gebhart/patrepeval huggingface dataset:
Dietary indoles and isothiocyanates that are generated from cruciferous vegetables can both stimulate apoptosis and confer protection against DNA damage in human colon cell lines. (2001)

The natural indoles 3,3'-diindolylmethane (DIM), ascorbigen (ASG), indole-3-carbinol (I3C), and indolo[3,2-b]carbazole (ICZ), as well as the natural isothiocyanates sulforaphane (SUL), benzyl isothiocyanate (BITC) and phenethyl isothiocyanate (PEITC), all possess cancer chemopreventive properties. It is now shown that DIM, ICZ, SUL, and BITC can each stimulate apoptosis in human colon adenocarcinoma LS-174 and Caco-2 cells. Treatment of LS-174 cells with nontoxic doses of DIM, ASG, I3C, or ICZ affected an increase of up to 21-fold in cytochrome P450 1A1 (CYP1A1). None of these indoles caused an elevation in either aldo-keto reductase 1C1 (AKR1C1) or the gamma-glutamylcysteine synthetase heavy subunit (GCS(h)), but DIM, I3C, and ICZ produced a very modest increase in NAD(P)H:quinone oxidoreductase 1 (NQO1). By contrast, nontoxic doses of SUL, BITC, or PEITC failed to induce expression of CYP1A1 in LS-174 cells, but caused an increase of between 11- and 17-fold in the protein levels of AKR1C1, NQO1, and GCS(h). Treatment of the colon cell line with ICZ or SUL caused increases in the levels of mRNA for CYP1A1, AKR1C1, and NQO1 that were consistent with the enzyme data. Exposure of Caco-2 cells to media containing indoles or isothiocyanates gave similar results to those obtained using LS-174 cells. Evidence is presented that the ability of indoles and isothiocyanates to stimulate either xenobiotic response element- or antioxidant response element-driven gene expression accounts for the two groups of phytochemicals inducing different gene batteries. Pretreatment of LS-174 cells for 24 h with ICZ and SUL before exposure for 24 h to benzo(a)pyrene (BaP) reduced to <20% the number of single-strand DNA breaks produced by the carcinogen. Neither ICZ alone nor SUL alone were able to confer the same degree of protection against DNA damage produced by BaP as they achieved in combination. Similar results were obtained with H(2)O(2) as the genotoxic agent. Together, these phytochemicals may prevent colon tumorigenesis by both stimulating apoptosis and enhancing intracellular defenses against genotoxic agents.
Hot hole induced damage in 1T-FBRAM on bulk FinFET (2011)

The reliability of a one Transistor Floating Body Random Access Memory (1T-FBRAM) bulk FinFET cell using Bipolar Junction Transistor (BJT) programming is investigated. It is shown that hot holes generated by impact ionization create interface defects close to the drain and positively charged oxide traps, especially at high transverse electric field. These created defects degrade the cell endurance. Moreover, this degradation is enhanced for shorter channel devices and narrower fin widths, which would be a limitation for the scaling of floating body RAM.
Obesity Increases the Severity of Acute Pancreatitis (2005)

Purpose: Obese patients appear to be at risk for more severe complications of acute pancreatitis (AP). APACHE-O score has been suggested to improve APACHE-II accuracy in predicting severe outcome in AP by adding a numerical score for obesity. Aims: (A) To determine if APACHE-O adds any significant predictive value to APACHE-II score and (B) to test the hypothesis that obese patients are at risk of more severe complications of AP than non-obese patients because of a more intense inflammatory response to pancreatic injury. Methods: 102 AP patients (mean age 50 years; 52 females, 50 males) were prospectively studied. Using a Body Mass Index (BMI) >30, 28% of the subjects were obese. Nineteen patients (19%) developed organ dysfunction and were classified as having severe AP (SAP). Receiver operating curves for prediction of SAP were calculated using admission APACHE-II and APACHE-O scores. Binary logistic regression was performed to assess if obesity is a risk for SAP and to determine the clinical factors associated with severe disease. Serum levels of IL-6, MCP-1 (early markers) and CRP and Ranson's scores (later markers) were compared between obese and non-obese patients with AP. Results: Admission APACHE-O (AUC: 0.895) and APACHE-II (AUC: 0.893) showed similar accuracy in predicting severe outcome. Admission APACHE-O cut-off value of 9 showed a sensitivity of 84%, specificity 82%, positive predictive value 52%, negative predictive value 96% and accuracy 83%. BMI was identified as a significant risk for SAP (OR: 2.8, p = 0.048). CRP levels and Ranson's score were significantly higher in obese than non-obese patients with AP (p = 0.0001 and p = 0.021 respectively). Admission IL-6 and MCP-1 levels showed a trend toward higher levels in obese patients but did not reach statistical significance (p = 0.368 and p = 0.325 respectively). Conclusions: Obesity is an independent risk for severe acute pancreatitis. Admission APACHE-O score is not more accurate than APACHE-II. Our study results suggest that obesity increases the severity of AP by amplifying the inflammatory response to injury. [figure 1]Figure
Modeling of nonlinear audio systems using swept-sine signals: application to audio effects (2009)

In this paper a new method for analysis and modeling of nonlinear audio systems is presented. The method is based on swept-sine excitation signal and nonlinear convolution firstly presented in [1, 2]. It can be used in nonlinear processing for audio applications, to simulate analog nonlinear effects (distortion effects, limiters) in digital domain. 1.
Redox control of transcription: sensors, response regulators, activators and repressers (1993)

In a growing number of cases, transcription of specific genes is known to be governed by oxidation or reduction of electron carriers with which the gene products interact. The biological function of such control is to activate synthesis of appropriate redox proteins, and to repress synthesis of inappropriate ones, in response to altered availability of specific electron sources and sinks. In prokaryotic systems this control appears to operate by two general classes of mechanism: by two-component regulation involving protein phosphorylation on histidine and aspartate; and by direct oxidation-reduction of gene repressors or activators. For the first class, termed 'two-component redox regulation', the term 'redox sensor' is proposed for any electron carrier that becomes phosphorylated upon oxidation or reduction and thereby controls phosphorylation of specific response regulators, while the term 'redox response regulator' is proposed for the corresponding sequence-specific DNA-binding protein that controls transcription as a result of its phosphorylation by one or more redox sensors. For the second class of redox regulatory mechanism, the terms 'redox activator protein' and 'redox repressor protein' are proposed for single proteins containing both electron transfer and sequence-specific DNA-binding domains. The structure, function and biological distribution of these components are discussed.
Subject-based reference values (1995)

Medical decisions based on comparison with group-based reference value have often less than desired sensitivity to significant changes in the biochemical or physiological state of an individual under investigation. Subgrouping of the reference values according to sex, age, or other criteria does frequently not solve this problem. The better solution is to compare new values with old results from the same individual, i.e., with subject-based reference values. Two types of criteria may be used: those based on critical differences between two results (the reference change limit) and those based on time-series models.
The ABSCISIC ACID INSENSITIVE 3 (ABI3) gene is modulated by farnesylation and is involved in auxin signaling and lateral root development in Arabidopsis (2003)

Genetic screens have identified a number of genes that regulate abscisic acid (ABA) responsiveness in Arabidopsis. Using a combination of suppressor screens and double mutant analysis, we have determined a genetic relationship for a number of these ABA response loci. Based on germination in the presence of exogenous ABA, the ABI1 and ABI2 phosphatases act at or upstream of the ERA1 farnesyl transferase and the ABI3 and ABI5 transcription factors act at or downstream of ERA1. In contrast with ABI3 and ABI5, the ABI4 transcription factor appears to act at or upstream of ERA1. Based on reporter gene constructs, the upstream regulation of ABI3 by ERA1 occurs at least partially at the level of transcription, suggesting that this lipid modification is required to attenuate ABI3 expression. Similar experiments also indicate that ABI3 is auxin inducible in lateral root primordia. Related to this, loss-of-function abi3 alleles show reduced lateral root responsiveness in the presence of auxin and an auxin transport inhibitor, and era1 mutants have increased numbers of lateral roots. These results suggest the possibility that genes identified through ABA responsive germination screens such as ERA1 and ABI3 have functions in auxin action in Arabidopsis.
New insights into the generation of Th2 immunity and potential therapeutic targets for the treatment of asthma (2010)

Studies of the role played by the innate immune system in the induction of Th2 responses have begun to unravel the cellular and molecular mechanisms potentially underlying the pathogenesis of allergic asthma. Further study in this area may lead to the discovery of new therapeutics for the treatment of allergic disease.
The butterfly: a broadband, aerodynamic antenna for airborne missile scoring using impulse radar (2002)

A description is given of the butterfly antenna which provides an aerodynamic replacement for the resistively loaded cone, for use with an airborne impulse radar. The missile-sensing system is described, and antenna requirements and developments are discussed. Results of measured performance are presented. The butterfly antenna is shown to give a clean pulse, although the pulse radiated sideways does have significant overshoot. The elevation pattern is broader and the efficiency is slightly higher than that in cones previously used.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Release of Glial Tissue–Specific Proteins After Acute Stroke (2000)

Our results indicate that postischemic release patterns of GFAP and S-100B protein may allow insight into the underlying pathophysiology of acute cerebral infarcts and may be used as a valuable tool of clinical stroke treatment.
Conotoxins-New Vistas for Peptide Therapeutics (2000)

There are approximately 500 species of predatory cone snails within the genus Conus. They comprise what is arguably the largest single genus of marine animals alive today. It has been estimated that the venom of each Conus species has between 50 and 200 components. These highly constrained sulfur rich components or conotoxins represent a unique arsenal of neuropharmacologically active peptides that have been evolutionarily tailored to afford unprecedented and exquisite selectivity for a wide variety of ion-channel subtypes. Remarkable divergence occurs when cone snails speciate. Consequently, the complement of venom peptides in any one Conus species is distinct from that of any other species. Hence many thousands of peptides that modulate ion channel function are present within Conus venoms. Evolutionary pressures have afforded a "pre-optimized," structurally sophisticated library that has been "fine tuned" over 50 million years. The statistics associated with sampling such libraries bear testimony to the validity and feasibility of this strategy. Although approximately 100 conotoxin sequences have been published in the scientific literature, representing a mere 0.2 % of the estimated library size, this sample has already afforded a peptide of proven clinical utility and several pre-clinical leads for CNS disorders. Conus libraries represent a rich pharmacopoeia and the potential to "therapeutically mine" such a resource appears limitless. The paucity of synthetic methodologies necessary to achieve the regioisomeric folding patterns present in these native peptides precludes access to synthetic conotoxin libraries, further validating the overall "mining" strategy. In this article, we will present a pragmatic overview of the molecular diversity as well as the neurobiological mechanisms that define each major class of conotoxin.
Streamlined quantification of absolute MBF at rest and stress with flurpiridaz F-18 injection PET in normal subjects and patients with coronary artery disease (CAD) (2011)

Surface critical behavior (SCB) refers to the singularities of physical quantities on the surface at the bulk phase transition. It is closely related to and even richer than the bulk critical behavior. In this work, we show that three types of SCB universality are realized in the dimerized Heisenberg models at the (2+1)-dimensional O(3) quantum critical points by engineering the surface configurations. The ordinary transition happens if the surface is gapped in the bulk disordered phase, while the gapless surface state generally leads to the multicritical special transition, even though the latter is precluded in classical phase transitions because the surface is in the lower critical dimension. An extraordinary transition is induced by the ferrimagnetic order on the surface of the staggered Heisenberg model, in which the surface critical exponents violate the results of the scaling theory and thus seriously challenge our current understanding of extraordinary transitions.
Regulation of methane monooxygenase genes in methanotrophs (2002)

Methanotrophs are bacteria capable of using methane as their sole carbon and energy source. Oxidation of methane by Methylosinus trichosporium OB3b is catalysed by the particulate (pMMO) and soluble (sMMO) methane monooxygenase enzymes. Transcription of the genes encoding pMMO (pmo) occurs at high copper-to-biomass ratio and sMMO (mmo) at low copper-to-biomass ratios. The aim of this work was to study the regulation of methane monooxygenase gene expression in response to copper ions- the "copper switch".&#13;\n&#13;\nPrimer extension and RT-PCR revealed putative transcriptional start sites 5' of the pmoC genes from Methylocystis sp. strain M and Methylosinus trichosporium OB3b that corresponded to a"-promoters. The pmo operons from both organisms possessed tandem promoters 5' of pmoC suggesting differential expression of the two sets of pmo genes. A qualitative analysis of pmo transcription from M trichosporium OB3b revealed that the pmo operon is transcribed at both high and low copper ion concentrations when M. trichosporium OB3b was grown on methane or methanol.&#13;\n&#13;\nThe gene encoding a" (rpoN) was cloned and sequenced, since previously Nielsen et al., (Mo! Microbiol (1997) 25, 399-409) had shown that transcription of the mmo genes from M trichosporium OB3b was shown to proceed from a a"-type promoter. Marker-exchange mutagenesis of rpoN verified its role in transcription of the mmo operon and also suggested its requirement for transcription of both nitrogen fixation and nitrate reduction genes. Sequencing of the region 5' of the mmo cluster (Ian McDonald, unpublished) revealed a gene possessing homology with a"-dependent transcriptional activators, named mmoR. Mutation of mmoR by marker-exchange mutagenesis showed it was also required for expression of the mmo operon. These data have allowed an improved model for the regulation of the pmo and mmo gene clusters by copper to be proposed.&#13;\n
Administrators Solving the Problems of Practice: Decision-Making Concepts, Cases, and Consequences (1994)

Publisher's description: This book describes eight different models of decision-making, compares the models, and illustrates how to use each model with actual cases from schools. The frameworks include classical, administrative, incremental, mixes scanning, political, and garbage-can models, as well as two models of shared decision-making. After illustrating the use of these decision-making models to analyze and develop solution strategies, students have the opportunity to explore about fifty actual cases to build their own analyses and solution strategies.
Non-cholinergic excitation in neurons after a chronic glutamate receptor blockade (2003)

Previous experiments revealed a dramatic increase in excitatory acetylcholine transmission in hypothalamic cultures during a chronic decrease in glutamate activity. Data suggested that in the absence of glutamate excitation, acetylcholine becomes the major excitatory neurotransmitter. However, non-cholinergic excitatory activity was also detected in some neurons. Here, using calcium imaging in hypothalamic cultures chronically subjected to the glutamate receptor blockade, we demonstrate the contribution of metabotropic glutamate receptors, P2-purinoreceptors, histamine receptors, adrenoreceptors, and gap junctions, but not nitric oxide to this non-cholinergic excitation. We also show that the sensitivity of neurons to receptor agonists is increased following the blockade. Data suggest that multiple components contribute to the excitatory activity in hypothalamic neurons during a long-term decrease in glutamate activity.
Spatial Interaction and the Statistical Analysis of Lattice Systems (1974)

Summary The formulation of conditional probability models for finite systems of spatially interacting random variables is examined. A simple alternative proof of the Hammersley–Clifford theorem is presented and the theorem is then used to construct specific spatial schemes on and off the lattice. Particular emphasis is placed upon practical applications of the models in plant ecology when the variates are binary or Gaussian. Some aspects of infinite lattice Gaussian processes are discussed. Methods of statistical analysis for lattice schemes are proposed, including a very flexible coding technique. The methods are illustrated by two numerical examples. It is maintained throughout that the conditional probability approach to the specification and analysis of spatial interaction is more attractive than the alternative joint probability approach.
UDPgalactose 4‐epimerase from Saccharomyces cerevisiae (2004)

UDPgalactose 4-epimerase (epimerase) catalyzes the reversible conversion between UDPgalactose and UDPglucose and is an important enzyme of the galactose metabolic pathway. The Saccharomyces cerevisiae epimerase encoded by the GAL10 gene is about twice the size of either the bacterial or human protein. Sequence analysis indicates that the yeast epimerase has an N-terminal domain (residues 1-377) that shows significant similarity with Escherichia coli and human UDPgalactose 4-epimerase, and a C-terminal domain (residues 378-699), which shows extensive identity to either the bacterial or human aldose 1-epimerase (mutarotase). The S. cerevisiae epimerase was purified to > 95% homogeneity by sequential chromatography on DEAE-Sephacel and Resource-Q columns. Purified epimerase preparations showed mutarotase activity and could convert either alpha-d-glucose or alpha-d-galactose to their beta-anomers. Induction of cells with galactose led to simultaneous enhancement of both epimerase and mutarotase activities. Size exclusion chromatography experiments confirmed that the mutarotase activity is an intrinsic property of the yeast epimerase and not due to a copurifying endogenous mutarotase. When the purified protein was treated with 5'-UMP and l-arabinose, epimerase activity was completely lost but the mutarotase activity remained unaffected. These results demonstrate that the S. cerevisiae UDPgalactose 4-epimerase is a bifunctional enzyme with aldose 1-epimerase activity. The active sites for these two enzymatic activities are located in different regions of the epimerase holoenzyme.
Integrated atom detector based on field ionization near carbon nanotubes (2009)

We demonstrate an atom detector based on field ionization and subsequent ion counting. We make use of field enhancement near tips of carbon nanotubes to reach extreme electrostatic field values of up to $9\ifmmode\times\else\texttimes\fi{}{10}^{9}\text{ }\text{V}/\text{m}$, which ionize ground-state rubidium atoms. The detector is based on a carpet of multiwall carbon nanotubes grown on a substrate and used for field ionization, and a channel electron multiplier used for ion counting. We measure the field enhancement at the tips of carbon nanotubes by field emission of electrons. We demonstrate the operation of the field ionization detector by counting atoms from a thermal beam of a rubidium dispenser source. By measuring the ionization rate of rubidium as a function of the applied detector voltage we identify the field ionization distance, which is below a few tens of nanometers in front of nanotube tips. We deduce from the experimental data that field ionization of rubidium near nanotube tips takes place on a time scale faster than ${10}^{\ensuremath{-}10}\text{ }\text{s}$. This property is particularly interesting for the development of fast atom detectors suitable for measuring correlations in ultracold quantum gases. We also describe an application of the detector as partial pressure gauge.
Pneumococcal Bacteremia in Charleston County, South Carolina (1990)

Since nationwide surveillance for pneumococcal bacteremia in the United States is not done, community-based studies are useful alternative methods to monitor trends in this disease. Data on the incidence of pneumococcal bacteremia in Charleston County, South Carolina, from 1974 to 1976, have been used to support cost-effective pneumococcal vaccine programs for the elderly. We reevaluated the incidence of pneumococcal bacteremia in Charleston County in 1986 and 1987 to assess whether earlier estimates remained valid given changes in medical practice. During 1986 and 1987, overall annual incidence of pneumococcal bacteremia in Charleston County was 18.7 per 100,000 (95% confidence limits, 13.7 to 23.6 per 100,000), which represents a 2.3-fold increase over the earlier rate. The increase coincided with a 2.2-fold increase in the annual number of blood cultures processed at four Charleston County hospital laboratories from 1975 to 1987 despite only a 1.1-fold increase in the number of patients discharged from these hospitals. Annualized rates increased 2.3-fold for adults more than or equal to 65 years old to 53 per 100,000 and 4.6-fold for children less than 2 years old to 162 per 100,000. The case-fatality rate of bacteremic patients was 18%, compared with 21% in the earlier study. The case-fatality rate for adults more than or equal to 65 years of age was 44%. Ninety-one percent of adults 19 to 64 years old with bacteremia had underlying medical conditions for which pneumococcal vaccine is recommended; all persons 55 to 64 years old had at least one underlying condition. The marked increases in pneumococcal bacteremia rates detected are likely due to more routine culturing of blood from symptomatic patients with pneumococcal disease. These findings emphasize the need for effective programs promoting use of pneumococcal vaccine in high-risk groups, particularly those more than or equal to 65 years old, and the development of a more immunogenic vaccine for children less than 2 years old.