gebhart/patrepeval huggingface dataset:
Recognition elements that determine affinity and sequence-specific binding to DNA of 2QN, a biosynthetic bis-quinoline analogue of echinomycin. (1999)

Footprinting experiments with DNase I provide a starting-point for investigating the molecular basis of nucleotide sequence recognition by 2QN, a bis-quinoline derivative of the quinoxaline antibiotic echinomycin produced by directed biosynthesis in Streptomyces echinatus. Using tyrT DNA molecules variously substituted with inosine and/or 2,6-diaminopurine residues it is shown that the location of the 2-amino group of purine nucleotides in the minor groove of the double helix exerts a dominant influence in determining where the antibiotic will bind, as it does for echinomycin. However, newly created binding sites in DNA molecules substituted with diaminopurine (D), all located round TpD steps, bind 2QN with so much higher affinity than the canonical CpG steps that the latter fail completely to appear as footprints in D-substituted DNA; indeed CpG sequences appear in regions of enhanced susceptibility to nuclease cleavage as do CpI steps in doubly D + I-substituted DNA. Quantitative footprinting plots confirm that sequences surrounding TpD steps bind 2QN several hundred-fold more tightly than do CpG-containing sequences, with dissociation constants of the order of 25 nM. To test the hypothesis that differences in stacking interactions between the chromophores of the drug and the DNA base pairs could account for the differences in binding affinities, models of 2QN bound to two DNA hexamers containing either a central CpG or a central TpD step were built. Calculation of the molecular electrostatic potential (MEP) of 2QN in solution using a continuum method revealed a distinctive pattern that is considered relevant to DNA binding. When the MEPs calculated for the two DNA hexamers in the complexed state were compared, substantial differences were found in the major groove and in the space between the base pairs that is occupied by the chromophores of the drug upon binding. The modelling data support the notion that electrostatic stacking interactions underlie the considerably preferred binding of echinomycin and 2QN around TpD steps rather than CpG steps.
Nitrogen Removal from Wastewater Using a Hybrid Membrane‐Biofilm Process: Pilot‐Scale Studies (2010)

The hybrid membrane biofilm process (HMBP) is a new approach to achieving total nitrogen removal from wastewater. Air-filled, hollow-fiber membranes are placed into an activated sludge basin and bulk aeration is suppressed. A nitrifying biofilm develops on the membranes, exporting nitrate and nitrite to the bulk liquid. The nitrate and nitrite are reduced by suspended biomass using influent BOD as the electron donor. Previous research demonstrated the HMBP concept at the bench scale and explored process fundamentals. This research explored the HMBP at the pilot scale, with a 120-L reaction tank, real wastewater, and a potentially scalable configuration. Nitrification rates averaged 0.5 g N m(-2)/d(-1), which were lower than found at the bench scale, and lower than predicted by a mathematical model, but still allowed effluent total nitrogen concentrations below 6 mg N/L with an average influent total nitrogen concentration of 25 mg N/L and a hydraulic retention time of 12 hours. More than 75% of the produced nitrate and nitrite was reduced with an average influent sCOD of only 68 mg/L and an average C:N ratio of 3.1. Mass balances on carbon and nitrogen suggest that nitrogen removal via nitrite occurred. This research confirms that the HMBP process is effective for BOD and nitrogen removal from wastewater, and suggests that the grid configuration is viable for scale-up.
Tell me who your friends are and I might be able to tell you what language(s) you speak: Social network analysis, multilingualism, and identity (2007)

Social network analysis has proved particularly useful in explaining why speakers in bilingual communities maintain or change their language behavior. Researchers have employed this sociolinguistic tool to investigate language shift and maintenance among longstanding stable bilingual communities. An underlying assumption in this analysis is that language, particularly the first language or mother tongue, is an integral part of collective identities, such as national, ethnic or cultural identities, and that maintenance of language across generations is a key factor to the maintenance of such identities. Certain bilingual communities may maintain this language ideology; however, multilingual communities present a more complex picture of the situation and may thus offer a challenge to the underlying assumptions of social network analysis. This article discusses the application of social network analysis to multilingual communities by taking a point of departure in the Filipino community in Oslo, the capital of Norway, with a view towards understanding linguistic and cultural maintenance. Results from the analyses provide support for the importance of social network in understanding language choice and cultural and linguistic maintenance; however, there were some notable exceptions. In this article we discuss language ideologies and the relationship between language and identity as complementary sources of explanation for language choice and language maintenance in this relatively speaking newly established multilingual community.
Is cadmium genotoxic? (1992)

Previous evidence that cadmium(II) causes gene mutations in bacteria or mammalian cells was weak. However, alterations in protocol have recently led to better evidence for its mutagenicity, especially in bacteria. Mutagenicity results may be confounded by tolerance mechanisms. Exposure of DNA in vitro to Cd2+ or to Cd2+ hydrogen peroxide does not result in strand breaks or alkali-labile sites. The fact that bacterial and mammalian cells appear to sustain some type of repairable DNA damage after exposure to Cd2+ suggests that the damage must be caused in an indirect manner. Recently, the ability of cadmium-metallothionein complex to cause DNA strand breaks has been described. Cd2+ also induces a "pro-oxidant state" by causing a depletion of cellular glutathione. This finding is consistent with the role of Cd2+ as a clastogen and may explain its weak mutagenicity at loci which cannot detect complex mutations. Cd2+ can also inhibit DNA repair, and can therefore act synergistically with certain mutagens and, presumably, carcinogens.
Numerical investigation on flow control effects of plasma actuators for subsonic aerofoils in turbine applications (2014)

Plasma actuators are all electrical devices capable of altering flow paths and reattaching separated boundary layers. The application to low pressure turbine stages in axial turbine engines indicates further fuel efficiency improvements at low Reynolds numbers. Using wind tunnel experiments, a numerical plasma model through steady-state simulations with RANS turbulence modeling was developed. Reasonable agreement has been observed in the calibration of the numerical plasma model to experimental data. Further parametric studies are considered, aiming to optimize control, reduce pressure loss for turbine stages, and reduce actuator power consumption.
TSA downregulates Wilms tumor gene 1 (Wt1) expression at multiple levels (2008)

The Wilms tumor gene WT1 encodes a zinc-finger transcription factor that is inactivated in a subset of pediatric kidney cancers. During embryogenesis, WT1 is expressed in a time- and tissue-specific manner in various organs including gonads and kidney but also in the hematopoietic system. Although widely regarded as a tumor suppressor gene, wild-type WT1 is overexpressed in a variety of hematologic malignancies, most notably in acute lymphoblastic leukemia as well as myelodysplastic syndromes. Reduction of WT1 expression levels leads to decrease of proliferation and apoptosis of leukemic cells, suggesting that in certain contexts WT1 might act as an oncogene. We show here that histone deacetylase inhibitors like Trichostatin A (TSA) can promptly and dramatically downregulate Wt1 expression levels in different cell lines. This effect was mostly due to the cessation of transcription and was mediated by sequences located in intron 3 of Wt1. In addition, TSA also caused enhanced degradation of the Wt1 protein by the proteasome. This was at least in part due to induction of the ubiquitin-conjugating enzyme UBCH8. Thus, downregulation of Wt1 expression might contribute to the beneficial effects of histone deacetylase inhibitors that are currently used in clinical trials as cancer therapeutics.
Biochemical and Genetic Analysis of the Mitochondrial Response of Yeast to BAX and BCL-X <sub>L</sub> (2000)

The BCL-2 family includes both proapoptotic (e.g., BAX and BAK) and antiapoptotic (e.g., BCL-2 and BCL-X(L)) molecules. The cell death-regulating activity of BCL-2 members appears to depend on their ability to modulate mitochondrial function, which may include regulation of the mitochondrial permeability transition pore (PTP). We examined the function of BAX and BCL-X(L) using genetic and biochemical approaches in budding yeast because studies with yeast suggest that BCL-2 family members act upon highly conserved mitochondrial components. In this study we found that in wild-type yeast, BAX induced hyperpolarization of mitochondria, production of reactive oxygen species, growth arrest, and cell death; however, cytochrome c was not released detectably despite the induction of mitochondrial dysfunction. Coexpression of BCL-X(L) prevented all BAX-mediated responses. We also assessed the function of BCL-X(L) and BAX in the same strain of Saccharomyces cerevisiae with deletions of selected mitochondrial proteins that have been implicated in the function of BCL-2 family members. BAX-induced growth arrest was independent of the tested mitochondrial components, including voltage-dependent anion channel (VDAC), the catalytic beta subunit or the delta subunit of the F(0)F(1)-ATP synthase, mitochondrial cyclophilin, cytochrome c, and proteins encoded by the mitochondrial genome as revealed by [rho(0)] cells. In contrast, actual cell killing was dependent upon select mitochondrial components including the beta subunit of ATP synthase and mitochondrial genome-encoded proteins but not VDAC. The BCL-X(L) protection from either BAX-induced growth arrest or cell killing proved to be independent of mitochondrial components. Thus, BAX induces two cellular processes in yeast which can each be abrogated by BCL-X(L): cell arrest, which does not require aspects of mitochondrial biochemistry, and cell killing, which does.
Renal synthesis of atriopeptin-like protein in physiology and pathophysiology (1991)

Atriopeptin is synthesized in mammalian atria as a 126-amino acid (14 kDa) prohormone, but it is secreted and circulates as a 28-amino acid (2.5 kDa) peptide. We have demonstrated the synthesis and secretion of an atriopeptin-like peptide in neonatal and adult rat kidney cell cultures. In this study, we evaluated the site of renal synthesis of this protein and its expression in normal rats and rats made nephrotic with puromycin aminonucleoside. The major form of atriopeptin in normal kidneys comigrated with an apparent molecular mass of 2.5 kDa assessed by gel filtration chromatography. However, the major form of this atriopeptin-like protein in nephrotic kidneys was determined to have an apparent molecular mass similar to the heart prohormone. No atriopeptin prohormone was detected in the plasma of nephrotic rats. Localization of this renal atriopeptin-like protein was accomplished by immunocytochemistry of rat kidney frozen sections. Using an antibody generated against either the COOH-terminal or NH3-terminal region of the cardiac atriopeptin prohormone, we detected specific immunostaining in the distal cortical nephron of the nephrotic kidney. This is the first report of the anatomic localization of a renal atriopeptin-like protein and its upregulation in nephrosis.
Non-NMDA and NMDA receptor-mediated excitotoxic neuronal deaths in adult brain are morphologically distinct: Further evidence for an apoptosis-necrosis continuum (1997)

Apoptosis and necrosis are generally recognized as two distinct pathways of cell death, based on biochemical and morphological characteristics. Despite rapid advances in elucidating molecular mechanisms of cell death, little is known about the morphological progression of death in neurons and the relationship between different mechanisms of neuronal death and the resulting subcellular alterations. With excitotoxicity, a clinically relevant model of neuronal death, apoptotic DNA laddering and morphologic evidence of necrosis can occur simultaneously in the same region of adult brain. Here, we tested the hypothesis that activation of N-methyl-D-aspartic acid (NMDA) and non-NMDA glutamate receptors (GluR) results in a spectrum of morphologically distinct phenotypes of neuronal death, with apoptosis and necrosis as its endpoints. The ultrastructural morphologies of newborn and adult neurons at different times following intrastriatal injections of non-NMDA and NMDA GluR agonists were compared to apoptosis, as established during naturally occurring neuronal death in the developing rat brain. Excitotoxic neuronal death in newborn striatum was morphologically indistinguishable from developmental apoptosis. In the adult, non-NMDA receptor agonist-induced neuronal death was characterized by extensive chromatin condensation that was reminiscent of, but not identical to, apoptosis during normal development. In contrast, quinolinate, an NMDA receptor agonist, produced only minor chromatin clumping and rapid cytoplasmic disintegration, which is suggestive of necrosis. These findings support the concept that degenerative phenotypes of excitotoxically injured neurons are influenced by the degree of brain maturity and GluR subtype stimulation, independent of the severity of excitotoxic insult, along a morphological continuum or gradient ranging from apoptosis to necrosis.
Parallel single-cell light-induced electroporation and dielectrophoretic manipulation (2009)

Electroporation is a common technique for the introduction of exogenous molecules across the, otherwise, impermeant cell membrane. Conventional techniques are limited by either low throughput or limited selectivity. Here we present a novel technique whereby we use patterned light to create virtual electrodes which can induce the parallel electroporation of single cells. This technique seamlessly integrates with optoelectronic tweezers to provide a single cell manipulation platform as well. We present evidence of parallel, single cell electroporation using this method through use of fluorescent dyes and dielectrophoretic responses. Additionally, through the use of integrated microfluidic channels, we show that cells remain viable following treatment in the device. Finally, we determine the optimal field dosage to inject propidium iodide into a HeLa cell and maintain cellular viability.
Mapping the amide I absorption in single bacteria and mammalian cells with resonant infrared nanospectroscopy (2016)

Infrared (IR) nanospectroscopy performed in conjunction with atomic force microscopy (AFM) is a novel, label-free spectroscopic technique that meets the increasing request for nano-imaging tools with chemical specificity in the field of life sciences. In the novel resonant version of AFM-IR, a mid-IR wavelength-tunable quantum cascade laser illuminates the sample below an AFM tip working in contact mode, and the repetition rate of the mid-IR pulses matches the cantilever mechanical resonance frequency. The AFM-IR signal is the amplitude of the cantilever oscillations driven by the thermal expansion of the sample after absorption of mid-IR radiation. Using purposely nanofabricated polymer samples, here we demonstrate that the AFM-IR signal increases linearly with the sample thickness t for t > 50 nm, as expected from the thermal expansion model of the sample volume below the AFM tip. We then show the capability of the apparatus to derive information on the protein distribution in single cells through mapping of the AFM-IR signal related to the amide-I mid-IR absorption band at 1660 cm(-1). In Escherichia Coli bacteria we see how the topography changes, observed when the cell hosts a protein over-expression plasmid, are correlated with the amide I signal intensity. In human HeLa cells we obtain evidence that the protein distribution in the cytoplasm and in the nucleus is uneven, with a lateral resolution better than 100 nm.
A High Power, Wide Torque Range, Efficient Engine with a Newly Developed Variable Geometry Turbocharger (1989)

<div class="htmlview paragraph">A turbocharger which has four pairs of fixed vanes and movable vanes inside the turbine scroll was developed. A 1.2-liter experimental gasoline engine with this turbocharger was made and mounted in the body of a passenger car. This variable-geometry mechanism did not need a waste-gate system. Results of bench tests showed that this engine generated a 93.3 kPa (700 mmHg) boost pressure over a 6,000 rpm range. This paper presents the mechanism, operation, and performance data of this variable-geometry turbocharger, as well as the performance data of the 1.2-liter experimental engine and this passenger car.</div>
Effects of Yogurt and Applesauce on the Oral Bioavailability of Nilotinib in Healthy Volunteers (2011)

Nilotinib, a potent orally bioavailable BCR-ABL tyrosine kinase inhibitor, is currently available as a hard gelatin capsule that must be swallowed whole. For patients who may have difficulty swallowing the intact capsule, an alternative mode of administration is desirable. The authors compared the bioavailability of nilotinib from the following administrations in 48 healthy subjects: (1) 400 mg nilotinib given as two 200-mg nilotinib intact capsules; (2) contents of two 200-mg nilotinib capsules, each capsule dispersed in 1 teaspoon of nonfat plain yogurt; and (3) contents of two 200-mg nilotinib capsules, each capsule dispersed in 1 teaspoon of applesauce. Nilotinib absorption was modestly increased following the administration of nilotinib dispersed in yogurt. The geometric mean ratios (90% confidence intervals) for nilotinib C(max), AUC(0-tlast), and AUC(0-inf) were 1.31 (1.22-1.41), 1.11 (1.05-1.16), and 1.08 (1.02-1.15), respectively. Administration of nilotinib dispersed in applesauce showed equivalent bioavailability compared with administration of nilotinib as intact capsules. The geometric mean ratios (90% confidence intervals) for nilotinib C(max), AUC(0-tlast), and AUC(0-inf) were 0.95 (0.88-1.02), 0.99 (0.94-1.04), and 0.97 (0.90-1.03), respectively. Each treatment was well tolerated in the study subjects. The data support a feasible alternative method of nilotinib administration; each capsule's contents may be dispersed in 1 teaspoon of applesauce and taken immediately.
[The mechanism of water transport in the epidermis]. (1991)

Possible mechanisms of water transport through Stratum Corneum (SC) in the process of insensible perspiration are investigated. Electrometric methods developed for measuring water flow density through SC are used. Data showing the reverse osmotic mechanism of water transport through the SC selective membrane are obtained. It is shown that the water flow density through SC controlling the evaporation rate from the skin surface in the process of insensible perspiration depends upon the skin capillary pressure.
<i>meta</i>‐Phenylene Units as Conjugation Barriers in Phenylenevinylene Chains (1992)

Independent of the chain length are the optical and redox chemical properties of the oligomers 1, because the formally continuous π conjugation in them is interrupted by the meta-phenylene units. This is valid for neutral as well as for ionic systems. The charge localization on a stilbene unit causes extremely long wavelength “intervalence” bands in the UV/VIS spectra of the radical ions of these compounds.
The impact of interface states on sub-threshold leakage and power management in CMOS devices and circuits (2007)

Space applications expose electronic systems to levels of radiation that are damaging to the individual components. Considerable effort has gone into the "hardening" of electronic components against total-dose damage by ionizing radiation. This thesis explores the degree to which commercial-of-the-shelf parts are affected by ionizing radiation. In particular, concentration is on the effect of interface state generation resulting from ionizing radiation on overall device performance. Various sized 0.13μm MOSFET devices were simulated, fabricated, irradiated and tested. Significant increases in the sub-threshold swing and leakage current were observed following a 1MRad total-dose gamma ray irradiation. Subsequently, logic inverter structures exhibited increased sub-threshold swing and total power dissipation following simulations that modeled increasing radiation exposure. Finally, an 11-stage ring oscillator experiment was conducted. A decrease in power for increased irradiations was observed in previous work [49], but without explanation. This work attempts to provide a logical framework for understanding this observation.
Antimetastatic effect of Triton WR 1339, a nonionic detergent, on rat ascites tumors. (1979)

The antimetastatic effect of Triton WR 1339 (TWR), a nonionic detergent, was evaluated in the rats bearing ascites tumor (Yoshida sarcoma or AH 66F). TWR did not inhibit the growth of primary tumor (ascites production). However, a marked inhibition of metastasis was observed in the lung and liver of rats treated with TWR. The results obtained suggest that TWR exerts antimetastatic effect before the entry of tumor cells into vascular channels. With other tests, it was found that TWR inhibits the release of tumor cells from tumor graft.