gebhart/patrepeval huggingface dataset:
Excision of a transposable element from a viral vector introduced into maize plants by agroinfection (1992)

The geminivirus maize streak virus (MSV) was used as a vector to introduce the maize transposable element Dissociation (Ds) and to study its excision in maize plants. MSV carrying Ds1 in its genome was introduced into maize plants by agroinfection. Excision of the Ds1 element from the MSV genome was detected only when functions from the transposable element Activator (Ac) were supplied in trans, either endogenously by the recipient maize plant or by co-transformation with Agrobacterium carrying a genomic Ac clone. The excision of Ds1 could easily be visualized by the appearance of viral symptoms induced by the revertant virus. The junction sequences left on the MSV genome after excision revealed 'footprints' typical of transposition as described for maize. From these results, we conclude that transposition functions in our system and that the use of the MSV replicon provides a rapid and simple tool for the investigation of the excision of transposable elements in maize plants.
Identification of the Starting Group on the First PE Chain Produced by the Phillips Catalyst (2019)

Upon contact with ethylene, the Phillips Cr/silica catalyst must self-alkylate before polymerization can begin. How this happens has been a mystery for over 60 years, being not only of scientific interest but also of commercial importance. Consequently, many controversial schemes have been proposed, including some that hold the initial PE chain to be different from all subsequent chains, starting with a vinyl group, instead of the usual methyl group. In this study, polymer chains produced by the Cr(II)/silica–titania catalyst at low yield were analyzed in an effort to identify the starting group on the first chain produced. The PE/Cr yield was deliberately kept low to avoid diluting that initial chain with other chains produced afterward. The polymer was then characterized by gel permeation chromatography and 13C NMR (natural abundance). Strong signals from methyl end groups were present, but terminal vinyl groups were not detected. Likewise, analysis by proton (1H) NMR also indicated a general lack of vinyl chain ends. An attempt was also made to identify the first species on the initial chain through isotopic labeling. Deutero-ethylene (C2D4), deutero-propylene (C3D6), or 13C-ethylene was first “preadsorbed” onto the divalent catalyst at −78 °C, where polymerization does not occur. After evacuating the excess isotopically labeled monomer, polymerization was conducted with unlabeled ethylene (C2H4) at higher temperatures. Deuterium (2H) NMR analysis of the polymers again indicated a strong methyl signal but no resonance from deuterium-containing vinyl chain ends. Comparison of the different NMR methods indicated a high degree of deuterium enrichment in the methyl chain ends. These results indicate that the initial chain in these experiments began with a methyl group, not a vinyl group as has sometimes been contemplated. Although helpful, this information still leaves the mechanism of site alkylation unclear because there is not enough hydrogen in ethylene to produce a methyl-initiated chain, without some other (still undefined) reaction also being involved to furnish the additional hydrogen, such as the creation of a permanent ligand.
Национальный корпус русского языка в образовании (2012)

Este trabajo describe el uso del Corpus Nacional Ruso (CNR) en la ensenanza de la lengua rusa. El CNR es un recurso electronico relativamente reciente, consistente en una enorme cantidad de textos rusos procesados de forma que permiten consultas bastante sofisticadas. En el articulo se analizan algunos usos posibles, incluida la ensenanza de la lengua rusa en los diferentes niveles de su ensenanza. El uso del CNR permite obtener facilmente un amplio numero de ejemplos que ilustran fenomenos linguisticos relevantes. Tomando como base estos ejemplos, los profesores pueden crear ejercicios y los estudiantes pueden llevar a cabo tareas creativas escritas. Los ejemplos estan tomados de textos escritos y orales comtemporaneos, que suministran al profesor de ruso los datos que con frecuencia echa en falta.
Building Directories from DNS: Experiences from WWWSeeker (1999)

This memo provides information for the Internet community. It does not specify an Internet standard of any kind. Distribution of this memo is unlimited. Copyright Notice Copyright (C) The Internet Society (1999). All Rights Reserved. There has been much discussion and several documents written about the need for an Internet Directory. Recently, this discussion has focused on ways to discover an organization’s domain name without relying on use of DNS as a directory service. This memo discusses lessons that were learned during InterNIC Directory and Database Services ’ development and operation of WWWSeeker, an application that finds a web site given information about the name and location of an organization. The back end database that drives this application was built from information obtained from domain registries via WHOIS and other protocols. We present this information to help future implementors avoid some of the blind alleys that we have already explored. This work builds on the Netfind system that was created by Mike Schwartz and his team at the University of Colorado at Boulder [1].
Plant genomic DNA isolation: An art or a science (2007)

Isolating quality DNA from tissues/cells presents a variety of problems in particular when plants are used as the source material. The specific characteristics of plants like the presence of rigid polysaccharide cell wall, pigments, chemical heterogeneity of secondary metabolites found in diverse species of plants, etc., necessitate special consideration and skill during isolation procedure. Until now, numerous protocols have been published for the purpose, but none is found to be universally applicable. Various factors starting from the selection of source material to the concentration of metabolites present in the plant decide the course of the isolation procedure. The present review is an update of various methods used for plant genomic DNA isolation, and it epitomizes the various problems faced and the solutions made to contend with them during DNA isolation from plant cells.
A multilevel matrix decomposition algorithm for analyzing scattering from large structures (1996)

A multilevel algorithm is presented for analyzing scattering from electrically large surfaces. The algorithm accelerates the iterative solution of integral equations that arise in computational electromagnetics. The algorithm permits a fast matrix-vector multiplication by decomposing the traditional method of moment matrix into a large number of blocks, with each describing the interaction between distant scatterers. The multiplication of each block by a trial solution vector is executed using a multilevel scheme that resembles a fast Fourier transform (FFT) and that only relies on well-known algebraic techniques. The computational complexity and the memory requirements of the proposed algorithm are O(N log/sup 2/ N).
Effect of SU11248 on gastrointestinal stromal tumor‐T1 cells: Enhancement of growth inhibition via inhibition of 3‐kinase/Akt/mammalian target of rapamycin signaling (2006)

SU11248 is an orally available type III and V receptor tyrosine kinase inhibitor. Clinical studies have shown the efficacy of SU11248 in individuals with gastrointestinal stromal tumors (GIST); however, the molecular mechanisms by which SU11248 inhibits the proliferation of these tumor cells remains to be fully elucidated. Taking advantage of GIST-T1 cells, which possess an activating mutation in exon 11 of the c-KIT gene, we examined the medicinal action of SU11248 in GIST cells. Clonogenic and MTT assays showed that SU11248 potently inhibited the proliferation of GIST-T1 cells with IC50 of approximately 1 nM and 40 nM, respectively. SU11248 (10 or 20 nM, 48 h) activated caspase-3 and induced apoptosis of GIST-T1 cells as measured by caspase assay, annexin V staining and cleavage of poly (ADP-ribose) polymerase. Western blot analyses found that SU11248 blocked autophosphorylation of c-KIT in association with inhibition of its downstream effectors, including Akt and extracellular signal-regulated kinase, but not signal transducers and activators of transcription. Interestingly, when phosphatidylinositol 3-kinase/Akt/mammalian target of rapamycin signaling was blocked simultaneously by either LY294002 or rapamycin, growth inhibition mediated by SU11248 was potentiated. Taken together, this study supports clinical studies of SU11248 for individuals with GIST, and the combination of SU11248 and inhibitors of 3-kinase/Akt/mammalian target of rapamycin signaling represents a promising novel treatment strategy.
Transport Layer Security Protocol Compression Methods (2004)

The Transport Layer Security (TLS) protocol (RFC 2246) includes features to negotiate selection of a lossless data compression method as part of the TLS Handshake Protocol and to then apply the algorithm associated with the selected method as part of the TLS Record Protocol. TLS defines one standard compression method which specifies that data exchanged via the record protocol will not be compressed. This document describes an additional compression method associated with a lossless data compression algorithm for use with TLS, and it describes a method for the specification of additional TLS compression methods.
Establishment of exponential growth after a nutritional shift-up in Escherichia coli B/r: accumulation of deoxyribonucleic acid, ribonucleic acid, and protein (1977)

The accumulation of deoxyribonucleic acid (DNA), ribonucleic acid (RNA), and protein was followed in cultures of Escherichia coli B/r during exponential growth in different media and for 2 h after a nutritional shift-up from succinate minimal medium (growth rate [mu1] = 0.67 doublings per h) to glucose plus amino acids medium (mu2 = 3.14 doublings per h). During postshift growth of the culture, the amounts of RNA (R), DNA (D), and protein (P) increased such that the ratios of the increments (delta R/delta P; delta D/delta P) were constants (k1, k2). This implies that the rates of accumulation of nuclei1:k2:1. These constants change from their preshift value to their final postshift value (i.e., k1 and k2) within a few minutes after the shift. k1 is a function of the activity of ribosomes, whereas k2 is related to the initiation of rounds of DNA replication. These parameters and the observed change in the doubling time of RNA (= mu2/mu1) were used to derive kinetic equations that describe the accumulation of DNA, RNA, protein, and cell mass during the 2- to 3-h transition period after a shift-up. The calculated kinetics agree closely with the observed kinetics.
RPGR ORF15 genotype and clinical variability of retinal degeneration in an Australian population (2009)

RPGR ORF15 mutations produce intrafamilial and interfamilial clinical variability with varying degrees of cone degeneration. In an Australian clinic population RPGR ORF15 mutations cause XLCORD in addition to XLRP.
PICS: Internet access controls without censorship (1996)

article Free AccessPICS: Internet access controls without censorship Authors: Paul Resnick Public Policy Research Department, AT&T Labs Public Policy Research Department, AT&T LabsView Profile , James Miller Massachusetts Institute of Technology's Laboratory for Computer Science Massachusetts Institute of Technology's Laboratory for Computer ScienceView Profile Authors Info & Claims Communications of the ACMVolume 39Issue 1001 October 1996pp 87–93https://doi.org/10.1145/236156.236175Published:01 October 1996Publication History 89citation3,742DownloadsMetricsTotal Citations89Total Downloads3,742Last 12 Months151Last 6 weeks16 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
The human macrophage mannose receptor directs Mycobacterium tuberculosis lipoarabinomannan-mediated phagosome biogenesis (2005)

Mycobacterium tuberculosis (M.tb) survives in macrophages in part by limiting phagosome-lysosome (P-L) fusion. M.tb mannose-capped lipoarabinomannan (ManLAM) blocks phagosome maturation. The pattern recognition mannose receptor (MR) binds to the ManLAM mannose caps and mediates phagocytosis of bacilli by human macrophages. Using quantitative electron and confocal microscopy, we report that engagement of the MR by ManLAM during the phagocytic process is a key step in limiting P-L fusion. P-L fusion of ManLAM microspheres was significantly reduced in human macrophages and an MR-expressing cell line but not in monocytes that lack the receptor. Moreover, reversal of P-L fusion inhibition occurred with MR blockade. Inhibition of P-L fusion did not occur with entry via Fcgamma receptors or dendritic cell-specific intracellular adhesion molecule 3 grabbing nonintegrin, or with phosphatidylinositol-capped lipoarabinomannan. The ManLAM mannose cap structures were necessary in limiting P-L fusion, and the intact molecule was required to maintain this phenotype. Finally, MR blockade during phagocytosis of virulent M.tb led to a reversal of P-L fusion inhibition in human macrophages (84.0 +/- 5.1% vs. 38.6 +/- 0.6%). Thus, engagement of the MR by ManLAM during the phagocytic process directs M.tb to its initial phagosomal niche, thereby enhancing survival in human macrophages.
Iron Molybdenum Cofactor: Catalyst In Dihydrogen Production And Nifen's Role In The Femo-co Biosynthetic Pathway (2012)

Humankind’s tremendous industrial and technological progress over the last two centuries has been driven by the natural abundance and availability of fossil fuels. As those reserves deplete, the prudent course of action would be to develop other readily available fuel sources. Some research efforts using biomolecules involve the hydrogenases and nitrogenases with the goal of evolving dihydrogen. At the nitrogenase active site, the iron-molybdenum cofactor (FeMo-co) catalyzes the reduction of dinitrogen and protons to form ammonia and dihydrogen. Toward the goal of producing dihydrogen passively as an alternative fuel, a novel advanced material has been developed. CdSe nanoparticles complexed with FeMo-co, in both aqueous and organic solvent systems showed complex formation. When the system was interrogated by EPR spectroscopy, evidence of electron transfer was observed. The CdSeMSA●NafY●FeMo-co system when illuminated with visible light evolved dihydrogen consistently in four different experimental sets under the same reaction conditions. NifEN protein plays an important role in the biosynthesis of FeMo-co in addition to the involvement of NifU, NifS, NifB, NifX, NifH and NafY. After NifB synthesizes a FeMo-co precursor, 6-Fe NifB-co, NifEN further incorporates additional Fe, S, Mo, and (R)-homocitrate to complete the synthesis of FeMo-co. Molybdenum is provided to NifEN as its oxoanion, Mo(VI)O4 2- ; however, in FeMo-co molybdenum is in the oxidation state of Mo(IV). EPR spectroscopic investigation of NifEN turnover samples showed a signal at g = 2.00 that was dependent on molybdate concentration. Power and temperature profiles gave evidence that the g iv = 2.00 EPR signal was distinct from the Fe-S clusters in NifEN. The species observed at g = 2.00 was assigned to the reduction of Mo(VI) to Mo(V). How to utilize the effectiveness of FeMo-co and complex it to photoactive materials for the purpose of evolving dihyrogen upon illumination, thus providing a sustainable alternative energy source is one subject of this dissertation. A related subject is to gain an understanding of the biosynthetic pathway of FeMo-co by investigation of NifEN turnover experiments. This understanding should contribute towards the development of improved catalysts for meeting future energy demands.
Epistasis analysis of suppressor mutations that allow HO expression in the absence of the yeast SW15 transcriptional activator. (1994)

We have examined mutations which overcome the requirement for SW15-dependent transcriptional activation of the Saccharomyces cerevisiae HO gene. We show that the RPD3 gene is the same as SDI2, and that SIN4 is the same as the TSF3 and SDI3 genes. We have also identified a new swi5 suppressor, RGR1. The RGR1 gene was identified originally as a negative regulator of SUC2. Epistasis analysis indicates that six swi5 suppressor genes function in four distinct pathways, with RPD3 and SIN3 in one pathway, RGR1 and SIN4 in a second pathway, and SDI4 and SIN5 each in distinct pathways. Finally, we show that complete suppression of the swi5 defect in HO expression by sin5 requires the wild-type ACE2 gene. This suggests that one function of SIN5 is to prevent ACE2, a SWI5 homolog, from activating HO expression.
Anti-fouling Coatings of Poly(dimethylsiloxane) Devices for Biological and Biomedical Applications (2015)

Fouling initiated by nonspecific protein adsorption is a great challenge in biomedical applications, including biosensors, bioanalytical devices, and implants. Poly(dimethylsiloxane) (PDMS), a popular material with many attractive properties for device fabrication in the biomedical field, suffers serious fouling problems from protein adsorption due to its hydrophobic nature, which limits the practical use of PDMS-based devices. Effort has been made to develop biocompatible materials for anti-fouling coatings of PDMS. In this review, typical nonfouling materials for PDMS coatings are introduced and the associated basic anti-fouling mechanisms, including the steric repulsion mechanism and the hydration layer mechanism, are described. Understanding the relationships between the characteristics of coating materials and the accompanying anti-fouling mechanisms is critical for preparing PDMS coatings with desirable anti-fouling properties.
Altered levels of laminin receptor mRNA in various human carcinoma cells that have different abilities to bind laminin. (1986)

The human laminin receptor was purified and molecularly cloned to investigate its biosynthetic regulation. Laminin receptor from normal and neoplastic tissue was preparatively affinity purified to homogeneity based on the high affinity of the receptor for laminin. The apparent molecular weight of the receptor from different carcinoma sources and from normal placental tissue is in the range of 68-72 kDa. Isoelectric focusing and two-dimensional gel electrophoresis indicated that the receptor protein consists of one major polypeptide chain with a pI value of 6.4 +/- 0.2. Laminin receptor cDNA clones were isolated after screening a human endothelial lambda gt11 cDNA library with a monoclonal antibody directed against a domain of the laminin receptor involved in ligand binding. Definitive identification of the cDNA clones was based on comparison of cDNA sequence with the amino acid sequence of a cyanogen bromide-generated octapeptide of purified placental laminin receptor. The laminin receptor mRNA is approximately 1700 bases long. The level of laminin receptor mRNA in a variety of human carcinoma-derived cell lines correlated with the number of laminin receptors on the cell surfaces of those cells. This suggests that the amount of laminin receptor mRNA may be a rate-limiting control step in the biosynthesis of the laminin receptor, and hence in the regulation of cellular attachment to basement membranes via laminin.
Reconstructing Images from Trichromatic Samples: From Basic Research to Practical Applications (1995)

The human retina encodes information about images through the responses of three classes of photoreceptor, often referred to as the L, M, and S cones. These photoreceptors are arranged in three interleaved mosaics; at any one retinal location only a single cone type samples the retinal image. To create our percept of a continuous colored world, the visual system must reconstruct the responses of the missing two cone types at each retinal location. The algorithm that performs this reconstruction works very well&#x2014;we rarely perceive artifacts that arise from the interleaved sampling arrangement.Most CCD based color cameras employ the same interleaved sampling architecture as the human retina. Yet for CCD cameras, color artifacts are quite common near sharp luminance boundaries. CCD cameras are more susceptible to these artifacts because their reconstruction algorithms are not as successful as the one employed by the human visual system.This talk will begin by reviewing basic research designed to elucidate reconstruction by the human visual system. We will then show how ideas that emerged from the basic research have led to a new algorithm for processing images acquired with CCD cameras.
New technologies for high precision dosage (1996)

This paper outlines the results of a new development in the field of liquid handling covering the range from 0.5 nanoliter to a few microliter. The company GeSiM designed a modular system consisting of microfluidic devices like miniaturised pumps, mixers and injectors. These basic elements may be used to build miniaturised manifolds providing complex fluidic, sensorial and electronic functions. Presently, the user of such products work in the field of biotechnology and genetic research. A specific application is the handling of biological cells in liquid solution. Furthermore a first project has been started investigating a new technology to apply medicines. Although the new microfluidic devices have been designed to handle aqueous solutions there are no restrictions to work with high viscous substances or solvents like ethanol, acetone, DMSO, DMF or acetonitrile. The authors focus on micro dosage technology. Based on the new microdroplet-pump, some new active and passive microfluidic devices are discussed. The main parts of most components are made from silicon and glass according to microsystem technology. The micropumps come with user-friendly hardware and software.
Ursodiol for the Long-Term Treatment of Primary Biliary Cirrhosis (1994)

Long-term ursodiol therapy slows the progression of primary biliary cirrhosis and reduces the need for liver transplantation.
Brain Regulation of Renin Secretion Involves Central Histaminergic Neurons (1990)

The possible involvement of histamine (HA) in the stress-induced increase in plasma renin activity (PRA) was investigated in male rats. Intracerebroventricular (ICV) infusion of histamine (HA; 3.8-60 micrograms) increased PRA dose-dependently, and the Kd (dissociation konstant) of HA was estimated to approximately 30 micrograms. ICV infusion of HA (30 micrograms) as well as 5 min of restraint stress increased plasma renin activity (PRA) 2- and 3-fold, respectively (p less than 0.01). These effects were abolished by prior ICV infusion of the H2-receptor antagonists cimetidine (100 micrograms) and ranitidine (125 micrograms) (p less than 0.01), which reduced the PRA to subbasal levels (p less than 0.05). When administered alone the H2-receptor antagonists had no effect on PRA. In contrast, the H1-receptor antagonist mepyramine (100 micrograms) increased the basal PRA level (p less than 0.01) and slightly augmented the HA- and stress-induced increase in PRA (p less than 0.05). HA as well as restraint stress increased the plasma levels of dopamine, norepinephrine and epinephrine almost 2-fold (p less than 0.01). The effect of the two stimuli was prevented by prior ICV infusion of mepyramine or cimetidine (p less than 0.01). Pretreatment with the beta-adrenergic receptor blocker propranolol (7 mg/kg i.p.) abolished the HA-induced and inhibited by 70% the stress-induced PRA increase. The results indicate that histaminergic neurons participate in the cerebral regulation of renin secretion. The H2-receptor-mediated PRA-increasing effect of HA involves activation of sympathetic nerves. In addition, HA seems to exert a minor inhibiting effect on PRA via H1-receptors.