gebhart/patrepeval huggingface dataset:
Fabrication and H<sub>2</sub>-Sensing Properties of SnO<sub>2</sub> Nanosheet Gas Sensors (2018)

Vertically formed and well-defined SnO<sub>2</sub> nanosheets are easy to fabricate, involving only a single process that is performed under moderate conditions. In this study, two different sizes of a SnO<sub>2</sub> nanosheet were concurrently formed on a Pt interdigitated electrode chip, with interconnections between the two. As the SnO<sub>2</sub> nanosheets were grown over time, the interconnections became stronger. The ability of the fabricated SnO<sub>2</sub> nanosheets to sense H<sub>2</sub> gas was evaluated in terms of the variation in their resistance. The resistance of a SnO<sub>2</sub> nanosheet decreased with the introduction of H<sub>2</sub> gas and returned to its initial level after the H<sub>2</sub> gas was replaced with air. Also, the response-recovery behaviors were improved as a result of the growth of the SnO<sub>2</sub> nanosheets owing to the presence of many reaction sites and strong interconnections, which may provide multipassages for the electron transfer channel, leading to the acceleration of the reaction between the H<sub>2</sub> gas and SnO<sub>2</sub> nanosheets.
Capturing the Herpes Simplex Virus Core Fusion Complex (gB-gH/gL) in an Acidic Environment (2011)

Herpes simplex virus (HSV) entry requires the core fusion machinery of gH/gL and gB as well as gD and a gD receptor. When gD binds receptor, it undergoes conformational changes that presumably activate gH/gL, which then activates gB to carry out fusion. gB is a class III viral fusion protein, while gH/gL does not resemble any known viral fusion protein. One hallmark of fusion proteins is their ability to bind lipid membranes. We previously used a liposome coflotation assay to show that truncated soluble gB, but not gH/gL or gD, can associate with liposomes at neutral pH. Here, we show that gH/gL cofloats with liposomes but only when it is incubated with gB at pH 5. When gB mutants with single amino acid changes in the fusion loops (known to inhibit the binding of soluble gB to liposomes) were mixed with gH/gL and liposomes at pH 5, gH/gL failed to cofloat with liposomes. These data suggest that gH/gL does not directly associate with liposomes but instead binds to gB, which then binds to liposomes via its fusion loops. Using monoclonal antibodies, we found that many gH and gL epitopes were altered by low pH, whereas the effect on gB epitopes was more limited. Our liposome data support the concept that low pH triggers conformational changes to both proteins that allow gH/gL to physically interact with gB.
Energy-harvesting microsystems (2015)

Summary form only given. Wireless microsensors and other miniaturized electronics cannot only monitor and better-manage power consumption in emerging small- and large-scale applications (for space, military, medical, agricultural, and consumer markets) but also add energy-saving and performance-enhancing intelligence to old, expensive, and difficult-to-replace infrastructures and tiny contraptions in difficult-to-reach places (like the human body). The energy these smart devices store, however, is often insufficient to power the functions they incorporate (such as telemetry, interface, processing, and others) for extended periods. Still more, replacing or recharging the batteries of hundreds of networked nodes is costly, and invasive in the case of the human body. Harvesting ambient energy to continually replenish a battery and wirelessly harnessing radiated energy periodically are therefore appealing alternatives, even if the development of relevant technologies today is, in relative terms, at its infancy. This talk discusses the state of the art and current research efforts in harnessing and conditioning energy and power from miniaturized transducers.
Comparative mutational analysis of peptidyl prolyl <i>cis/trans</i> isomerases: active sites of <i>Escherichia coli</i> trigger factor and human FKBP12 (1997)

A low degree of amino acid sequence similarity to FK506-binding proteins (FKBPs) has been obtained for the peptidyl prolyl cis/trans isomerase (PPIase) domain of E. coli trigger factor (TF) that was thought to be significant with regard to the enzymatic properties of the bacterial enzyme. We examined whether the alteration of a negatively charged side-chain at position 37 (FKBP numbering) and a phenylalanine at position 99, both highly conserved through both types of enzymes, leads to parallel effects on the catalytic activity of both FKBP12 and TF-PPIase domain in a series of tetrapeptide substrates with different P1 subsites. For the latter enzyme, substitution of Glu178 by Val or Lys, which aligns to Asp37 in human FKBP12, enhanced the PPIase activity, whereas a strongly decreased enzymatic activity was determined for the Asp37Leu and Asp37Val variants of FKBP12. Regardless of the P1 subsite of the substrate used for the assay, mutation of Phe233Tyr generated a protein variant of the TF-PPIase domain with about 1% of the wild type PPIase activity. Dependent on the substrate nature, a moderate decrease as well as a 4.8-fold increase in k(cat)/K(M) could be determined for the corresponding Phe99Tyr FKBP12 variant. Neither of the mutations of the TF-PPIase domain was able to implant FK506 inhibition found as a major characteristic of the FKBP family of PPIases.
Supplementary Figure S1 from Blood-Based Diagnosis and Risk Stratification of Patients with Pancreatic Intraductal Papillary Mucinous Neoplasm (IPMN) (2023)

&lt;p&gt;Diagnostic performance of serum protein panels.&lt;/p&gt;
Restriction site polymorphism at the LPA (Lp(a) apoliprotein; apoliprotein(a)) locus (1990)

A restriction site polymorphism in the Lp(a) apolipoprotein gene (the LPA gene) is reported. The basis for the polymorphism is presence or absence of an MspI restriction site that appears to be 3' to the last kringle IV structure of the gene. The "1" gene (presence of the restriction site) has a frequency of 0.316 and the "2" gene (absence of the restriction site) has a frequency of 0.684. Both members of each of 67 monozygotic (MZ) twin pairs had the same genotype and there was Mendelian segregation of the DNA variants in 40 families with a total of 75 children. There was a lower proportion of people with genotype 1-1 in the top quartile than in the 3 bottom quartiles of the population distribution of Lp(a) lipoprotein levels but the difference did not reach statistical significance.
Analysing the Correlation between Lexical Ambiguity and Translation Quality in a Multimodal Setting using WordNet (2022)

Ali Hatami, Paul Buitelaar, Mihael Arcan. Proceedings of the 2022 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies: Student Research Workshop. 2022.
Characterization of<i>Francisella tularensis</i>Outer Membrane Proteins (2006)

Francisella tularensis is a gram-negative coccobacillus that is capable of causing severe, fatal disease in a number of mammalian species, including humans. Little is known about the proteins that are surface exposed on the outer membrane (OM) of F. tularensis, yet identification of such proteins is potentially fundamental to understanding the initial infection process, intracellular survival, virulence, immune evasion and, ultimately, vaccine development. To facilitate the identification of putative F. tularensis outer membrane proteins (OMPs), the genomes of both the type A strain (Schu S4) and type B strain (LVS) were subjected to six bioinformatic analyses for OMP signatures. Compilation of the bioinformatic predictions highlighted 16 putative OMPs, which were cloned and expressed for the generation of polyclonal antisera. Total membranes were extracted from both Schu S4 and LVS by spheroplasting and osmotic lysis, followed by sucrose density gradient centrifugation, which separated OMs from cytoplasmic (inner) membrane and other cellular compartments. Validation of OM separation and enrichment was confirmed by probing sucrose gradient fractions with antibodies to putative OMPs and inner membrane proteins. F. tularensis OMs typically migrated in sucrose gradients between densities of 1.17 and 1.20 g/ml, which differed from densities typically observed for other gram-negative bacteria (1.21 to 1.24 g/ml). Finally, the identities of immunogenic proteins were determined by separation on two-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis and mass spectrometric analysis. This is the first report of a direct method for F. tularensis OM isolation that, in combination with computational predictions, offers a more comprehensive approach for the characterization of F. tularensis OMPs.
Investigation of Kerr effect in a blue phase liquid crystal using wedge-cell technique (2017)

In this work an alternative method for refractive index measurement of blue phase liquid crystal in the Kerr effect has been described. The proposed wedge method uses simple goniometric setup, allowing for direct index measurements for any wavelengths and index values. This is significant advantage comparing to other methods, usually having limitations of the measurement range as well as necessity complicated calculation to obtain refractive indices values. The results are reliable and agree well with the subject literature. Full Text: PDF ReferencesW. Cao et al., "Lasing in a three-dimensional photonic crystal of the liquid crystal blue phase II", Nat. Mater. 1, 111-113 (2002). CrossRef S. Meiboom, M. Sammon, W.F. Brinkman, "Lattice of disclinations: The structure of the blue phases of cholesteric liquid crystals", Phys. Rev. A. 27, 438 (1983). CrossRef S. Tanaka et al., "Double-twist cylinders in liquid crystalline cholesteric blue phases observed by transmission electron microscopy", Sci. Rep. 5, 16180 (2015). CrossRef Y. Li and S.-T. Wu, "Polarization independent adaptive microlens with a blue-phase liquid crystal", Opt. Express 19(9), 8045-8050 (2011). CrossRef N. Rong et al., "Polymer-Stabilized Blue-Phase Liquid Crystal Fresnel Lens Cured With Patterned Light Using a Spatial Light Modulator", J. of Disp. Technol. 12(10), 1008-1012 (2016). CrossRef J.-D. Lin et al., "Spatially tunable photonic bandgap of wide spectral range and lasing emission based on a blue phase wedge cell", Opt. Express 22(24), 29479-29492 (2014). CrossRef P. Joshi et al., "Tunable light beam steering device using polymer stabilized blue phase liquid crystals", Photon. Lett. Poland 9(1), 11-13 (2017). CrossRef Ch.-W. Chen et al., "Temperature dependence of refractive index in blue phase liquid crystals", Opt. Mater. Express 3(5), 527-532 (2013). CrossRef Y.-H. Lin et al., "Measuring electric-field-induced birefringence in polymer stabilized blue-phase liquid crystals based on phase shift measurements", J. Appl. Phys. 109, 104503 (2011). CrossRef J. Yan et al., "Direct measurement of electric-field-induced birefringence in a polymer-stabilized blue-phase liquid crystal composite", Opt. Express 18(11), 11450-11455 (2010). CrossRef K.A. Rutkowska, K. Orzechowski, M. Sierakowski, "Wedge-cell technique as a simple and effective method for chromatic dispersion determination of liquid crystals", Photon. Lett. Poland 8(2), 51-53 (2016). CrossRef O. Chojnowska et al., "Electro-optical properties of photochemically stable polymer-stabilized blue-phase material", J. Appl. Phys. 116, 213505 (2014). CrossRef J. Yan et al., "Extended Kerr effect of polymer-stabilized blue-phase liquid crystals", Appl. Phys. Lett. 96, 071105 (2010). CrossRef M. Chen et al., "Electrically assisting crystal growth of blue phase liquid crystals", Opt. Mater. Express 4(5), 953-959 (2014). CrossRef J. Kerr, Philos. Mag. 50, 337 (1875).
Synthesis of a biologically active fluorescent probe for labeling neurotensin receptors. (1994)

We synthesized a fluorescent derivative of the tridecapeptide neurotensin (NT), with the aim of providing a new tool for the pharmacological characterization and anatomic localization of NT receptors in mammalian brain. Fluoresceinylated NT (N alpha-fluoresceinyl thiocarbamyl (FTC)-[Glu1]NT; fluo-NT) was synthesized using solid-phase methodology and purified to 99% homogeneity by preparative high-pressure liquid chromatography (HPLC). Analytical HPLC, acidic and carboxypeptidase Y hydrolysis, and fast atom bombardment-mass spectroscopy confirmed that the purified compound was selectively labeled on the [Glu1] terminus and that a single FTC moiety was coupled to each molecule of [Glu1]NT. Flow cytometric analysis of the binding of fluo-NT to SN17 septal neuroblastoma cells indicated that the fluorescent derivative bound neural NT receptors with an affinity comparable to that of monoiodinated NT([125I]-NT). Competition experiments on mouse brain membrane preparations showed fluo-NT to inhibit specific [125I]-NT binding with a coefficient of inhibition (KI) virtually identical to that of the native peptide (0.67 vs 0.55 nM). Conventional epifluorescence and confocal microscopic analysis of specific fluo-NT binding to sections of the rat midbrain revealed a topographic distribution of the bound fluorescent ligand similar to that previously observed with autoradiography using [125I]-NT. However, fluo-NT provided markedly higher cell resolution and enabled, in particular, the detection of hitherto unnoted intracytoplasmic receptor clusters. Binding of fluo-NT to live SN17 hybrid cells indicated that the fluorescent ligand had retained its ability to internalize in vivo and confirmed that this internalization process was both time- and temperature-dependent. In sum, the present study demonstrates that fluo-NT is applicable to both the pharmacological study of NT binding sites using flow cytometry and to the regional and cellular localization of these sites by conventional epifluorescence and confocal microscopy.
CRISPR‐Cas, Horizontal Gene Transfer, and the Flexible (Pan) Genome (2022)

Most known CRISPR-Cas systems primarily provide acquired, heritable immunity to bacteria and archaea against invasion by selfish DNA elements. Consequently, the main activity of these systems is to destroy incoming DNA that matches their immune memory–spacers within the CRISPR array. This chapter discusses, the evidence for and against such a trade off between CRISPR-Cas and the ability to maintain high genomic diversity (and the benefits that come with it) via horizontal gene transfer. Most viruses that infect bacteria and archaea and are capable of a temperate (nonlytic) lifestyle can integrate into the genomes of their hosts. Integrated proviruses represent an important part of microbial pangenomes, can provide a benefit to the host under a variety of stresses and environmental conditions and can contribute to bacterial virulence.
Broadband slow-wave modulation in posterior and anterior cortex tracks distinct states of propofol-induced unconsciousness (2019)

A controversy 5 has developed in recent years over the role that frontal and posterior cortices play in mediating consciousness and unconsciousness. One hypothesis proposes that posterior sensory and association cortices are the principal mediators of consciousness, citing evidence that strong slow-wave activity over posterior cortex during sleep disrupts the contents of dreaming. A competing hypothesis proposes that frontal-posterior interactions are critical to ignite a conscious percept, since activation of frontal cortex appears necessary for perception and can reverse unconsciousness under anesthesia. In both cases, EEG slow-waves (&lt; 1 Hz) are considered evidence that up- and down-states are disrupting cortical activity necessary for consciousness. Here, we used anesthesia to study the interaction between the slow-wave and higher frequency activity in humans. If slow-waves are derived from underlying up and down-states, then they should modulate activity across a broad range of frequencies. We found that this broadband slow-wave modulation does occur: broadband slow-wave modulation occurs over posterior cortex when subjects initially become unconscious, but later encompasses both frontal and posterior cortex when subjects are more deeply anesthetized and likely unarousable. Based on these results, we argue that unconsciousness under anesthesia comprises several shifts in brain state that disrupt the sensory contents of consciousness distinct from arousal and awareness of those contents. Significance Statement The roles of frontal and posterior cortices in mediating consciousness and unconsciousness are controversial. Disruption of posterior cortex during sleep appears to suppress the contents of dreaming, yet activation of frontal cortex appears necessary for perception and can reverse unconsciousness under anesthesia. We studied the time course of regional cortical disruption, as mediated by slow-wave modulation of broadband activity, during anesthesia-induced unconsciousness in humans. We found that broadband slow-wave modulation covered posterior cortex when subjects initially became unconscious, but later encompassed both frontal and posterior cortex when subjects were deeply anesthetized and likely unarousable. This suggests that unconsciousness under anesthesia comprises several shifts in brain state that disrupt the contents of consciousness distinct from arousal and awareness of those contents.
Synthesis and Characterization of Repeating Sequence Copolymers of Fluorene and Methylene Monomers (2007)

A series of well-defined multiblock (mb) copolymers consisting of alternating 9,9-dihexylfluorene and methylene segments has been prepared. Poly(9,9-dihexylfluorene-mb-methylene)s (PFMs) with repeat units of FxMy (x = 1−4, y = 10, 18 and x = 5−8, y = 18) were assembled by tandem metal-catalyzed acyclic diene metathesis (ADMET) polymerization/hydrogenation from α,ω-olefin bearing precursors. The polymers exhibited weight-average molecular weights ranging from Mw = 10 to 57 kDa. The PFMs exhibit photophysical properties, absorbance, and emission consistent with the length of the fluorene sequence. Glass and melting transition temperatures also increase with fluorene segment length.
Interaction network among <i>de novo</i> purine nucleotide biosynthesis enzymes in <i>Escherichia coli</i> (2023)

In human cells, de novo purine nucleotide biosynthesis is known to be regulated through the formation of a metabolon called purinosome. Here, we employed a bacterial two-hybrid approach to characterize the protein-protein interactions network among the corresponding enzymes of Escherichia coli. Our study revealed a dense network of binary interactions that connect most purine nucleotide biosynthesis enzymes. Notably, PurK, an exclusive prokaryotic enzyme, appears as one of the central hubs of this network. We further showed that modifications in PurK, which disrupted several interactions in the network, affected the purine nucleotide pools and altered the bacterial fitness. Our data suggest that the bacterial de novo purine nucleotide biosynthesis enzymes can assemble in a supramolecular complex and that proper interactions among the components of this complex can contribute to bacterial fitness.
Description of Neolamprologus timidus, new species, and review of N. furcifer from Lake Tanganyika (Teleostei: Cichlidae) (2013)

Neolamprologus timidus, new species, is described from Ulwile Island and adjacent localities on the Tanzanian coast of Lake Tanganyika. The species was observed or collected along about 100 km of coastline from KolwePoint, Cape Mpimbwe, south to Kisi Island. It is distinguished from the most similar species, N. furcifer, by presenceof scales on most of the cheek, long pectoral fin and pelvic fin with the second ray longer than the first. Neolamprologus timidus is sympatric with N. furcifer at Kolwe Point and south to Kampempa Point, and at Lupitaand Ulwile Islands south to Kisi Island, but N. furcifer is otherwise absent from the range of N. timidus. Two morphologically distinct forms are recognized in N. furcifer. Samples of N. furcifer from Ulwile Island and slightly more southern localities possess a caudal fin with rounded lobes and long middle rays, appearing onlyslightly emarginate. Samples of N. furcifer from Udachi and nearby localities possess pointed caudal-fin lobeswith greatly elongated streamers, similar to N. timidus and to N. furcifer from other parts of Lake Tanganyika, including the type specimens from the southern part of the lake. The variation in caudal-fin shape may be an expression of character displacement as it occurs in the area of sympatry between N. timidus and N. furcifer. MitochondrialDNA sequences are nearly identical in samples of N. furcifer with pointed or rounded caudal fin. A molecular phylogenetic analysis of a large set of lamprologin cichlids using two mitochondrial genes corroborates earlier analyses and places N. furcifer and N. timidus in different clades with different species of Neolamprologus, Julidochromis, Chalinochromis, and Telmatochromis despite sharing a unique combination of fin and bodyshape, and colour pattern. A 4648 base-pair multiloci analysis of a smaller number of species using fragments ofthree mitochondrial and two nuclear genes resolves N. furcifer and N. timidus in sister clades, but the N. timidus clade also includes Telmatochromis brachygnathus, and N. furcifer is sister species of Chalinochromis brichardi.
Thermodynamic Trends in Carbon−Hydrogen Bond Activation in Nitriles and Chloroalkanes at Rhodium (2009)

Several transition-metal systems have been used to establish correlations between metal-carbon and carbon-hydrogen bonds. Here, the [Tp'RhL] fragment, where Tp' = tris(3,5-dimethylpyrazolyl)borate and L = neopentyl isocyanide, is used to investigate C-H bond activation in a series of linear alkylnitriles and chloroalkanes. Using a combination of kinetic techniques, relative free energies can be found for the compounds TpRhL(CH(3))H, Tp'RhL[(CH(2))(n)CN]H (n = 1-5), and Tp'RhL[(CH(2))(m)Cl]H (m = 1, 3, 4, 5). It is found that the CN and Cl substituents dramatically strengthen the M-C bond more than anticipated if in the alpha-position, with the effect on bond strength diminishing substantially as the X group moves further from the metal (i.e, beta, gamma, delta). Examination of M-C vs C-H bond strengths shows that the Tp'RhL(CH(2)X)H compounds (X = phenyl, vinyl, CN, Cl) all show a good correlation, as do the alkyl, aryl, and vinyl derivatives. The compounds in the former group, however, have stronger M-C bonds than expected based on the C-H bond strengths and consequently, their correlation is separate from the other unsubstituted compounds.
Potentiation of Bacillus thuringiensis insecticidal activity by serine protease inhibitors (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPotentiation of Bacillus thuringiensis insecticidal activity by serine protease inhibitorsSusan C. MacIntosh, Ganesh M. Kishore, Frederick J. Perlak, Pamela G. Marrone, Terry B. Stone, Steve R. Sims, and Roy L. FuchsCite this: J. Agric. Food Chem. 1990, 38, 4, 1145–1152Publication Date (Print):April 1, 1990Publication History Published online1 May 2002Published inissue 1 April 1990https://pubs.acs.org/doi/10.1021/jf00094a051https://doi.org/10.1021/jf00094a051research-articleACS PublicationsRequest reuse permissionsArticle Views520Altmetric-Citations103LEARN 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