gebhart/patrepeval huggingface dataset:
A small cache of large ranges: Hardware methods for efficiently searching, storing, and updating big dataflow tags (2008)

Dynamically tracking the flow of data within a microprocessor creates many new opportunities to detect and track malicious or erroneous behavior, but these schemes all rely on the ability to associate tags with all of virtual or physical memory. If one wishes to store large 32-bit tags, multiple tags per data element, or tags at the granularity of bytes rather than words, then directly storing one tag on chip to cover one byte or word (in a cache or otherwise) can be an expensive proposition. We show that dataflow tags in fact naturally exhibit a very high degree of spatial-value locality, an observation we can exploit by storing metadata on ranges of addresses (which cover a non-aligned contiguous span of memory) rather than on individual elements. In fact, a small 128 entry on-chip range cache (with area equivalent to 4KB of SRAM) hits more than 98% of the time on average. The key to this approach is our proposed method by which ranges of tags are kept in cache in an optimally RLE-compressed form, queried at high speed, swapped in and out with secondary memory storage, and (most important for dataflow tracking) rapidly stitched together into the largest possible ranges as new tags are written on every store, all the while correctly handling the cases of unaligned and overlapping ranges. We examine the effectiveness of this approach by simulating its use in definedness tracking (covering both the stack and the heap), in tracking network-derived dataflow through a multi-language web application, and through a synthesizable prototype implementation.
Inhibition of Low-Density Lipoprotein Oxidation by Astaxanthin (2000)

Marine animals produce astaxanthin which is a carotenoid and antioxidant. In this study we determined the in vitro and ex vivo effects of astaxanthin on LDL oxidation. The oxidation of LDL was measured in a 1 ml reaction system consisting of increasing concentrations of astaxanthin (12.5, 25.0, 50.0 microg/ml), 400 microM V-70 (2, 2'-azobis(4-methoxy-2, 4-dimethylvaleronitrile)), and LDL (70 microg/ml protein). Astaxanthin dose, dependently significantly prolonged the oxidation lag time (31.5, 45.4, 65.0 min) compared with the control (19.9 min). For the ex vivo study 24 volunteers (mean age 28.2 [SD 7.8] years) consumed astaxanthin at doses of 1.8, 3.6,14.4 and 21.6 mg per day for 14 days. No other changes were made in the diet. Fasting venous blood samples were taken at days 0, +14. LDL lag time was longer (5.0, 26.2, 42.3 and 30.7% respectively) compared with day 0 after consuming astaxanthin at doses of 1.8, 3.6,14.4 and 21.6 mg for 14 days compared with day 0, but there was no difference in oxidation of LDL between day 0 (lag time 59.9+/-7.2 min) and day 14 (57.2+/-6.0 min) in the control group. Our results provide evidence that consumption of marine animals producing astaxanthin inhibits LDL oxidation and possibly therefore contributes to the prevention of atherosclerosis.
Comparative effects of pravastatin and lovastatin on nighttime sleep and daytime performance (1992)

Pravastatin and lovastatin, two HMG-CoA reductase inhibitors with similar cholesterol-lowering effects, differ in their lipid solubility. The hydrophilic characteristics of pravastatin may explain why the drug has not been detected in cerebrospinal fluid. On the other hand, lovastatin, a lipophilic compound, has been detected in the cerebrospinal fluid. Previous reports have suggested that lovastatin administration may be associated with insomnia, which reflects an action in the central nervous system. The effects of the two drugs on nocturnal sleep and day-time performance in young, healthy men have been assessed in randomized, double-blind, placebo-controlled studies. Computer-based performance tests were administered on two consecutive days before drug administration and at the end of a 3-week active drug or placebo treatment period. Results from both sites were combined for analysis. Neither pravastatin nor lovastatin significantly affected nocturnal sleep or daytime sleepiness in this study population, but lovastatin significantly affected daytime performance. In subjects treated with lovastatin, the results showed that two measures of performance, divided attention (p less than 0.05) and vigilance (p less than 0.01), worsened significantly from baseline as did global performance (p less than 0.01). Performance was not affected in the pravastatin and placebo groups. These results provide preliminary evidence of an adverse effect of lovastatin on daytime performance.
Cloning of cDNAs from Arabidopsis thaliana that encode putative protein phosphatase 2C and a human DM-like protein by transformation of a fission yeast mutant (1994)

We characterized three Arabidopsis thaliana cDNA clones that could rescue the sterile phenotype of the Schizosaccharomyces pombe pde1 mutant, which is defective in cAMP phosphodiesterase. The first clone had a coding capacity of 399 amino acids that is 35% identical with rat protein phosphatase 2C (PP2C). The second had a coding capacity of 159 amino acids that is 41% identical with human Dr1. Dr1 has been shown to interact with TATA-binding protein (TBP) and block its ability to activate transcription. The third encoded Arabidopsis TBP itself. Saccharomyces cerevisiae TBP also could suppress the sterile phenotype if expressed in S.pombe pde1 cells, but overexpression of S.pombe TBP could do so very poorly. These observations suggest preliminarily that PP2C may counteract cAMP-dependent protein kinase in fission yeast cells, and that the heterologous TBPs and Dr1 may interfere with the general transcription factors of S.pombe so that the gene expression in the host cell becomes affirmative of sexual development. Furthermore, the identification of a Dr1-like protein in A.thaliana strongly argues for the ubiquity of this protein among eukaryotic genera and for a conserved mechanism to regulate transcription initiation that involves Dr1.
Exosomes secreted by mesenchymal stem cells promote endothelial cell angiogenesis by transferring miR-125a (2016)

Angiogenesis plays crucial roles in various physiological processes including wound healing and tissue repair. It requires a tight interaction between endothelial cells and their surrounding environment. Mesenchymal stem cells (MSCs), one of the non-endothelial cell types present in the perivascular environment, have been shown to secret exosomes to modulate intercellular communications between MSCs and their target cells. In this study, we initially isolated exosomes secreted by human adipose-derived MSCs (adMSC-Exo) and examined their roles in angiogenesis. We found that adMSC-Exo could be taken up by endothelial cells and significantly promote angiogenesis in vitro and in vivo Further study showed that miR-125a was enriched in adMSC-Exo, and repressed the expression of the angiogenic inhibitor delta-like 4 (DLL4) by targeting its 3' untranslated region. Additionally, adMSC-Exo and its exosomal transferred miR-125a could repress DLL4 expression and modulate endothelial cell angiogenesis through promoting formation of endothelial tip cells. In conclusion, our study indicates that adMSC-Exo can transfer miR-125a to endothelial cells and promote angiogenesis by repressing DLL4. adMSC-Exo, as a pro-angiogenic factor, might be a promising candidate for therapeutical tissue repair.
Analysis of Antibody Titers to Epstein-Barr Virus Nuclear Antigens in Sera of Patients with Sjogren's Syndrome and with Rheumatoid Arthritis (1991)

To examine if Epstein-Barr virus (EBV) infection is associated with the two autoimmune diseases, Sjögren's syndrome and rheumatoid arthritis, IgG antibody titers of sera from patients with the disorders were evaluated for five constituents of EBV nuclear antigens (EBNA-1, -2, -3, -4, and -6). To circumvent interference by autoantibodies in the sera, fusion proteins synthesized in Escherichia coli were used as specific antigens. By ELISA the average IgG antibody titers to domains of the five EBNAs, especially the amino-terminal domain of EBNA-2, in sera of patients with Sjögren's syndrome were slightly higher than those in normal sera. The tendency of sera from Sjögren's syndrome patients to have higher reactivities to the EBNA domains was also observed by immunoblotting. By comparison, few heightened serologic responses to EBNAs were observed in sera from patients with rheumatoid arthritis. Further analyses are required to determine if EBV is associated with Sjögren's syndrome in any way.
Selective blockade of CD28 and not CTLA-4 with a single-chain Fv–α1-antitrypsin fusion antibody (2003)

B7-1 and B7-2 are costimulatory molecules expressed on antigen-presenting cells. The CD28/B7 costimulation pathway is critical for T-cell activation, proliferation, and Th polarization. Blocking both cytotoxic T-lymphocyte-associated antigen 4 (CTLA-4) and CD28 interactions with a CTLA-4/Ig fusion protein inhibits various immune-mediated processes in vivo, such as allograft rejection and autoimmunity. However, selective blockade of CD28 may represent a better strategy for immunosuppression than B7 blockade, because CTLA-4/B7 interactions have been shown to participate in the extinction of the T-cell receptor-mediated activation signal and to be required for the induction of immunologic tolerance. In addition, selective CD28 inhibition specifically decreases the activation of alloreactive and autoreactive T cells, but not the activation of T cells stimulated by exogenous antigens presented in the context of self major histocompatibility complex (MHC) molecules. CD28 blockade cannot be obtained with anti-CD28 dimeric antibodies, which cluster their target and promote T-cell costimulation, whereas monovalent Fab fragments can block CD28 and reduce alloreactivity. In this study, we report the construction of a monovalent single-chain Fv antibody fragment from a high-affinity antihuman CD28 antibody (CD28.3) that blocked adhesion of T cells to cells expressing the CD28 receptor CD80. Genetic fusion with the long-lived serum protein alpha1-antitrypsin led to an extended half-life without altering its binding characteristics. The anti-CD28 fusion molecule showed biologic activity as an immuno-suppressant by inhibiting T-cell activation and proliferation in a mixed lymphocyte reaction.
Stochastic discourse modeling in spoken dialogue systems using semantic dependency graphs (2006)

This investigation proposes an approach to modeling the discourse of spoken dialogue using semantic dependency graphs. By characterizing the discourse as a sequence of speech acts, discourse modeling becomes the identification of the speech act sequence. A statistical approach is adopted to model the relations between words in the user's utterance using the semantic dependency graphs. Dependency relation between the headword and other words in a sentence is detected using the semantic dependency grammar. In order to evaluate the proposed method, a dialogue system for medical service is developed. Experimental results show that the rates for speech act detection and task-completion are 95.6% and 85.24%, respectively, and the average number of turns of each dialogue is 8.3. Compared with the Bayes' classifier and the Partial-Pattern Tree based approaches, we obtain 14.9% and 12.47% improvements in accuracy for speech act identification, respectively.
Expression of an X-linked gene from an inactive human X chromosome in mouse-human hybrid cells: further evidence for the noninactivation of the steroid sulfatase locus in man. (1980)

Somatic cell hybrid clones were derived from the fusion of hypoxanthine phosphoribosyltransferase (HPRT; EC 2.4.2.8)-deficient mouse cells and two different human fibroblast strains, each carrying an X chromosome-autosome translocation. One of these had an X/11 translocation [46,X,t(X;11)(p21;q13)] and the other had an X/19 translocation [46,X,t(X;19)(q22;q13)]. The structurally normal human X chromosome is the late-replicating (genetically inactive) chromosome in these two cell strains; the rearranged X chromosome is early replicating (genetically active). One primary hybrid clone carrying both the translocated X chromosome and the structurally normal X chromosome was isolated in hypoxanthine/aminopterin/thymidine medium from each of these two cell fusion experiments. These clones were then selected in medium containing 8-azaguanine to achieve the loss of the active human HPRT locus. Five subclones from the cell hybrid with the X/11 translocation failed to express two known human X-chromosome markers [glucose-6-phosphate dehydrogenase (G6PD; EC 1.1.1.49) and phosphoglycerate kinase (PGK; EC 2.7.2.3)] but did express human microsomal steroid sulfatase (STS; sterol-sulfate sulfohydrolase, EC 3.1.6.2). Three of these were cytogenetically analyzed and found to contain a structurally normal human X chromosome but not the X/11 translocation. Two subclones were isolated in 8-azaguanine from the hybrid with the X/19 translocation. Cytogenetic analysis of these two clones showed the presence of a structurally normal human X chromosome; the X/19 translocation was not present. They did not express human G6PD, PGK, or HPRT but did express human STS. These results indicate that human STS is expressed from a locus on the inactive human X chromosome and support our earlier finding that the STS locus escapes X-inactivation in man.
Identification of soluble and membrane-bound isoforms of the murine flt3 ligand generated by alternative splicing of mRNAs. (1995)

We have recently described a novel hematopoietic growth factor, referred to as the flt3 ligand, that stimulates the proliferation of sub-populations of hematopoietic cells that are enriched for stem and progenitor cells. This factor is a transmembrane protein that undergoes proteolytic cleavage to generate a soluble form of the protein. We have isolated additional flt3 ligand isoforms by PCR that contain an extra exon and encode what are predicted to be either a soluble form of the ligand or a longer version of the transmembrane protein. We have also isolated cDNAs from murine T cell libraries that encode an isoform of the flt3 ligand that has an unusual C-terminus. This isoform results from a failure to splice out an intron during mRNA processing. The protein encoded by this cDNA is expressed on the cell surface, where it is biologically active. However, this novel isoform does not appear to give rise to a soluble form of the protein. Regulation of mRNA splicing is likely to control the generation of cell bound or soluble forms of this hematopoietic growth factor. Genetic mapping studies localize the gene encoding the flt3 ligand to the proximal portion of mouse chromosome 7 and to human chromosome 19q13.3.
Effect of 2′-O-methyl/thiophosphonoacetate-modified antisense oligonucleotides on huntingtin expression in patient-derived cells (2014)

Optimizing oligonucleotides as therapeutics will require exploring how chemistry can be used to enhance their effects inside cells. To achieve this goal it will be necessary to fully explore chemical space around the native DNA/RNA framework to define the potential of diverse chemical modifications. In this report we examine the potential of thiophosphonoacetate (thioPACE)-modified 2'-O-methyl oligoribonucleotides as inhibitors of human huntingtin (HTT) expression. Inhibition occurred, but was less than with analogous locked nucleic acid (LNA)-substituted oligomers lacking the thioPACE modification. These data suggest that thioPACE oligonucleotides have the potential to control gene expression inside cells. However, advantages relative to other modifications were not demonstrated. Additional modifications are likely to be necessary to fully explore any potential advantages of thioPACE substitutions.
Toxic effect of ethanolic extract of Nerium oleander (Apocynaceae) leaves against different developmental stages of Muscina stabulans (Diptera-Muscidae). (1996)

Nerium oleander (Apocynaceae) is evergreen shrubs widely used for ornamental purpose in mediterranean region. The present investigation, revealed for the first time the insecticidal effect of ethanolic extract from leaves of this plant against 2nd instar larvae of the medically important false stable fly Muscina stabulans (Diptera: Muscidae). LC50 of the extract was 113.66 ppm. This dose delayed larval and pupal duration suppressed oviposition and decreased adult longevity of the survivors. Morphogenic abnormalities were recorded and photographed in larval, pupal and adult stages, which were produced from treating 2nd instar larvae with different concentrations of the extract.
Decreased expression of cyclin G2 is significantly linked to the malignant transformation of papillary carcinoma of the thyroid. (2003)

Our results suggest that lack of cyclin G2 plays an important role in the malignant transformation of papillary carcinoma. Also, it may play an adjuvant role in the transformation of follicular adenoma to carcinoma. This is the first study of the expression of cyclin G2, a novel cyclin having a role opposite to that of conventional cyclins, in human carcinoma.
Partial characterization of the phosphotransferase system of human central-nervous-system myelin (1983)

The phosphotransferase system of human central-nervous-system myelin was investigated. Evidence obtained indicated the presence of at least two different phosphotransferase systems (cyclic nucleotide-dependent and -independent) in myelin, which were found to be firmly associated with the membrane. The cyclic AMP-dependent kinase of myelin and white-matter cytosol preferentially phosphorylated certain histone fractions and displayed only modest activity with basic protein as substrate. On the other hand, the cyclic nucleotide-independent system showed specificity toward basic protein. Its activity was not only dependent on Mg2+ but it was greatly enhanced by this bivalent cation. Whereas the cyclic nucleotide-dependent kinase could be extracted with buffers containing Triton X-100, the bivalent cation-regulated kinase resisted solubilization from myelin under these conditions.
AMERICIUM IN THE BEAGLE DOG: BIOKINETIC AND DOSIMETRIC MODEL (2006)

A biokinetic model of the systemic distribution of americium in the beagle dog is presented. The model is based on a previous biokinetic model of plutonium. The data sets used for the development of the model were the measurements of excreted activity (urine and feces) and organ burdens (skeleton, liver, and other soft tissues) for different levels of initial injected activity. In developing the model, the compartmental structure of the skeleton of the plutonium model was adopted, and only the numerical values of parameters were adapted. The model well describes the fractions of americium in the skeleton, liver, and soft tissues and the total fraction excreted in urine and feces. The tuning of the liver clearance parameter provides a realistic description of the change in the partitioning between liver and skeleton for different injection levels. The most significant features of the biokinetics and dosimetry of americium and plutonium in beagles are compared. The total fractions of the clearance to the skeleton and the liver are roughly equal to the value for plutonium, but the partitioning of americium between these organs is reversed with respect to the partitioning of plutonium. 241Am doses to liver and skeleton are similar to 239Pu doses, owing to some counteracting factors. For the highest injection level, the liver mass is dependent on the time post injection. For the skeletal tissues, the dose to the cortical endosteum by far exceeds the dose to the trabecular endosteum and the red marrow. The model provides the basis for statistical survival analyses and risk estimates.
Does olanzapine have antidepressant properties? A retrospective preliminary study (2000)

Olanzapine appears to be moderately effective in open add-on treatment in patients with mainly depressive symptoms. Accumulating evidence suggests that olanzapine, and atypical antipsychotics in general, possess mild to moderate adjunctive antidepressant properties.
Intranodal injection of semimature monocyte-derived dendritic cells induces T helper type 1 responses to protein neoantigen (2003)

Dendritic cells (DCs) represent the most potent antigen-presenting cells of the immune system capable of initiating primary immune responses to neoantigens. Here we characterize the primary CD4 T-cell immune response to protein keyhole limpet hemocyanin (KLH) in 5 metastatic melanoma patients undergoing a tumor peptide-based dendritic cell vaccination trial. Monocyte-derived dendritic cells displaying a semimature phenotype, as defined by surface markers, were loaded ex vivo with antigen and injected intranodally at weekly intervals for 4 weeks. All patients developed a strong and long-lasting delayed-type hypersensitivity reactivity to KLH, which correlated with the induction of KLH-dependent proliferation of CD4 T cells in vitro. Secondary in vitro stimulation with KLH showed significant increase in interferon-gamma and interleukin-2 (IL-2) but not IL-4, IL-5, nor IL-10 secretion by bulk T cells. On the single-cell level, most TH1 cells among in vitro-generated KLH-specific T-cell lines confirmed the preferential induction of a KLH-specific type 1 T helper immune response. Furthermore, the induction of KLH-specific antibodies of the IgG2 subtype may reflect the induction of a type 1 cytokine profile in vivo after vaccination. Our results indicate that intranodal vaccination with semimature DCs can prime strong, long-lasting CD4 T-cell responses with a TH1-type cytokine profile in cancer patients.
Three-dimensional Brillouin confocal microscopy (2007)

We present Brillouin confocal microscopy for non-invasively measuring mechanical properties of material with three-dimensional spatial resolution and high sensitivity.
Anti-tumor effect of gallic acid on LL-2 lung cancer cells transplanted in mice (2001)

We previously reported that gallic acid (3,4,5-trihydroxybenzoic acid), a naturally occurring plant phenol, can induce apoptosis in four kinds of human lung cancer cell lines in vitro. The present study further investigated the in vivo anti-tumor effects of orally administered gallic acid. Gallic acid reduced cell viability of LL-2 mouse lung cancer cells in vitro dose dependently, with a 50% inhibitory concentration (IC50) value of around 200 microM. C57Black mice were transplanted with LL-2 cells, and administered gallic acid (1 mg/ml in drinking water, ad libitum) and/or cisplatin (4 mg/kg i.p. injection, once a week). The average weight of the transplanted tumors, obtained at 29 days after transplantation, in the mice of control, gallic acid-treated cisplatin-treated and cisplatin plus gallic acid-treated groups was 4.02, 3.65, 3.19 and 1.72 g, respectively. The average tumor weight of the mice treated with cisplatin combined with gallic acid was significantly smaller than that of the control group (p<0.05). The amount of apoptotic cells in the tumor tissues of mice treated with gallic acid and/or cisplatin was significantly higher than those of the control mice. Combination of gallic acid and cisplatin increased the tumor cell apoptosis compared with the treatment with cisplatin alone. The present findings suggest that the combination of gallic acid with an anti-cancer drug, including cisplatin, may be an effective protocol for lung cancer therapy.
Caesarean section increases the risk of hospital care in childhood for asthma and gastroenteritis (2003)

There is a significant increase of the risk for developing symptoms of asthma and/or gastroenteritis that motivates admission for hospital care in CS children older than 1 year. It is speculated that a disturbed intestinal colonization pattern in CS children may be a common pathogenic factor.