gebhart/patrepeval huggingface dataset:
[Amplification of portions of the genome in mammalian somatic cells resistant to colchicine. VI. Restriction analysis of the amplified DNA sequences]. (1983)

Fragments specific for the amplified regions in DNA of Djungarian hamster colchicine-resistant cells were studied after restriction endonuclease digestion. We used three different methods of detection of these fragments: a) comparison of the wild type and resistant cell DNA electroforegramms stained by ethidium bromide; b) blotting of DNA from sensitive and resistant variants onto nitrocellulose filters and their hybridization with nick-translated DNA from resistant cells, in the presence of the excess of unlabelled DNA from the wild type cells (competitive hybridization); c) investigation of autonomously replicating DNA from sensitive and colchicine-resistant sublines. The highest resolution was found using the third method. However, the competitive hybridization is evidently a more universal approach to restriction analysis of DNA amplified sequences, because it gives quite high resolution and may be used for studying both autonomously and non-autonomously replicating sequences.
Bilayer graphene nanoribbon nanoelectromechanical system device: A computational study (2009)

A bilayer graphene nanoribbon nanoelectromechanical device is investigated via first-principle simulations. The output characteristics as a function of interlayer distance are calculated, with the proposed device acting as a displacement and a force sensor. The operating mechanism of a bistable switch based on this device structure is also explored, and in the present floating gate design, a switching gate bias of 5.6 V is required, resulting in an ON-OFF current ratio of 3 orders at a device bias of 20 mV. This minuscule bistable device could potentially be implemented in future semiconductor memory devices and radio frequency communication circuitry.
Abstraction in databases (1980)

This paper surveys current research and practice concerning abstraction in database systems. Classical and semantic database models are reviewed and emphasized, as fundamental database abstraction mechanisms.
Potential Mechanisms of Muscle Mitochondrial Dysfunction in Aging and Obesity and Cellular Consequences (2009)

Mitochondria play a key role in the energy metabolism in skeletal muscle. A new concept has emerged suggesting that impaired mitochondrial oxidative capacity in skeletal muscle may be the underlying defect that causes insulin resistance. According to current knowledge, the causes and the underlying molecular mechanisms at the origin of decreased mitochondrial oxidative capacity in skeletal muscle still remain to be elucidated. The present review focuses on recent data investigating these issues in the area of metabolic disorders and describes the potential causes, mechanisms and consequences of mitochondrial dysfunction in the skeletal muscle.
Improved LINC power transmission using a quadrature outphasing technique (2005)

A new improved approach to LINC power transmission is presented based on a quadrature outphasing technique, which depends on the constant envelope decomposition of the in-phase and quadrature parts of the input signal. In this approach, the processing of the resultant constant envelope components requires a bandwidth far smaller than if a simple LINC transmission technique were used, resulting in reduced sensitivity to components mismatch, far less spectral regrowth and superior linearity than the simple LINC approach. Experimental results at HF band show that the new technique improves the spectral re-growth by more than 10 dB for an 8-ary DPSK signal compared to the regular LINC transmission.
Brca2-Null Embryonic Survival is Prolonged on the BALB/c Genetic Background (2000)

Women who inherit mutations in the BRCA2 cancer susceptibility gene have an 85% chance of developing breast cancer. The function of the BRCA2 gene remains elusive, but there is evidence to support its role in transcriptional transactivation, tumor suppression, and the maintenance of genomic integrity. Individuals with identical BRCA2 mutations display a different distribution of cancers, suggesting that there are low-penetrance genes that can modify disease outcome. We hypothesized that genetic background could influence embryonic survival of a Brca2 mutation in mice. Brca2-null embryos with a 129/SvEv genetic background (129(B2-/-)) died before embryonic day 8. 5. Transfer of this Brca2 mutation onto the BALB/cJ genetic background (BALB/c(B2-/-)) extended survival to embryonic day 10.5. These results indicate that the BALB/c background harbors genetic modifiers that can prolong Brca2-null embryonic survival. The extended survival of BALB/c(B2-/-) embryos enabled us to ask whether transcriptional regulation of the Brca1 and Brca2 genes is interdependent. The interdependence of Brca1 and Brca2 was evaluated by studying Brca2 gene expression in BALB/c(B1-/-) embryos and Brca1 gene expression in BALB/c(B2-/-) embryos. Nonisotopic in situ hybridization demonstrated that Brca2 transcript levels were comparable in BALB/c(B1-/-) embryos and wild-type littermates. Likewise, reverse transcriptase-polymerase chain reactions confirmed Brca1 mRNA expression in embryonic day 8.5 BALB/c(B2-/-) embryos that was comparable to Brca2-heterozygous littermates. Thus, the Brca1 and Brca2 transcripts are expressed independently of one another in Brca1- and Brca2-null embryos. Mol. Carcinog. 28:174-183, 2000.
Designed Phosphoprotein Recognition in <i>Escherichia coli</i> (2014)

Protein phosphorylation is a central biological mechanism for cellular adaptation to environmental changes. Dysregulation of phosphorylation signaling is implicated in a wide variety of diseases. Thus, the ability to detect and quantify protein phosphorylation is highly desirable for both diagnostic and research applications. Here we present a general strategy for detecting phosphopeptide-protein interactions in Escherichia coli. We first redesign a model tetratricopeptide repeat (TPR) protein to recognize phosphoserine in a sequence-specific fashion and characterize the interaction with its target phosphopeptide in vitro. We then combine in vivo site-specific incorporation of phosphoserine with split mCherry assembly to observe the designed phosphopeptide-protein interaction specificity in E. coli. This in vivo strategy for detecting and characterizing phosphopeptide-protein interactions has numerous potential applications for the study of natural interactions and the design of novel ones.
Molecular epidemiology of Escherichia coli O157:H7 by restriction fragment length polymorphism using Shiga-like toxin genes (1995)

The purpose of this study was to assess a simplified method for interstrain differentiation of Escherichia coli O157:H7 and other Shiga-like toxin-producing E. coli (SLTEC) strains. A method based on the use of nucleic acid probes from Shiga-like toxin (SLT) I and II structural genes was used to generate restriction fragment length polymorphism (RFLP) patterns of SLTEC strains, (SLT-RFLP patterns) resulting from digestion of isolated genomic DNA with four different restriction enzymes (BamHI, EcoRI, HindIII, and PvuII) used separately. A total of 165 SLTEC strains from clinical, food, and environmental sources, including O157:H7 isolates from four food-borne outbreaks in Canada and the United States, were analyzed in the study. SLT-RFLP demonstrated that E. coli O157:H7 strains from each food-borne outbreak had the same unique SLT-RFLP pattern. Fifty-two SLT-RFLP types were found among 96 E. coli O157:H7 isolates from sporadic cases of hemorrhagic colitis and hemolytic uremic syndrome in Washington state. The use of the SLT probes proved to be a very powerful method for interstrain differentiation of SLTEC strains. Although the use of each of the enzymes alone did not give enough differentiative power to be used in epidemiological studies, the combination of patterns generated by two restriction enzymes (EcoRI and PvuII, used separately) provided the desired sensitivity for such studies. The results clearly demonstrate the usefulness of the method for studying the molecular epidemiology of E. coli O157:H7. The method is also suitable for establishing an epidemiological database, in terms of both sensitivity and ease of compilation and interpretation of results.
Another world: inside artificial reality (1989)

To elucidate prognostic implications of recipient cytomegalovirus infection before heart transplantation, we prospectively followed the clinical outcome of 21 transplant recipients whose explanted hearts (myocardium and coronary arteries) were first examined for the presence of cytomegalovirus DNA with polymerase chain reaction. Subsequently, serial endomyocardial biopsy tissue samples obtained from the allograft during routine evaluation for rejection were analyzed by polymerase chain reaction for both an immediate early and late cytomegalovirus gene region of cytomegalovirus DNA. Humoral cytomegalovirus immunoglobulin G antibodies were also measured by radioimmunoassay. Both early and late antigens were present in 14 of 21 (67%) explants from patients with (12 of 15 explants) and without (2 of 6 explants) pretransplant cytomegalovirus antibodies. Although the presence of both early and late antigens was uncommon in allografts the first week after transplantation (5 of 20 allografts, 25%), their presence significantly increased at 1 month (14 of 21 allografts, 67%) and 2 to 3 months (13 of 17 allografts, 77%) regardless of pretransplantation cytomegalovirus antibody status. The presence of both early and late antigens in explant tissue strongly predicted allograft virus status during the follow-up periods. Of five patients in whom clinical cytomegalovirus disease subsequently developed, all had explants positive for both early and late antigens, and all allografts were positive for early and late antigens within 1 month after transplantation. These are the first prospective data to correlate pretransplantation serum antibodies and explant polymerase chain reaction status with the development of future allograft infections and overall clinical outcome.
Synthesis of VHDL concurrent processes (1994)

This paper presents two methods for synthesis of VHDL specifications containing concurrent processes. Our main objective is to preserve simulation/synthesis correspondence during high-level synthesis and to produce hardware that operates with a high degree of parallelism. The first method supports an unrestricted use of signals and wait statements and synthesizes synchronous hardware with global control of process synchronization for signal update. The second method allows hardware synthesis without the strict synchronization imposed by the VHDL simulation cycle. Experimental results have shown that the proposed methods are efficient for a wide spectrum of digital systems.
Resistance of Aerosolized Bacterial Viruses to Relative Humidity and Temperature (2015)

The use of aerosolized bacteriophages as surrogates for hazardous viruses might simplify and accelerate the discovery of links between viral components and their persistence in the airborne state under diverse environmental conditions. In this study, four structurally distinct lytic phages, MS2 (single-stranded RNA [ssRNA]), ϕ6 (double-stranded RNA [dsRNA]), ϕX174 (single-stranded DNA [ssDNA]), and PR772 (double-stranded DNA [dsDNA]), were nebulized into a rotating chamber and exposed to various levels of relative humidity (RH) and temperature as well as to germicidal UV radiation. The aerosolized viral particles were allowed to remain airborne for up to 14 h before being sampled for analysis by plaque assays and quantitative PCRs. Phages ϕ6 and MS2 were the most resistant at low levels of relative humidity, while ϕX174 was more resistant at 80% RH. Phage ϕ6 lost its infectivity immediately after exposure to 30°C and 80% RH. The infectivity of all tested phages rapidly declined as a function of the exposure time to UVC radiation, phage MS2 being the most resistant. Taken altogether, our data indicate that these aerosolized phages behave differently under various environmental conditions and highlight the necessity of carefully selecting viral simulants in bioaerosol studies.
Phase Transitions of the Lennard-Jones System (1969)

Monte Carlo computations have been performed in order to determine the phase transitions of a system of particles interacting through a Lennard-Jones potential. The fluid-solid transition has been investigated using a method recently introduced by Hoover and Ree. For the liquid-gas transition a method has been devised which forces the system to remain always homogeneous. A comparison is made with experiment in the case of argon. An indirect determination of the phase transition of the hard-sphere gas is made which is essentially in agreement with the results of the more direct calculations.
Hybrid Rigid/Soft and Biologic/Synthetic Materials: Polymers Grafted onto Cellulose Microcrystals (2011)

Rigid nanoscale polymer rods were prepared by grafting preformed amine-terminated poly(styrene) and poly(tert-butyl acrylate) onto oxidized cellulose microcrystals. Low polydispersity polymers, grown using atom transfer radical polymerization, were characterized and purified prior to cellulose attachment. Oxidation of the cellulose microcrystal led to the formation of carboxylic acids on the surface of the microcrystals. Covalent attachment of the polymers onto the cellulose microcrystals was achieved via a carbodiimide-mediated amidation reaction. The length and diameter of the polymer-cellulose composites increased upon surface modification. Typically, polymer-cellulose composites are synthesized by a grafting-from method because it can be difficult to obtain sufficient graft density using a grafting-to preparation. However, the composites reported here comprised 60-64% grafted polymer by mass. This degree of grafting-to allowed the composite to form stable suspensions in organic solvents.
Über hexagoanale Perowskite mit Kationenfehlstellen. IV. Ba<sub>8</sub>Re<sub>3</sub>M<sup>v</sup>W□<sub>3</sub>O<sub>24</sub> mit M<sup>v</sup> = Nb, Ta – Perowskitstapelvarianten vom 24 L‐Typ (1978)

Abstract Die gelben Perowskitstapelvarianten Ba 8 Re 3 NbW□ 3 O 24 und Ba 8 Re 3 TaW□ 3 O 24 besitzen eine rhomboedrische Schichtstruktur von 24 L‐Typ mit 3 Formeleinheiten für die trigonal aufgestellte Zelle (Ba 8 Re 3 NbW□ 3 O 24 : a = 5,82 1 Å; c = 55,6 1 Å; Be 8 Re 3 TaW□ 3 O 24 : a = 5,82 1 Å; c = 55,6 1 Å).
The Effect of 15‐Hour Fat Infusions of Varying Dosage on Bilirubin Binding to Albumin (1985)

Intravenous fat emulsions (1, 2, and 3 g/kg) were administered over 15 hr to 20 appropriate for gestational age premature infants with physiologic hyperbilirubinemia to determine the effect of fat infusions on the serum free fatty acid:albumin molar ratio (F/A) and on unbound bilirubin. Significant increases (p less than 0.05) in F/A occurred with each increase in lipid dose in infants less than 30 wk gestation, but not in infants greater than or equal to 30 wk gestation. There was a direct linear correlation (r = 0.65, p less than 0.001) between F/A ratio and unbound bilirubin (estimated fluorometrically by the ratio of albumin-bound bilirubin/reserve bilirubin binding capacity, B/R). The largest increases in unbound bilirubin (albumin-bound bilirubin/reserve bilirubin binding capacity) were seen in infants with F/A greater than 4.0. The gestational age of infants with F/A greater than 4.0 was significantly less (p less than 0.01) than infants with F/A less than 4.0 (28.7 +/- 0.47 vs. 31.1 +/- 0.40 wk, mean +/- SEM). In 10/58 infusions there was a fall in unbound bilirubin, unrelated to birthweight, gestational age, postnatal age, however, during these infusions the end-infusion F/A was greater than or equal to 3.0. We conclude that 1 g/kg of lipid emulsion infused over a 15-hr period has minimal risk of decreasing bilirubin binding in premature infants less than 30 wk gestation. As doses of 2 or 3 g/kg are used, these infants may be at risk of decreased bilirubin binding, due to elevations in the F/A ratio. Monitoring of the F/A ratio may identify infants at risk for decreased bilirubin binding during lipid infusion and provide guidelines for determining the appropriate lipid dose.
Biodegradation of the anionic surfactant dialkyl sulphosuccinate (1993)

Abstract A range of Organisation for Economic Cooperation and Development (OECD) guideline test systems was used to determine the extent and possible mechanisms of biodegradation of dialkyl sulphosuccinate (DASS, C6/C8). Primary biodegradation of DASS was virtually complete in OECD guideline tests and in simulations of activated sludge sewage treatment systems under both optimal and adverse conditions, and of an anaerobic digester. Ultimate biodegradation increased from about 50% in ready tests to 94% in more powerful inherent tests. [14C]DASS was used to determine the fate of the surfactant in activated sludge and in surface waters. Mechanistic studies were performed to ascertain the biodegradative pathway of [14C]DASS. A putative degradation pathway for DASS is proposed.
A Mycobacterium avium subsp. paratuberculosis LuxR regulates cell envelope and virulence (2009)

Mycobacterium avium subsp. paratuberculosis adapts to the environment via the regulation of genes affecting its envelope's composition. Bacteria grown in milk (in vivo conditions) presented differences in the cell wall-associated lipids and in the expression of genes involved in lipid metabolism (FadE8, FadE6 and MAP1420) and host cell invasion (MAP1203, LprL). A different lipid profile was also observed in the envelope of intracellular bacteria after 1 h of infection. Intracellular bacteria showed up-regulation of a LuxR regulator which controls the envelope's composition by up-regulation of FadE8, MAP1420, MAP1203 and LprL and by down-regulation of pks12, mmpL2 and MAP2594. A LuxR-overexpressing strain with a lipid-deficient envelope phenotype, infected epithelial cells more efficiently than the wild-type bacteria; however, it was not more resistant than the wild-type strain to the action of bactericidal proteins. Here we show that LuxR regulates virulence determinants and is involved in mycobacteria adaptation to the host.
Environmental Induction of White–Opaque Switching in Candida albicans (2008)

Candida albicans strains that are homozygous at the mating type locus (MTLa or MTLalpha) can spontaneously switch at a low frequency from the normal yeast cell morphology (white) to an elongated cell type (opaque), which is the mating-competent form of the fungus. The ability to switch reversibly between these two cell types also contributes to the pathogenicity of C. albicans, as white and opaque cells are differently adapted to specific host niches. We found that in strain WO-1, a strain in which genomic alterations have occurred, but not in other tested strains, switching from the white to the opaque phase can also be induced by environmental conditions. Transient incubation of white cells under anaerobic conditions programmed the cells to switch en masse to the opaque phase. The anaerobic induction of white-opaque switching was controlled by the transcription factor CZF1, which in heterozygous MTLa/alpha cells regulates filamentous growth under embedded, hypoxic conditions. Intriguingly, passage of white cells of strain WO-1 through the mouse intestine, a host niche in which the cells are likely to be exposed to anaerobic conditions, resulted in a strongly increased frequency of switching to the opaque phase. These results demonstrate that white-opaque switching is not only a spontaneous process but, in combination with genomic alterations, can also be induced by environmental signals, suggesting that switching and mating of C. albicans may occur with high efficiency in appropriate niches within its human host.
Decrease in linoleic acid metabolites as a potential mechanism in cancer risk reduction by conjugated linoleic acid (1999)

Previous research suggested that conjugated linoleic acid (CLA) feeding during the period of pubescent mammary gland development in the rat resulted in diminished mammary epithelial branching which might account for the reduction in mammary cancer risk. Terminal end buds (TEB) are the primary sites for the chemical induction of mammary carcinomas in rodents. One of the objectives of the present study was to investigate the modulation of TEB density by increasing levels of dietary CLA and to determine how this might affect the risk of methylnitrosourea-induced mammary carcinogenesis. The data show a graded and parallel reduction in TEB density and mammary tumor yield produced by 0.5 and 1% CLA. No further decrease in either parameter was observed when CLA in the diet was raised to 1.5 or 2%. Thus, optimal CLA nutrition during pubescence could conceivably control the population of cancer-sensitive target sites in the mammary gland. Since both CLA and linoleic acid are likely to share the same enzyme system for chain desaturation and elongation, it is possible that increased CLA intake may interfere with the further metabolism of linoleic acid. Fatty acid analysis of total lipid showed that CLA and CLA metabolites continued to accumulate in mammary tissue in a dose-dependent manner over the range 0.5-2% CLA. There was no perturbation in tissue linoleic acid, however, linoleic acid metabolites (including 18:3, 20:3 and 20:4) were consistently depressed by up to 1% CLA. Of particular interest was the significant drop in 20:4 (arachidonic acid), which is the substrate for the cyclooxygenase and lipoxygenase pathways of eicosanoid biosynthesis. Thus the CLA dose-response effect on arachidonic acid suppression corresponded closely with the CLA dose-response effect on cancer protection in the mammary gland. This information is critical in providing new insights regarding the biochemical action of CLA.
Quantitative profiling of biomarkers related to B‐vitamin status, tryptophan metabolism and inflammation in human plasma by liquid chromatography/tandem mass spectrometry (2009)

Vitamins B2 and B6 serve as cofactors in enzymatic reactions involved in tryptophan and homocysteine metabolism. Plasma concentrations of these vitamins and amino acids are related to smoking and inflammation, and correlate with other markers of immune activation. Large-scale studies of these relations have been hampered by lack of suitable analytical methods. The assay described includes riboflavin, five vitamin B6 forms (pyridoxal 5'-phosphate, pyridoxal, 4-pyridoxic acid, pyridoxine and pyridoxamine), tryptophan and six tryptophan metabolites (kynurenine, kynurenic acid, anthranilic acid, 3-hydroxykynurenine, xanthurenic acid and 3-hydroxyanthranilic acid), cystathionine, neopterin and cotinine. Trichloroacetic acid containing 13 isotope-labelled internal standards was added to 60 microL of plasma, the mixture was centrifuged, and the resulting supernatant used for analysis. The analytes were separated within 5 min on a stable-bond C8 column by a gradient-type mobile phase containing acetonitrile, heptafluorobutyric acid and high concentration (650 mmol/L) of acetic acid, and detected using electrospray ionization tandem mass spectrometry (ESI-MS/MS). The mobile phase ensured sufficient separation and high ionization efficiency of all analytes. Recoveries were 75-123% and within-day and between-day coefficients of variance (CVs) were 2.5-9.5% and 5.4-16.9%, respectively. Limits of detection ranged from 0.05 to 7 nmol/L. The method enables quantification of endogenous plasma concentrations of 16 analytes related to B-vitamin status and inflammation, and may prove useful in large-scale epidemiological studies.