gebhart/patrepeval huggingface dataset:
A Case Study: What Doses of <i>Amanita phalloides</i> and Amatoxins Are Lethal to Humans? (2015)

There are few data estimating the human lethal dose of amatoxins or of the toxin level present in ingested raw poisonous mushrooms. Here, we present a patient who intentionally ingested several wild collected mushrooms to assess whether they were poisonous. Nearly 1 day after ingestion, during which the patient had nausea and vomiting, he presented at the emergency department. His transaminase levels started to increase starting from hour 48 and peaking at hour 72 (alanine aminotransferase 2496 IU/L; aspartate aminotransferase 1777 IU/L). A toxin analysis was carried out on the mushrooms that the patient said he had ingested. With reversed-phase high-performance liquid chromatography analysis, an uptake of approximately 21.3 mg amatoxin from nearly 50 g mushroom was calculated; it consisted of 11.9 mg alpha amanitin, 8.4 mg beta amanitin, and 1 mg gamma amanitin. In the urine sample taken on day 4, 2.7 ng/mL alpha amanitin and 1.25 ng/mL beta amanitin were found, and there was no gamma amanitin. Our findings suggest that the patient ingested approximately 0.32 mg/kg amatoxin, and fortunately recovered after serious hepatotoxicity developed.
Contributions of Long-Term Research and Time-Series Observations to Marine Ecology and Biogeochemistry (2008)

Time-series observations form a critical element of oceanography. New interdisciplinary efforts launched in the past two decades complement the few earlier, longer-running time series to build a better, though still poorly resolved, picture of lower-frequency ocean variability, the climate processes that drive variability, and the implications for food web dynamics, carbon storage, and climate feedbacks. Time series also enlarge our understanding of ecological processes and are integral for improving models of physical-biogeochemical-ecological ocean dynamics. The major time-series observatories go well beyond simple monitoring of core ocean properties, although that important activity forms the critical center of all time-series efforts. Modern ocean time series have major process and experimental components, entrain ancillary programs, and have integrated modeling programs for deriving a better understanding of the observations and the changing, three-dimensional ocean in which the observatories are embedded.
Case histories of dc resistivity measurements to map shallow coal mine workings (2003)

Two recent events have focused attention on the need for mapping underground mine workings: the failure of the Martin County Coal Corporation tailings impoundment near Inez, Kentucky on 11 October 2000 and the 24 July 2002 Quecreek Mine inundation that trapped nine miners for 77 hours in Somerset County, Pennsylvania. In both cases, unexpected conditions related to abandoned mines were the sources of the accidents. In the first case, the overburden between an abandoned mine and the base of a slurry impoundment was too thin and the slurry broke into the mine. The consequence was that the slurry broke out and flooded two separate watersheds with coal refuse. In the second case, miners accidentally excavated into the flooded workings of the abandoned Saxman Mine, which they thought was hundreds of feet away.
Proprietary arabinogalactan extract increases antibody response to the pneumonia vaccine: a randomized, double-blind, placebo-controlled, pilot study in healthy volunteers (2010)

ISRCTN98817459.
Matrix GLA Protein Modulates Differentiation Induced by Bone Morphogenetic Protein-2 in C3H10T1/2 Cells (2001)

Matrix GLA protein (MGP) is ubiquitously expressed with high accumulation in bone and cartilage, where it was found to associate with bone morphogenetic proteins (BMP) during protein purification. To test whether MGP affects BMP-induced differentiation, three sets of experiments were performed. First, pluripotent C3H10T1/2 cells transfected with human MPG (hMGP) or antisense to hMGP (AS-hMGP) were treated with BMP-2. In cells overexpressing hMGP, osteogenic and chondrogenic differentiation was inhibited indicating decreased BMP-2 activity. Conversely, in cells overexpressing AS-hMGP, BMP-2 activity was enhanced. Second, cells were prepared from homozygous and heterozygous MPG-deficient mice aortas. When treated with BMP-2, these cells underwent chondrogenic and osteogenic differentiation, respectively, whereas controls did not. Third, FLAG-tagged hMGP with the same biological effect as native hMGP inhibited BMP-induced differentiation, when exogenously added to culture media. Together, these results suggest that MGP modulates BMP activity. To test whether hMGP fragments would retain the effect of full-length hMGP, three subdomains were overexpressed in C3H10T1/2 cells. In cells expressing the mid-region, alone (amino acids (aa) 35-54) or in combination with the N terminus (aa 1-54) but not the C terminus (aa 35-84), osteogenic differentiation was enhanced and occurred even without added BMP-2. Thus, two subdomains had the opposite effect of full-length hMGP, possibly due to different expression levels or domain characteristics.
Oxidative Cross-Coupling of <i>N</i>-(2‘-Phenylphenyl)benzene- sulfonamides or Benzoic and Naphthoic Acids with Alkenes Using a Palladium−Copper Catalyst System under Air (1998)

N-(2‘-Phenylphenyl)benzenesulfonamides react with acrylate esters accompanied via cleavage of the C−H bond at their 2‘-position in the presence of a catalyst system of Pd(OAc)2 and Cu(OAc)2 and a base under air to produce 5,6-dihydro-5-(benzenesulfonyl)phenanthridine-6-acetate derivatives in high yields. The reactions of benzoic acid with butyl acrylate and styrene can also give 3-[(butoxycarbonyl)methyl]phthalide and 3-phenylisocoumarin, respectively.
Exact analytical loop closure in proteins using polynomial equations (1999)

Loop closure in proteins has been studied actively for over 25 years. Using spherical geometry and polynomial equations, several loop-closure problems in proteins are solved exactly by reducing them to the determination of the real roots of a polynomial. Loops of seven, eight, and nine atoms are treated explicitly, including the tripeptide and disulfide-bonded loop-closure problems. The number of valid loop closures can be evaluated by the method of Sturm chains, which counts the number of real roots of a polynomial. Longer loops can be treated by three methods: by sampling enough dihedral angles to reduce the problem to a soluble loop-closure problem; by applying the loop-closure algorithm hierarchically; or by decimating the chain into independently moving rigid elements that can be reconnected using loop-closure algorithms. Applications of the methods to docking, homology modeling and NMR problems are discussed. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 819-844, 1999.
Classical Swine Fever Virus E <sup>rns</sup> Deletion Mutants: <i>trans</i> -Complementation and Potential Use as Nontransmissible, Modified, Live-Attenuated Marker Vaccines (2000)

An SK6 cell line (SK6c26) which constitutively expressed the glycoprotein E(rns) of classical swine fever virus (CSFV) was used to rescue CSFV E(rns) deletion mutants based on the infectious copy of CSFV strain C. The biochemical properties of E(rns) from this cell line were indistinguishable from those of CSFV E(rns). Two E(rns) deletion mutants were constructed, virus Flc23 and virus Flc22. Virus Flc23 encoded only the utmost N- and C-terminal amino acids of E(rns) (deletion of 215 amino acids) to retain the original protease cleavage sites. Virus Flc22 is not recognized by a panel of E(rns) antibodies, due to a deletion of 66 amino acids in E(rns). The E(rns) deletion mutants Flc22 and Flc23 could be rescued in vitro only on the complementing SK6c26 cells. These rescued viruses could infect and replicate in SK6 cells but did not yield infectious virus. Virus neutralization by E(rns)-specific antibodies was similar for the wild-type virus and the recombinant viruses, indicating that E(rns) from SK6c26 cells was incorporated in the viral particles. Pigs vaccinated with Flc22 or Flc23 were protected against a challenge with a lethal dose of CSFV strain Brescia. This is the first demonstration of trans-complementation of defective pestivirus RNA with a pestiviral structural protein and opens new ways to develop nontransmissible modified live pestivirus vaccines. In addition, the absence of (the antigenic part of) E(rns) in the recombinant viral particles can be used to differentiate between infected and vaccinated animals.
Exon 5 deletion variant estrogen receptor messenger RNA expression in relation to tamoxifen resistance and progesterone receptor/pS2 status in human breast cancer. (1995)

The exon 5 deletion splice variant of estrogen receptor (delta 5 ER), which in vitro is constitutively active in the absence of estrogens, may have a role in conferring both tamoxifen resistance and ER-related phenotype in breast cancer. We have investigated the expression of this variant in vivo (at the level of mRNA) in relation to known tamoxifen resistance and expression of the estrogen-regulated genes progesterone receptor (PgR) and pS2. The amount of delta 5 ER mRNA relative to wild type (WT) ER mRNA (% delta 5/WT) was assayed in 70 tamoxifen-resistant and 50 primary breast carcinomas using reverse transcription/PCR. Both WT and delta 5 ER mRNA were detected in the majority of tumors, although delta 5 ER was detected only in the presence of WT ER. Overall no significant difference was seen in % delta 5/WT ER between tamoxifen-resistant and primary control tumors (medians, 13 and 15%, respectively). Tumors in both control and resistant groups which expressed PgR/pS2 in the absence of measurable ER protein (ER- PgR+ and ER- pS2+) had significantly higher delta 5 ER mRNA levels compared with other phenotypes (P < 0.002). This association with ER-/pS2+ tumors has not been demonstrated previously. In ER+ tumors which expressed pS2, significantly greater delta 5 ER mRNA expression was observed in tamoxifen-resistant compared with control tumors (P = 0.05). A similar although nonsignificant trend was observed in ER+ PgR+ tumors. While delta 5 ER mRNA is unlikely to be responsible for tamoxifen resistance in most breast cancers, elevated delta 5 ER mRNA levels may be important in some tumors, especially those which continue to express high levels of PgR/pS2.
Mutational analysis of the damage-recognition and catalytic mechanism of human SMUG1 DNA glycosylase (2004)

Single-strand selective monofunctional uracil-DNA glycosylase (SMUG1), previously thought to be a backup enzyme for uracil-DNA glycosylase, has recently been shown to excise 5-hydroxyuracil (hoU), 5-hydroxymethyluracil (hmU) and 5-formyluracil (fU) bearing an oxidized group at ring C5 as well as an uracil. In the present study, we used site-directed mutagenesis to construct a series of mutants of human SMUG1 (hSMUG1), and tested their activity for uracil, hoU, hmU, fU and other bases to elucidate the catalytic and damage-recognition mechanism of hSMUG1. The functional analysis of the mutants, together with the homology modeling of the hSMUG1 structure based on that determined recently for Xenopus laevis SMUG1, revealed the crucial residues for the rupture of the N-glycosidic bond (Asn85 and His239), discrimination of pyrimidine rings through pi-pi stacking to the base (Phe98) and specific hydrogen bonds to the Watson-Crick face of the base (Asn163) and exquisite recognition of the C5 substituent through water-bridged (uracil) or direct (hoU, hmU and fU) hydrogen bonds (Gly87-Met91). Integration of the present results and the structural data elucidates how hSMUG1 accepts uracil, hoU, hmU and fU as substrates, but not other oxidized pyrimidines such as 5-hydroxycytosine, 5-formylcytosine and thymine glycol, and intact pyrimidines such as thymine and cytosine.
Membrane microdomain switching: a regulatory mechanism of amyloid precursor protein processing (2008)

Neuronal activity has an impact on beta cleavage of amyloid precursor protein (APP) by BACE1 to generate amyloid-beta peptide (Abeta). However, the molecular mechanisms underlying this effect remain to be elucidated. Cholesterol dependency of beta cleavage prompted us to analyze immunoisolated APP-containing detergent-resistant membranes from rodent brains. We found syntaxin 1 as a key molecule for activity-dependent regulation of APP processing in cholesterol-dependent microdomains. In living cells, APP associates with syntaxin 1-containing microdomains through X11-Munc18, which inhibits the APP-BACE1 interaction and beta cleavage via microdomain segregation. Phosphorylation of Munc18 by cdk5 causes a shift of APP to BACE1-containing microdomains. Neuronal hyperactivity, implicated in Abeta overproduction, promotes the switching of APP microdomain association as well as beta cleavage in a partially cdk5-dependent manner. We propose that microdomain switching is a mechanism of cholesterol- and activity-dependent regulation of APP processing in neurons.
Main Magnetic Focus Ion Trap, new tool for trapping of highly charged ions (2014)

It is proposed to produce the highly charged ions in the local ion trap formed by a rippling electron beam in the focusing magnetic field. The experimental results demonstrate the presence of iridium ions with charges up to 50+. According to estimates, the average electron current density in the local ion trap can reach the value of the order of 10 kA/cm^2. The pilot examples of devices of this type with the electron beam energies within the range 3-10 keV are also presented.
Analysis of oblate spheroidal antenna (2002)

An oblate spheroidal antenna with linearly polarized excitation is analyzed numerically, and its radiation patterns are examined. The beamwidth of the E-plane radiation pattern becomes wider as the antenna height is increased. The integral equation method can be easily applied to the case of circularly polarized excitation.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Validation of a web-based ESL test (2003)

The web offers new opportunities to realize some of the current ideals for interactive language assessment by providing learners information about their language ability at their convenience. If such tests are to be trusted to provide learners with information that might help to improve their language ability, the tests need to undergo validation processes, but validation theory does not offer specific guidance about what should be included in a validity argument. Conventional wisdom suggests that low-stakes tests require less rigorous validation than high-stakes tests, but what are the factors that affect decisions about the validation process for either? Attempting to make these contributing factors explicit, this article examines the ways in which the purpose of a low-stakes web-based ESL (English as a second language) test guided its design and the validation process. The validity argument resulting from the first phase of the validation process is illustrated.
An approach to implement contracts as trusted intermediaries (2004)

In a virtual enterprise context, business process interoperability and cooperative process enactment are important in order to achieve a common objective despite the distribution in space, time and organizations. A contract is a facility used to deploy cross-organizational processes, to monitor and to enforce the composition and the enactment of these processes both inside and outside the organization's boundaries. This paper presents a contract model for describing clauses that address business interactions, for deploying cross-organizational activities (called synchronization points) and for enforcing and controlling policies. The contract is an XML document used to describe how process Web services cooperates and how synchronization points enforce contract clauses.
The Art of Scientific Investigation (1954)

Though this book is written by an eminent biologist, no excuse is necessary for bringing it to the attention of physicists; the principles with which Prof. Beveridge is concerned are common to all branches of science. In the preface he seems to imply that he is writing mainly for the benefit of the young scientist who is a beginner in research, but the book will be enjoyed by research workers and scientists of all ages.
The sarcomeric actin CArG-binding factor is indistinguishable from the c-fos serum response factor. (1989)

The c-fos serum response element (SRE) and a sarcomeric actin promoter element (CArG box) are similar in sequence and are recognized, respectively, by the serum response factor (SRF) and the CArG-binding factor (CBF). Although the transcriptional controls for the c-fos and sarcomeric actin genes are rather different, SRF and CBF have been found to be indistinguishable by all criteria tested. They exhibited similar chromatographic properties, sedimentation rates, and temperature stabilities. In mobility shift assays, the SRE competed more strongly than the actin CArG box for formation of either the SRF-SRE or the CBF-CArG complex. The symmetric inverted repeat of the left side of the Xenopus cytoskeletal actin SRE also competed, even more strongly, for each complex. The site-specific binding of each protein was inhibited both by orthophenanthroline, whose effects were reversed by zinc addition, and by treatment with potato acid phosphatase. Furthermore, immune serum raised against the c-fos SRF also recognized the actin CBF. We discuss how transcriptional control of these diverse genes might be obtained with a single similar factor.
Smaller fleas ... ad infinitum: therapeutic bacteriophage redux. (1996)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
The Effect of an Audience on the Gakel-Call and Other Frustration Behaviours in the Laying Hen (<i>Gallus Gallus Domesticus</i>) (2003)

Abstract When thwarted in a behaviour, laying hens show an increase in stereotyped pacing, displacement preening and a specific vocalisation known as the ‘gakel-call’. How these behaviours, which might serve as indicators of welfare, are influenced by social factors is not yet known. In this study, we investigated the effect of an audience (another bird or a human) on the expression of the gakel-call and other behaviours indicating frustration. Twenty-four Lohman Brown hens were trained to gain free access to food in a test cage. Sixteen hens were used as test birds and eight as non-test audience birds. The food-deprived test hens were tested for 15 min in a non-thwarting situation (food freely available) and for 15 min in a thwarting situation (food covered but visible). For both situations we investigated four different treatments: no audience in the adjacent cage; a non-thwarted audience bird in the adjacent cage; a thwarted audience bird in the adjacent cage; and finally a human audience. The durations of stereotyped pacing and displacement preening were significantly higher in test birds during thwarting than during non-thwarting; thwarted birds also gave significantly more gakel-calls compared to non-thwarted birds. The test birds, and also the audience birds, gave more gakel-calls when thwarted in the presence of a thwarted conspecific than when in the presence of a non-thwarted bird, but there were no significant differences in stereotyped pacing or displacement preening, which are usually associated with frustration. In conclusion, this study supports the view that the gakel-call signals frustration in laying hens. Furthermore, the state of the audience influences the occurrence of gakel-calls in thwarted hens. Thus, when using the gakel-call as a welfare-indicator, the social aspects of the vocal expression of frustration in laying hens should not be overlooked.
Chitosan inserts for periodontitis: Influence of drug loading, plasticizer and crosslinking on in vitro metronidazole release (2007)

Chitosan based metronidazole (MZ) inserts were fabricated by the casting method and characterized with respect to mass and thickness uniformity, metronidazole loading and in vitro metronidazole release kinetics. The fabricated inserts exhibited satisfactory physical characteristics. The mass of inserts was in the range of 5.63 +/- 0.42 to 6.04 +/- 0.89 mg. The thickness ranged from 0.46 +/- 0.06 to 0.49 +/- 0.08 mm. Metronidazole loading was in the range of 0.98 +/- 0.09 to 1.07 +/- 0.07 mg except for batch CM3 with MZ loading of 2.01 +/- 0.08 mg. The inserts exhibited an initial burst release at the end of 24 h, irrespective of the drug to polymer ratio, plasticizer content or cross-linking. However, further drug release was sustained over the next 6 days. Cross-linking with 10% (m/m) of glutaraldehyde inhibited the burst release by approximately 30% and increased the mean dissolution time (MDT) from 0.67 to 8.59 days. The decrease in drug release was a result of reduced permeability of chitosan due to cross-linking.
Analyzing regression test selection techniques (1996)

Regression testing is a necessary but expensive maintenance activity aimed at showing that code has not been adversely affected by changes. Regression test selection techniques reuse tests from an existing test suite to test a modified program. Many regression test selection techniques have been proposed, however, it is difficult to compare and evaluate these techniques because they have different goals. This paper outlines the issues relevant to regression test selection techniques, and uses these issues as the basis for a framework within which to evaluate the techniques. The paper illustrates the application of the framework by using it to evaluate existing regression test selection techniques. The evaluation reveals the strengths and weaknesses of existing techniques, and highlights some problems that future work in this area should address.
Oral passive immunization against dental caries in rats by use of hen egg yolk antibodies specific for cell-associated glucosyltransferase of Streptococcus mutans (1991)

The effect of polyclonal egg yolk immunoglobulin G antibodies (yIgG) raised against whole cells, cell-free (CF) glucosyltransferase (GTase), or cell-associated (CA) GTase of serotype c Streptococcus mutans was examined in terms of in vitro inhibition of virulence-related factors of S. mutans and protection of S. mutans-infected rats against the development of dental caries. Hens (18 weeks old) were immunized with formalin-treated whole cells, purified CF-GTase, or CA-GTase together with Freund's complete adjuvant. In addition, yIgG to surface protein antigen was used in some in vitro experiments for comparison with other antibodies. yIgG was purified by ammonium sulfate precipitation followed by DEAE-Sephacel column chromatography or fractional precipitation with ethanol. Purified yIgG was found to be a 220-kDa protein, which was dissociated into heavy and light chains upon addition of 2-mercaptoethanol. yIgG to whole cells and surface protein antigen gave a heavy aggregation of S. mutans organisms, while yIgG to CF- and CA-GTase specifically inhibited the enzymatic activity of the respective GTase. yIgG to CA-GTase and whole cells was found to clearly suppress the adherence of S. mutans cells to a glass surface. Specific-pathogen-free Sprague-Dawley rats that had been infected heavily and repeatedly with S. mutans and fed diet no. 2000 developed severe dental caries, while rats fed diet 2000 containing greater than or equal to 0.1% yIgG to CA-GTase showed a statistically significant reduction in dental plaque accumulation and caries development. Administration of yIgG to CF-GTase and whole cells failed to protect against caries. These results clearly suggest that yIgG to S. mutants CA-GTase specifically inhibited a virulence factor of this organism, i.e., insoluble glucan-synthesizing CA-GTase, resulting in a significant reduction in the development of dental caries.