gebhart/patrepeval huggingface dataset:
Modifications of DNA by different haloethylnitrosoureas. (1982)

The modification of DNA by the haloethylnitrosoureas is probably responsible for their antitumor activity. A current hypothesis relates this cytotoxic action to the transfer of haloethyl groups from the nitrosourea to DNA followed by a second reaction of the haloethyl group with the opposite DNA strand. However, other modifications besides interstrand cross-links are introduced into DNA, raising the question whether the choice of the particular nitrosourea could affect the distribution of DNA modifications in a way which would maximize cytotoxic activity. To investigate this point, DNA was reacted with the following compounds: N,N'-bis(2-chloroethyl)-N-nitrosourea (NSC 409962); N-(2-chloroethyl)-N'-cyclohexyl-N-nitrosourea (NSC 79037); N-(2-chloroethyl N'-(2,6-dihydroxycyclohexyl)-N-nitrosourea (NsC 264395); N-(2-chloroethyl)-N-nitrosourea (NSC 47547); and N-(2-fluoroethyl(-N'-cyclohexyl-N-nitrosourea (NSC 87974). Reacted DNA was depurinated, and the distribution of guanine derivatives was obtained by high-pressure liquid chromatography. These studies have shown that the distribution of products obtained is markedly influenced by the chemical structure of the nitrosourea. Differences are noted in the relative amounts of 6- versus 7-substituted guanines, in the amount of hydroxyethylation versus haloethylation, and in the amount of diguanylethane formation. Thus, it may be possible to modulate the biological effect obtained from a nitrosourea by changing its molecular structure.
Analysis of a Dual-Rotor, Toroidal-Winding, Axial-Flux Vernier Permanent Magnet Machine (2017)

In this paper, a vernier permanent magnet (VPM) machine with dual-rotor toroidal-winding axial-flux topology is analyzed. Through the combination of toroidal windings with the rotor-stator-rotor topology, the end winding length of the proposed machine is significantly reduced compared with that of the regular VPM machine. Based on the airgap permeance function, the back-EMF and torque expressions are derived and the nature of the machine is revealed. The influence of pole ratio (ratio of rotor pole pair number to stator pole pair number) and main geometric parameters, such as slot opening, magnet thickness, etc., on electromagnetic performance is then analytically investigated in detail. Both the quasi-three-dimensional (quasi-3D) finite element analysis (FEA) and 3-D FEA are applied to verify the derived equations. Finally, a prototype of the proposed machine has been manufactured and experimentally evaluated. The test results agree well with both theoretical and FEA analyses. With the current density of 5.8 A/mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> and slot fill factor of 0.35, the torque density of the proposed machine prototype can reach 31.9 kNm/m <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> .
The role of spontaneous cap domain mutations in haloalkane dehalogenase specificity and evolution (1994)

The first step in the utilization of the xenobiotic chlorinated hydrocarbon 1,2-dichloroethane by Xanthobacter autotrophicus is catalyzed by haloalkane dehalogenase (Dh1A). The enzyme hydrolyses 1-haloalkanes to the corresponding alcohols. This allows the organism to grow also on short-chain (C2-C4) 1-chloro-n-alkanes. We have expressed Dh1A in a strain of Pseudomonas that grows on long-chain alcohols and have selected 12 independent mutants that utilize 1-chlorohexane. Six different mutant enzymes with improved Km or Vmax values with 1-chlorohexane were obtained. The sequences of the mutated dh1A genes showed that several mutants had the same 11-amino acid deletion, two mutants carried a different point mutation, and three mutants had different tandem repeats. All mutations occurred in a region encoding the N-terminal part of the cap domain of Dh1A, and it is concluded that this part of the protein is involved in the evolution of activity toward xenobiotic substrates.
Effect of curing-tip diameter on the accuracy of dental radiometers. (1999)

The purpose of this study was to determine the accuracy of four commercially available radiometers when curing tips of different diameters were used. A visible-light curing unit (Optilux 500) with a new 80-watt quartz-halogen bulb (OptiBulb) was used as the light source for all measurements. The unit's irradiance value was measured using three hand-held radiometers (Demetron model #100, Cure-Rite model #644726, and Coltolux Light Meter) and a built-in visible-light curing unit radiometer (Optilux 500). Measurements were made with four curing tips of diameters 4 mm, 7.5 mm, 10.5 mm, and 12 mm. For each tip, trials were made with five radiometers of each model. Student's t-tests at the 0.05 level of significance were used to compare the mean irradiance measured by each model of radiometer, to the irradiance value measured by a laboratory-grade power meter. A one-way analysis of variance at the 0.05 level of significance was used to compare the irradiance values among the five samples of each commercially available radiometer model. Except for the Optilux 500 built-in radiometer with the 10.5-mm tip, all the commercially available radiometers exhibited irradiance values significantly different from those of the laboratory-grade power meter. There were no statistically significant differences among the five samples of each commercially available radiometer model.
Current strategies for the prevention of breast cancer (2014)

Due to the high incidence of breast cancer in the United States, optimal strategies for its prevention are imperative. This entails identification of women who are at an increased risk for breast cancer and an integrative approach that includes effective screening methods as well as nutritional, pharmacologic, and surgical management. Several breast cancer risk-assessment tools, such as the Gail and Claus models, can help clinicians determine the quantitative risk of breast cancer. The role of selective estrogen receptor modulators, such as tamoxifen and raloxifene, for the prevention of breast cancer has been well established. Several other agents, such as aromatase inhibitors, are currently being investigated. The potential adverse effects of these chemopreventive agents, which include an impact on the quality of life, must be discussed with the patient before deciding on this approach. Additionally, breast cancer risk factors have been identified over the years; some of them are modifiable, but others are not. Although there is no conclusive evidence to suggest the protective role of specific dietary components, alcohol consumption and obesity are associated with an increased breast cancer risk; thus lifestyle changes can lead to a lower risk of developing breast cancer. Surgical approaches, including bilateral risk-reduction mastectomy and salpingo-oophorectomy, are usually limited to women with a hereditary predisposition to development of breast cancer. The objective of this review is to summarize the various approaches directed at reducing the incidence of breast cancer.
The Production of "Experimental Neurosis" in the White Rat* (1939)

Psychiatric Clinic for Children, University of Minnesota Hospitals and Department of Psychology, University of Minnesota
THE TAGGING OF RED CELLS AND PLASMA PROTEINS WITH RADIOACTIVE CHROMIUM 1 (1950)

In preparation for the present study, arc spectrography 3 was used to demonstrate the presence of trace amounts of chromium in human tissues, including the blood. Tissue analyses were performed on samples of normal human blood by means of a colorimetric method (2) with the finding of mean values of 20 y % for packed red cells and 14 y % for plasma. The present report is concerned with a new biological tracer, radioactive chromium (Cr51), which is bound by the red cells and plasma proteins. Both anionic hexavalent (Na2Cr51O4) and cationic trivalent (Cr51Cl3) states of the element have been studied.
Apodizing functions for Fourier transform spectroscopy (2007)

Apodizing functions are used in Fourier transform spectroscopy (FTS) to reduce the magnitude of the sidelobes in the instrumental line shape (ILS), which are a direct result of the finite maximum optical path difference in the measured interferogram. Three apodizing functions, which are considered optimal in the sense of producing the smallest loss in spectral resolution for a given reduction in the magnitude of the largest sidelobe, find frequent use in FTS [J. Opt. Soc. Am.66, 259 (1976)]. We extend this series to include optimal apodizing functions corresponding to increases in the width of the ILS ranging from factors of 1.1 to 2.0 compared with its unapodized value, and we compare the results with other commonly used apodizing functions.
Satellites free the mobile phone (1998)

A variety of satellite systems, soon to go into orbit, will bounce voice and data between wireless handheld phones anywhere on Earth. Peripatetic users will be able to switch at will between conventional terrestrial service and the new satellite systems wherever they roam. Some of the satellite-based land mobile services are or will be worldwide, others cover broad geographical regions. All are characterized by the magnitude of the capital being invested-in the billions of US dollars-and by sweeping transnational business alliances. Virtually every one of these wireless efforts has given rise to international partnerships, often involving satellite manufacturers, cellular service providers, electronic equipment companies, and telecommunications entities. In addition, satellite systems are going into orbit to supply other services besides dialup telephones.
IL-4 Biology: Impact on Normal and Leukemic CLL B Cells (2003)

This review provides a perspective on the role of IL-4 in relation to both normal and leukemic CLL B cells. IL-4 is a well-characterized cytokine known to be produced by normal T cells and have impact on normal B cell differentiation and proliferation. This cytokine and its receptor are now known to exist on CLL B cells. An autocrine pathway for CLL B cells is strongly supported by signaling events, alteration of apoptotic proteins and changes in apoptosis resistance. Based on the increasing knowledge regarding the IL-4 pathway unique opportunities for therapy are now available in B-CLL.
Brain Basis of Phonological Awareness for Spoken Language in Children and Its Disruption in Dyslexia (2011)

Phonological awareness, knowledge that speech is composed of syllables and phonemes, is critical for learning to read. Phonological awareness precedes and predicts successful transition from language to literacy, and weakness in phonological awareness is a leading cause of dyslexia, but the brain basis of phonological awareness for spoken language in children is unknown. We used functional magnetic resonance imaging to identify the neural correlates of phonological awareness using an auditory word-rhyming task in children who were typical readers or who had dyslexia (ages 7-13) and a younger group of kindergarteners (ages 5-6). Typically developing children, but not children with dyslexia, recruited left dorsolateral prefrontal cortex (DLPFC) when making explicit phonological judgments. Kindergarteners, who were matched to the older children with dyslexia on standardized tests of phonological awareness, also recruited left DLPFC. Left DLPFC may play a critical role in the development of phonological awareness for spoken language critical for reading and in the etiology of dyslexia.
<i>In situ</i>data collection and structure refinement from microcapillary protein crystallization (2005)

In situ X-ray data collection has the potential to eliminate the challenging task of mounting and cryocooling often fragile protein crystals, reducing a major bottleneck in the structure determination process. An apparatus used to grow protein crystals in capillaries and to compare the background X-ray scattering of the components, including thin-walled glass capillaries against Teflon, and various fluorocarbon oils against each other, is described. Using thaumatin as a test case at 1.8 Å resolution, this study demonstrates that high-resolution electron density maps and refined models can be obtained from in situ diffraction of crystals grown in microcapillaries.
A robust estimation of distribution algorithm for power electronic circuits design (2010)

The automated synthesis and optimization of power electronic circuits (PECs) is a significant and challenging task in the field of power electronics. Traditional methods such as the gradient-based methods, the hill-climbing techniques and the genetic algorithms (GA), are either prone to local optima or not efficient enough to find highly accurate solutions for this problem. To better optimize the design of PECs, this paper presents an extended histogram-based estimation of distribution algorithm with an adaptive refinement process (EDA/a-r). In the EDA/a-r, the histogram-based estimation of distribution algorithm is used to roughly locate the global optimum, while the adaptive refinement process is used to improve the accuracy of solutions. The adaptive refinement process, with its search radius adjusted adaptively during the evolution, is executed to search the surrounding region of the best-so-far solution in every generation. To maintain the diversity, a historic learning strategy is used in constructing the probabilistic model and a mutation strategy is hybridized in the sampling operation. The proposed EDA/a-r has been successfully used to optimize the design of a buck regulator. Experimental results show that compared with the GA and the particle swarm optimization (PSO), the EDA/a-r can obtain much better mean solution quality and is less likely to be trapped into local optima.
Selection of reference genes for qPCR in hairy root cultures of peanut (2011)

This work constitutes the first effort to validate reference genes for RT-qPCR in hairy roots. While these genes were selected under conditions of NaOAc and MeJA treatment, we anticipate these genes to provide good targets for reference genes for hairy roots under a variety of stress conditions. The lead reference genes were a gene encoding for a TATA box binding protein (TBP2) and a gene encoding a ribosomal protein (RPL8C). A commonly used reference gene GAPDH showed low stability of expression suggesting that its use may lead to inaccurate gene expression profiles when used for data normalization in stress-stimulated hairy roots. Likewise the A. rhizogenes transgene rolC showed less expression stability than GAPDH. This study proposes that a minimum of two reference genes should be used for a normalization procedure in gene expression profiling using elicited hairy roots.
Induction of Angiogenesis by Controlled Delivery of Vascular Endothelial Growth Factor Using Nanoparticles (2012)

Dex-GMA and gelatin-based nanoparticles could provide sustained release of VEGF and may serve as a new way for angiogenesis.
Hedgehog signaling is essential for normal wound healing (2008)

The hedgehog family of morphogens (sonic [Shh], Indian, and desert hedgehog) are central regulators of embryologic growth and tissue patterning. Although recent work implicates Shh in postnatal tissue repair and development, conclusive evidence is lacking. Here, we demonstrated the importance of Shh in wound repair, by examining the effects of cyclopamine, a specific inhibitor of the Shh signaling cascade, on tissue repair. Using a murine-splinted excisional wound model, which attenuates wound contraction in this loose-skinned rodent, we established that, by all measures (wound closure, epithelialization, granulation formation, vascularity, and proliferation), wound healing was profoundly impaired when Shh signaling was disrupted. Because embryonic disruption of Shh is associated with distinct phenotypic defects, our findings invite investigation of the potential role of Shh signaling under postnatal conditions associated with disregulated wound healing.
On point estimation of the abnormality of a Mahalanobis index (2016)

Mahalanobis distance may be used as a measure of the disparity between an individual's profile of scores and the average profile of a population of controls. The degree to which the individual's profile is unusual can then be equated to the proportion of the population who would have a larger Mahalanobis distance than the individual. Several estimators of this proportion are examined. These include plug-in maximum likelihood estimators, medians, the posterior mean from a Bayesian probability matching prior, an estimator derived from a Taylor expansion, and two forms of polynomial approximation, one based on Bernstein polynomial and one on a quadrature method. Simulations show that some estimators, including the commonly-used plug-in maximum likelihood estimators, can have substantial bias for small or moderate sample sizes. The polynomial approximations yield estimators that have low bias, with the quadrature method marginally to be preferred over Bernstein polynomials. However, the polynomial estimators sometimes yield infeasible estimates that are outside the 0-1 range. While none of the estimators are perfectly unbiased, the median estimators match their definition; in simulations their estimates of the proportion have a median error close to zero. The standard median estimator can give unrealistically small estimates (including 0) and an adjustment is proposed that ensures estimates are always credible. This latter estimator has much to recommend it when unbiasedness is not of paramount importance, while the quadrature method is recommended when bias is the dominant issue.
Toward Understanding Molecular Mechanisms of Abiotic Stress Responses in Rice (2008)

Abstract Plants have evolved delicate mechanisms to cope with environmental stress. Following exposure to environmental stimuli, extracellular signals are perceived and transmitted through signal transduction cascades. Upon receipt and transmission of the signals, a number of stress-related genes are induced, leading to stress adaptation in plant cells. Rice, which is a critical food grain for a large portion of the world’s population, is frequently impacted by several abiotic stressors, the most important of which are drought, salinity, and cold. Exposure to environmental conditions outside of acceptable tolerance ranges can negatively affect rice growth and production. In this paper, a review of rice responses to abiotic stress is presented, with particular attention to the genes and pathways related to environmental stress tolerance. It is apparent that, while progress has been made in identifying genes involved in stress adaptation, many questions remain. Understanding the mechanisms of stress response in rice is important for all research designed to develop new rice varieties with improved tolerance.
Monolingual Distributional Profiles for Word Substitution in Machine Translation (2018)

Out-of-vocabulary (OOV) words present a significant challenge for Machine Translation. For low-resource languages, limited training data increases the frequency of OOV words and this degrades the quality of the translations. Past approaches have suggested using stems or synonyms for OOV words. Unlike the previous methods, we show how to handle not just the OOV words but rare words as well in an Example-based Machine Translation (EBMT) paradigm. Presence of OOV words and rare words in the input sentence prevents the system from finding longer phrasal matches and produces low quality translations due to less reliable language model estimates. The proposed method requires only a monolingual corpus of the source language to find candidate replacements. A new framework is introduced to score and rank the replacements by efficiently combining features extracted for the candidate replacements. A lattice representation scheme allows the decoder to select from a beam of possible replacement candidates. The new framework gives statistically significant improvements in English-Chinese and English-Haitian translation systems.
Inhibitory effect of a genistein derivative on pigmentation of guinea pig skin (2017)

This study demonstrated the mechanisms of the inhibitory effects of GD against UVB-induced pigmentation in guinea pig skin.
Influence of template strandedness on in vitro replication of mutagen-damaged DNA (1987)

We analyzed the ability of DNA polymerases to bypass damage on single- and double-stranded templates. In vitro DNA synthesis was studied on UV-irradiated and polyaromatic hydrocarbon reacted (benzo[a]pyrenediol epoxide and oxiranylpyrene) double-stranded templates by a protocol involving initiation on a uniquely nicked circular double-stranded template. The template was prepared by treating single-stranded (+)M13mp2 circular strands with mutagen and then hybridizing with restricted M13 RFmp2, followed by isolation of the nicked RFII forms. The protocol permits either (+), (-), or both strands to carry lesions. We found that the rules for termination and bypass of lesions previously observed with single-stranded DNA templates also hold for double-stranded templates. Termination of synthesis occurs primarily one nucleotide 3' to the lesion in the template strand. Bypass of UV-induced lesions can be followed in a series of three partial reactions in the presence of Mn2+ and dGMP, which relax the specificity of nucleotide insertion and 3'----5' exonuclease activity, respectively. There is no evidence for greater permissivity of bypass in double-as opposed to single-stranded templates. As with single-stranded templates, purines and preferentially deoxyadenosine (dA) are inserted opposite lesions. Lesions in the nontemplate strand elicit neither termination nor pausing. The addition of Rec A protein resulted in a measurable increase of bypass in this system.
Formation of Lung Alveolar-Like Structures in Collagen–Glycosaminoglycan Scaffolds <i>in Vitro</i> (2005)

The objective of this study was to investigate the histology of tissue formed when fetal rat lung cells were grown in a collagen-glycosaminoglycan (GAG) tissue-engineering scaffold. The goal was the formation of lung histotypic structures in the tissue-engineering scaffolds in vitro. Achieving this goal would facilitate future investigations of the effects of selected scaffold design parameters on processes that may underlie aspects of lung regeneration in vivo. Lung cells were obtained from Sprague-Dawley rats after 16 and 19 days of gestation. These dissociated cells were seeded into type I collagen-chondroitin 6-sulfate matrices, 8 mm in diameter by 2 mm in thickness, cross-linked and sterilized by dehydrothermal treatment. Approximately 28 million cells were seeded into each spongelike sample. Histological and immunohistochemical studies were performed at termination periods of 2 days and 1, 2, and 3 weeks. The enzymatically dissociated 19-day gestation fetal rat lung cells formed and maintained alveolar-like structures, 50-60 microm in diameter, in the collagen- GAG scaffold. A novel finding was that all of the cell-seeded scaffolds underwent cell-mediated contraction that appeared to be associated with the finding by immunohistochemistry of expression of alpha-smooth muscle actin in some cells. These results demonstrate the capability of dissociated lung cells to form lung histotypic structures in collagen-GAG tissue-engineering scaffolds in vitro. This culture system may be of value in facilitating exploration of strategies for preparing such scaffolds for the regeneration of lung tissue in vivo.