gebhart/patrepeval huggingface dataset:
Full-length structure of a monomeric histidine kinase reveals basis for sensory regulation (2014)

Although histidine kinases (HKs) are critical sensors of external stimuli in prokaryotes, the mechanisms by which their sensor domains control enzymatic activity remain unclear. Here, we report the full-length structure of a blue light-activated HK from Erythrobacter litoralis HTCC2594 (EL346) and the results of biochemical and biophysical studies that explain how it is activated by light. Contrary to the standard view that signaling occurs within HK dimers, EL346 functions as a monomer. Its structure reveals that the light-oxygen-voltage (LOV) sensor domain both controls kinase activity and prevents dimerization by binding one side of a dimerization/histidine phosphotransfer-like (DHpL) domain. The DHpL domain also contacts the catalytic/ATP-binding (CA) domain, keeping EL346 in an inhibited conformation in the dark. Upon light stimulation, interdomain interactions weaken to facilitate activation. Our data suggest that the LOV domain controls kinase activity by affecting the stability of the DHpL/CA interface, releasing the CA domain from an inhibited conformation upon photoactivation. We suggest parallels between EL346 and dimeric HKs, with sensor-induced movements in the DHp similarly remodeling the DHp/CA interface as part of activation.
Generalized Epilepsy with Febrile Seizures Plus (GEFS<sup>+</sup>): Clinical Spectrum in Seven Italian Families Unrelated to <i>SCN1A, SCN1B</i>, and <i>GABRG2</i> Gene Mutations (2004)

The most frequently observed phenotypes matched those reported in families with mutations of the SCN1A, SCN1B, and GABRG2 genes. IGE and GEFS+ may overlap in some families, suggesting a shared genetic mechanism. The observation that 13% of affected individuals had focal epilepsy confirms previously reported rates and should prompt a reformulation of the "GEFS+" concept to include focal epileptogenesis.
Hop acids can efficiently replace antibiotics in ethanol production. (2006)

This study was carried out at the Fermentation Technology Institute of the University of Hohenheim. The aim of the study was to evaluate the potential of hop acids as natural antibacterials in distillery mashes for alcoholic fermentation. Lactostab™ and Isostab™ were investigated for their effect on growth and lactic acid production by two selected strains of lactobacilli. The potential of improving ethanol yields by use of Lactostab™ and Isostab™ during alcoholic fermentation of wheat mash and sugar beet molasses mash was monitored. Penicillin G and Virginiamycin were used as referential substances for comparison of antibacterial activity. Lactostab™ and Isostab™ prevented growth of lactobacilli and production of lactic acid at ppm levels. Production of lactic acid and acetic acid was blocked at inhibitory concentrations of Lactostab™ and Isostab™. Both substances acted bactericidal when inhibitory concentrations were doubled. Virginamycin and Penicillin G were tested as conventional antibacterial reference. Of all tested antibacterials, Virginiamycin was most effective and acted bactericidal at a concentration of only 0.5 ppm. However, ethanol yields obtained at inhibitory/ bactericidal concentrations of hop acids were in every respect comparable to those obtained with inhibitory/ bactericidal concentrations of antibiotics. Penicillin G, at a concentration of only 0.25 ppm, inhibited bacteria growth in most trials, but induced resistance in L. fermentum in wheat mash fermentation. Lactostab™ and Isostab™ consist of hop components contained in beer and spent hops and bear no risk for human or animal health. Thus, they provide an excellent, safe alternative to control bacteria in ethanol fermentations.
(<i>P</i>)-Helicene Displays Chiral Selection in Binding to Z-DNA (2004)

Enantiomeric helicenes of (P)-A and (M)-A were synthesized. The binding of the helicenes to B- and Z-DNA was studied quantitatively by CD, equilibrium dialysis, and fluorescence spectroscopy. Enantiomeric (P)-A not only bound selectively to Z-DNA but also effectively converted the B-DNA conformation to Z-DNA. The enantioselectivity of the helicenes offers a new route for the rational design of inhibitors of biological functions that may depend on Z-DNA.
Molecular Analysis of <i>Clostridium difficile</i> Strains Isolated from 18 Cases of Recurrent <i>Clostridium difficile</i> -Associated Diarrhea (2003)

Recurrence of Clostridium difficile-associated diarrhea (CDAD) occurs in 15 to 20% of patients after discontinuation of treatment. Arbitrarily primed PCR was used to investigate the epidemiology of recurrent CDAD in 18 patients. Reinfection with a new strain occurred in 6 of 18 patients (33.3%), while 12 patients relapsed with the original strain shortly after discontinuation of treatment. These data suggest that reinfection with exogenous C. difficile is a common problem and that not all recurrences are due to relapse.
A reduced basis element method for the steady Stokes problem: Application to hierarchical flow systems (2005)

In this thesis we consider the reduced basis element method for approximating the solution of parameter dependent problems described by partial differential equations. In particular we focus on fluid flow in pipes, bifurcations and hierarchical systems, where the flow is described by the steady Stokes equations, or the steady Navier-Stokes equations. The thesis consists of four papers and this introduction.The reduced basis element method is different from traditional reduced basis methods in that it combines these methods with domain decomposition. A given geometry is decomposed into building blocks with the same topology as a few reference domains, e.g. a rectangle and a reference bifurcation. Relative to each reference domain we precompute and store basis functions found on a preselected set of deformations of the respective reference domains. A reduced basis solution is then found by mapping the basis functions from their respective reference domains to corresponding domains in the domain decomposition. A local approximation of the “true” solution on one domain is found using the basis functions belonging to that specific domain, and the global approximation is found by “gluing” the local approximations together with constraints across domain interfaces. Geometries where building blocks of the same topology are reused many times are attractive candidates for the reduced basis element method. When there is only one domain in the geometry, the reduced basis element method is seen as a traditional reduced basis method where the geometry of the domain is one of the independent parameters.In the first part of the introduction we present the reduced basis method and the reduced basis element method. In the second part of the introduction we motivate the work done in the thesis, and give a summary of the papers.
Engineered antibody fragments for immuno-PET imaging of endogenous CD8 <sup>+</sup> T cells in vivo (2014)

The noninvasive detection and quantification of CD8(+) T cells in vivo are important for both the detection and staging of CD8(+) lymphomas and for the monitoring of successful cancer immunotherapies, such as adoptive cell transfer and antibody-based immunotherapeutics. Here, antibody fragments are constructed to target murine CD8 to obtain rapid, high-contrast immuno-positron emission tomography (immuno-PET) images for the detection of CD8 expression in vivo. The variable regions of two anti-murine CD8-depleting antibodies (clones 2.43 and YTS169.4.2.1) were sequenced and reformatted into minibody (Mb) fragments (scFv-CH3). After production and purification, the Mbs retained their antigen specificity and bound primary CD8(+) T cells from the thymus, spleen, lymph nodes, and peripheral blood. Importantly, engineering of the parental antibodies into Mbs abolished the ability to deplete CD8(+) T cells in vivo. The Mbs were subsequently conjugated to S-2-(4-isothiocyanatobenzyl)-1,4,7-triazacyclononane-1,4,7-triacetic acid for (64)Cu radiolabeling. The radiotracers were injected i.v. into antigen-positive, antigen-negative, immunodeficient, antigen-blocked, and antigen-depleted mice to evaluate specificity of uptake in lymphoid tissues by immuno-PET imaging and ex vivo biodistribution. Both (64)Cu-radiolabeled Mbs produced high-contrast immuno-PET images 4 h postinjection and showed specific uptake in the spleen and lymph nodes of antigen-positive mice.
Smart, clean surfaces (2003)

Fed up with cleaning dusty windows, soiled shoes, and dirty paintwork? A series of products are now emerging on the market that claim to have self-cleaning surfaces, apparently removing the need for regular washing, scrubbing, and polishing with chemical agents. But consumers should refrain from throwing away all their cloths and detergents just yet. Questions regarding the longevity of such products, the optimal technology, and the most suitable applications have yet to be settled.
Multicomponent Reactions Involving 2-Methyleneaziridines:  Rapid Synthesis of 1,3-Disubstituted Propanones (2002)

Ring opening of 1-alkyl-2-methyleneaziridines 1 or 2 is accomplished with organocopper reagents (R(2)CuLi or RMgX/CuI) in the presence of boron trifluoride diethyl etherate giving 1-substituted propan-2-ones 3-9 in 42-88% yield. Ring opening with RMgCl/CuI in the absence of the Lewis acid allows further alkylation of the metalloenamine (metalated imine) intermediate in a regiocontrolled manner. The sequential formation of two new intermolecular carbon-carbon bonds in this reaction provides a rapid entry into a variety of 1,3-disubstituted propan-2-ones, including 11 and 14-23. The scope and mechanism of this multicomponent reaction (MCR) has been assessed. It is established that this MCR tolerates alkyl, aryl, and benzylic Grignard reagents and a wide range of electrophiles, including alkyl iodides, bromides, and tosylates, as well as epoxides and aldehydes. In addition, gem-dimethyl substitution on the exocyclic double bond of the 2-methyleneaziridine is tolerated. This MCR has been applied to the one-pot synthesis of (Z)-6-heneicosen-11-one, 25, an important sex attractant of the Tussock moth. Using 3-deuterio-1-(1-phenylethyl)-2-methyleneaziridine, 26, we determined that this MCR occurs predominantly by direct ring opening at the sp(3)-hybridized aziridine carbon atom (C-3).
Bioinorganic Chemistry: Inorganic Elements in the Chemistry of Life: An Introduction and Guide (1994)

Partial table of contents: Historical Background, Current Relevance and Perspectives. Some General Principles. Metals at the Center of Photosynthesis: Magnesium and Manganese. Catalysis Through Hemoproteins: Electron Transfer, Oxygen Activation and Metabolism of Inorganic Intermediates. Iron--Sulfur and Other Nonheme Iron Proteins. Uptake, Transport and Storage of an Essential Element as Exemplified by Iron. Copper-Containing Proteins: An Alternative to Biological Iron. Zinc: Structural and Gene-Regulatory Functions and the Enzymatic Catalysis of Hydrolysis or Condensation Reactions. Biological Functions of the Nonmetallic Inorganic Elements. Chemotherapy with Compounds of Some Nonessential Elements. Bibliography. Glossary. List of Inserts. Index.
Reactive Characteristics and Adsorption Heat of Ni/ZnO–SiO<sub>2</sub>–Al<sub>2</sub>O<sub>3</sub> Adsorbent by Reactive Adsorption Desulfurization (2011)

Reactive adsorption desulfurization (RADS) experiments of fluid catalytic cracking (FCC) gasoline and a model gasoline over an Ni/ZnO–SiO2–Al2O3 adsorbent were carried out in a fixed-fluidized bed reactor at low pressures in an H2 atmosphere. The results show that hydrogenation, hydrogen transfer, and polymerization reactions accompany RADS. Sulfidation and carbon deposits, which can lead to decreases in the regeneration rate and amount of activated Ni, are crucial to the decay of desulfurization and the olefin-hydrogenation capability of the adsorbents. The obvious reduction of C5 and C6 olefins in FCC gasoline mainly contribute to the drop in octane number of the desulfurization product. The desulfurization experiment on model gasoline and the adsorption heats of model compounds show that RADS removes sulfur from sulfur-containing compound through S–M interactions rather than by π-complexation over the Ni/ZnO–SiO2–Al2O3 adsorbent. The adsorption heat of sulfur-containing compound is proportional to the electron density of sulfur atoms.
Automatic routing and ad-hoc retrieval using SMART: TREC 2 (1993)

The Smart information retrieval project emphasizes completely automatic approaches to the understanding and retrieval of large quantities of text. We continue our work in the TREC 2 environment, performing both routing and ad-hoc experiments. The ad-hoc work extends our investigations into combining global similarities, giving an overall indication of how a document matches a query, with local similarities identifying a smaller part of the document which matches the query. The performance of the ad-hoc runs is good, but it is clear we are not yet taking full advantage of the available local information. Our routing experiments use conventional relevance feedback approaches to routing, but with a much greater degree of query expansion than was done in TREC 1. The length of a query vector is increased by a factor of 5 to 10 by adding terms found in previously seen relevant documents. This approach improves effectiveness by 30--40% over the original query. Introduction For over 30 years...
HYPOTrace: Image Analysis Software for Measuring Hypocotyl Growth and Shape Demonstrated on Arabidopsis Seedlings Undergoing Photomorphogenesis (2009)

Analysis of time series of images can quantify plant growth and development, including the effects of genetic mutations (phenotypes) that give information about gene function. Here is demonstrated a software application named HYPOTrace that automatically extracts growth and shape information from electronic gray-scale images of Arabidopsis (Arabidopsis thaliana) seedlings. Key to the method is the iterative application of adaptive local principal components analysis to extract a set of ordered midline points (medial axis) from images of the seedling hypocotyl. Pixel intensity is weighted to avoid the medial axis being diverted by the cotyledons in areas where the two come in contact. An intensity feature useful for terminating the midline at the hypocotyl apex was isolated in each image by subtracting the baseline with a robust local regression algorithm. Applying the algorithm to time series of images of Arabidopsis seedlings responding to light resulted in automatic quantification of hypocotyl growth rate, apical hook opening, and phototropic bending with high spatiotemporal resolution. These functions are demonstrated here on wild-type, cryptochrome1, and phototropin1 seedlings for the purpose of showing that HYPOTrace generated expected results and to show how much richer the machine-vision description is compared to methods more typical in plant biology. HYPOTrace is expected to benefit seedling development research, particularly in the photomorphogenesis field, by replacing many tedious, error-prone manual measurements with a precise, largely automated computational tool.
Predictive microfluidic control of regulatory ligand trajectories in individual pluripotent cells (2012)

Local (cell-level) signaling environments, regulated by autocrine and paracrine signaling, and modulated by cell organization, are hypothesized to be fundamental stem cell fate control mechanisms used during development. It has, however, been challenging to demonstrate the impact of cell-level organization on stem cell fate control and to relate stem cell fate outcomes to autocrine and paracrine signaling. We address this fundamental problem using a combined in silico and experimental approach in which we directly manipulate, using laminar fluid flow, the local impact of endogenously secreted gp130-activating ligands and their activation of signal transducer and activator of transcription3 (STAT3) signaling in mouse embryonic stem cells (mESC). Our model analysis predicted that flow-dependent changes in autocrine and paracrine ligand binding would impact heterogeneity in cell- and colony-level STAT3 signaling activation and cause a gradient of cell fate determination along the direction of flow. Interestingly, analysis also predicted that local cell density would be inversely proportional to the degree to which endogenous secretion contributed to cell fate determination. Experimental validation using functional activation of STAT3 by secreted factors under microfluidic perfusion culture demonstrated that STAT3 activation and consequently mESC fate were manipulable by flow rate, position in the flow field, and local cell organization. As a unique demonstration of how quantitative control of autocrine and paracrine signaling can be integrated with spatial organization to elicit higher order cell fate effects, this work provides a general template to investigate organizing principles due to secreted factors.
EXPERIMENTAL INCLUSION CONJUNCTIVITIS IN MAN (1966)

Journal Article EXPERIMENTAL INCLUSION CONJUNCTIVITIS IN MAN: II. PARTIAL RESISTANCE TO REINFECTION Get access CHANDLER DAWSON, CHANDLER DAWSON Search for other works by this author on: Oxford Academic PubMed Google Scholar ERNEST JAWETZ, ERNEST JAWETZ Search for other works by this author on: Oxford Academic PubMed Google Scholar LAVELLE HANNA, LAVELLE HANNA Search for other works by this author on: Oxford Academic PubMed Google Scholar LAWRENCE ROSE, LAWRENCE ROSE Search for other works by this author on: Oxford Academic PubMed Google Scholar T. RODMAN WOOD, T. RODMAN WOOD Search for other works by this author on: Oxford Academic PubMed Google Scholar PHILLIPS THYGESON PHILLIPS THYGESON 1Department of Microbiology, and F. I Proctor Foundation for Research in Ophthalmology, University of California, San Francisco Medical CenterSan Francisco, California 94122 Search for other works by this author on: Oxford Academic PubMed Google Scholar American Journal of Epidemiology, Volume 84, Issue 3, November 1966, Pages 411–425, https://doi.org/10.1093/oxfordjournals.aje.a120654 Published: 01 November 1966 Article history Received: 29 November 1965 Published: 01 November 1966
High Broad‐Band Photoresponsivity of Mechanically Formed InSe–Graphene van der Waals Heterostructures (2015)

High broad-band photoresponsivity of mechanically formed InSe-graphene van der Waals heterostructures is achieved by exploiting the broad-band transparency of graphene, the direct bandgap of InSe, and the favorable band line up of InSe with graphene. The photoresponsivity exceeds that for other van der Waals heterostructures and the spectral response extends from the near-infrared to the visible spectrum.
Triglyceride composition of native and rearranged butter and coconut oils (1964)

Abstract Triglyceride gas chromatography was used for quantitative fractionation by carbon number of native and rearranged butter and coconut oils. Significant differences in the triglyceride type distributions between the corresponding native and chemically modified fats were found. Increased proportions of both short and long chain triglycerides occurred in the rearranged butterfat. In reconstituted coconut oil there was a shift towards the shorter chain length triglycerides. The natural and the rearranged triglyceride distributions of the two oils were shown to differ from the random distributions calculated for the corresponding fatty acid complements. The butterfat triglyceride compositions showed greater deviations from random than did the coconut oils. The modified oils approached random distributions more closely than did the native ones. In both cases the deviations from truly random populations appeared to be in the direction anticipated on the basis of chemical reactivity.
Analysis of MIMO Diversity Improvement Using Circular Polarized Antenna (2014)

MIMO (Multiple Input Multiple Output) technique is one of the important means to enhance the system capacity. Diversity gain could be acquired by using traditional ±45° dual-polarized antenna, but in the scenario where multipath scattering is not strong, power-unbalance in two polarizations caused by polarization mismatching between transmitting and receiving antennas will reduce diversity gain. This problem can be effectively solved by using circular polarized antennas. In this paper, through theory analysis and test, the improvement of MIMO diversity gain using circular polarization antenna is analyzed.
Molecular-beam epitaxy growth of device-compatible GaAs on silicon substrates with thin (∼80nm) Si1−xGex step-graded buffer layers for high-κ III-V metal-oxide-semiconductor field effect transistor applications (2007)

The authors report the fabrication of TaN–HfO2–GaAs metal-oxide-semiconductor capacitors on silicon substrates. GaAs was grown by migration-enhanced epitaxy (MEE) on Si substrates using an ∼80-nm-thick Si1−xGex step-graded buffer layer, which was grown by ultrahigh vacuum chemical vapor deposition. The MEE growth temperatures for GaAs were 375 and 400°C, with GaAs layer thicknesses of 15 and 30nm. We observed an optimal MEE growth condition at 400°C using a 30nm GaAs layer. Growth temperatures in excess of 400°C resulted in semiconductor surfaces rougher than 1nm rms, which were unsuitable for the subsequent deposition of a 6.5-nm-thick HfO2 gate dielectric. A minimum GaAs thickness of 30nm was necessary to obtain reasonable capacitance-voltage (C-V) characteristics from the GaAs layers grown on Si substrates. To improve the interface properties between HfO2 and GaAs, a thin 1.5nm Ge interfacial layer was grown by molecular-beam epitaxy in situ after the GaAs growth. The Ge-passivated GaAs samples were then transferred in air for the subsequent ex situ HfO2 formation. This Ge interfacial layer in between HfO2 and GaAs was necessary to avoid relatively flat C-V characteristics that are symptomatic of high interface state densities.
Joint strength and microstructures of brazed joints of stainless steel with Fe-based filler (2014)

For thermal conversion parts of electrical equipment which are required high corrosion resistance, stainless steel is often used. The joining of such materials is generally conducted with brazing with Ni-based filler. Since Ni is a rare and high-cost material, the substitute filler material which is low-Ni or Ni-free is expected to be developed. Fe-based filler has been developed as one candidate. In this study, joint strength and the microstructure of stainless steel type 304 brazed joint with Fe-based filler were investigated. As the results, it was clarified that shear strength of the joint with Fe-based filler is the almost same level as that with conventional Ni-based filler. Moreover, the effect of joint clearance on the joint strength and the microstructure was also investigated. When joint clearance is more than 50 μm, the final solidified area which consists of Fe-Cr-Ni-Si phases and P-rich phases forms in the center of the brazed joint. The formation of P-rich phases causes the joint strength reduction.
Zero Reversion Loss, High-Efficiency Charge Pump for Wide Output Current Load Range (2018)

Switched-capacitor charge pumps provide fully-integrated voltage conversion in integrated circuits, without the need for large area inductors. Traditional cross-coupled charge pump topologies are limited by reversion loss, where charge flows backward during a pumping cycle due to non-ideal switch control clocks. In this work, we present two modified charge pump topologies that eliminate reversion loss while adding minimal control complexity. A detailed comparison with recent published approaches is presented. The single-stage charge pump Designs I and II are implemented in a standard 180 nm CMOS process and exhibit peak efficiency of 81.9% and 83.2%, respectively, and more than 70% power efficiency is achieved across a load current range from 100-900 μA for Design II. The presented approach improves efficiency while decreasing required stage capacitance several-fold, achieving over 87 mW/mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> power density.