gebhart/patrepeval huggingface dataset:
A cis-acting element present in multiple genes serves as a repressor protein binding site for the yeast CAR1 gene. (1990)

Induction of the arginase (CAR1) gene expression in Saccharomyces cerevisiae has previously been shown to require participation of a cis-dominantly regulated upstream repression sequence (URS). Deletion of this element results in high-level expression of the CAR1 gene without inducer. To determine the structure of the CAR1 URS element, we performed a saturation mutagenesis. Results of the mutagenic analysis indicated that the CAR1 URS was a 9-base-pair palindromic sequence, 5'-AGCCGCCGA-3'. A DNA fragment containing this sequence was shown to bind one or more proteins by a gel shift assay. DNA fragments containing point mutations that completely eliminated URS function were not effective competitors in this assay, whereas those which supported URS function were effective competitors. Sequences in the 5'-flanking regions of 14 other genes were found to be homologous to the CAR1 URS. These sequences were shown to support varying degrees of URS function in the expression vector assay, to bind protein as demonstrated by the gel shift assay, and to compete with a DNA fragment containing the CAR1 URS for protein binding. These results indicate that the CAR1 URS element possesses the characteristics of a repressor binding site. Further, they are consistent with the suggestion that sites homologous to the CAR1 URS may be situated in the 5'-flanking regions of multiple unrelated yeast genes. The widespread occurrence of this element raises the possibility that it is the target site for one or more negatively acting general transcription factors.
A Self-Assembled Monolayer for the Binding and Study of Histidine-Tagged Proteins by Surface Plasmon Resonance (1996)

This paper reports the generation of a self-assembled monolayer (SAM) that selectively binds proteins whose primary sequence terminates with a His-tag: a stretch of six histidines commonly incorporated in recombinant proteins to simplify purification. The SAM was prepared by the adsorption onto a gold surface of a mixture of two alkanethiols: one thiol that terminated with a nitrilotriacetic acid (NTA) group, a group that forms a tetravalent chelate with Ni(II), and a second thiol that terminated with a tri(ethylene glycol) group, a group that resists protein adsorption. His-tagged proteins bound to the SAM by interaction of the histidines with the two vacant sites on Ni(II) ions chelated to the surface NTA groups. Studies with model proteins showed the binding was specific for His-tagged proteins and required the presence of Ni(II) on the surface. Immobilized His-tagged proteins were kinetically stable in buffered saline at pH 7.2 but could be desorbed by treatment with 200 mM imidazole. Surface plasmon resonance studies for two model systems showed that His-tagged proteins adsorbed on the NTA-SAM retained a greater ability to participate in binding interactions with proteins in solution than protein immobilized in a thin dextran gel layer by covalent coupling.
Dynamic vectorization in the E2 dynamic multicore architecture (2010)

Previous research has shown that Explicit Data Graph Execution (EDGE) instruction set architectures (ISA) allow for power efficient performance scaling. In this paper we describe the preliminary design of a new dynamic multicore processor called E2 that utilizes an EDGE ISA to allow for the dynamic composition of physical cores into logical processors. We provide details of E2's support for dynamic reconfigurability and show how the EDGE ISA facilities outof- order vector execution.
A Quantitative Histological Study of Strain-Dependent Differences in the Effects of Irradiation on Mouse Lung during the Early Phase (1989)

Strain differences in the radiation response of mouse lung during the early phase (before 28 weeks postirradiation) were investigated histologically. The nine strains tested were divided into three groups on the basis of the nature of the edema present, the occurrence of hyaline membranes, and the presence of fibrosis. Group 1 mice, three C57 strains, developed hyaline membranes, focal fibrosis, and a protein-rich edema containing fibrin. Group 3, CBA and two C3H strains, had only a protein-poor edema with little fibrin and developed no visible fibrosis. Group 2 mice had both types of edema and small quantities of focal fibrosis. The degree of lung impairment in mice dying of respiratory insufficiency was assessed by scoring lung acini as nonfunctional or open and presumably functional. Over 70% of acini were nonfunctional as a result of airflow obstruction. This was considered sufficient to account for death. Carbon perfusion immediately before sacrifice indicated that all types of lesions were at least partially perfused with blood. Pleural effusions were found in some individuals of two strains. The proportion of nonfunctional acini was similar in mice of the same strain with and without effusions, which would not be expected if the effusions contributed appreciably to respiratory distress in the early phase.
Induction of apoptosis (programmed cell death) in tumour cell lines by widely diverging stimuli (1990)

Conference Article| April 01 1990 Induction of apoptosis (programmed cell death) in tumour cell lines by widely diverging stimuli SEAMUS V. LENNON; SEAMUS V. LENNON 1Department of Biology, St Patrick's College, Maynooth, Co. Kildare, Republic of Ireland Search for other works by this author on: This Site PubMed Google Scholar SEAMUS J. MARTIN; SEAMUS J. MARTIN 1Department of Biology, St Patrick's College, Maynooth, Co. Kildare, Republic of Ireland Search for other works by this author on: This Site PubMed Google Scholar THOMAS G. COTTER THOMAS G. COTTER 1Department of Biology, St Patrick's College, Maynooth, Co. Kildare, Republic of Ireland Search for other works by this author on: This Site PubMed Google Scholar Biochem Soc Trans (1990) 18 (2): 343–345. https://doi.org/10.1042/bst0180343 Article history Received: September 18 1989 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn Email Cite Icon Cite Get Permissions Citation SEAMUS V. LENNON, SEAMUS J. MARTIN, THOMAS G. COTTER; Induction of apoptosis (programmed cell death) in tumour cell lines by widely diverging stimuli. Biochem Soc Trans 1 April 1990; 18 (2): 343–345. doi: https://doi.org/10.1042/bst0180343 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBiochemical Society Transactions Search Advanced Search © 1990 Biochemical Society1990 Article PDF first page preview Close Modal You do not currently have access to this content.
Microcalorimetric Studies of CO and H2 Adsorption on Nickel Powders Promoted with Potassium and Cesium (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMicrocalorimetric Studies of CO and H2 Adsorption on Nickel Powders Promoted with Potassium and CesiumB. E. Spiewak, J. Shen, and J. A. DumesicCite this: J. Phys. Chem. 1995, 99, 49, 17640–17644Publication Date (Print):December 1, 1995Publication History Published online1 May 2002Published inissue 1 December 1995https://pubs.acs.org/doi/10.1021/j100049a026https://doi.org/10.1021/j100049a026research-articleACS PublicationsRequest reuse permissionsArticle Views341Altmetric-Citations40LEARN 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 options Get e-Alerts
Interleukin-23 drives innate and T cell–mediated intestinal inflammation (2006)

Inflammatory bowel disease (IBD) is a chronic inflammatory disorder of the gastrointestinal tract involving aberrant activation of innate and adaptive immune responses. We have used two complementary models of IBD to examine the roles of interleukin (IL)-12 family cytokines in bacterially induced intestinal inflammation. Our results clearly show that IL-23, but not IL-12, is essential for the induction of chronic intestinal inflammation mediated by innate or adaptive immune mechanisms. Depletion of IL-23 was associated with decreased proinflammatory responses in the intestine but had little impact on systemic T cell inflammatory responses. These results newly identify IL-23 as a driver of innate immune pathology in the intestine and suggest that selective targeting of IL-23 represents an attractive therapeutic approach in human IBD.
Antioxidant activity of rosemary (Rosmarinus officinalis L.) essential oil and its hepatoprotective potential (2014)

Our results demonstrate that rosemary essential oil, beside exhibiting free radical scavenging activity determined by DPPH assay, mediates its hepatoprotective effects also through activation of physiological defense mechanisms.
"Slow light" gyroscope based on coupled resonator waveguide structure (2007)

We propose to utilize the highly dispersive coupled resonator structure for sensitive rotation sensing. The coupled resonator induced transparency based "slow light" gyroscope is analyzed and an AB-init FDTD method is proposed for device designing.
Model-based evaluation: from dependability to security (2004)

The development of techniques for quantitative, model-based evaluation of computer system dependability has a long and rich history. A wide array of model-based evaluation techniques is now available, ranging from combinatorial methods, which are useful for quick, rough-cut analyses, to state-based methods, such as Markov reward models, and detailed, discrete-event simulation. The use of quantitative techniques for security evaluation is much less common, and has typically taken the form of formal analysis of small parts of an overall design, or experimental red team-based approaches. Alone, neither of these approaches is fully satisfactory, and we argue that there is much to be gained through the development of a sound model-based methodology for quantifying the security one can expect from a particular design. In this work, we survey existing model-based techniques for evaluating system dependability, and summarize how they are now being extended to evaluate system security. We find that many techniques from dependability evaluation can be applied in the security domain, but that significant challenges remain, largely due to fundamental differences between the accidental nature of the faults commonly assumed in dependability evaluation, and the intentional, human nature of cyber attacks.
Danazol Increases the Anticoagulant Effect of Warfarin (1992)

Based on this report and other published cases, clinicians must be aware that danazol may increase the anticoagulant effect of warfarin. Patients receiving warfarin who are prescribed danazol must be monitored closely to prevent excessive anticoagulation and subsequent bleeding. Studies are needed to determine the frequency of this interaction and its underlying mechanisms.
Metal-Catalyzed Oxidation of Phenylalanine-Sensitive 3-Deoxy- d - arabino -Heptulosonate-7-Phosphate Synthase from Escherichia coli : Inactivation and Destabilization by Oxidation of Active-Site Cysteines (1999)

The in vitro instability of the phenylalanine-sensitive 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase [DAHPS(Phe)] from Escherichia coli has been found to be due to a metal-catalyzed oxidation mechanism. DAHPS(Phe) is one of three differentially feedback-regulated isoforms of the enzyme which catalyzes the first step of aromatic biosynthesis, the formation of DAHP from phosphoenolpyruvate and D-erythrose-4-phosphate. The activity of the apoenzyme decayed exponentially, with a half-life of about 1 day at room temperature, and the heterotetramer slowly dissociated to the monomeric state. The enzyme was stabilized by the presence of phosphoenolpyruvate or EDTA, indicating that in the absence of substrate, a trace metal(s) was the inactivating agent. Cu2+ and Fe2+, but none of the other divalent metals that activate the enzyme, greatly accelerated the rate of inactivation and subunit dissociation. Both anaerobiosis and the addition of catalase significantly reduced Cu2+-catalyzed inactivation. In the spontaneously inactivated enzyme, there was a net loss of two of the seven thiols per subunit; this value increased with increasing concentrations of added Cu2+. Dithiothreitol completely restored the enzymatic activity and the two lost thiols in the spontaneously inactivated enzyme but was only partially effective in reactivation of the Cu2+-inactivated enzyme. Mutant enzymes with conservative replacements at either of the two active-site cysteines, Cys61 or Cys328, were insensitive to the metal attack. Peptide mapping of the Cu2+-inactivated enzyme revealed a disulfide linkage between these two cysteine residues. All results indicate that DAHPS(Phe) is a metal-catalyzed oxidation system wherein bound substrate protects active-site residues from oxidative attack catalyzed by bound redox metal cofactor. A mechanism of inactivation of DAHPS is proposed that features a metal redox cycle that requires the sequential oxidation of its two active-site cysteines.
Membrane topology of peripheral myelin protein 22 (2000)

Peripheral myelin protein 22 (PMP22) is a structural component of compact peripheral nerve myelin and is likely to play a role in the modulation of cell proliferation and cell spreading. Molecular genetics revealed that mutations affecting the PMP22 gene are responsible for the most common forms of hereditary motor and sensory neuropathies in humans. Computer analysis predicts a tetraspan-membrane structure for the PMP22 protein. We have assessed the topology of PMP22 experimentally using chimeric proteins consisting of different PMP22 domains fused to reporter genes and internally tagged molecules. Based on in vitro transcription/translation assays and immunohistochemical analysis of transfected cells, we propose that PMP22 can adopt a non-tetraspan topology that has functional implications in normal and disease processes.
WebShield: Enabling Various Web Defense Techniques without Client Side Modifications (2011)

Today, web attacks are increasing in frequency, severity and sophistication. Existing solutions are either hostbased which suffer deployment problems or middlebox approaches that can only accommodate certain security protection mechanisms with limited protection. In this paper, we propose four design principles for general middlebox frameworks of web protection, and apply these principles to design WebShield, which can enable various host-based security mechanisms. In particular, we run all the JavaScript from remote web servers only at shadow browser instances inside the middlebox, and only run our trusted JavaScript rendering agent at client browsers. The trusted rendering agent turns browsers into a thin web terminal by reconstructing the encoded DOM of a webpage. We implement a prototype of WebShield. Evaluation demonstrates that a general JavaScript rendering agent can render webpages precisely and be just slightly slower than direct access. We further demonstrate that our design can work well with interactive web applications such as JavaScript games. WebShield can detect attacks deeply embedded in dynamic HTML pages including the ones in complex Web 2.0 applications, and can also detect both known and unknown vulnerabilities. We further show that WebShield is scalable for deployment.
Identification of an intermediate-segregation regime in a diblock copolymer system (1996)

We have studied the scaling behavior of the bulk structure in a symmetric diblock copolymer system using small-angle scattering. We have identified a crossover between the inter mediate-segregation regime and the strong-segregation limit at χN ≃ 29. In the inter mediate-segregation regime (χN ≃ 5 − 29), the characteristic length scale, D, scales with chain length, N, as D ∝ N0.83. In the strong-segregation limit (χN > 29), the scaling behavior D ∝ N0.61 is found. The observed crossover is consistent with theoretical predictions.
Effect of Heparin and Heparin Fractions on Platelet Aggregation (1980)

Porcine intestinal mucosal heparin induced aggregation of platelets in citrated platelet-rich plasma and enhanced platelet aggregation and serotonin secretion induced by other agents. This action of heparin was blocked by substances that elevate platelet cyclic AMP and by EDTA but not by inhibitors of platelet cyclooxygenase. The effect was not inhibited by apyrase or by N-amylthio-5'-AMP and therefore did not require the action of ADP, nor was there activation of platelet phospholipase. Platelet aggregation by heparin required a plasma cofactor different from the cofactor required for ristocetin. Fractionation of heparin yielded preparations that varied in molecular weight and, within a given molecular weight fraction, in affinity for antithrombin III. Fractions of high molecular weight (average 20,000) were more reactive with platelets than were fractions of low molecular weight (7,000). Anticoagulant activity did not parallel the platelet reactivity of heparin fractions. Among high molecular weight fractions, preparations of high or low antithrombin affinity were equally active in induction of platelet aggregation. In low molecular weight fractions, there was an inverse relationship between platelet reactivity and anticoagulant activity in normal platelet-rich plasma, but, in platelet-rich plasma depleted of antithrombin, low molecular weight fractions of high and low antithrombin affinity reacted equally with platelets. These results suggest that formation of an antithrombin-heparin complex protected platelets from aggregation by heparin. Selection of heparin fractions of low molecular weight and high antithrombin affinity may improve anticoagulant therapy and development of thromboresistant heparin-coated artificial materials.
Prevention of Typhoid Fever in Nepal with the VI Capsular Polysaccharide ofSalmonella Typhi (1987)

We conducted a pilot study followed by a large clinical trial in Nepal of the use of the capsular polysaccharide of Salmonella typhi (Vi) as a vaccine to prevent typhoid fever. In the pilot study, involving 274 Nepalese, there were no significant side effects of the Vi vaccine; about 75 percent responded with a rise in serum antibodies of fourfold or more. In the clinical trial, residents of five villages were given intramuscular injections of either Vi or, as a control, pneumococcus vaccine dispensed in coded, randomly arranged, single-dose syringes. There were 6907 participants, of whom 6438 were members of the target population (5 to 44 years of age); each was visited every two days. Those with temperatures of 37.8 degrees C or higher for three consecutive days were examined and asked to give blood for culture. Typhoid was diagnosed as either blood culture-positive or clinically suspected on the basis of bradycardia, splenomegaly, and fever, with a negative blood culture. Seventeen months after vaccination, the codes were broken for the 71 patients meeting the criteria for either culture-positive or clinically suspected typhoid. The attack rate of typhoid was 16.2 per 1000 among the controls and 4.1 per 1000 among those immunized with Vi (P less than 0.00001). The efficacy of Vi was 72 percent in the culture-positive cases, 80 percent in the clinically suspected cases, and 75 percent in the two groups combined. These data provide evidence that Vi antibodies confer protection against typhoid. Surveillance continues to determine the duration of Vi-induced immunity.
Targeting colon cancer stem cells using a new curcumin analogue, GO-Y030 (2011)

Our results indicate that STAT3 is a novel therapeutic target in colon cancer stem cells, and inhibition of activated STAT3 in cancer stem cells by GO-Y030 may offer an effective treatment for colorectal cancer.
Crystallization of ricin A chain obtained from a cloned gene expressed in Escherichia coli. (1987)

Ricin is a heterodimeric toxin of the form AB, where B is a lectin which binds cell surfaces, triggering endocytosis. The B chain then aids the A chain in escaping from the endosome. The A chain enzymatically attacks and inactivates ribosomes, thereby killing the intoxicated cell. We have recently solved the three-dimensional structure of whole ricin. Here we report that the A chain, expressed from a gene cloned into Escherichia coli has been crystallized in a suitable form for high resolution x-ray analysis. The crystals are monoclinic space group P2(1) with a = 42.6, b = 68.1, c = 50.2 A and beta = 112.9 degrees. There is evidence that the A chain undergoes a conformational change, resulting in activation, when it is released from the B chain. Comparison of the two structures should facilitate an analysis of this process.
Draft Genome Sequence of Bacillus thuringiensis Serovar Tolworthi Strain Na205-3, an Isolate Toxic for Helicoverpa armigera (2014)

We report here the complete annotated 6,510,053-bp draft genome sequence of Bacillus thuringiensis serovar tolworthi strain Na205-3, which is toxic for Helicoverpa armigera. This strain potentially contains nine insecticidal toxin genes homologous to cry1Aa12, cry1Ab1, cry1Ab8, cry1Ba1, cry1Af1, cry1Ia10, vip1Bb1, vip2Ba2, and vip3Aa6.
The single laser flow cytometric micronucleus test: a time course study using colchicine and urethane in rat and mouse peripheral blood and acetaldehyde in rat peripheral blood (2002)

A single laser flow cytometric procedure to quantify micronucleus frequency in rat and mouse peripheral blood was evaluated. Reticulocytes express the transferrin receptor (also known as the CD71-defined antigen). When combined with a DNA stain, antibodies against this antigen can be used to differentially label and quantify micronucleated reticulocytes. The object of this study was to evaluate the method for rat and mouse peripheral blood using flow cytometry and compare the results obtained between two laboratories (GlaxoWellcome and Litron Laboratories). The compounds selected were the rodent carcinogens colchicine, urethane and acetaldehyde. Colchicine gives a positive response in the rat bone marrow micronucleus assay and an inconclusive result in the rat peripheral blood micronucleus assay. The latter two are both established rat carcinogens readily detected in both the bone marrow and peripheral blood micronucleus assays. In these experiments both rat and mice were treated with either colchicine or urethane and rats alone treated with acetaldehyde. After a single treatment, repeat sampling of peripheral blood was made at 0, 24, 48 and 72 h. Replicate blood samples were obtained and fixed for flow cytometric analysis at both facilities. The micronucleated reticulocyte frequency of each blood sample was determined by analysing 20 000 total reticulocytes per blood sample. The data suggest that the single laser flow cytometric procedure resulted in consistent reticulocyte and micronucleated reticulocyte frequencies between laboratories. Furthermore, these flow cytometric data compare favourably with previously published data.