gebhart/patrepeval huggingface dataset:
Strand Invasion of Supercoiled DNA by Oligonucleotides with a Triplex Guide Sequence (1998)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTStrand Invasion of Supercoiled DNA by Oligonucleotides with a Triplex Guide SequenceHoward B. Gamper,, Ya-Ming Hou, Michael R. Stamm, Mikhail A. Podyminogin, and Rich B. MeyerView Author Information Epoch Pharmaceuticals, Inc., 1725 220th Street SE # 104, Bothell, Washington 98021 Department of Biochemistry and Molecular Pharmacology Thomas Jefferson University, 233 South 10th Street Philadelphia, Pennsylvania 19107 Cite this: J. Am. Chem. Soc. 1998, 120, 9, 2182–2183Publication Date (Web):February 24, 1998Publication History Received2 May 1997Published online24 February 1998Published inissue 1 March 1998https://pubs.acs.org/doi/10.1021/ja971397ihttps://doi.org/10.1021/ja971397irapid-communicationACS PublicationsCopyright © 1998 American Chemical SocietyRequest reuse permissionsArticle Views192Altmetric-Citations15LEARN 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 SUBJECTS:Alcohols,Cells,Crystal cleavage,Genetics,Post-translational modification Get e-Alerts
Differential Binding of Ligands to the Apolipoprotein E Receptor 2 (2003)

Apolipoprotein E receptor 2 (apoER2) is an important participant in the Reelin signaling pathway that directs cell positioning during embryogenesis. ApoER2 is a cell surface molecule that elicits intracellular signal transduction through binding of Reelin. The structural requirements for Reelin binding to apoER2 and the receptor domains involved in this process are unclear at present. Using a series of receptor mutants, we characterized the interaction of apoER2 with Reelin and compared this interaction to that of apoER2 with the receptor-associated protein (RAP), an apoER2 ligand that does not induce signaling. By surface plasmon resonance we demonstrate that apoER2 exhibits 6-fold higher affinity for Reelin than the very low density lipoprotein receptor (VLDLR), which also functions as a Reelin receptor (K(D) 0.2 nM versus K(D) 1.2 nM). Acidic amino acid residues in complement-type repeat domains 1 and 3 of apoER2 are required for Reelin binding. The same regions of the receptor are also bound by RAP with a 25-fold lower affinity (K(D) 5 nM). Whereas RAP binds to apoER2 with a 1:1 stoichiometry, experimental evidence suggests that Reelin associates with two or more receptor molecules simultaneously to achieve high-affinity interaction. This finding indicates that aggregation of apoER2 by multivalent ligands such as Reelin may be the structural basis for signal transduction.
Plant biotechnology: the genetic manipulation of plants (2003)

Introduction 1. Plant genomes - the organisation and expression of plant genes 2. Plant tissue culture 3. Techniques for plant transformation 4. Binary vectors for plant transformation 5. The genetic manipulation of herbicide resistance 6. The genetic manipulation of pest resistance 7. Plant disease resistance 8. Reducing the effects of viral diseases 9. Strategies for stress tolerance 10. The improvement of crop yield and quality 11. Molecular farming / pharming 12. Future prospects for GM crops
Novel Short-term Hypothermic Oxygenated Perfusion (HOPE) System Prevents Injury in Rat Liver Graft From Non-Heart Beating Donor (2006)

We demonstrate a beneficial effect of HOPE by preventing reperfusion injury in a clinically relevant NHBD model.
Purification and Characterization of the RecA Protein from Neisseria gonorrhoeae (2011)

The strict human pathogen Neisseria gonorrhoeae is the only causative agent of the sexually transmitted infection gonorrhea. The recA gene from N. gonorrhoeae is essential for DNA repair, natural DNA transformation, and pilin antigenic variation, all processes that are important for the pathogenesis and persistence of N. gonorrhoeae in the human population. To understand the biochemical features of N. gonorrhoeae RecA (RecA(Ng)), we overexpressed and purified the RecA(Ng) and SSB(Ng) proteins and compared their activities to those of the well-characterized E. coli RecA and SSB proteins in vitro. We observed that RecA(Ng) promoted more strand exchange at early time points than RecA(Ec) through DNA homologous substrates, and exhibited the highest ATPase activity of any RecA protein characterized to date. Further analysis of this robust ATPase activity revealed that RecA(Ng) is more efficient at displacing SSB from ssDNA and that RecA(Ng) shows higher ATPase activity during strand exchange than RecA(Ec). Using substrates created to mimic the cellular processes of DNA transformation and pilin antigenic variation we observed that RecA(Ec) catalyzed more strand exchange through a 100 bp heterologous insert, but that RecA(Ng) catalyzed more strand exchange through regions of microheterology. Together, these data suggest that the processes of ATP hydrolysis and DNA strand exchange may be coupled differently in RecA(Ng) than in RecA(Ec). This difference may explain the unusually high ATPase activity observed for RecA(Ng) with the strand exchange activity between RecA(Ng) and RecA(Ec) being more similar.
Are Toll-like receptor gene polymorphisms associated with prostate cancer? (2012)

The suggestion that there is a connection between chronic intraprostatic inflammation and prostate cancer was declared some years ago. As Toll-like receptors (TLRs) are the key players in the processes of chronic intraprostatic inflammation, there is a hypothesis that TLR gene polymorphisms may be associated with prostate cancer risk. Although a number of comprehensive studies have been conducted on large samples in various countries, reliable connections between these single nucleotide polymorphisms and prostate cancer risk, stage, grade, aggressiveness, ability to metastasize, and mortality have not been detected. Results have also varied slightly in different populations. The data obtained regarding the absence of connection between the polymorphisms of the genes encoding interleukin-1 receptor-associated kinases (IRAK1 and IRAK4) and prostate cancer risk might indicate a lack of association between inherited variation in the TLR signaling pathway and prostate cancer risk. It is possible to consider that polymorphisms of genes encoding TLRs and proteins of the TLR pathway also do not play a major role in the etiology and pathogenesis of prostate cancer. Feasibly, it would be better to focus research on associations between TLR single nucleotide polymorphisms and cancer risk in other infection-related cancer types.
Artificial Salmonella vaccines: O-antigenic oligosaccharide-protein conjugates induce protection against infection with Salmonella typhimurium (1979)

Outbred mice were vaccinated with various artificial Salmonella vaccines and subsequently challenged intraperitoneally with graded doses of virulent Salmonella typhimurium. The Salmonella vaccines used were: (i) octasaccharide, obtained by hydrolysis of the O-antigenic polysaccharide chain of S. typhimurium strain SH 4809 with phage P22-associated endo-rhamnosidase and covalently linked to either diphtheria toxin or edestine; (ii) purified outer membrane proteins (porins) from S. typhimurium; and (iii) octasaccharide covalently linked to porins. All vaccines induced significant protection against experimental infection of mice with S. typhimurium. However, vaccination with the octasaccharide-porin conjugate resulted in better protection than that obtained by vaccination with octasaccharide or porin vaccines separately. Rabbit antibodies raised against the different vaccines were also passively administered intravenously to mice. Such mice were protected against challenge with virulent S. typhimurium by antibodies specific for the S. typhimurium O-antigen or for the porins. Thus, active immunization with more than one surface component of Salmonella bacteria improved the efficacy of the vaccine. The data from the passive immunization experiments also emphasized the role of humoral immunity for protection against S. typhimurium infection.
The FDA alert on serotonin syndrome with combined use of SSRIs or SNRIs and Triptans: an analysis of the 29 case reports. (2007)

Triptans when administered with SSRIs or SNRIs might rarely precipitate serotonin syndrome. The data do not support prohibiting the use of triptans with SSRIs or SNRIs. With increased physician awareness of serotonin syndrome, it is possible that additional cases may be reported.
THE EFFECT OF IMIPENEM/CILASTATIN ON ACUTE CYCLOSPORIN NEPHROTOXICITY IN HEART/LUNG TRANSPLANT PATIENTS (1995)

Ali, Baghaie; Maryam, Bayat; Cyril, Abobo; Golden, Zenon; Theodore, Bates Author Information
Insecticidal Properties of <i>d</i>-Limonene (1988)

リモネンのチャバネゴキブリ, イエバエ, ココクゾウ, ヒゲナガハムシに対する作用を, 経皮, くん蒸, 経口, 忌避, 残効, 殺卵, 殺幼虫性の生物検定法で検討した. チャバネゴキブリとイエバエにはわずかながら経皮毒性があり, ピペロニルブトキサイドの共力作用も認められた. 高濃度蒸気にさらされたチャバネゴキブリとココクゾウは死亡した. 経口投与による作用ではチャバネゴキブリの成虫, 若虫に殺虫活性はなく, かえって若虫の成育を促進した. 処理した表面の素材の如何にかかわらず, チャバネゴキブリ成虫に対する残効性は認められなかった. 高濃度処理でヒゲナガハムシの卵の艀化を抑制し, 土壌中で3齢幼虫に殺虫活性が認められた. 以上の実験から限られた範囲ではあるがリモネンの殺虫作用が認められた.
Minimizing the risk of hypoglycemia in patients with type 2 diabetes mellitus (2010)

Hypoglycemia is a major barrier to achieving glycemic goals in patients with diabetes. Both acute and chronically recurrent hypoglycemic events appear to have long-term consequences for patients with type 2 diabetes mellitus (T2DM). Chronically recurrent hypoglycemia may lead to an impairment of the counterregulatory system, with the potential for the development of hypoglycemia unawareness syndrome, increased severe hypoglycemia-associated hospitalization, and increased mortality. Hypoglycemic events may also have negative implications in cardiovascular disease and/or dementia. Avoidance of hypoglycemia by treating with appropriate, individualized regimens for patients with T2DM should be a primary focus of physicians. Utilizing traditional agents (eg, metformin and thiazolidinediones) that do not promote hypoglycemia, in combination with newer agents such as dipeptidyl peptidase-4 inhibitors and incretin mimetics, could offer a therapeutic advantage when trying to help patients reach their hemoglobin A(1c) goal without the added risk of hypoglycemia.
Crystal structure of a γδ T-cell receptor specific for the human MHC class I homolog MICA (2011)

γδ T cells play important roles in bridging innate and adaptive immunity, but their recognition mechanisms remain poorly understood. Human γδ T cells of the V(δ)1 subset predominate in intestinal epithelia and respond to MICA and MICB (MHC class I chain-related, A and B; MIC) self-antigens, mediating responses to tumorigenesis or viral infection. The crystal structure of an MIC-reactive V(δ)1 γδ T-cell receptor (TCR) showed expected overall structural homology to antibodies, αβ, and other γδ TCRs, but complementary determining region conformations and conservation of V(δ)1 use revealed an uncharacteristically flat potential binding surface. MIC, likewise, serves as a ligand for the activating immunoreceptor natural killer group 2, D (NKG2D), also expressed on γδ T cells. Although MIC recognition drives both the TCR-dependent stimulatory and NKG2D-dependent costimulatory signals necessary for activation, interaction analyses showed that MIC binding by the two receptors was mutually exclusive. Analysis of relative binding kinetics suggested sequential recognition, defining constraints for the temporal organization of γδ T-cell/target cell interfaces.
Structural Analogues of the Calanolide Anti-HIV Agents. Modification of the trans-10,11-Dimethyldihydropyran-12-ol Ring (Ring C) (1997)

(+)-Calanolide A is a potent inhibitor of reverse transcriptase from human immunodeficiency virus type 1 (HIV-1), which was isolated from an extract of Calophyllum lanigerum, along with seven related compounds. In order to examine the structure-activity relationships of the trans-10,11-dimethyldihydropyran-12-ol ring (designated ring C), a series of structural analogues were prepared and evaluated using a whole cell cytopathicity assay (XTT). Removal of the 10-methyl group resulted in decreased activity, with only one epimer exhibiting anti-HIV activity. Substituting the 10-methyl group with an ethyl chain maintained anti-HIV activity, with only a 4-fold reduction in potency relative to racemic calanolide A. Substitution of the 10-methyl group with an isopropyl moiety completely eliminated the anti-HIV activity. Addition of an extra methyl group at either the 10- or 11-position maintained the basic stereochemical features of the parent calanolide system while removing the chirality at the respective carbon, but resulted in decreased activity relative to calanolide A. In all the above examples, analogues containing a cis relationship between the 10- and 11-alkyl moieties were completely devoid of activity. Synthetic intermediates in which the 12-hydroxyl group was in the ketone oxidation state exhibited suppressing anti-HIV activity, with EC50 values only 5-fold less potent than that of calanolide A for both the 10,11-cis (6) and -trans (5) series. These ketones represent the first derivatives in the calanolide series to exhibit anti-HIV activity while not containing a 12-hydroxyl group. Likewise, ketone derivative 6 was the first example of a compound in the calanolide series having a cis relationship between the 10- and 11-methyl groups found to exhibit anti-HIV activity. Analogues which showed anti-HIV activity in the CEM-SS cytoprotection assay were further confirmed to be inhibitors of HIV-1 reverse transcriptase.
Best practice in the treatment of nonmuscle invasive bladder cancer (2011)

Bladder carcinoma is the most common malignancy of the urinary tract. Approximately 75-85% of patients with bladder cancer present with a disease that is confined to the mucosa (stage Ta, carcinoma in situ) or submucosa (stage T1). These categories are grouped as nonmuscle invasive bladder cancer (NMIBC). Although the management of NMIBC tumours has significantly improved during the past few years, it remains difficult to predict the heterogeneous outcome of such tumours, especially if high-grade NMIBC is present. Transurethral resection is the initial treatment of choice for NMIBC. However, the high rates of recurrence and significant risk of progression in higher-grade tumours mandate additional therapy with intravesical agents. We discuss the role of various intravesical agents currently in use, including the immunomodulating agent bacillus Calmette-Guérin (BCG) and chemotherapeutic agents. We also discuss the current guidelines and the role of these therapeutic agents in the context of higher-grade Ta and T1 tumours. Beyond the epidemiology, this article focuses on the risk factors, classification and diagnosis, the prediction of recurrence and progression in NMIBC, and the treatments advocated for this invasive disease.
Studies on the Synthesis of the Fe-S Cluster of Dihydroxy-acid Dehydratase in Escherichia coli Crude Extract (1996)

The apoprotein of Escherichia coli dihydroxy-acid dehydratase, which contains a catalytically essential [4Fe-4S] cluster in its active form, has been used as a substrate to investigate Fe-S cluster synthesis. The inactive apoprotein could be reactivated in vitro by factors present in the crude extract of E. coli and to a much smaller extent in the presence of Fe3+, S2-, and dithiothreitol. This reactivation occurs as a result of Fe-S cluster synthesis. It is anticipated that the Fe-S cluster synthesis observed in crude extracts in vitro may involve some of the components that participate in Fe-S cluster synthesis in vivo. The origin of the sulfur used to form Fe-S clusters was investigated. Four enzymatic activities in the crude extract of E. coli were found that can provide sulfur for Fe-S cluster synthesis in vitro by mobilizing the sulfur from cysteine. The purification of the proteins responsible for three of these activities is reported in this paper. The three proteins have been identified as O-acetylserine sulfhydrylase A, O-acetylserine sulfhydrylase B, and beta-cystathionase. The rate and extent of sulfide mobilization from cysteine in the reaction catalyzed by O-acetylserine sulfhydrylases A and B depend on the presence of nucleophiles that can add to the aminoacrylate formed on the enzyme following the removal of sulfide from cysteine. A new amino acid is formed when the nucleophiles add to the aminoacrylate. Sulfur mobilization by beta-cystathionase does not require a nucleophile, and the reaction is a minor variation on the cleavage of beta-cystathionine, with pyruvate, ammonia, and sulfide being the products. Once sulfur is mobilized by these enzymes, its efficient use in Fe-S cluster synthesis seems to be affected by the presence of yet unidentified factors present in crude extract. In crude extract and partially purified preparations from E. coli where these factors are present, the rapidity with which Fe-S clusters are formed and the efficiency with which sulfur is used imply an orderly controlled formation of Fe-S clusters that is generally typified by enzymatic reactions.
Liquid Crystal Displays: Addressing Schemes and Electro-Optical Effects (2001)

In this second edition of Liquid Crystal Displays, Ernst Lueder provides a timely update to his successful text. His unique combination of theory and practice presents all the information required for the development and manufacture of modern high performance and energy saving LCDs. The author also strives for an easy to understand description of complex facts. The second edition focuses on a variety of liquid crystal cells and their electronic addressing, and outlines new developments including: High performance VA cells, especially for TV, due to two subpixels with excellent -correction also at oblique viewing Short optical response times in the range of 1 ms also for inter-gray transitions due to novel addressing waveforms Fringe field switching for acceleration of rise and decay of luminance eliminating frame memories Reduction of motion blur by scanning backlights, high frequency frames, edge enhancement and motion blur modeling Very thin LCDs with power saving LED backlights exhibiting unmatched color purity and larger than NTSC color gamut Printed layers on hydrophobic and hydrophilic areas replacing photolithography Practicing electrical engineers, physicists, chemists and display specialists will find this a valuable resource. Researchers will appreciate the practical guidance given for the design of improved LCDs, whilst students are provided with a useful overview of the field.
Controlling Motion at the Nanoscale: Rise of the Molecular Machines (2015)

As our understanding and control of intra- and intermolecular interactions evolve, ever more complex molecular systems are synthesized and assembled that are capable of performing work or completing sophisticated tasks at the molecular scale. Commonly referred to as molecular machines, these dynamic systems comprise an astonishingly diverse class of motifs and are designed to respond to a plethora of actuation stimuli. In this Review, we outline the conditions that distinguish simple switches and rotors from machines and draw from a variety of fields to highlight some of the most exciting recent examples of opportunities for driven molecular mechanics. Emphasis is placed on the need for controllable and hierarchical assembly of these molecular components to display measurable effects at the micro-, meso-, and macroscales. As in Nature, this strategy will lead to dramatic amplification of the work performed via the collective action of many machines organized in linear chains, on functionalized surfaces, or in three-dimensional assemblies.
Hydrogen sulfide‐induced apoptosis of human aorta smooth muscle cells via the activation of mitogen‐activated protein kinases and caspase‐3 (2004)

The endogenous production of hydrogen sulfide (H2S) and its physiological functions, including membrane hyperpolarization and smooth muscle cell relaxation, position this gas well in the family of gasotransmitters together with nitric oxide (NO) and carbon monoxide (CO). In this study, we demonstrate that H2S at physiologically relevant concentrations induced apoptosis of human aorta smooth muscle cells (HASMCs). Exposure of HASMCs to H2S did not induce necrosis as verified with Trypan blue exclusion and LDH release analysis. After inhibiting endogenous H2S production, exogenous H2S induced much more significant apoptosis, which was not altered by the presence of albumin or glutathione. H2S treatment increased the activities of ERK and p38 mitogen-activated protein kinase (MAPK), but not c-Jun N-terminal kinase activity. Suppression of extracellular signal-regulated kinase (ERK) activity, but not of p38 activity, inhibited the H2S-induced apoptosis of HASMCs. The activation of ERK by H2S in HASMCs was accompanied by increased caspase-3 activity. Inhibition of caspase-3 by AC-DEVD-CHO attenuated the H2S-induced cell apoptosis. Inhibition of ERK by U0126 decreased caspase-3 activity, whereas AC-DEVD-CHO did not alter ERK activity. In conclusion, exogenous H2S induces apoptosis of HASMCs, which is significantly affected by the endogenous H2S level. Of the three investigated MAPKs, only ERK played an active role in mediating H2S-induced apoptosis of HASMCs by activating caspase-3. These findings may help reveal novel mechanisms for many diseases linked to H2S-related abnormal cellular proliferation and apoptosis.
Translocation of RecA-Coated Double-Stranded DNA through Solid-State Nanopores (2008)

We report translocation of double-stranded DNA (dsDNA) molecules that are coated with RecA protein through solid-state nanopores. Translocation measurements show current-blockade events with a wide variety in time duration (10-4-10-1 s) and conductance blockade values (3-14 nS). Large blockades (11.4+/-0.7 nS) are identified as being caused by translocations of RecA-dsDNA filaments. We confirm these results through a variety of methods, including changing molecular length and using an optical tweezer system to deliver bead-functionalized molecules to the nanopore. We further distinguish two different regimes of translocation: a low-voltage regime (<150 mV) in which the event rate increases exponentially with voltage, and a high-voltage regime in which it remains constant. Our results open possibilities for a variety of future experiments with (partly) protein-coated DNA molecules, which is interesting for both fundamental science and genomic screening applications.