gebhart/patrepeval huggingface dataset:
Despite slow catalysis and confused substrate specificity, all ribulose bisphosphate carboxylases may be nearly perfectly optimized (2006)

The cornerstone of autotrophy, the CO(2)-fixing enzyme, d-ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco), is hamstrung by slow catalysis and confusion between CO(2) and O(2) as substrates, an "abominably perplexing" puzzle, in Darwin's parlance. Here we argue that these characteristics stem from difficulty in binding the featureless CO(2) molecule, which forces specificity for the gaseous substrate to be determined largely or completely in the transition state. We hypothesize that natural selection for greater CO(2)/O(2) specificity, in response to reducing atmospheric CO(2):O(2) ratios, has resulted in a transition state for CO(2) addition in which the CO(2) moiety closely resembles a carboxylate group. This maximizes the structural difference between the transition states for carboxylation and the competing oxygenation, allowing better differentiation between them. However, increasing structural similarity between the carboxylation transition state and its carboxyketone product exposes the carboxyketone to the strong binding required to stabilize the transition state and causes the carboxyketone intermediate to bind so tightly that its cleavage to products is slowed. We assert that all Rubiscos may be nearly perfectly adapted to the differing CO(2), O(2), and thermal conditions in their subcellular environments, optimizing this compromise between CO(2)/O(2) specificity and the maximum rate of catalytic turnover. Our hypothesis explains the feeble rate enhancement displayed by Rubisco in processing the exogenously supplied carboxyketone intermediate, compared with its nonenzymatic hydrolysis, and the positive correlation between CO(2)/O(2) specificity and (12)C/(13)C fractionation. It further predicts that, because a more product-like transition state is more ordered (decreased entropy), the effectiveness of this strategy will deteriorate with increasing temperature.
Hydrogenolysis of polychlorinated biphenyls by sodium borohydride with homogeneous and heterogeneous nickel catalysts (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTHydrogenolysis of polychlorinated biphenyls by sodium borohydride with homogeneous and heterogeneous nickel catalystsJerome A. Roth, Srikanth R. Dakoji, Robert C. Hughes, and Robert E. CarmodyCite this: Environ. Sci. Technol. 1994, 28, 1, 80–87Publication Date (Print):January 1, 1994Publication History Published online1 May 2002Published inissue 1 January 1994https://pubs.acs.org/doi/10.1021/es00050a012https://doi.org/10.1021/es00050a012research-articleACS PublicationsRequest reuse permissionsArticle Views317Altmetric-Citations46LEARN 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
Advances in Holographic Optical Trapping (2013)

Holographic optical trapping (HOT) is a technique for non-invasive dynamic anipulation of multiple microscopic objects, which has been used for many applications in the life sciences during the past decade. The technique uses holographic beam steering with a spatial light modulator (SLM) to direct light to the desired positions of optical traps. In many cases, the control of the optical intensity of the traps is impaired by imperfections in the SLM. This has limited the use of HOT for applications sensitive to variations in the trap intensities, such as optical force measurement (OFM). Also, the algorithms for optimization of holograms used in HOT are computationally demanding, and real-time manipulation with optimized holograms has not been possible. In this thesis, four different methods for improving the accuracy of holographic beam steering are presented, along with a novel application for the combination of HOT and position measurement. The control of trap intensities is improved by compensating for crosstalk between pixels, and for spatial variations of the phase response of the SLM; and by dumping a controlled amount of light to specified regions away from the traps. Variations in trap intensities occurring when updating the SLM with new holograms are suppressed by enforcing a stronger correlation between consecutive holograms. The methods consist of modifications of the algorithm used for hologram generation, or alternative methods for post-processing of generated holograms. Applications with high stability requirements, such as OFM with HOT, will benefit from the presented improvements. A method for reducing computation time for hologram optimization is also presented, allowing the accuracy improvements to be used also for time critical applications. Further, it is shown that position measurement of nanowires, held by multiple optical traps, can be used to probe the orientational structure and defects in liquid crystal materials.
<i>Recent Progress in Microcalorimetry</i> (1964)

Share Icon Share Twitter Facebook Reddit LinkedIn Reprints and Permissions Cite Icon Cite Search Site Citation E. Calvet, H. Prat, H. A. Skinner, Joseph G. Hoffman; Recent Progress in Microcalorimetry. Physics Today 1 April 1964; 17 (4): 67–68. https://doi.org/10.1063/1.3051541 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentPhysics Today Search Advanced Search
Infection of Human Hepatocyte Chimeric Mouse With Genetically Engineered Hepatitis B Virus * (2005)

Studies of hepatitis B virus (HBV) mutants have been hampered by the lack of a small animal model with long-term infection of cloned HBV. Using a mouse model in which liver cells were highly replaced with human hepatocytes that survived over a long time with mature human hepatocyte function, we performed transmission experiments of HBV. Human serum containing HBV and the virus produced in HepG2 cell lines that transiently or stably transfected with 1.4 genome length HBV DNA were inoculated. Genetically modified e-antigen-negative mutant strain also was produced and inoculated into the mouse model. A high-level (approximately 10(10) copies/mL) viremia was observed in mice inoculated with HBV-positive human serum samples. The level of viremia tended to be high in mice with a continuously high human hepatocyte replacement index. High levels and long-lasting viremia also were observed in mice injected with the in vitro generated HBV. The viremia continued up to 22 weeks until death or killing. Passage experiments showed that the serum of these mice contained infectious HBV. Genetically engineered hepatitis B e antigen-negative mutant clone also was shown to be infectious. Lamivudine effectively reduced the level of viremia in these infected mice. In conclusion, this mouse model of HBV infection is a useful tool for the study of HBV virology and evaluation of anti-HBV drugs. Our results indicate that HBeAg is dispensable for active viral production and transmission.
N-terminal fatty-acylation of sonic hedgehog enhances the induction of rodent ventral forebrain neurons (2001)

The adult basal ganglia arise from the medial and lateral ganglionic eminences, morphologically distinct structures found in the embryonic telencephalon. We have previously shown that temporal changes in sonic hedgehog (Shh) responsiveness determine the sequential induction of embryonic neurons that populate the medial and lateral ganglionic eminences. In this report, we show that Shh-mediated differentiation of neurons that populate the lateral ganglionic eminence express different combinations of the homeobox-containing transcription factors Dlx, Mash1 and Islet 1/2. Furthermore, we show that N-terminal fatty-acylation of Shh significantly enhances its ability to induce the differentiation of rat E11 telencephalic neurons expressing Dlx, Islet 1/2 or Mash1. Recent evidence indicates that in utero injection of the E9.5 mouse forebrain with retroviruses encoding wild-type Shh induces the ectopic expression of Dlx2 and severe deformities in the brain. In this report, we show that Shh containing a mutation at the site of acylation prevents either of these phenotypes. These results suggest that N-terminal fatty-acylation of Shh may play an important role in Shh-dependent signaling during rodent ventral forebrain formation.
Electrosynthesis, characterization, and application of novel hybrid materials based on carbon nanotube–polyaniline–nickel hexacyanoferrate nanocomposites (2005)

Incorporating nanoclusters of nickel hexacyanoferrates (NiHCF) onto a porous polyaniline (PANI)–carbon nanotube (CNT) matrix provides a novel class of hybrid materials with a good ion exchange capacity, high stability, and selectivity for caesium ions. The CNT–PANI–NiHCF nanocomposite films have been synthesized by step-by-step electrodeposition on glassy carbon electrodes and characterized with cyclic voltammetry (CV), scanning electron microscopy (SEM), transmission electron microscopy (TEM), and X-ray photoelectron spectroscopy (XPS) techniques. CV and XPS investigations confirmed the formation of PANI and NiHCF on the surface of CNTs. The microstructure of NiHCF hybrid materials was characterized by SEM and TEM; the size of NiHCF particles is approximately 20 to 50 nm. The porous high surface area CNT matrix provides a high loading capacity for the deposition of NiHCF nanoparticles, while the PANI thin-film further stabilizes the nanoparticles. The selectivity for caesium ion adsorption of the hybrid materials was investigated. The high selectivity for caesium provides a basis for the development of a novel electrochemical ion exchange process for the treatment of nuclear waste and radioactive caesium contaminated waters.
Tactile microsensor elements prepared from aligned superelastic carbon microcoils and polysilicone matrix (2006)

Superelastic carbon microcoils (SE-CMC) with coil diameters of 10–15 µm and high elasticity were prepared by the Ni catalysed pyrolysis of acetylene. The SE-CMC could be extended and contracted to 5–10 times their original coil length; these effects accompanied changes in electrical parameters. The extension of the bulk SE-CMC sheets was highly sensitive to the applied load, and could respond to very low applied loads of the order of milligrams. Using the SE-CMCs as the sensing material and polysilicone resin as the composite matrix, tactile sensor elements with different alignments were prepared. It was found that the sensor elements had the high sensitivity of 1 mgf (1 Pa). The smallest dimensions of the SE-CMC microsensor elements obtained were 80 × 80 × 80 µm3 (the sensor was very small and the smallest detectable force was hard to measure). It was also found that the SE-CMC alignments in the matrix and the method of placement on the electrodes dramatically affected the sensing properties.
SISTEM INFORMASI PENGOLAHAN DATA SERVIS ELECTRONIC DI PT. LG ELECTRONIC INDONESIA (CABANG JAMBI) (2012)

Penulisan ilmiah ini menjelaskan mengenai Aplikasi pengolahan data servis electronic dan karya ilmiah electronic PT. LG Electronic Indonesia (Cabang Jambi) dengan tujuan mempermudah pencatatan data servis electronic serta mengurangi resiko kesalahan pencatatan dan mempermudah dalam pembuatan karya ilmiah. Pembuatan Aplikasi pengolahan data servis electronic dan karya ilmiah servis PT. LG Electronic Indonesia (Cabang Jambi) ini menggunakan Visual Basic 6.0, dan Microsoft Access sebagai database, serta untuk membuat karya ilmiah mengunakan Data Report. Data atau informasi berkaitan dengan penelitian ini didapat melalui studi lapangan dan studi pustaka. Kesimpulan yang di dapat oleh penulis dalam pembuatan aplikasi ini adalah pencatatan data servis electronic dan karya ilmiah servis electronic dapat dilakukan secara terkomputerisasi, mengurangi resiko kesalahan dalam pembuatan karya ilmiah yang cepat dan akurat
Zwitterionic Metallocenes Derived from<i>rac</i>and<i>meso</i>-Ethylenebisindenyl Zirconocene Olefin Complexes and Pentafluorophenyl-Substituted Boranes (1999)

Trimethylphosphine-stabilized ethylene complexes 1 of the ethylenebisindenyl-supported zirconocene fragment are prepared via magnesium reduction of rac-(EBI)ZrCl2 in the presence of ethylene and PMe3. When the reaction is halted after 6 h, good yields of a mixture containing rac-(EBI)Zr(η2-CH2CH2)PMe3, rac-1, and the racemic diastereomer of the zirconacyclopentane derivative (EBI)Zr(η2-CH2CH2CH2CH2), rac-2, are obtained. This mixture may be converted to pure rac-1 if treated with excess PMe3. If the magnesium reduction of rac-(EBI)ZrCl2 is left for 3 days in the presence of magnesium chloride, complete epimerization to meso-1 is observed. Thus, both diastereomers of 1 are available. Compounds meso-1 and rac-2 have been characterized crystallographically. The coordinated ethylene ligands in compounds 1 are susceptible to electrophilic attack by the pentafluorophenyl-substituted boranes HB(C6F5)2 and B(C6F5)3, forming zwitterionic metallocene products. For reactions involving HB(C6F5)2, the products meso-3 and rac-3 are characterized by a strong zirconium−hydrido borate interaction, as well as a weak Zr−Cβ bonding. In addition to complete solution characterization, the structure of meso-3 was determined crystallographically. Upon treatment of rac-1 with B(C6F5)3, a more charge-separated zwitterion, rac-4, was formed. In addition to retaining its PMe3 ligand, the complex is stabilized by a strong β-CH2 interaction, as determined by X-ray crystallography and NMR spectroscopy. Structural comparisons between the compounds reported herein and previous examples in metallocene chemistry are presented.
Project Jukebox: An Innovative Way to Access and Preserve Oral History Records (1991)

This article will introduce oral history curators, archivists, librarians, researchers, and others interested in the preservation and accessibility of oral history recordings to a fascinating project at the Alaska and Polar Regions Department, Elmer E. Rasmuson Library, University of Alaska Fairbanks. Project Jukebox is an exciting, unique approach to age-old problems of preservation, storage, and retrieval of oral history records. Using state-of-the-art technology, Project Jukebox allows a researcher to find an appropriate interview, to listen to the interview, to look at historical photographs relative to the interview, to locate the site of the interview on a map, and when available, to read a transcript of the interview. The original records are not subject to damage from handling because the patron works from a digitized record on the computer.
Inhibition of the growth of Neisseria meningitidis by reduced ferritin and other iron-binding agents (1979)

Serogroups of N. meningitidis were characterized as virulent or avirulent according to their capacity to establish meningococcal infection in mice. An agar plate diffusion technique demonstrated that iron had a definite growth-supporting role for both of these meningococcal types. The avirulent strains could use ionic or chelated iron as well as the virulent strains. Iron-reversible growth inhibition occurred to the same extent for both bacterial types in the presence of the synthetic iron-chelating agents Desferal and ethylenediamine-di-orthohydroxy phenylacetic acid. A difference in response was demonstrated for these bacterial types when grown in the presence of various iron-binding proteins from animal body fluids and tissues. The growth of the avirulent strain was inhibited to a greater degree by egg white conalbumin. The humoral iron-binding protein transferrin showed a significant inhibitory capacity only when used in conjunction with bicarbonate. Under conditions of increased iron saturation of this protein, the avirulent strain was inhibited to the furthest extent. In the presence of ferritin, the cellular iron-binding protein, which had been reduced, inhibition of the growth of either strain type did not occur on iron-poor media (less than 5 micrograms/100 ml). However, with the incorporation of iron into the media, the inhibitory effect of the protein became evident. As the concentration of iron increased, the inhibition increased to a certain level and subsequently declined. A substantial difference in the ability of the avirulent type to grow in the presence of reduced horse spleen ferritin was observed. For this microorganism, a correlation appears to exist between the capacity to grow by utilizing the available iron in the presence of reduced ferritin and the ability to establish infection. The host protein ferritin, in the reduced state, apart from simply being a storage protein for iron, can prevent the growth of a procaryotic organism. Our experiments suggest a role for ferritin in the prevention of emningococcal disease. A cehmotherapeutic potential for Desferal is also implied.
The Response of Nannochloropsis gaditana to Nitrogen Starvation Includes <i>De Novo</i> Biosynthesis of Triacylglycerols, a Decrease of Chloroplast Galactolipids, and Reorganization of the Photosynthetic Apparatus (2013)

Microalgae of the genus Nannochloropsis are capable of accumulating triacylglycerols (TAGs) when exposed to nutrient limitation (in particular, nitrogen [N]) and are therefore considered promising organisms for biodiesel production. Here, after nitrogen removal from the medium, Nannochloropsis gaditana cells showed extensive triacylglycerol accumulation (38% TAG on a dry weight basis). Triacylglycerols accumulated during N deprivation harbored signatures, indicating that they mainly stemmed from freshly synthesized fatty acids, with a small proportion originating from a recycling of membrane glycerolipids. The amount of chloroplast galactoglycerolipids, which are essential for the integrity of thylakoids, decreased, while their fatty acid composition appeared to be unaltered. In starved cells, galactolipids were kept at a level sufficient to maintain chloroplast integrity, as confirmed by electron microscopy. Consistently, N-starved Nannochloropsis cells contained less photosynthetic membranes but were still efficiently performing photosynthesis. N starvation led to a modification of the photosynthetic apparatus with a change in pigment composition and a decrease in the content of all the major electron flow complexes, including photosystem II, photosystem I, and the cytochrome b(6)f complex. The photosystem II content was particularly affected, leading to the inhibition of linear electron flow from water to CO(2). Such a reduction, however, was partially compensated for by activation of alternative electron pathways, such as cyclic electron transport. Overall, these changes allowed cells to modify their energetic metabolism in order to maintain photosynthetic growth.
Peptoids successfully inhibit the growth of gram negative E. coli causing substantial membrane damage (2017)

Peptoids are an alternative approach to antimicrobial peptides that offer higher stability towards enzymatic degradation. It is essential when developing new types of peptoids, that mimic the function of antimicrobial peptides, to understand their mechanism of action. Few studies on the specific mechanism of action of antimicrobial peptoids have been described in the literature, despite the plethora of studies on the mode of action of antimicrobial peptides. Here, we investigate the mechanism of action of two short cationic peptoids, rich in lysine and tryptophan side chain functionalities. We demonstrate that both peptoids are able to cause loss of viability in E. coli susceptible cells at their MIC (16-32 μg/ml) concentrations. Dye leakage assays demonstrate slow and low membrane permeabilization for peptoid 1, that is still higher for lipid compositions mimicking bacterial membranes than lipid compositions containing Cholesterol. At concentrations of 4 × MIC (64-128 μg/ml), pore formation, leakage of cytoplasmic content and filamentation were the most commonly observed morphological changes seen by SEM in E. coli treated with both peptoids. Flow cytometry data supports the increase of cell size as observed in the quantification analysis from the SEM images and suggests overall decrease of DNA per cell mass over time.
450 mm dual frequency capacitively coupled plasma sources: Conventional, graded, and segmented electrodes (2010)

Wafer diameters for microelectronics fabrication will soon transition from 300 to 450 mm at a time when excitation frequencies for capacitively coupled plasmas (CCPs) are increasing to 200 MHz or higher. Already for 300 mm tools, there is evidence that wave behavior (i.e., propagation, constructive, and destructive interference) affects the uniformity of processing. The increase in diameter to 450 mm is likely to exacerbate these effects, perhaps requiring nontraditional tool designs. This is particularly important in dual frequency (DF) CCP tools in which there are potential interactions between frequencies. In this paper, results from a two-dimensional computational investigation of Ar plasma properties in a 450 mm DF-CCP reactor, incorporating a full-wave solution of Maxwell’s equations, are discussed. As in 300 mm DF-CCP reactors, the electron density collapses toward the center of the reactor with increasing high frequency (HF), however, with more pronounced finite wavelength effects. Graded conductivity electrodes with multilayer of dielectrics are computationally demonstrated as a possible means to suppress wave effects thereby increasing plasma uniformity. Segmentation of the HF electrode also improves the plasma uniformity by making the electrical distance between the feeds and the sheath edges as uniform as possible.
Ligand solvation in molecular docking (1999)

Solvation plays an important role in ligand-protein association and has a strong impact on comparisons of binding energies for dissimilar molecules. When databases of such molecules are screened for complementarity to receptors of known structure, as often occurs in structure-based inhibitor discovery, failure to consider ligand solvation often leads to putative ligands that are too highly charged or too large. To correct for the different charge states and sizes of the ligands, we calculated electrostatic and non-polar solvation free energies for molecules in a widely used molecular database, the Available Chemicals Directory (ACD). A modified Born equation treatment was used to calculate the electrostatic component of ligand solvation. The non-polar component of ligand solvation was calculated based on the surface area of the ligand and parameters derived from the hydration energies of apolar ligands. These solvation energies were subtracted from the ligand-receptor interaction energies. We tested the usefulness of these corrections by screening the ACD for molecules that complemented three proteins of known structure, using a molecular docking program. Correcting for ligand solvation improved the rankings of known ligands and discriminated against molecules with inappropriate charge states and sizes.