gebhart/patrepeval huggingface dataset:
OrfX, a Nucleomodulin Required for Listeria monocytogenes Virulence (2017)

<i>Listeria monocytogenes</i> is a bacterial pathogen causing severe foodborne infections in humans and animals. <i>Listeria</i> can enter into host cells and survive and multiply therein, due to an arsenal of virulence determinants encoded in different loci on the chromosome. Several key <i>Listeria</i> virulence genes are clustered in <i>Listeria</i> pathogenicity island 1. This important locus also contains <i>orfX</i> (<i>lmo0206</i>), a gene of unknown function. Here, we found that OrfX is a small, secreted protein whose expression is positively regulated by PrfA, the major transcriptional activator of <i>Listeria</i> virulence genes. We provide evidence that OrfX is a virulence factor that dampens the oxidative response of infected macrophages, which contributes to intracellular survival of bacteria. OrfX is targeted to the nucleus and interacts with the regulatory protein RybP. We show that in macrophages, the expression of OrfX decreases the level of RybP, which controls cellular infection. Collectively, these data reveal that <i>Listeria</i> targets RybP and evades macrophage oxidative stress for efficient infection. Altogether, OrfX is after LntA, the second virulence factor acting directly in the nucleus.<b>IMPORTANCE</b><i>Listeria monocytogenes</i> is a model bacterium that has been successfully used over the last 30 years to refine our understanding of the molecular, cellular, and tissular mechanisms of microbial pathogenesis. The major virulence factors of pathogenic <i>Listeria</i> species are located on a single chromosomal locus. Here, we report that the last gene of this locus encodes a small secreted nucleomodulin, OrfX, that is required for bacterial survival within macrophages and in the infected host. This work demonstrates that the production of OrfX contributes to limiting the host innate immune response by dampening the oxidative response of macrophages. We also identify a target of OrfX, RybP, which is an essential pleiotropic regulatory protein of the cell, and uncover its role in host defense. Our data reinforce the view that the secretion of nucleomodulins is an important strategy used by microbial pathogens to promote infection.
Self-consistency and self-sufficiency of the photocarrier grating technique (1988)

The recently suggested photocarrier grating technique appears to be the most reliable method available for the determination of the ambipolar diffusion length in hydrogenated amorphous silicon. We show that the technique can be made simpler than originally suggested, and that it is self-sufficient in the sense that all the required parameters can be determined by the same experimental setup. It is demonstrated that the various results obtained by the technique are self-consistent and that extremely accurate values of the ambipolar diffusion length can be determined.
Continuous synthesis of palladium nanorods in oxidative segmented flow (2015)

Laminar and segmented flow methods are presented for producing Pd rod‐shaped nanostructures from Na 2 PdCl 4 in mixtures of water, ethylene glycol, polyvinyl pyrrolidone, and KBr. Synthesis in laminar flow produced an evolution from Pd nanoparticles to short nanorods with residence time. Use of air as the segmentation gas tuned the oxidative environment promoting anisotropic growth of Pd. Moreover, the elevated temperatures (160°C and 190°C) and pressure (0.8 MPa) reduced the synthesis time from hours for most batch systems to 2 min. The ratio of polyol and Pd precursor metal flow streams controlled the anisotropic growth, obtaining nanorods with a diameter approximately 4 nm and an aspect ratio up to 6. Nanorods were single crystal with the {100} lattice spacing of fcc structure, and without any dislocation, stacking fault, or twin defects. The resulting Pd nanorods had high activity at moderate temperature (40ºC) and pressure (0.2 MPa) in the catalytic hydrogenation of styrene. © 2015 American Institute of Chemical Engineers AIChE J , 62: 373–380, 2016
Grain Boundaries in Multi-Seeded Melt-Grown Superconductors (2005)

Future applications of high temperature superconductors require bulk materials of a complex shape. The multi-seeded-melt-growth process (MSMG) represents a promising technique for obtaining qualitatively well oriented bulk materials with different kinds of shape. In the MSMG process, several seeds are placed on a precursor pellet, from which the growth of the bulk starts. A certain problem of the MSMG process is that grain boundaries become inevitable when the growth fronts of two neighboring seeds collide. These grain boundaries are responsible for a reduction of the critical currents and pose a problem for high current applications. By polishing the sample step by step, the influence of the grain boundaries was investigated by scanning Hall probe measurements and by the magnetoscan technique. Additionally, optical microscopy and electron microscopy were employed to investigate the details of the microstructure.
Structure-Based Virtual Screening to Discover Potential Lead Molecules for the SARS-CoV-2 Main Protease (2020)

The COVID-19 disease is caused by a new strain of the coronavirus family (SARS-CoV-2), and it has affected at present millions of people all over the world. The indispensable role of the main protease (M<sup>pro</sup>) in viral replication and gene expression makes this enzyme an attractive drug target. Therefore, inhibition of SARS-CoV-2 M<sup>pro</sup> as a proposition to halt virus ingression is being pursued by scientists globally. Here we carried out a study with two objectives: the first being to perform comparative protein sequence and 3D structural analysis to understand the effect of 12 point mutations on the active site. Among these, two mutations, viz., Ser46 and Phe134, were found to cause a significant change at the active sites of SARS-CoV-2. The Ser46 mutation present at the entrance of the S5 subpocket of SARS-CoV-2 increases the contribution of other two hydrophilic residues, while the Phe134 mutation, present in the catalytic cysteine loop, can cause an increase in catalytic efficiency of M<sup>pro</sup> by facilitating fast proton transfer from the Cys145 to His41 residue. It was observed that active site remained conserved among M<sup>pro</sup> of both SARS-CoVs, except at the entrance of the S5 subpocket, suggesting sustenance of substrate specificity. The second objective was to screen the inhibitory effects of three different data sets (natural products, coronaviruses main protease inhibitors, and FDA-approved drugs) using a structure-based virtual screening approach. A total of 73 hits had a combo score >2.0. Eight different structural scaffold classes were identified, such as one/two tetrahydropyran ring(s), dipeptide/tripeptide/oligopeptide, large (approximately 20 atoms) cyclic peptide, and miscellaneous. The screened hits showed key interactions with subpockets of the active site. Further, molecular dynamics studies of selected screened compounds confirmed their perfect fitting into the subpockets of the active site. This study suggests promising structures that can fit into the SARS-CoV-2 M<sup>pro</sup> active site and also offers direction for further lead optimization and rational drug design.
Poly[ferricenium-1,2(1,3:1,1')-diylmethylene tetrachloroferrate(III)], a hydrophilic polysalt for biomedical applications (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPoly[ferricenium-1,2(1,3:1,1')-diylmethylene tetrachloroferrate(III)], a hydrophilic polysalt for biomedical applicationsEberhard W. Neuse and Fathima B. D. KhanCite this: Macromolecules 1986, 19, 2, 269–272Publication Date (Print):February 1, 1986Publication History Published online1 May 2002Published inissue 1 February 1986https://pubs.acs.org/doi/10.1021/ma00156a004https://doi.org/10.1021/ma00156a004research-articleACS PublicationsRequest reuse permissionsArticle Views69Altmetric-Citations17LEARN 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
Diamond turning of aluminum image slicers for astronomical applications (2019)

Image slicers have become a standard equipment in the field of astronomical spectroscopy. They are now widely used in most integral field spectrographs (IFSes) in order to detect and characterize distant galaxies or extra- solar planets. However, they are notoriously difficult to manufacture due to their multiple small tilted surfaces, but equipment such as that of AOFI (Advanced Optical Fabrication Infrastructure) of Universite Laval eases the process. In this regard, the team at AOFI has been tasked with the fabrication of the image slicer for the GIRMOS instrument. This paper presents the characterization of diamond turned RSA-6061 and AA-6061 T6 aluminum, and the definition of the different machining parameters, such as step size and tool radius, that could improve the surface quality of an aluminum image slicer. It also discusses the fabrication of the first prototypes at AOFI, that will eventually prove useful in the fabrication of the image slicer for GIRMOS, effectively lowering its risks.
Complete amino acid sequence of pig kidney fructose-1,6-bisphosphatase. (1982)

The covalent structure of the pig kidney fructose-1,6-bisphosphatase (D-fructose-1,6-bisphosphate 1-phosphohydrolase, EC 3.1.3.11) subunit has been determined. Placement of the 335 amino acid residues in the polypeptide chain was based largely on automated Edman degradation of eight purified cyanogen bromide fragments generated from the S-carboxymethylated protein. The determination of the amino acid sequence of the largest cyanogen bromide fragment (154 residues) required additional analysis of subfragments obtained by tryptic cleavage at arginyl residues and by mild acid cleavage of an Asp-Pro peptide bond. Alignment of the cyanogen bromide fragments was accomplished by analysis of a product of limited proteolysis by an endogenous protease and by characterization of the tryptic peptides isolated from S-[14C]carboxymethylated fructose-1,6-bisphosphatase. This sequence information has permitted the identification of several reactive sites of functional and structural significance in pig kidney fructose-1,6-bisphosphatase.
Tunable Thin-Film Crystalline Structures and Field-Effect Mobility of Oligofluorene–Thiophene Derivatives (2007)

Air-stable p-type semiconducting oligofluorene–thiophene derivatives were vacuum-deposited on octadecyltriethoxysilane-treated SiO2/Si substrates. Effects of end-substituents and substrate deposition temperature (TD) on molecular orientation, crystalline morphologies, and structures in these thin films were investigated by two-dimensional grazing incidence X-ray diffraction and atomic force microscopy, and those results were correlated with charge mobility in top-contacted devices. Crystalline morphologies of the first monolayer thin film in direct contact with the dielectric surface, influenced by TDs (25, 90, and 140 °C) and end-substituted groups (hydrogen, hexyl, and dodecyl), could be categorized as dendrite, compact disk, and single-crystal-like layered grains. The results of grazing incidence X-ray diffraction strongly support that molecular orientation in the films can be finely tuned through controlling substrate, TD, and molecular architecture, resulting in high air stability and field-effect mobility in a top-contacted electrode of organic thin film transistors.
Electrical equipment for a combined wind/PV isolated generating system (1996)

Wind and solar photovoltaic generating systems have advanced rapidly in recent years, but both suffer from the intermittent nature of their resource. A secure stand-alone power supply based on either requires a substantial energy store. Combining the two creates a supply with smaller storage requirement since the fluctuations have a statistical tendency to cancel. The system developed for a 10 kW application comprises wind and solar collectors, each of 5 kW rating, with a lead-acid battery for storage and a 10 kW PWM inverter for the final output. The wind turbine generator is a 5 kW, 200 RPM, direct-drive, permanent-magnet, axial-flux machine based on the 'Torus' configuration. The three-phase output is rectified to form a variable voltage DC link. The power converter uses two DC-DC power converters connected in series, each with a bypass diode which conducts continuously when the corresponding source is not available.
The use of tramadol hydrochloride in the treatment of post-anesthetic shivering. (1990)

Tramadol at the dosage of 1 mg per kg body weight was given intravenously to 110 adult patients who developed postoperative shivering. All patients were cured of the shivering after 45 seconds to 6 minutes. Seventy-four per cent stopped within 2 minutes after the injection. There were five patients who had recurrence of shivering after 10 to 30 minutes and this was easily stopped by another dosage of the drug. There were very few minor side effects and they required no medical treatment.
Resistance to sliding of orthodontic appliances in the dry and wet states: Influence of archwire alloy, interbracket distance, and bracket engagement (2000)

Having established dimensional and mechanical characteristics, the resistances to sliding (RS) were measured in vitro for various archwires against stainless steel brackets. Using stainless steel ligatures, a constant normal force (300g) was maintained while second-order angulation (straight theta) was varied from -12 degrees to +12 degrees. Using miniature bearings to simulate contiguous teeth, five experiments each were run in the dry or wet states with human saliva at 34 degrees C as a function of four archwire alloys, five interbracket distances, and two bracket engagements. Outcomes were objectively analyzed to establish when theta=0, and the relative contact angles ( theta(r)) were replotted. Critical contact angles (theta(c)) that were determined via experimentation were in good agreement with theory. Slopes and y-intercepts were tabulated from linear regression equations of RS against theta plots in both the passive (theta < or = theta (c)) and active ( theta > or = theta(c)) configurations, for which theta = theta(c) identified the boundary between classical friction and binding phenomena. Stiffer archwires and shorter interbracket distances exacerbated binding, whereas, once corrected for differing bracket engagement, RS was independent of slot dimension. Unlike earlier results in the passive configuration, in the active configuration couples comprised of titanium alloys (NiTi and (beta-Ti) had higher RS values in the wet versus the dry state. For those archwire alloys evaluated, two empirical expressions were adduced that comprise the binding component, the yield strength or elastic limit, and the beam length, which implicitly represent the stiffness, flexibility, and interbracket distance.
Mycobacterium chelonaeCausing Otitis Media in an Ear-Nose-and-Throat Practice (1988)

Seventeen cases of otitis media caused by Mycobacterium chelonae were detected among patients seen at a single ear-nose-and-throat (ENT) office (Office A) in Louisiana between May 5 and September 15, 1987. All the patients had a tympanotomy tube or tubes in place or had one or more tympanic-membrane perforations, with chronic otorrhea that was unresponsive to standard therapy with antimicrobial agents. Middle-ear exploration in six patients revealed abundant granulation tissue; multiple granulomas and acid-fast bacilli were demonstrated on a section of tissue from one patient with a nonhealing mastoidectomy incision. Thirteen of the 14 ear isolates obtained from patients seen in Office A had the same unusual pattern of high-level resistance to aminoglycosides. M. chelonae and other nontuberculous mycobacteria were recovered from several sources of water in Office A, as well as in another ENT office (Office B) in a neighboring city that was visited by the index patient. Only one additional case was detected in Office B during the same period. Otologic instruments in Office A were cleaned in an ultrasonic bath with tap water and a liquid detergent; the contents of the bath were changed only once weekly. Instruments in Office B were placed in boiling water between patient examinations. This outbreak establishes M. chelonae as an agent of otitis media and underscores the need for high-level disinfection or sterilization of ENT instruments between examinations to prevent the transmission of this organism to patients in the office setting.
Inhibition of Notch signaling induces apoptosis of myeloma cells and enhances sensitivity to chemotherapy (2007)

Drug resistance remains a critical problem in the treatment of patients with multiple myeloma. Recent studies have determined that Notch signaling plays a major role in bone marrow (BM) stroma-mediated protection of myeloma cells from de novo drug-induced apoptosis. Here, we investigated whether pharmacologic inhibition of Notch signaling could affect the viability of myeloma cells and their sensitivity to chemotherapy. Treatment with a gamma-secretase inhibitor (GSI) alone induced apoptosis of myeloma cells via specific inhibition of Notch signaling. At concentrations toxic for myeloma cell lines and primary myeloma cells, GSI did not affect normal BM or peripheral blood mononuclear cells. Treatment with GSI prevented BM stroma-mediated protection of myeloma cells from drug-induced apoptosis. The cytotoxic effect of GSI was mediated via Hes-1 and up-regulation of the proapoptotic protein Noxa. In vivo experiments using xenograft and SCID-hu models of multiple myeloma demonstrated substantial antitumor effect of GSI. In addition, GSI significantly improved the cytotoxicity of the chemotherapeutic drugs doxorubicin and melphalan. Thus, this study demonstrates that inhibition of Notch signaling prevents BM-mediated drug resistance and sensitizes myeloma cells to chemotherapy. This may represent a promising approach for therapeutic intervention in multiple myeloma.
Synthetic auxotrophy remains stable after continuous evolution and in co-culture with mammalian cells (2020)

Abstract Understanding the evolutionary stability and possible context-dependence of biological containment techniques is critical as engineered microbes are increasingly under consideration for applications beyond biomanufacturing. While batch cultures of synthetic auxotrophic Escherichia coli previously exhibited undetectable escape throughout 14 days of monitoring, the long-term effectiveness of synthetic auxotrophy is unknown. Here, we report automated continuous evolution of a synthetic auxotroph using custom chemostats that supply a decreasing concentration of essential biphenylalanine (BipA). After 100 days of evolution in three separate trials, populations exhibit no observable escape and are capable of normal growth rates at 10-fold lower BipA concentration than the ancestral synthetic auxotroph. Allelic reconstruction of three proteins implicated in small molecule transport reveals their contribution to increased fitness at low BipA concentrations. Mutations do not appear in orthogonal translation machinery nor in synthetic auxotrophic markers. Based on its evolutionary stability, we introduce the progenitor synthetic auxotroph directly to mammalian cell culture. We observe containment of bacteria without detrimental effects on HEK293T cells. Overall, our findings reveal that synthetic auxotrophy is effective on timescales and in contexts that enable diverse applications. One Sentence Summary To ascertain whether life inevitably finds a way, we continuously evolve an Escherichia coli strain that was not able to escape from engineered biocontainment before, and we find that it does not escape even after 100 days of evolution, nor does it escape when added to mammalian cell culture.
Adsorption of core-shell nanoparticles at liquid–liquid interfaces (2011)

The use of nanoparticles as building blocks for the self-assembly of functional materials has been rapidly increasing in recent years. In particular, two-dimensional materials can be effectively self-assembled at liquid interfaces thanks to particle localization and mobility at the interface in combination with tailoring of specific interactions. Many recent advances have been made in the understanding of the adsorption and assembly at liquid interfaces of small hydrophobic nanoparticles stabilized by short-chain rigid dispersants but the corresponding studies on core-shell nanoparticles sterically stabilized by extended hydrophilic polymer brushes are presently missing. Such particles offer significant advantages in terms of fabrication of functional, responsive and bio-compatible materials. We present here a combination of experimental and numerical data together with an intuitive and simple model aimed at elucidating the mechanisms governing the adsorption of iron oxide nanparticles (5–10 nm) stabilized by low molecular weight poly(ethylene glycol) (1.5–10 kDa). We show that the adsorption dynamics and the structure of the final assembly depend on the free energy of the particles at the interface and discuss the thermodynamics of the adsorption in terms of the polymer solubility in each phase.