gebhart/patrepeval huggingface dataset:
A New TetR Family Transcriptional Regulator Required for Morphogenesis inStreptomyces coelicolor (2007)

Both morphogenesis and antibiotic production in the streptomycetes are initiated in response to starvation, and these events are coupled. We previously described a transposon-generated mutant in Streptomyces coelicolor, SE293, that resulted in a bld strain that overproduced the antibiotic actinorhodin. The SCO1135 open reading frame identified by the insertion encodes a member of the TetR family of transcriptional regulators. Here we show that a constructed deletion of the SCO1135 open reading frame resulted in the same morphological and antibiotic production phenotype as the insertion mutant. The constructed deletion also resulted in constitutive expression of SCO1135 transcript, as well as that of the gene cluster immediately adjacent to it, SCO1134-1132, which encodes a putative molybdopterin binding complex. A His6-tagged version of the SCO1135 protein product was shown to bind the intergenic region between SCO1135 and SCO1134, which contains the apparent transcription start sites for each gene mapped by primer extension analysis. Increased expression of the SCO1134-1132 transcript in the SCO1135 deletion mutant also resulted in increased expression of xanthine dehydrogenase activity, confirming the predictions about these open reading framed based on protein similarity. We have designated the SCO1134-1142 gene cluster xdhABC and the regulator encoded by SCO1135 xdhR. We speculate that the inappropriate expression of xanthine dehydrogenase affects purine salvaging pathways at the onset of development, creating artificially high concentrations of both GTP and ppGpp and perturbing the pathways these molecules participate in for the initiation of morphogenesis and antibiotic production.
Nickel-catalyzed reactions involving strained .sigma. bonds. III. Nickel(0)-catalyzed reaction of bicyclo[2.1.0]pentane with olefins (1971)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTNickel-catalyzed reactions involving strained .sigma. bonds. III. Nickel(0)-catalyzed reaction of bicyclo[2.1.0]pentane with olefinsR. Noyori, T. Suzuki, and H. TakayaCite this: J. Am. Chem. Soc. 1971, 93, 22, 5896–5897Publication Date (Print):November 1, 1971Publication History Published online1 May 2002Published inissue 1 November 1971https://pubs.acs.org/doi/10.1021/ja00751a054https://doi.org/10.1021/ja00751a054research-articleACS PublicationsRequest reuse permissionsArticle Views153Altmetric-Citations23LEARN 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
Identification of a Novel Family of Ankyrin Repeats Containing Cofactors for p160 Nuclear Receptor Coactivators (2004)

Members of the p160 nuclear receptor coactivators interact with liganded nuclear receptors to enhance transcription of target genes. Here we identify a novel family of ankyrin repeats containing cofactors (ANCOs) that interact with the p160 coactivators. ANCO-1 binds to the conserved Per-Arnt-Sim (PAS) region of the p160 coactivators. It encodes a large nuclear protein with five ankyrin repeats, and parts of its sequences have been reported as nasopharyngeal carcinoma susceptibility protein and medulloblastoma antigen. Immunofluorescence staining reveals discrete nuclear foci of ANCO-1 that are distinct from known nuclear structures. Intriguingly, ANCO-1 also colocalizes and interacts with histone deacetylases. Transient reporter gene assay shows that ANCO-1 expression inhibits ligand-dependent transactivation by both steroid and nonsteroid nuclear receptors. Taken together, we have identified a novel family of ankyrin repeats containing cofactors that may recruit histone deacetylases to the p160 coactivators/nuclear receptor complex to inhibit ligand-dependent transactivation.
200  A randomized, placebo-controlled study of galcanezumab in patients with treatment-resistant migraine: double-blind results from CONQUER (2022)

Objective CONQUER assessed galcanezumab efficacy and safety in patients with episodic or chronic migraine who had multiple migraine preventive treatment failures. Methods In this phase 3, double-blind study, patients (aged 18–75 years) met criteria for migraine, had 4–29 monthly migraine headache days, and 2–4 migraine preventive medication category failures in the past 10 years. Patients were randomized to receive galcanezumab 120mg/month (with 240-mg loading dose; N=232) or placebo (N=230). Primary endpoint: overall mean change from baseline in number of monthly migraine headache days across Months 1–3. Key secondary endpoints: ≥50%, ≥75%, or 100% reduction in monthly migraine headache days and change on Migraine-Specific Quality of Life-Role Function Restrictive domain. Results Galcanezumab-treated patients averaged 4.1 fewer monthly migraine headache days from a baseline of 13.4 versus placebo patients’ average of 1.0 fewer from a baseline of 13.0 (between-group difference 3.1; p&lt;0.0001; 95%CI: -3.9, -2.3; effect size=0.72). Galcanezumab was superior to placebo on all key secondary endpoints and did not differ from placebo in terms of safety. Conclusion Galcanezumab was superior to placebo in preventive treatment of migraine and was safe and well tolerated in patients with previous failures to standard-of-care preventive treatments. pain_andrew@lilly.com
Ferrous Mono-α,α′-dipyridyl (1949)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTFerrous Mono-α,α′-dipyridylP. KrumholzCite this: J. Am. Chem. Soc. 1949, 71, 11, 3654–3656Publication Date (Print):November 19, 1949Publication History Published online1 May 2002Published inissue 19 November 1949https://pubs.acs.org/doi/10.1021/ja01179a021https://doi.org/10.1021/ja01179a021research-articleACS PublicationsRequest reuse permissionsArticle Views133Altmetric-Citations25LEARN 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
A Practical Attack to De-anonymize Social Network Users (2010)

Social networking sites such as Facebook, LinkedIn, and Xing have been reporting exponential growth rates and have millions of registered users. In this paper, we introduce a novel de-anonymization attack that exploits group membership information that is available on social networking sites. More precisely, we show that information about the group memberships of a user (i.e., the groups of a social network to which a user belongs) is sufficient to uniquely identify this person, or, at least, to significantly reduce the set of possible candidates. That is, rather than tracking a user's browser as with cookies, it is possible to track a person. To determine the group membership of a user, we leverage well-known web browser history stealing attacks. Thus, whenever a social network user visits a malicious website, this website can launch our de-anonymization attack and learn the identity of its visitors. The implications of our attack are manifold, since it requires a low effort and has the potential to affect millions of social networking users. We perform both a theoretical analysis and empirical measurements to demonstrate the feasibility of our attack against Xing, a medium-sized social network with more than eight million members that is mainly used for business relationships. Furthermore, we explored other, larger social networks and performed experiments that suggest that users of Facebook and LinkedIn are equally vulnerable.
Measurement Units and Scales for Object-Relational Database Metrics (2008)

Metrology in software engineering, as a discipline of study, requires that metrics and measurements be formally evaluated and validated. These validated metrics need to be formally calibrated against standard measuring scales. Object-relational databases (ORDB), complex in its design and functionality, require that their metrics be accepted in the science of measurement. Hence, we attempt in this work to calibrate five ORDB metrics and derive scales for them. Also the unit of measurements for the relevant metrics are also interpreted and argued, so that the metrics become meaningful in its numeral existence. The work is concluded with a focus on open issues on the database metrics.
Low-voltage C 8 -BTBT thin-film transistors for flexible electronics (2017)

During the last decades several research groups and companies have been focused on the development of innovative products in the area of transparent and flexible electronics. Thin-film transistors (TFTs) are the fundamental electronic elements of this technology responsible for the current modulation in the system. Especially for portable gadgets, it is important that the integrated electronic circuits operate at low-voltages. To increase the charge carrier density in the channel region at a specific voltage, the capacitive coupling between the semiconductor and gate can be improved applying dielectrics with high permittivity without losing the malleability of the device. In this article, we analyze the frequency-dependent dielectric constant of a commercially available organic-inorganic nanocomposite and the influence of a titanium interlayer in-between the capacitor’s bottom electrode and the applied insulating film. Afterwards, an integration process for low-voltage C8-BTBT-based TFTs on freestanding polyethylene terephthalate (PET) substrates employing this hybrid dielectric is presented and the electrical characteristics of the transistors were evaluated.
Structure-retention relations in the reversed-phase high performance liquid chromatography of purine and pyrimidine compounds (1980)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStructure-retention relations in the reversed-phase high performance liquid chromatography of purine and pyrimidine compoundsPhyllis R. Brown and Eli. GrushkaCite this: Anal. Chem. 1980, 52, 8, 1210–1215Publication Date (Print):July 1, 1980Publication History Published online1 May 2002Published inissue 1 July 1980https://pubs.acs.org/doi/10.1021/ac50058a012https://doi.org/10.1021/ac50058a012research-articleACS PublicationsRequest reuse permissionsArticle Views156Altmetric-Citations45LEARN 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
Local Backbone Geometry Plays a Critical Role in Determining Conformational Preferences of Amino Acid Residues in Proteins (2022)

The definition of the structural basis of the conformational preferences of the genetically encoded amino acid residues is an important yet unresolved issue of structural biology. In order to gain insights into this intricate topic, we here determined and compared the amino acid propensity scales for different (φ, ψ) regions of the Ramachandran plot and for different secondary structure elements. These propensities were calculated using the Chou-Fasman approach on a database of non-redundant protein chains retrieved from the Protein Data Bank. Similarities between propensity scales were evaluated by linear regression analyses. One of the most striking and unexpected findings is that distant regions of the Ramachandran plot may exhibit significantly similar propensity scales. On the other hand, contiguous regions of the Ramachandran plot may present anticorrelated propensities. In order to provide an interpretative background to these results, we evaluated the role that the local variability of protein backbone geometry plays in this context. Our analysis indicates that (dis)similarities of propensity scales between different regions of the Ramachandran plot are coupled with (dis)similarities in the local geometry. The concept that similarities of the propensity scales are dictated by the similarity of the NC<sup>α</sup>C angle and not necessarily by the similarity of the (φ, ψ) conformation may have far-reaching implications in the field.
Molecular Imaging of Atherosclerotic Plaques Using a Human Antibody Against the Extra-Domain B of Fibronectin (2004)

Current imaging modalities of human atherosclerosis, such as angiography, ultrasound, and computed tomography, visualize plaque morphology. However, methods that provide insight into plaque biology using molecular tools are still insufficient. The extra-domain B (ED-B) is inserted into the fibronectin molecule by alternative splicing during angiogenesis and tissue remodeling but is virtually undetectable in normal adult tissues. Angiogenesis and tissue repair are also hallmarks of advanced plaques. For imaging atherosclerotic plaques, the human antibody L19 (specific against ED-B) and a negative control antibody were labeled with radioiodine or infrared fluorophores and injected intravenously into atherosclerotic apolipoprotein E-null (ApoE-/-) or normal wild-type mice. Aortas isolated 4 hours, 24 hours, and 3 days after injection exhibited a selective and stable uptake of L19 when using radiographic or fluorescent imaging. L19 binding was confined to the plaques as assessed by fat staining. Comparisons between fat staining and autoradiographies 24 hours after 125I-labeled L19 revealed a significant correlation (r=0.89; P<0.0001). Minimal antibody uptake was observed in normal vessels from wild-type mice receiving the L19 antibody and in atherosclerotic vessels from ApoE-/- mice receiving the negative control antibody. Immunohistochemical studies revealed increased expression of ED-B not only in murine but also in human plaques, in which it was found predominantly around vasa vasorum and plaque matrix. In summary, we demonstrate selective targeting of atheromas in mice using the human antibody to the ED-B domain of fibronectin. Thus, our findings may set the stage for antibody-based molecular imaging of atherosclerotic plaques in the intact organism.
Calculation of static longitudinal aerodynamic characteristics of STOL aircraft with upper surface blown flaps (1975)

An existing prediction method developed for EBF aircraft configurations was applied to USB configurations to determine its potential utility in predicting USB aerodynamic characteristics. An existing wing-flap vortex-lattice computer program was modified to handle multiple spanwise flap segments at different flap angles. A potential flow turbofan wake model developed for circular cross-section jets was used to model a rectangular cross-section jet wake by placing a number of circular jets side by side. The calculation procedure was evaluated by comparison of measured and predicted aerodynamic characteristics on a variety of USB configurations. The method is limited to the case where the flow and geometry of the configuration are symmetric about a vertical plane containing the wing root chord. Comparison of predicted and measured lift and pitching moment coefficients were made on swept wings with one and two engines per wing panel, various flap deflection angles, and a range of thrust coefficients. The results indicate satisfactory prediction of lift for flap deflections up to 55 and thrust coefficients less than 2. The applicability of the prediction procedure to USB configurations is evaluated, and specific recommendations for improvements are discussed.
Free-radical chemistry of organophosphorus compounds. III. .alpha. vs. .beta. Scission in reactions of alkoxy and thiyl radicals with trivalent organophosphorus derivatives (1973)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTFree-radical chemistry of organophosphorus compounds. III. .alpha. vs. .beta. Scission in reactions of alkoxy and thiyl radicals with trivalent organophosphorus derivativesWesley G. Bentrude, Eric R. Hansen, Wajid A. Khan, Tae B. Min, and Peter E. RogersCite this: J. Am. Chem. Soc. 1973, 95, 7, 2286–2293Publication Date (Print):April 1, 1973Publication History Published online1 May 2002Published inissue 1 April 1973https://pubs.acs.org/doi/10.1021/ja00788a031https://doi.org/10.1021/ja00788a031research-articleACS PublicationsRequest reuse permissionsArticle Views744Altmetric-Citations27LEARN 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
Functionalization of parylene during its chemical vapor deposition (2011)

Abstract Two possible mechanisms for the reaction of four halogenated (metha)acrylate‐based molecules with Parylene [poly (paraxylylene)] during its chemical vapor deposition were proposed. The chemical reactivity of acrylate double bond with the paraxylylene biradical was calculated for all four (metha)acrylate‐based molecules. These calculations allowed the evaluation of the energetically favorable mechanism and indeed a direct correlation was found between both predicted and experimental reactivities. Next, the reactivity of the (metha)acrylate‐modified Parylene films was evaluated through their reaction with different amines. The obtained amidated Parylene films were characterized with X‐ray photoelectron spectroscopy, Kaiser test for primary amines, and fluorescence microscopy. The strong reactivity of (metha)acrylate‐modified Parylene films toward nucleophilic substitution emphasizes a general method for the functionalization of self‐supported Parylene films grown on the reacting solutions using the novel solid on liquid deposition process. This paves the way to the development of multifunctional materials in a one‐step process resulting from the deposition Parylene over liquid patterns. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2011
Sensitivity analysis of magnetic field measurements for magnetic resonance electrical impedance tomography (MREIT) (2017)

The efficiencies observed with the optimized sequence parameters will likely render in-vivo human brain MREIT feasible. Magn Reson Med 79:748-760, 2018. © 2017 International Society for Magnetic Resonance in Medicine.
Exhaled nitric oxide comes of age (2012)

The measurement of exhaled nitric oxide (NO) made its way as a new lung function from basic discovery to clinical application in less than a decade. As was the case with spirometry, after the initial bloom of the field, making and following basic discoveries, contradictory findings and unexpected discoveries brought the area to a halt, and scientists have been prompted to take a fresh look at all of the available data and the future horizon.
Impact of Stavudine Phenotype and Thymidine Analogues Mutations on Viral Response to Stavudine plus Lamivudine in Altis 2 Anrs Trial (2002)

These results argue for a phenotypic and genotypic cross resistance between stavudine and zidovudine. Modest increases of IC50 and IC50 for stavudine had an important impact on the virological response during the trial and plead for a new definition of the threshold value for stavudine phenotypic index.
Triple Versus Dual Therapy for Eradicating Helicobacter pylori and Preventing Ulcer Recurrence: A Randomized, Double-Blind, Multicenter Study of Lansoprazole, Clarithromycin, and/or Amoxicillin in Different Dosing Regimens (1998)

In patients with active or a recent history of duodenal ulcer, a 14-day course of lansoprazole-based triple therapy without additional acid suppression therapy is highly effective in the eradication of H. pylori and in preventing ulcer recurrence. Among the dual therapies, higher eradication rates occurred when lansoprazole (with amoxicillin) or clarithromycin (with lansoprazole) was administered t.i.d. vs b.i.d., but the rates were still significantly lower than with lansoprazole triple therapy with all three drugs administered b.i.d.
Crystalline order and melting behavior of isotactic polypropylene (α form) (1984)

Abstract Samples of isotactic polypropylene in the α form may have different degrees of order in the up and down positioning of the chains. By suitable programming of the crystallization history of unoriented samples it is possible to show, from DSC and WAXS data, that a strict correlation exists between the melting behavior and the degree of ordering of the chains. The process of ordering at annealing temperatures above 150°C may lead to a “continuum” of modifications of the α form from less ordered to highly ordered ones; correspondingly we observe an increase in the melting point by as much as 15°C.