gebhart/patrepeval huggingface dataset:
On the molecular basis of uracil recognition in DNA: comparative study of T-A versus U-A structure, dynamics and open base pair kinetics (2010)

Uracil (U) can be found in DNA as a mismatch paired either to adenine (A) or to guanine (G). Removal of U from DNA is performed by a class of enzymes known as uracil-DNA-glycosylases (UDG). Recent studies suggest that recognition of U-A and U-G mismatches by UDG takes place via an extra-helical mechanism. In this work, we use molecular dynamics simulations to analyze the structure, dynamics and open base pair kinetics of U-A base pairs relative to their natural T-A counterpart in 12 dodecamers. Our results show that the presence of U does not alter the local conformation of B-DNA. Breathing dynamics and base pair closing kinetics are only weakly dependent on the presence of U versus T, with open T-A and U-A pairs lifetimes in the nanosecond timescale. Additionally, we observed spontaneous base flipping in U-A pairs. We analyze the structure and dynamics for this event and compare the results to available crystallographic data of open base pair conformations. Our results are in agreement with both structural and kinetic data derived from NMR imino proton exchange measurements, providing the first detailed description at the molecular level of elusive events such as spontaneous base pair opening and flipping in mismatched U-A sequences in DNA. Based on these results, we propose that base pair flipping can occur spontaneously at room temperature via a 3-step mechanism with an open base pair intermediate. Implications for the molecular basis of U recognition by UDG are discussed.
Integrated gas chromatography-mass spectrometry (1973)

Mass spectrometric analysis of organic compounds was in the early 1950s done mostly for quantitative determination of petroleum products. The use of the mass spectrometer for qualitative analysis of solid organic material samples was shown by O'Neil & Wier (1951) and since then a continuous increase in mass spectrometric studies of different classes of organic compounds has been noted. After the gas chromatograph was developed by James & Martin (1952) the quantitative analysis of complex mixtures of organic compounds was possible and after a few years the gas chromatographic method was considered as routine. The first connection of a gas chromatograph (GC) to a mass spectrometer (MS) was made by Holmes & Morell (1957). They studied gases using a splitter system where only a small part or less than 1% of the effluent from a packed column was transferred to the ion source of the mass spectrometer. The next step in GC—MS development was made by Gohlke (1959), who studied compounds of low molecular weight using capillary column directly connected to a time-of-flight mass spectrometer. This was possible due to the fact that the carrier gas flow rate could be limited to about 1 ml/min. To avoid the sample loss resulting from using a packed column with the splitter system a jet molecular separator was constructed as an interphase between the packed column and a mass spectrometer with magnetic sector analyser (Ryhage, 1964). Mixtures of fatty acids and of hydrocarbons with a molecular weight of up to about 420 were studied. In this study spectra were taken at irregular intervals.
QPQ Technology and Quality Control (2006)

QPQ technology is a new surface modification and strengthening technology for metals. This paper examines some process and quality control methods of QPQ technology.
Tetramethyl Rhodamine Methyl Ester (TMRM) is Suitable for Cytofluorometric Measurements of Mitochondrial Membrane Potential in Cells Treated with Digitonin (1999)

A new method for cytofluorometric analysis of mitochondrial membrane potential deltapsi has been developed by using TMRM as a cationic, mitochondrial selective probe. The method is based on limited treatment of cultured cells with digitonin which permeabilises the plasma membrane and leaves mitochondria intact. The resulting signal of TMRM-stained cells thus represents only the probe accumulated in mitochondria. Fibroblasts and cybrids were used as a model cell systems and optimal conditions for digitonin treatment and staining by TMRM were described. The TMRM signal collapsed by valinomycin, KCN and antimycin A and FCCP titration was used to gradually lower deltapsi and characterise the stability of deltapsi. The method is suitable for sensitive measurement of deltapsi in different types of cultured cells.
Design of Shrinkage Margin for Thin Panel Welded Structure during Manufacturing Process (2005)

The purpose of this study is to establish a design tool for the shrinkage margin of a deckhouse caused by welding and flame straightening. In order to do it, the effects of heat intensity and internal/external restraint condition on the shrinkage of the simple weldments were investigated, in order to identify the principal factors controlling shrinkage caused by welding process and flame straightening. Based on the results, predictive equations for longitudinal and transverse shrinkage at the welded structure were formulated as the function of heat intensity and in-plane rigidity. These equations were verified by comparing predicted results with the measured results at a panel structure of deckhouse.
Effect of on‐farm interventions in the aftermath of an outbreak of hypervirulent verocytotoxin‐producing <i>Escherichia coli</i> O157:H7 in Sweden (2018)

In 2007, human infections with a hypervirulent strain of verocytotoxin-producing <i>Escherichia coli</i> O157:H7 increased in Sweden and especially in the Halland County. A connection between the cases and a local beef cattle farm with an on-farm abattoir and meat processing plant was established. In this observational study the control measures implemented on the infected farm and the dynamics of infection in the herd are described. In May 2008, when measures were initiated and animals put to pasture, the prevalence of positive individuals was 40 per cent and 18 carcasses out of 24 slaughtered animals were contaminated. During summer the monthly prevalence of positive carcasses varied between 8 and 41 per cent and at turning-in 22 out of 258 individually sampled animals were shedding the pathogen. After January 2009 no positive carcasses were found at slaughter and follow-up samplings of environment and individuals remained negative until the study period ended in May 2010. The results indicate that on-farm measures have potential to reduce the prevalence of the pathogen in a long-term perspective. However, as self-clearance cannot be excluded the effectiveness of the suggested measures needs to be confirmed.
Upregulation of Bone Morphogenetic Protein-1/Mammalian Tolloid and Procollagen C-Proteinase Enhancer-1 in Corneal Scarring (2014)

Bone morphogenetic protein-1/mTLD and PCPE-1 are upregulated in corneal scars. Both proteins may therefore contribute to the process of corneal scarring.
National Cholesterol Education Program recommendations for measurement of low-density lipoprotein cholesterol: executive summary. The National Cholesterol Education Program Working Group on Lipoprotein Measurement (1995)

Journal Article National Cholesterol Education Program recommendations for measurement of low-density lipoprotein cholesterol: executive summary. The National Cholesterol Education Program Working Group on Lipoprotein Measurement Get access P S Bachorik, P S Bachorik Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA Search for other works by this author on: Oxford Academic Google Scholar J W Ross J W Ross Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA Search for other works by this author on: Oxford Academic Google Scholar Clinical Chemistry, Volume 41, Issue 10, 1 October 1995, Pages 1414–1420, https://doi.org/10.1093/clinchem/41.10.1414 Published: 01 October 1995
Design and development of a practical muscle fatigue monitor (2009)

The purpose of the study is to develop a method to monitor the patient during the exercise and advice him to stop as he is approaching the fatigue condition. The median frequency of the EMG signal has been recognized as the best indicator of the muscular fatigue during the voluntary contraction of skeletal muscles. The EMG signal is picked up from the body using a pair of biopotential electrodes. A special preamplifier and a band-pass filer are designed to process the raw signal. The signal is applied into a personal computer (PC) via the sound card. The power spectrum of the signal is calculated using the Fast Fourier Transform (FFT) algorithm in MATLAB. The median frequency is calculated and plotted against time during the exercise. Experiments are designed to test the procedure in the lab. The fluctuations in the median frequency are eliminated using averaging over time. The tests indicate a drop in the mean value of the median frequency before the test subject feels the fatigue.
An XML Plagiarism Detection Model for Procedural Programming Languages (2003)

Plagiarism is a common place in academics, especially in courses involving programming. In this paper, XPDec, an XML-based model is introduced to detect similarities among programs that arise under plagiarism. Based upon the syntax of a specific programming language, XPDec uses an XML scheme that is suitable for the detection of plagiarism. XML documents are generated from given program sources and XQuery is used to extract information relevant to the detection of plagiarism. The XML’s tree-like representation of query results is exploited to ignore common forms of reordering that arise in plagiarism. The level of similarity between a pair of programs is numerically quantified and reported. The usefulness of XPDec in detection of plagiarism is discussed. XPDec has been implemented, and its architecture is presented.
Interaction between growth arrest-DNA damage protein 34 and Src kinase Lyn negatively regulates genotoxic apoptosis (2001)

Genotoxic stresses activate intracellular signaling molecules, which lead to growth arrest, DNA repair, and/or apoptosis. Among these molecules are the growth arrest and DNA damage protein 34 (GADD34) and the Src-related protein tyrosine kinase Lyn. Here, we report that these two proteins physically and functionally interact to regulate DNA damage-induced apoptosis. Multiple isolates of GADD34 and the related murine protein MyD116 were identified as binding partners of Lyn in a yeast two-hybrid screen. The specific interaction was confirmed by in vitro association of GADD34 with glutathione S-transferase fusion proteins containing the Src Homology 3 (SH3) domain of Lyn, as well as coimmunoprecipitation of GADD34 and Lyn from mammalian cells. GADD34 was tyrosine-phosphorylated in vivo in a Lyn-dependent manner. Lyn efficiently phosphorylated affinity-purified GADD34 in vitro. Lyn negatively regulated the proapoptotic function of GADD34 in a kinase-dependent manner. Expression of wild-type, but not kinase-inactive, Lyn weakened promotion of apoptosis by GADD34 following treatment with methyl-methanesulfonate or ionizing radiation in HEK293 and HeLa cells. In contrast, pretreatment of cells with the Src-specific tyrosine kinase inhibitor PP1 strengthened promotion of apoptosis by GADD34. We propose that Lyn regulates the proapoptotic function of GADD34 by binding and phosphorylating it.
One-step synthesis of substituted 6,8-dioxabicyclo[3.2.1]octanes: easy preparation of racemic frontalin, brevicomins, and related systems (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTOne-step synthesis of substituted 6,8-dioxabicyclo[3.2.1]octanes: easy preparation of racemic frontalin, brevicomins, and related systemsMiguel Yus and Diego J. RamonCite this: J. Org. Chem. 1992, 57, 2, 750–751Publication Date (Print):January 1, 1992Publication History Published online1 May 2002Published inissue 1 January 1992https://pubs.acs.org/doi/10.1021/jo00028a065https://doi.org/10.1021/jo00028a065research-articleACS PublicationsRequest reuse permissionsArticle Views226Altmetric-Citations52LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Polymorphism of HLA class I genes in Meizhou Han population of Guangdong, China (2007)

Summary Human leukocyte antigen (HLA) is an invaluable marker for anthropological studies because of its extreme polymorphism. Most of the studies carried out in Chinese populations are about HLA class II genes, but few about class I genes. In the present study, we investigated HLA class I polymorphism using polymerase chain reaction‐sequencing‐based typing (PCR‐SBT) method in 104 unrelated Han individuals in Meizhou of Guangdong, southern China. Twenty‐three HLA‐A, 43 HLA‐B and 27 HLA‐C alleles were identified and allele frequencies and two‐locus (C/B) and three‐locus (A/C/B) haplotypes were statistically analysed. The most frequent HLA‐A allele is A*110101 with a frequency of 30.3%, followed by A*24020101 (22.2%) and A*2420 (11.6%). Among the 43 detected HLA‐B alleles, B*5801 (17.0%), B*400101 (15.5%) and B*4601 (10.0%) were frequently observed. Among the 27 detected C alleles, the most predominant one is Cw*07020101 (25.8%), followed by Cw*0717 (14.7%). The most frequent HLA‐C/B two‐locus haplotype is Cw*07020101/B*400101 (10.1%). The most common HLA‐A/C/B three‐locus haplotype in Meizhou Han is A*110101/Cw*07020101/B*400101 (3.4%). Phylogenetic tree based on HLA class I allele frequencies genetically suggested that Meizhou Han has an affinity to southern Asian populations. The result may also reflect an admixture of Han and ethnic minorities of southern China.
Human anelloviruses and the central nervous system (2010)

Torque teno virus and related anelloviruses are a recent addition to the list of agents that cause chronic productive infections and high levels of plasma viraemia in humans. Many aspects of the natural history and pathogenesis of these under many respects surprising viruses are still poorly understood. In this review, we briefly outline the general properties of anelloviruses, examine what is currently known about the interactions they establish with the central nervous system (CNS), and discuss the possible pathological consequences.
Intravenous Immunoglobulin for the Prevention of Infection in Chronic Lymphocytic Leukemia (1988)

In a double-blind study, we randomly assigned 84 patients with chronic lymphocytic leukemia who were judged to be at increased risk of bacterial infection to receive intravenous immunoglobulin G (400 mg per kilogram of body weight) or a placebo every three weeks for one year. Eligible patients had hypogammaglobulinemia, a history of infection, or both. The patients receiving immunoglobulin had significantly fewer bacterial infections during the study period than those receiving placebo (23 vs. 42; P = 0.01). This reduction was most striking in the patients who completed a full year of treatment (14 vs. 36; P = 0.001). The period from study entry to the first serious bacterial infection was significantly longer in the patients receiving immunoglobulin (P = 0.026). There was no significant difference between the two groups in the incidence of nonbacterial infection. Immunoglobulin therapy was tolerated well; there were no serious adverse reactions, and the incidence of minor reactions was low. We conclude that selected patients with chronic lymphocytic leukemia who are at risk of bacterial infection can be substantially protected from this complication by the regular intravenous administration of immunoglobulin.
Survival-factor-induced phosphorylation of Bad results in its dissociation from Bcl-xL but not Bcl-2 (2001)

The pro-apoptotic Bcl-2-family protein Bad heterodimerizes with Bcl-2 and Bcl-xL in the outer mitochondrial membranes, nullifying their anti-apoptotic activities and promoting cell death. We report that interleukin-3 (IL-3) stimulation induces Bad phosphorylation and triggers its translocation from mitochondria to cytoplasm in cells expressing Bcl-xL but not Bcl-2. Overexpression of Bad sensitized Bcl-xL-expressing FL5.12 cells to apoptosis induced by IL-3 deprivation, but had no effect on the viability of cells expressing Bcl-2. IL-3 stimulation induced Bad phosphorylation at Ser-112, impairing its binding to Bcl-xL and resulting in its association with 14-3-3 proteins in the cytosol. However, Ser-112 phosphorylation could not trigger Bad dissociation from mitochondria in FL5.12 cells expressing Bcl-2. In 293T cells expressing Bcl-xL, Bad was phosphorylated at three serines, 112, 136 and 155, and was largely localized in the cytosolic fraction. In contrast, overexpression of Bcl-2 prevented phosphorylation of Bad at Ser-136 and Ser-155, sequestering this protein in the mitochondrial membranes. When the N-terminal regions of Bcl-2 and Bcl-xL were swapped with each other, the Bcl-xL(N)–Bcl-2 chimaeric protein (containing the N-terminal region of Bcl-xL) failed to prevent Bad phosphorylation in cells and was unable to block the cytosolic distribution of this pro-apoptotic protein. Additional experiments with the Bcl-2(N)–Bcl-xL chimaeric protein (containing the N-terminal region of Bcl-2) indicated that, although the N-terminal region of Bcl-2 is necessary, it is not sufficient for sequestering Bad in the mitochondrial membranes. These observations suggest that growth-factor-mediated phosphorylation of Bad contributes to the cytoprotective function of Bcl-xL but not Bcl-2.
Tradition’s Use of Burns: The Legendary Tradition (1984)

Burns’ own milieu was a traditional one: on the very personal level, he unconsciously accepted many of its practices and concerns; as an artist in words he drew from it in a multiplicity of ways; and as a collector of folksongs he recorded one aspect of that on-going oral tradition, folksongs, for posterity. As inheritor of a cultural tradition, he lived in large measure by it, taking from it, and giving back to it. Unwittingly, he also provided the ever-developing tradition with an immense body of additional material, for he became the central figure in a legendary tradition, which at different times has largely included three narrative genres — personal experience stories, legends, jokes and anecdotes — which reflect changing attitudes and perspectives towards Burns.
A current-sourced DC-DC converter derived via the duality principle from the half-bridge converter (1993)

A current-sourced switch-mode power supply topology is developed by applying a duality principle to a voltage-sourced half-bridge converter. The converter has boost converter characteristics and is suited to low-voltage high-current input applications. It is shown to compare favorably with the center-tapped transformer converter. Two optional enhancements-nondissipative snubber networks and inductor clamping windings-are also examined. Some results obtained with a low-power prototype are presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
The Variation of Breast Parenchymal Patterns with Age (1985)

The Wolfe classification of mammographic parenchymal patterns has been applied to 9036 women attending a Breast Cancer Screening Unit. Overall, two thirds fell into high risk categories (P2 and DY). The incidence of DY decreases with age, while the low risk categories (N1 and P1) increase with age. P2 remains constant over most of the age range. The implications of these findings are discussed and comparison is made with other series.
Utility of <u>In Situ</u> Assays for Detecting Environmental Pollutants (1990)

In Situ bioassays are toxicity determining techniques applied to or designed for use under real world conditions outside of the control of the laboratory. A number of plants and animals, domestic and wild, are used in situ to measure and monitor mutagenesis, carcinogenesis and other biological endpoints; for example, growth, nitrogen fixation, excretion of urinary δ-aminolevulinic acid, blood cell abnormalities, etc. The organisms include corn, soybean, spiderwort, white footed mouse, wild house mouse, mudminnow, white croaker and brown bullhead fish, sea urchin and mussel.
Endothelial cells from cord blood CD133<sup>+</sup>CD34<sup>+</sup> progenitors share phenotypic, functional and gene expression profile similarities with lymphatics (2008)

The existence of endothelial progenitor cells (EPC) with high cell-cycle rate in human umbilical cord blood has been recently shown and represents a challenging strategy for therapeutic neovascularization. To enhance knowledge for future cellular therapy, we compared the phenotypic, functional and gene expression differences between EPC-derived cells generated from cord blood CD34(+) cells, and lymphatic and macrovascular endothelial cells (EC) isolated from human foreskins and umbilical veins, respectively. Under appropriate culture conditions, EPC developed into fully matured EC with expression of similar endothelial markers as lymphatic and macrovascular EC, including CD31, CD36, von Willebrand factor FVIII, CD54 (ICAM-1), CD105 (endoglin), CD144 (VE-cadherin), Tie-1, Tie-2, VEGFR-1/Flt-1 and VEGFR-2/Flk-1. Few EPC-derived cells became positive for LYVE-1, indicating their origin from haematopoietic stem cells. However they lacked expression of other lymphatic cell-specific markers such as podoplanin and Prox-1. Functional tests demonstrated that the cobblestone EPC-derived cells up-regulated CD54 and CD62E expression in response to TNF-alpha, incorporated DiI-acetylated low-density liproprotein and formed cord- and tubular-like structures with capillary lumen in three-dimensional collagen culture--all characteristic features of the vascular endothelium. Structures compatible with Weibel-Palade bodies were also found by electron microscopy. Gene microarray profiling revealed that only a small percentage of genes investigated showed differential expression in EPC-derived cells and lymphatic EC. Among them were adhesion molecules, extracellular matrix proteins and cytokines. Our data point to the close lineage relationship of both types of vascular cells and support the theory of a venous origin of the lymphatic system.