gebhart/patrepeval huggingface dataset:
Double bands in DNA gel elctrophoresis caused by bis-intercalating dyes (1995)

Many bis-intercalating dyes used for fluorescence detection of DNA in electrophoresis have been reported to give band-splitting and band-broadening, which results in poor resolution and a decreased detection sensitivity. We have studied the dimeric dye YOYO-1, and to some extent also TOTO-1 and EthD-1, and found that in complex with DNA these dyes give rise to two components with different electrophoretic mobilities. Electrophoresis experiments and spectroscopic measurements on the two components show that they differ in that the DNA molecules have different amounts of dye bound. Our results exclude that the extra bands are caused by intermolecular cross-linking. Incubation of the samples for increasing times before electrophoresis makes the bands move closer and closer to each other as the dye molecules become more homogeneously distributed among the DNA molecules. Finally, the two bands merge into one at an intermediate position. This equilibration process is extremely slow at room temperature (days), and is therefore not a practical method to eliminate band-splitting in routine analysis. However, we find that if the temperature is raised to 50 degrees C, the dye-DNA complexes equilibrate completely in only 2 h.
Lipoxygenase product formation and cell adhesion during neutrophil-glomerular endothelial cell interaction (1995)

Leukotriene (LT) and lipoxin (LX) levels were monitored in ionophore-stimulated coincubations of polymorphonuclear neutrophils (PMN) and microvascular kidney glomerular endothelial cells (GEN) to determine the profile of lipoxygenase (LO) products generated during cell-cell interactions and the relative contributions of transcellular pathways to LO product biosynthesis in this setting. LTB4 and LTC4 were the major products formed, as determined by reverse-phase high-performance liquid chromatography and radioimmunoassay. LTB4 and LTC4 levels were increased by 23 and 185%, respectively, in coincubations of PMN and GEN, compared with incubations of PMN alone. In contrast, LXA4 and LXB4 levels were not changed in the presence of GEN. These data suggested that GEN utilize PMN-derived LTA4 to generate LT. In keeping with this hypothesis, LT biosynthesis was enhanced if PMN were primed with human granulocyte-macrophage colony-stimulating factor (GM-CSF), a cytokine that augments LTA4 biosynthesis by activated PMN. The influence of LT on PMN adhesion to GEN was also assessed, since adhesion appears to be a pivotal event in recruitment of PMN in acute glomerulonephritis. Under basal conditions, LTB4 provoked low levels of adhesion via a PMN-directed CD11/CD18-dependent mechanism. The level of adhesion was markedly enhanced by prior priming of PMN with GM-CSF or activation of GEN with tumor necrosis factor-alpha (TNF). LTB4 was as potent in this regard as the complement component C5a, platelet-activating factor (PAF), and interleukin-8 (IL-8), other mediators that contribute to the entrapment of PMN in inflamed glomeruli. LTC4 also provoked PMN-GEN adhesion via a CD11/CD18-dependent mechanism, but, in contrast to LTB4, via actions with GEN. This action of LTC4 appeared to be mediated, at least in part, by induction of PAF synthesis by GEN. Interestingly, LT-induced PMN-GEN adhesion was markedly attenuated following remodeling of PMN phospholipids with 15(S)-hydroxyeicosatetraenoic acid, a product of 15-LO, which has been implicated as an anti-inflammatory eicosanoid in some experimental and human inflammatory diseases. Taken together, these results provide further evidence that 1) transcellular biosynthetic pathways may amplify the profiles of inflammatory mediators and thereby contribute to leukocyte recruitment in acute glomerulonephritis and 2) that products of the 5-LO and 15-LO pathways may exert opposing actions on PMN trafficking during glomerular inflammation in vivo.
Comparative genomic and transcriptomic analyses reveal the hemibiotrophic stage shift of <i>Colletotrichum</i> fungi (2012)

Hemibiotrophic fungal plant pathogens represent a group of agronomically significant disease-causing agents that grow first on living tissue and then cause host death in later, necrotrophic growth. Among these, Colletotrichum spp. are devastating pathogens of many crops. Identifying expanded classes of genes in the genomes of phytopathogenic Colletotrichum, especially those associated with specific stages of hemibiotrophy, can provide insights on how these pathogens infect a large number of hosts. The genomes of Colletotrichum orbiculare, which infects cucurbits and Nicotiana benthamiana, and C. gloeosporioides, which infects a wide range of crops, were sequenced and analyzed, focusing on features with potential roles in pathogenicity. Regulation of C. orbiculare gene expression was investigated during infection of N. benthamiana using a custom microarray. Genes expanded in both genomes compared to other fungi included sequences encoding small, secreted proteins (SSPs), secondary metabolite synthesis genes, proteases and carbohydrate-degrading enzymes. Many SSP and secondary metabolite synthesis genes were upregulated during initial stages of host colonization, whereas the necrotrophic stage of growth is characterized by upregulation of sequences encoding degradative enzymes. Hemibiotrophy in C. orbiculare is characterized by distinct stage-specific gene expression profiles of expanded classes of potential pathogenicity genes.
The management of Behçet's syndrome. (2007)

Behçet syndrome (BS) is a multisystem vasculitis characterized by skin and mucosa lesions and musculoskeletal, ocular, gastrointestinal, neurological and major vessel involvement. It is seen mainly in the Mediterranean basin, Middle East and the Far East. The disease runs a more severe course among young males and the severity diminishes with age. This review describes the management of this disease, which should be individualized and varies according to site and gender.
Release of cytokines induced by Salmonella typhimurium porins (1993)

Salmonella typhimurium SH5014 porins induce the release of tumor necrosis factor alpha (TNF-alpha), interleukin 1 alpha (IL-1 alpha), and IL-6 by human monocytes and of gamma interferon (IFN-gamma) and IL-4 by human lymphocytes. Porins at 1 microgram/ml induce the greatest release of TNF-alpha, IL-1 alpha, and IL-6 by monocytes and of IL-4 by lymphocytes, while porins at 5 micrograms/ml induce the greatest release of IFN-gamma by lymphocytes. The R form of lipopolysaccharide (LPS-R) induces the greatest release of TNF-alpha and IL-1 alpha by monocytes when used at a low concentration (1 microgram/ml). At higher concentrations (5 and 10 micrograms/ml, respectively), LPS-R induces the maximal release of IL-6 from monocytes and the maximal release of IL-4 from lymphocytes. The S form of LPS (LPS-S) induces the greatest release of TNF-alpha, IL-1 alpha, and IL-6 by monocytes and that of IL-4 by lymphocytes when used at a concentration of 1 microgram/ml. After stimulation with LPS-S, the largest quantity of TNF-alpha and IL-1 alpha released was less than that obtained after stimulation with LPS-R at the same concentration, while the quantity of IL-6 released was found to be slightly higher than that obtained after stimulation with porins or LPS-R. LPS-S (1 microgram/ml) induces IFN-gamma release from lymphocytes in notably smaller quantities than that obtained with LPS-R and slightly larger quantities than that obtained with porins. The preparation of porins used was found to be contaminated with 10 pg of LPS per 10 micrograms of porins, a quantity which was found to have no biological effect; furthermore, porin preparations with the addition of polymyxin B gave the same results.
Inhibition of CD26 in Human Cord Blood CD34 <sup>+</sup> Cells Enhances Their Engraftment of Nonobese Diabetic/Severe Combined Immunodeficiency Mice (2007)

CD26, a surface serine dipeptidylpeptidase IV (DPPIV) expressed on different cell types, cleaves the amino-terminal dipeptide from some chemokines, including stromal-derived factor-1 (SDF-1/CXCL12). SDF-1/CXCL12 plays important roles in hematopoietic stem cell (HSC) homing, engraftment, and mobilization. Inhibition of CD26 peptidase activity enhances homing, engraftment, and competitive repopulation in congenic mouse bone marrow cell transplants. Our studies evaluated a role for CD26 in in vivo engraftment of HSCs from human umbilical cord blood (CB) into nonobese diabetic/severe combined immunodeficiency (NOD/SCID) mice. Pretreating purified CD34(+) human CB cells with Diprotin A, a DPPIV inhibitor, for 15 min significantly enhanced engraftment. Treatment did not affect differentiation of CD34(+) cells in vivo, as measured phenotypically by human markers CD33, CD38, CD19, and CD34. We found that the percentage of CD26(+) cells within the more immature cells (CD34(+)CD38()) was significantly higher than in the more mature population (CD34(+)CD38(+)). These results suggest that inhibition of CD26 may be one way to enhance engraftment of limiting numbers of stem cells during CB transplantation.
High power laser diode driver based on power converter technology (1997)

This paper describes the design of a high speed semiconductor laser diode driver designed for driving 500 mW to 1.5 W diodes at full optical power modulation up to frequencies of 10 MHz. The duty cycle of the modulation may be varied. A switching power-converter based current source allows a higher power delivery efficiency to the diode than in previous designs, allowing for a more modest power supply and dissipation requirements. A dynamic ripple cancellation circuit reduces the power converter output current ripple to less than 1% of full-scale current. The circuit is capable of delivering up to 2.5 A to a laser load, with a 10-90% switching risetime from laser threshold to full on of less than 20 ns.
Nonlinear Model Predictive control (NMPC) of fixed pitch variable speed wind turbine (2008)

Wind power has become one of the most attractive energy systems in several decades due to its rich wind power available and high turn back value than other types of renewable energy systems. The classical wind turbines are normally fixed pitch constant speed which have less power efficient and high dynamics loads that results in reducing life cycle of system. To overcome this disadvantage, modern generation of wind turbine with variable speed is now widely used. However, wind energy conversion system that includes complex combination of aero dynamics and electrical phenomena together with anonymous action of wind speed making control system sophisticated. Despite if a great deal of research has been focus on wind turbines in the literature. In this paper, we present advanced control algorithm Nonlinear Model Predictive Control (NMPC) regulating shaft speed to capture as much as possible power and keep it below maximum level at high wind speed. Because of the limitation of power electronics devices, the generation torque is also restricted below maximum value. All these constraints are naturally handled by NMPC algorithm which is promising control theory interested by many researchers resent years. The algorithm is validated by simulation and later is hardware realization of controller.
Study of n-type gallium arsenide- and gallium phosphide-based photoelectrochemical cells. Stabilization by kinetic control and conversion of optical energy to electricity (1977)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStudy of n-type gallium arsenide- and gallium phosphide-based photoelectrochemical cells. Stabilization by kinetic control and conversion of optical energy to electricityArthur B. Ellis, Jeffrey M. Bolts, Steven W. Kaiser, and Mark S. WrightonCite this: J. Am. Chem. Soc. 1977, 99, 9, 2848–2854Publication Date (Print):April 1, 1977Publication History Published online1 May 2002Published inissue 1 April 1977https://pubs.acs.org/doi/10.1021/ja00451a002https://doi.org/10.1021/ja00451a002research-articleACS PublicationsRequest reuse permissionsArticle Views465Altmetric-Citations63LEARN 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-Alertsclose Get e-Alerts
The expression and characterization of human recombinant proinsulin-like growth factor II and a mutant that is defective in the O-glycosylation of its E domain. (1996)

In humans, newly synthesized proinsulin-like growth factor II (pro-IGF-II), i.e. IGF-II with an E domain extension of 89 amino acids, is 0-glycosylated on Thr75. As an approach to define the role that glycosylation of the E domain serves in the processing, secretion, and biological activities of IGF-II and to identify the sites of endoproteolytic processing, we constructed a mutant that encodes carbohydrate-free prepro-IGF-II. The mutant and wild-type prepro-IGF-II were expressed in NIH-3T3 cells, and the protein products were analyzed by SDS-PAGE followed by immunoblots with antipeptide antibodies to human and homologous rat E domain sequences. Transfectants that express glycosylated pro-IGF-II, i.e. xz97 and G11 cells, have intracellular forms of the growth factor with apparent Mr (appMr) of 21, 23, and 27K. NIH-3T3 xz95 cells, i.e. transfected with DNA that is missing the 0-glycosylation sequence, could also synthesize pro-IGF-II with an appMr of 21K. However, they did not accumulate the 23K and 27K forms of presumably glycosylated growth factor. None of the transfected NIH 3T3 cells processed much pro-IGF-II intracellularly, as the appMr 21K, 23K, and 27K forms had terminal E domain amino acid sequences that were recognized by antibodies to the homologous rat peptide sequence Met117 to Gln156. Subsequent to their secretion, the IGF-II in xz97 and G11 cells accumulated in the conditioned medium mostly as two partially processed species with appMr, of 17K and 14K, respectively. The IGF-II that accumulated in the conditioned medium of the xz95 cells had an appMr of 11K. As evidenced by a decrease in mass after treatment with neuraminidase and 0-glycosidase, the 17-kDa form of pro-IGF-II secreted by the NIH-3T3 xz97 cells was 0-glycosylated, whereas that secreted by the xz95 cells was oligosaccharide free. All of the pro-IGF-II forms have E domain amino acid sequences that reacted with antipeptide Ab to the Asp69 to Lys88 sequence. However, appMr 17K IGF-II, but not 14K IGF-II, also contained a larger E domain that was recognized by Ab to the sequence Phe89 to Arg101. The final step in the processing of 11- to 17-kDa IGF-II at Arg68 and the generation of mature IGF-II did not occur in the NIH-3T3 transfectants and is similar to what has been observed in human embryonic cells and mesenchymal tumors. The failure to remove the glycosylated E domain peptide from appMr, 14K and 17K IGF-II did not affect their binding to IGF-II/cation-independent mannose-6 phosphate receptors or presumably to IGF-I receptors, because in in vitro mitogenic assays they were equipotent with mature IGF-II. Unglycosylated pro-IGF-II from the NIH-3T3 xz95 cells also bound to these receptors. However, it was about 10 times more potent than IGF-II in stimulating thymidine incorporation into NIH-3T3 i24 IGF-IR cells, possibly because of the absence of negatively charged sialic acid and/or steric occlusion.
Spectral Geometry Processing with Manifold Harmonics (2008)

Abstract We present an explicit method to compute a generalization of the Fourier Transform on a mesh. It is well known that the eigenfunctions of the Laplace Beltrami operator (Manifold Harmonics) define a function basis allowing for such a transform. However, computing even just a few eigenvectors is out of reach for meshes with more than a few thousand vertices, and storing these eigenvectors is prohibitive for large meshes. To overcome these limitations, we propose a band‐by‐band spectrum computation algorithm and an out‐of‐core implementation that can compute thousands of eigenvectors for meshes with up to a million vertices. We also propose a limited‐memory filtering algorithm, that does not need to store the eigenvectors. Using this latter algorithm, specific frequency bands can be filtered, without needing to compute the entire spectrum. Finally, we demonstrate some applications of our method to interactive convolution geometry filtering. These technical achievements are supported by a solid yet simple theoretic framework based on Discrete Exterior Calculus (DEC). In particular, the issues of symmetry and discretization of the operator are considered with great care.
On the Design of Transitions Between a Metal and Inverted Strip Dielectric Waveguide for Millimeter Waves (1981)

The results of a study of three types of transitions between the rectangular metal waveguide and the inverted strip guide are reported. Reflected power measurements from each type of transition and insertion-loss measurements for configurations involving the three transitions have also been carried out. The procedure of determining the optimum parameters for the transition is quite general, and has the potential for being extended to other dielectric structures.
Challenges in the design of CMOS transceivers for the IEEE 802.11 wireless LANs: past, present and future (2005)

The paper presents the challenges involved in the design of integrated IEEE 802.11 wireless LAN transceivers with focus on radio architecture and circuit implementation. In particular, examples of critical blocks in the receiver and transmitter are discussed.
Differential regulation of antigen presentation in high‐ and low‐IgE responder mice (1991)

Strains of mice differ greatly in their capacity to produce interleukin (IL) 4 and high levels of serum IgE. The contribution of macrophages (M phi) in enhancing the production of IL4 by T cells in high-IgE responder mice was studied. M phi from BALB/c mice (high-IgE responder strain) developed an augmented capacity to present antigen to IL 4-producing T helper type 2 (Th2) clones, when the M phi were pretreated by exposure to the lymphokines IL 4 and IL 5. In contrast, identical treatment of M phi from H-2-identical DBA/2 mice (low-IgE responder strain) resulted in inhibition of the capacity to stimulate Th2 clones. The impairment of antigen presentation by DBA/2 M phi was closely paralleled by a decrease of cell surface class II major histocompatibility complex (MHC) expression and an abrogation of IL 1 production by these cells, while identical treatment of BALB/c M phi enhanced class II MHC expression and did not inhibit secretion of IL 1. Our studies demonstrate that IL 4 and IL 5 can exert different effects on M phi from high- and low-IgE responder strains of mice, resulting in down-regulation of the expansion of IL 4-producing cells in low-but not high-IgE responder mice.
The Arabidopsis AGL8 MADS Box Gene Is Expressed in Inflorescence Meristems and Is Negatively Regulated by APETALA1 (1995)

M. Alejandra Mandel, Martin F. Yanofsky, The Arabidopsis AGL8 MADS Box Gene Is Expressed in Inflorescence Meristems and Is Negatively Regulated by APETALA1, The Plant Cell, Vol. 7, No. 11 (Nov., 1995), pp. 1763-1771
Chemistry and Logical Structures (1970)

Abstract The utility of the basic structures of modern mathematics for chemistry is discussed; general set theory, topology, and group theory are shown to pervade almost all static and dynamic aspects of chemistry. Chemical analogy, the systematic classification of molecules and a corresponding nomenclature system, conformational transformations, polyhedral rearrangements, and the relations between starting materials, transition complexes, and final products of chemical reactions are examples of where we apply the elements of modern mathematics to the solution of chemical problems.
Social Network Analysis for Automatic Role Recognition (2011)

The computing community has shown a significant interest for the analysis of social interactions in the last decade. Different aspects of social interactions have been studied such as dominance, emotions, conflicts, etc. However, the recognition of roles has been neglected whereas these are a key aspect of social interactions. In fact, sociologists have shown not only that people play roles each time they interact, but also that roles shape behavior and expectations of interacting participants. The aim of this thesis is to fill this gap by investigating the problem of automatic role recognition in a wide range of interaction settings, including production environments, e.g. news and talk-shows, and spontaneous exchanges, e.g. meetings. The proposed role recognition approach includes two main steps. The first step aims at representing the individuals involved in an interaction with feature vectors accounting for their relationships with others. This step includes three main stages, namely segmentation of audio into turns (i.e. time intervals during which only one person talks), conversion of the sequence of turns into a social network, and use of the social network as a tool to extract features for each person. The second step uses machine learning methods to map the feature vectors into roles. The experiments have been carried out over roughly 90 hours of material. This is not only one of the largest databases ever used in literature on role recognition, but also the only one, to the best of our knowledge, including different interaction settings. In the experiments, the accuracy of the percentage of data correctly labeled in terms of roles is roughly 80% in production environments and 70% in spontaneous exchanges (lexical features have been added in the latter case). The importance of roles has been assessed in an application scenario as well. In particular, the thesis shows that roles help to segment talk-shows into stories, i.e. time intervals during which a single topic is discussed, with satisfactory performance. The main contributions of this thesis are as follows: To the best of our knowledge, this is the first work where social network analysis is applied to automatic analysis of conversation recordings. This thesis provides the first quantitative measure of how much roles constrain conversations, and a large corpus of recordings annotated in terms of roles. The results of this work have been published in one journal paper, and in five conference articles.