) gene was delivered to the lungs of neonatal mice via transpulmonary injection. A bidirectional promoter construct coexpressing both HO-1 and a luciferase reporter gene was used so that in vivo gene expression patterns could be monitored in real time. HO-1 expression levels were also modulated with doxycycline and assessed in vivo with bioluminescent light transmitted through the tissues from the coregulated luciferase reporter. As a model of oxidative stress and HO-1-mediated protection, groups of animals were exposed to hyperoxia. After gene transfer, elevated levels of HO-1 were detected predominantly in alveolar type II cells by immunocytochemistry. With overexpression of HO-1, increased oxidative injury was observed. Furthermore, this model demonstrated a cell-specific effect of lung HO-1 overexpression in oxidative stress. Specific control of expression for therapeutic genes is possible in vivo. The transpulmonary approach may prove useful in targeting gene expression to cells of the alveolar epithelium or to circumscribed areas of the lung.
Patterned magnetic nanostructures and quantized magnetic disks (1997)

Nanofabrication, offering unprecedented capabilities in the manipulation of material structures and properties, opens up new opportunities for engineering innovative magnetic materials and devices, developing ultra-high-density magnetic storage, and understanding micromagnetics. This paper reviews the recent advances in patterned magnetic nanostructures, a fast-emerging field, including (1) state-of-the-art technology for patterning of magnetic nanostructures as small as 10 nm; (2) engineering of unique magnetic properties (such as domain structures, domain switching, and magnetoresistance) by patterning and controlling the size, shape, spacing, orientation, and compositions of magnetic materials; (3) quantized magnetic disks-a new paradigm for ultra-high-density magnetic storage based on patterned single-domain elements that have demonstrated a storage density of 65 Gb/in/sup 2/ (nearly two orders of magnitude higher than that in current commercial magnetic disks) and a capability of 400 Gb/in/sup 2/; (4) novel magnetoresistance sensors based on unique properties of magnetic nanostructures; (5) other applications of nanoscale patterning in magnetics such as the quantification of magnetic force microscopy (MFM) and a new ultra-high-resolution MFM tip; and (6) sub-10-nm imprint lithography-a new low-cost, high-throughput technology for manufacturing magnetic nanostructures.
Reduced elimination of IgG antibodies by engineering the variable region (2010)

Fc engineering to increase the binding affinity of IgG antibodies to FcRn has been reported to reduce the elimination of IgG antibodies. Herein, we present a novel non-FcRn-dependent approach to reduce the elimination of IgG antibodies. Pharmacokinetic studies conducted in normal mice of various humanized IgG4 antibodies, which had identical constant regions but different variable region sequences, revealed that an antibody with a lower isoelectric point (pI) has a longer half-life. These antibodies exhibited comparable binding affinity to FcRn, and with the antibodies with lower pIs, a longer half-life was also observed in beta2-microglobulin knockout mice, suggesting that differences in the pharmacokinetics were due to a non-FcRn-dependent mechanism. On the basis of our findings, we attempted to engineer the pharmacokinetic properties of a humanized anti-IL6 receptor IgG1 antibody. Selected substitutions in the variable region, without substitution in the Fc region, lowered the pI but did not reduce the biological activity and showed a significant reduction in the clearance of the antibody in cynomolgus monkey. These results suggest that lowering the pI by engineering the variable region could reduce the elimination of IgG antibodies and could provide an alternative to Fc engineering of IgG antibodies.
Use of Biodiesel-Derived Crude Glycerol for Producing Eicosapentaenoic Acid (EPA) by the Fungus Pythium irregulare (2009)

Crude glycerol is a major byproduct for the biodiesel industry. Producing value-added products through microbial fermentation on crude glycerol provides opportunities to utilize a large quantity of this byproduct. The objective of this study is to explore the potential of using crude glycerol for producing eicosapentaenoic acid (EPA, 20:5 n-3) by the fungus Pythium irregulare . When P. irregulare was grown in medium containing 30 g/L crude glycerol and 10 g/L yeast extract, EPA yield and productivity reached 90 mg/L and 14.9 mg/L x day, respectively. Adding pure vegetable oils (flaxseed oil and soybean oil) to the culture greatly enhanced the biomass and the EPA production. This enhancement was due to the oil absorption by the fungal cells and elongation of shorter chain fatty acids (e.g., linoleic acid and alpha-linolenic acid) into longer chain fatty acid (e.g., EPA). The major impurities contained in crude glycerol, soap and methanol, were inhibitory to fungal growth. Soap can be precipitated from the liquid medium through pH adjustment, whereas methanol can be evaporated from the medium during autoclaving. The glycerol-derived fungal biomass contained about 15% lipid, 36% protein, and 40% carbohydrate, with 9% ash. In addition to EPA, the fungal biomass was also rich in the essential amino acids lysine, arginine, and leucine, relative to many common feedstuffs. Elemental analysis by inductively coupled plasma showed that aluminum, calcium, copper, iron, magnesium, manganese, phosphorus, potassium, silicon, sodium, sulfur, and zinc were present in the biomass, whereas no heavy metals (such as mercury and lead) were detected. The results show that it is feasible to use crude glycerol for producing fungal biomass that can serve as EPA-fortified food or feed.