gebhart/patrepeval huggingface dataset:
Deterministic platform software for hard real-time systems using multi-core COTS (2015)

Future generations of avionic equipments are expected to embed multi-core processors. Using Components Off-The-Shelf (COTS) processors is considered both by the industrial and academic communities, as well as certification authorities. However, in the safety-critical domain, a common issue with COTS multi-core processors is their lack of predictability, directly linked to the difficulty to foresee and manage inter-core interferences due to shared hardware resources.
Transcription Is Required to Establish Maternal Imprinting at the Prader-Willi Syndrome and Angelman Syndrome Locus (2011)

The Prader-Willi syndrome (PWS [MIM 17620]) and Angelman syndrome (AS [MIM 105830]) locus is controlled by a bipartite imprinting center (IC) consisting of the PWS-IC and the AS-IC. The most widely accepted model of IC function proposes that the PWS-IC activates gene expression from the paternal allele, while the AS-IC acts to epigenetically inactivate the PWS-IC on the maternal allele, thus silencing the paternally expressed genes. Gene order and imprinting patterns at the PWS/AS locus are well conserved from human to mouse; however, a murine AS-IC has yet to be identified. We investigated a potential regulatory role for transcription from the Snrpn alternative upstream exons in silencing the maternal allele using a murine transgene containing Snrpn and three upstream exons. This transgene displayed appropriate imprinted expression and epigenetic marks, demonstrating the presence of a functional AS-IC. Transcription of the upstream exons from the endogenous locus correlates with imprint establishment in oocytes, and this upstream exon expression pattern was conserved on the transgene. A transgene bearing targeted deletions of each of the three upstream exons exhibited loss of imprinting upon maternal transmission. These results support a model in which transcription from the Snrpn upstream exons directs the maternal imprint at the PWS-IC.
Differential Roles for αMβ2 Integrin Clustering or Activation in the Control of Apoptosis via Regulation of Akt and ERK Survival Mechanisms (2000)

The role of integrins in leukocyte apoptosis is unclear, some studies suggest enhancement, others inhibition. We have found that beta(2)-integrin engagement on neutrophils can either inhibit or enhance apoptosis depending on the activation state of the integrin and the presence of proapoptotic stimuli. Both clustering and activation of alpha(M)beta(2) delays spontaneous, or unstimulated, apoptosis, maintains mitochondrial membrane potential, and prevents cytochrome c release. In contrast, in the presence of proapoptotic stimuli, such as Fas ligation, TNFalpha, or UV irradiation, ligation of active alpha(M)beta(2) resulted in enhanced mitochondrial changes and apoptosis. Clustering of inactive integrins did not show this proapoptotic effect and continued to inhibit apoptosis. This discrepancy was attributed to differential signaling in response to integrin clustering versus activation. Clustered, inactive alpha(M)beta(2) was capable of stimulating the kinases ERK and Akt. Activated alpha(M)beta(2) stimulated Akt, but not ERK. When proapoptotic stimuli were combined with either alpha(M)beta(2) clustering or activation, Akt activity was blocked, allowing integrin activation to enhance apoptosis. Clustered, inactive alpha(M)beta(2) continued to inhibit stimulated apoptosis due to maintained ERK activity. Therefore, beta(2)-integrin engagement can both delay and enhance apoptosis in the same cell, suggesting that integrins can play a dual role in the apoptotic progression of leukocytes.
Regulation of Cell Proliferation and Migration by Keratin19-Induced Nuclear Import of Early Growth Response-1 in Breast Cancer Cells (2013)

KRT19 is a potential tumor suppressor that negatively regulates Akt signaling through modulation of Egr1 nuclear localization.
Cloning and sequencing show that 4-hydroxybenzoate hydroxylase (PobA) is required for uptake of 4-hydroxybenzoate in Rhizobium leguminosarum (1994)

Mutants of Rhizobium leguminosarum bv. viciae MNF300 and R. leguminosarum bv. trifolii WU95 unable to accumulate 4-hydroxybenzoate lack 4-hydroxybenzoate hydroxylase. The capacity of these mutants to take up and grow on 4-hydroxybenzoate was restored by a 2.0 kb EcoRI-PstI DNA fragment. This contained only one ORF which had over 60% DNA sequence similarity with the structural gene for 4-hydroxybenzoate hydroxylase (pobA) from Pseudomonas spp. and Acinetobacter. Reported effects of metabolic inhibitors and substrate analogues on the apparent uptake of 4-hydroxybenzoate have now been shown to be due to their direct effect on 4-hydroxybenzoate hydroxylase. We propose that uptake of 4-hydroxybenzoate is via a metabolic 'drag' mechanism dependent on the activity of the pobA gene product.
All-polymer thin film transistors fabricated by high-resolution ink-jet printing (2002)

All-polymer thin film transistors (TFTs) are fabricated by ink-jet printing for the first time. Source/drain electrodes are printed using a conducting polymer (PEDOT) solution on substrates with patterned wetting-and-dewetting regions. A channel length down to 5 /spl mu/m has been achieved without short-circuits. The TFTs show a high mobility of 0.02 cm/sup 2//V/spl middot/s and on/off ratio of more than 10/sup 5/. These characteristics are equal or better than reference devices with gold electrodes. The fabrication of printed inverters is also demonstated, in which components such as gate electrodes, interconnections, via-holes or resistors, are patterned with the ink-jet technique.
Synthesis of 1-(3-Azido-2,3-dideoxy-β-D-ribo-hexofuranosyl)-, 1-(2,3-Dideoxy-β-D-erythro-hexofuranosyl)- and 1-(2,3-Dideoxy-β-D-erythro-hex-2-enofuranosyl)pyrimidine Nucleosides (1994)

1-(3-Azido-2,3-dideoxy-β-D- ribo -hexofuranosyl)uracil ( XXII ) and 1-(2,3-dideoxy-β-D- erythro -hex-2-enofuranosyl)uracil ( VIII ) were prepared starting from 1-(2- O -acetyl-3,5,6-tri- O -benzoyl-β-D-glucofuranosyl)uracil ( I ) by a procedure described previously for thymine analogs. 1-(2,3-Dideoxy-β-D- erythro -hexofuranosyl)uracil ( XIII ) was obtained by catalytic hydrogenation of 1-(5,6-di- O -benzoyl-2,3-dideoxy-β-D- erythro -hex-2-enofuranosyl)uracil ( VII ) and subsequent methanolysis. Reaction of dibenzoyl derivative VII , 1-(5,6-di- O -benzoyl-2,3-dideoxy-β-D- erythro -hexofuranosyl)uracil ( XII ) and the diacetate prepared by acetylation of azido derivative XXII with Lawesson's reagent, followed by methanolysis, afforded 1-(2,3-dideoxy-β-D- erythro -hex-2-enofuranosyl)-4-thiouracil ( X ), 1-(2,3-dideoxy-β-D- erythro -hexofuranosyl)-4-thiouracil ( XV ) and 1-(3-azido-2,3-dideoxy-β-D- ribo -hexofuranosyl)-4-thiouracil ( XXIII ), respectively. Heating of thio derivatives X , XV and XXIII with methanolic ammonia at 100 °C gave 1-(2,3-dideoxy-β-D- erythro -hex-2-enofuranosyl)cytosine ( XI ), 1-(2,3-dideoxy-β-D- erythro -hexofuranosyl)cytosine ( XVI ) and 1-(3-azido-2,3-dideoxy-β-D- ribo -hexofuranosyl)cytosine ( XXIV ).
Efficient Piecewise Training of Deep Structured Models for Semantic Segmentation (2016)

Recent advances in semantic image segmentation have mostly been achieved by training deep convolutional neural networks (CNNs). We show how to improve semantic segmentation through the use of contextual information, specifically, we explore 'patch-patch' context between image regions, and 'patch-background' context. For learning from the patch-patch context, we formulate Conditional Random Fields (CRFs) with CNN-based pairwise potential functions to capture semantic correlations between neighboring patches. Efficient piecewise training of the proposed deep structured model is then applied to avoid repeated expensive CRF inference for back propagation. For capturing the patch-background context, we show that a network design with traditional multi-scale image input and sliding pyramid pooling is effective for improving performance. Our experimental results set new state-of-the-art performance on a number of popular semantic segmentation datasets, including NYUDv2, PASCAL VOC 2012, PASCAL-Context, and SIFT-flow. In particular, we achieve an intersection-overunion score of 78:0 on the challenging PASCAL VOC 2012 dataset.
The Gamma Interferon (IFN-γ) Mimetic Peptide IFN-γ(95-133) Prevents Encephalomyocarditis Virus Infection both in Tissue Culture and in Mice (2006)

We have demonstrated previously that the C-terminal gamma interferon (IFN-gamma) mimetic peptide consisting of residues 95 to 133 [IFN-gamma(95-133)], which contains the crucial IFN-gamma nuclear localization sequence (NLS), has antiviral activity in tissue culture. Here we evaluate the efficacy of this peptide and its derivatives first in vitro and then in an animal model of lethal viral infection with the encephalomyocarditis (EMC) virus. Deletion of the NLS region from the IFN-gamma mimetic peptide IFN-gamma(95-133) resulted in loss of antiviral activity. However, the NLS region does not have antiviral activity in itself. Replacing the NLS region of IFN-gamma(95-133) with the NLS region of the simian virus 40 large T antigen retains the antiviral activity in tissue culture. IFN-gamma(95-133) prevented EMC virus-induced lethality in mice in a dose-dependent manner compared to controls. Mice treated with IFN-gamma(95-133) had no or low EMC virus titers in their internal organs, whereas control mice had consistently high viral titers, especially in the heart tissues. Injection of B8R protein, which is encoded by poxviruses as a defense mechanism to neutralize host IFN-gamma, did not inhibit IFN-gamma(95-133) protection against a lethal dose of EMC virus, whereas mice treated with rat IFN-gamma were not protected. The data presented here show that the IFN-gamma mimetic peptide IFN-gamma(95-133) prevents EMC virus infection in vivo and in vitro and may have potential against other lethal viruses, such as the smallpox virus, which encodes the B8R protein.
Molecular mobility and nucleocytoplasmic flux in hepatoma cells. (1986)

Fluorescence microphotolysis (photobleaching) was used to measure, in single polyethylene glycol-induced polykaryons of hepatoma tissue culture cells, nucleocytoplasmic flux and intracellular mobility for a series of dextrans ranging in molecular mass from 3 to 150 kD and for bovine serum albumin. For the dextrans, the cytoplasmic and the nucleoplasmic translational diffusion coefficients amounted to approximately 9 and approximately 15%, respectively, of the value in dilute buffer. The diffusion coefficients depended inversely on molecular radius, suggesting that diffusion was dominated by viscosity effects. By application of the Stokes-Einstein equation, cytoplasmic and nucleoplasmic viscosities were derived to be 6.6 and 8.1 cP, respectively, at 23 degrees C. Between 10 and 37 degrees C nucleoplasmic diffusion coefficients increased by approximately 45-85%, whereas cytoplasmic diffusion coefficients were virtually independent of temperature. In contrast to that of the dextrans, diffusion of bovine serum albumin was more restricted. In the cytoplasm the diffusion coefficient was approximately 1.5% of the value in dilute buffer; in the nucleus albumin was largely immobile. This indicated that albumin mobility is dominated by association with immobile cellular structures. Nucleocytoplasmic flux of dextrans depended inversely on molecular mass with an exclusion limit between 17 and 41 kD. This agrees with previous measurements on primary hepatocytes (Peters, R., 1984, EMBO [Eur. Mol. Biol. Organ.] J. 3:1831-1836), suggesting that in both cell types the nuclear envelope has properties of a molecular sieve with a functional pore radius of approximately 55 A.
The SNARE Protein SNAP23 and the SNARE-Interacting Protein Munc18c in Human Skeletal Muscle Are Implicated in Insulin Resistance/Type 2 Diabetes (2010)

We have translated our previous in vitro results into humans by showing that there is a change in the distribution of SNAP23 to the interior of the cell in skeletal muscle from patients with type 2 diabetes. We also showed that Munc18c is a potential regulator of SNAP23.
Human Embryonic Stem Cell Telomere Length Impacts Directly on Clonal Progenitor Isolation Frequency (2007)

The pluripotentiality of human embryonic stem cells is expected to yield an abundance of clinically useful cell types. Using physiologic oxygen culture systems, we show that it is possible to isolate highly proliferative clonal progenitor cells from partially differentiated human embryonic stem cells. These progenitors have similar, though not identical, immunophenotypes with a resemblance to bone marrow-derived adherent stem cells. Through telomere length analysis of multiple early senescing clones, we were able to show that the starting telomere length of a human embryonic stem cell line impacts on the proliferative potential of clonally isolated partially differentiated mortal progeny. Proliferative clones undergo growth arrest with telomere lengths consistent with telomere-driven replicative senescence. To bypass this phenomenon, we transduced progenitor cells with ectopic hTERT (the limiting catalytic component of telomerase). This enabled telomerase immortalization without affecting differentiation potential or immunophenotype. In summary we describe the derivation of clonal progenitor cells from human embryonic stem cells and the relevance of parental cell telomere length to the frequency of highly proliferative clone isolation.
Cloning and Characterization of a G Protein-Activated Human Phosphoinositide-3 Kinase (1995)

Phosphoinositide-3 kinase activity is implicated in diverse cellular responses triggered by mammalian cell surface receptors and in the regulation of protein sorting in yeast. Receptors with intrinsic and associated tyrosine kinase activity recruit heterodimeric phosphoinositide-3 kinases that consist of p110 catalytic subunits and p85 adaptor molecules containing Src homology 2 (SH2) domains. A phosphoinositide-3 kinase isotype, p110 gamma, was cloned and characterized. The p110 gamma enzyme was activated in vitro by both the alpha and beta gamma subunits of heterotrimeric guanosine triphosphate (GTP)-binding proteins (G proteins) and did not interact with p85. A potential pleckstrin homology domain is located near its amino terminus. The p110 gamma isotype may link signaling through G protein-coupled receptors to the generation of phosphoinositide second messengers phosphorylated in the D-3 position.
Limited Antibody‐Dependent Cellular Cytotoxicity Antibody Response Induced by a Herpes Simplex Virus Type 2 Subunit Vaccine (2000)

The humoral response to a herpes simplex virus (HSV) type 2 subunit vaccine containing recombinant glycoproteins B (gB2) and D (gD2) was tested in 3 groups of patients. These included HSV-seronegative, HSV-1-seropositive, and HSV-2-seropositive individuals. There were excellent antibody responses, as measured by gB2- and gD2-specific ELISAs and HSV-2 neutralization assays. However, in 2 HSV-2 antibody-dependent cellular cytotoxicity (ADCC) assays, there were relatively low antibody responses, especially among HSV-seronegative individuals. The low ADCC responses may be associated with the poor efficacy of this vaccine observed in clinical trials.
Polymorphisms of the IL-1 gene complex in coal miners with silicosis (2001)

This is the first report showing an association between the IL-1RA (+ 2018) polymorphism and silicosis, and suggests that this polymorphism may confer increased risk for the development of the disease.
Methylmalonic Acid Measured in Plasma and Urine by Stable-Isotope Dilution and Electrospray Tandem Mass Spectrometry (2000)

This method is well suited for large-scale MMA testing (> or =100 samples per day) where a shorter analytical time is highly desirable. Reagents are less expensive than the anion-exchange/cyclohexanol-HCl method, and sample preparation of batches up to 100 specimens is completed in less than 8 h and is automated.
Bioactivation of the Selective Estrogen Receptor Modulator Desmethylated Arzoxifene to Quinoids:  4‘-Fluoro Substitution Prevents Quinoid Formation (2005)

Although selective estrogen receptor modulators (SERMs) are useful in the treatment and prevention of breast cancer, the SERM tamoxifen has been associated with an increased risk of endometrial cancer possibly due to metabolism to electrophilic quinoids. Another SERM, arzoxifene is currently in clinical trials for the treatment of breast cancer, and since it has similar structural characteristics to tamoxifen, it also has the potential to form quinoids. In the current study, the active form of arzoxifene in vivo, desmethylated arzoxifene (DMA), was synthesized and chemically or enzymatically oxidized to DMA diquinone methide. The half-life of DMA diquinone methide at physiological pH and temperature was approximately 15 s. Reaction of DMA diquinone methide with glutathione (GSH) gave four mono-GSH conjugates, two di-GSH conjugates, and one tri-GSH conjugate. In incubations of DMA with GSH and either rat or human liver microsomes, DMA o-quinone-GSH conjugates were detected in addition to DMA diquinone methide-GSH conjugates. A DMA diquinone methide-deoxyguanosine adduct was detected following the incubation of DMA diquinone methide with deoxynucleosides. In preliminary studies with a human breast cancer cell line, DMA induced dose-dependent DNA damage and was more effective at causing DNA damage than raloxifene. These results suggest that DMA can be metabolized to electrophilic/redox-active quinoids, which have the potential to cause toxicity in vivo. A new fluorinated derivative unable to form a diquinone methide, 4'-F-DMA, was synthesized. 4'-F-DMA showed similar estrogen receptor (ER) binding affinity as compared to DMA. The antiestrogenic activity as measured by inhibition of estradiol-mediated induction of alkaline phosphatase activity in Ishikawa cells showed 10-fold lower activity for 4'-F-DMA compared to DMA; however, the antiestrogenic activity was comparable to raloxifene. In microsomal incubations of 4'-F-DMA in the presence of GSH, no GSH adducts were detected. These data suggest that 4'-F-DMA might be a promising SERM with similar activity to DMA and raloxifene and less toxicity.
Lidocaine patch 5 for carpal tunnel syndrome: how it compares with injections: a pilot study. (2006)

This pilot trial demonstrated that the lidocaine patch 5% was efficacious in reducing pain associated with CTS and was well tolerated. The lidocaine patch 5% may offer patients with CTS effective, noninvasive treatment for the management of their symptoms. Further controlled trials are warranted.
A MUTANT GENOTYPE OF FLAX (Linum usitatissimum L.) CONTAINING VERY LOW LEVELS OF LINOLENIC ACID IN ITS SEED OIL (1986)

Two flax (Linum usitatissimum L.) mutants having reduced linolenic acid content in their seed oil (M1589 = 19.1% linolenic; M1722 = 23.4% linolenic) were crossed to determine whether further reductions could be achieved by recombination of the mutant genes. Extensive transgressive segregation was evident in the F 2 for both linolenic acid (1.2–36.6%) and linoleic acid (14.7–55.2%), which were strongly negatively correlated (r = −0.97). F 2 plants homozygous for both the M1589 and M1722 mutations had very low levels of linolenic acid (&lt;2%) and high levels of linoleic acid (&gt;46%).Key words: Flax, linseed, Linum usitatissimum, linoleic acid, linolenic acid, seed oil
Contribution of socioeconomic status to black/white differences in cancer incidence (1989)

Blacks and Whites have very different cancer incidence rates for many sites, but this may largely be due to the racial differences in socioeconomic status (SES). The authors tested this hypothesis by determining the effect of adjustment for SES on the black/white incidence ratios for 12 cancer sites. Race-specific census tract-level SES variables (median family income, percent below poverty level, and years of education) were obtained from the 1980 US census and applied to approximately 20,000 black and 88,000 white cancer cases from the National Cancer Institute's Surveillance, Epidemiology, and End Results (SEER) program for the years 1978 to 1982. For each cancer site (with each sex considered separately), Poisson regression was used to produce age-adjusted black/white incidence ratios, with and without adjustment for SES. The SES variable with the strongest adjusting power was percent below poverty level. For many sites (breast, in situ and invasive cervix, esophagus, male lung, pancreas, stomach) poverty accounted for much or all of the racial differences. For several sites (bladder, multiple myeloma, prostate, uterine corpus), large racial differences persisted after adjustment for poverty, and these findings suggest directions for investigating the etiology of these cancers.
Insulin stimulates the translocation of protein kinase C in rat adipocytes (1989)

Insulin-induced changes in protein kinase C were examined in cytosol and membrane fractions of rat adipocytes enzymatically after Mono Q column chromatography and by immunoblotting. During a 5-20 min period of insulin treatment, cytosolic protein kinase C decrease by approximately 50%, whereas membrane protein kinase C increased nearly 2-fold. These findings suggest that insulin stimulates the translocation of protein kinase C in rat adipocytes.
The Effect of Mild Hyperuricemia on Urinary Transforming Growth Factor Beta and the Progression of Chronic Kidney Disease (2007)

Although mild hyperuricemia is common in patients with renal disease, it has usually been considered a marker of reduced nephron mass rather than a risk factor for progression of kidney disease. On the other hand, experiments in a rat model demonstrated important deleterious effects of mild hyperuricemia on several aspects of renal structure and function. In the present investigation, the impact of the discontinuation of allopurinol therapy on the control of hypertension and the rate of progression of chronic kidney disease was considered. The present work involved 50 patients, suffering from stage 3 and 4 chronic kidney disease. All of them were on chronic allopurinol therapy for the treatment of mild hyperuricemia. Their blood pressure, serum creatinine and uric acid levels were followed for 12 months following allopurinol withdrawal. Urinary transforming growth factor beta-1 (TGF-beta1) was assayed by a solid-phase enzyme-linked immunosorbent assay. After allopurinol withdrawal, significant worsening of hypertension, significant acceleration of the rate of loss of kidney function and a significant increase in the urinary excretion of TGF-beta1 were observed in the group of patients who were not receiving pharmacological blockers of the renin-angiotensin system. In conclusion, asymptomatic hyperuricemia has a deleterious effect on the progression of chronic kidney disease and the control of hypertension. This effect was blocked by treatment with renin-angiotensin system blockers.
<title>Calibration of a CCD camera on a hybrid coordinate measuring machine for industrial metrology</title> (1991)

A methodology for the calibration of a CCD low-cost camera mounted on a CMM machine is described. Several kinds of geometric distortion are taken into account in the camera model. Five distortion parameters are introduced modeling both radial and non-radial effects. A two- phase methodology is developed for the parameter estimation. In the first phase, a closed-form solution is reached for the intrinsic and the extrinsic parameters neglecting distortion effects. In the second phase, an iterative procedure estimates separately the distortion and the non- distortion parameters, to avoid harmful interactions. The main novelty of the solution is the use of only linear systems, avoiding any non-linear optimization process. Low-level image processing used for calibration images is described. Experimental results and comparisons with more simplified camera models and estimation strategies are presented.