gebhart/patrepeval huggingface dataset:
Inferring branching pathways in genome-scale metabolic networks (2009)

ReTrace is a useful method in metabolic path finding tasks, combining some of the best aspects in constraint-based and graph-theoretic methods. It finds use in a multitude of tasks ranging from metabolic engineering to metabolic reconstruction of recently sequenced organisms.
Periplasmic superoxide dismutase protects<i>Salmonella</i>from products of phagocyte NADPH-oxidase and nitric oxide synthase (1997)

Superoxide dismutase (SOD) catalyzes the conversion of superoxide radical to hydrogen peroxide. Periplasmic localization of bacterial Cu,Zn-SOD has suggested a role of this enzyme in defense against extracellular phagocyte-derived reactive oxygen species. Sequence analysis of regions flanking the Salmonella typhimurium sodC gene encoding Cu,Zn-SOD demonstrates significant homology to lambda phage proteins, reflecting possible bacteriophage-mediated horizontal gene transfer of this determinant among pathogenic bacteria. Salmonella deficient in Cu,Zn-SOD has reduced survival in macrophages and attenuated virulence in mice, which can be restored by abrogation of either the phagocyte respiratory burst or inducible nitric oxide synthase. Moreover, a sodC mutant is extremely susceptible to the combination of superoxide and nitric oxide. These observations suggest that SOD protects periplasmic or inner membrane targets by diverting superoxide and limiting peroxynitrite formation, and they demonstrate the ability of the respiratory burst and nitric oxide synthase to synergistically kill microbial pathogens in vivo.
Regulation of the <i>Escherichia coli</i> K5 Capsule Gene Cluster: Evidence for the Roles of H-NS, BipA, and Integration Host Factor in Regulation of Group 2 Capsule Gene Clusters in Pathogenic <i>E. coli</i> (2000)

The expression of Escherichia coli group 2 capsules (K antigens) is temperature dependent, with capsules only being expressed at temperatures above 20 degrees C. Thermoregulation is at the level of transcription, with no detectable transcription at 20 degrees C. Using the E. coli K5 capsule gene cluster as a model system, we have shown that the nucleoid-associated protein H-NS plays a dual role in regulating transcription of group 2 capsule gene clusters at 37 and 20 degrees C. At 37 degrees C H-NS is required for maximal transcription of group 2 capsule gene clusters, whereas at 20 degrees C H-NS functions to repress transcription. The BipA protein, previously identified as a tyrosine-phosphorylated GTPase and essential for virulence in enteropathogenic E. coli, was shown to play a similar role to H-NS in regulating transcription at 37 and 20 degrees C. The binding of integration host factor (IHF) to the region 1 promoter was necessary to potentiate transcription at 37 degrees C and IHF binding demonstrated by bandshift assays. The IHF binding site was 3' to the site of transcription initiation, suggesting that sequences in the 5' end of the first gene (kpsF) in region 1 may play a role in regulating transcription from this promoter at 37 degrees C. Two additional cis-acting sequences, conserved in both the region 1 and 3 promoters, were identified, suggesting a role for these sequences in the coordinate regulation of transcription from these promoters. These results indicate that a complex regulatory network involving a number of global regulators exists for the control of expression of group 2 capsules in E. coli.
Novel Document Level Features for Statistical Machine Translation (2015)

In this paper, we introduce document level features that capture necessary information to help MT system perform better word sense disambiguation in the translation process. We describe enhancements to a Maximum Entropy based translation model, utilizing long distance contextual features identified from the span of entire document and from both source and target sides, to improve the likelihood of the correct translation for words with multiple meanings, and to improve the consistency of the translation output in a document setting. The proposed features have been observed to achieve substantial improvement of MT performance on a variety of standard test sets in terms of TER/BLEU score.
Chemical Evidence for Thiyl Radical Addition to the C6-Position of a Pyrimidine Nucleoside and Its Possible Relevance to DNA Damage Amplification (2000)

ADVERTISEMENT RETURN TO ISSUEPREVNoteNEXTChemical Evidence for Thiyl Radical Addition to the C6-Position of a Pyrimidine Nucleoside and Its Possible Relevance to DNA Damage AmplificationK. Nolan Carter, Thomas Taverner, Carl H. Schiesser, and Marc M. GreenbergView Author Information Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, and School of Chemistry, The University of Melbourne, Victoria 3010, Australia [email protected]Cite this: J. Org. Chem. 2000, 65, 24, 8375–8378Publication Date (Web):October 28, 2000Publication History Received15 May 2000Published online28 October 2000Published inissue 1 December 2000https://pubs.acs.org/doi/10.1021/jo0007433https://doi.org/10.1021/jo0007433brief-reportACS PublicationsCopyright © 2000 American Chemical SocietyRequest reuse permissionsArticle Views397Altmetric-Citations23LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Hydrocarbons,Nucleic acids,Physiology,Pyrimidine,Thiols Get e-Alerts
Determination of the Position of the Conformational Equilibrium of a Trans 1,2-Disubstituted Cyclohexane by NMR Spectroscopy. An Experiment in Physical Organic Chemistry for Undergraduate Students (2001)

An experiment using NMR spectroscopy to determine the relative amounts of the two chair conformations of trans-1-chloro-2-(2-nitrophenythio)cyclohexane is described. The cyclohexane derivative is prepared in an NMR tube by the addition of 2-nitrophenylsulfenyl chloride to cyclohexene. The coupling constants for the hydrogens adjacent to the chlorine and sulfur are used to calculate the percentage of each conformer in the equilibrium mixture. The coupling constants for these hydrogens in the individual conformers are obtained by application of the Karplus equation. The needed dihedral angles are obtained by a molecular mechanics calculation, although idealized angles can also be used. The reaction is conducted in two solvents, chloroform-d and acetonitrile-d3, so the effect of solvent polarity on the equilibrium is also investigated.
Spectrophotometric Analysis of the Cyanide Metabolite 2-Aminothiazoline-4-Carboxylic Acid (ATCA) (2006)

Methods of directly evaluating cyanide levels are limited by the volatility of cyanide and by the difficulty of establishing steady-state cyanide levels with time. We investigated the measurement of a stable, toxic metabolite, 2-aminothiazoline-4-carboxylic acid (ATCA), in an attempt to circumvent the challenge of directly determining cyanide concentrations in aqueous media. This study was focused on the spectrophotometric ATCA determination in the presence of cyanide, thiocyanate (SCN(-)), cysteine, rhodanese, thiosulfate, and other sulfur donors. The method involves a thiazolidine ring opening in the presence of p-(hydroxy-mercuri)-benzoate, followed by the reaction with diphenylthiocarbazone (dithizone). The product is spectrophotometrically analyzed at 625 nm in carbon tetrachloride. The calibration curve was linear with a regression line of Y = 0.0022x (R(2) = 0.9971). Interference of cyanide antidotes with the method was determined. Cyanide, thiosulfate, butanethiosulfonate (BTS), and rhodanese did not appreciably interfere with the analysis, but SCN(-) and cysteine significantly shifted the standard curve. This sensitive spectrophotometric method has shown promise as a substitute for the measurement of the less stable cyanide.
Stress-dependent seismic anisotropy of shales (1999)

Abstract A simple theory for the stress-dependent seismic anisotropy of shales can be obtained in terms of a second-rank tensor and a fourth-rank tensor that depend on the orientation distribution of contacts between clay platelets. The theory allows the normal and shear stiffness of the contact regions between clay platelets to be obtained as a function of stress from measurements of seismic P- and S-wave velocities for shales. The ratio of the normal-to-shear compliance, B N /B T , of the contact regions between clay particles is found to be sensitive to the saturation state of the shale. Inversion of velocity measurements for fully saturated shales shows a low value of B N /B T when compared with measurements on air-dry shales, consistent with the expected reduction in normal compliance in a fluid-saturated, low-permeability rock. For all shales considered, B N /B T is found to be less than unity. The contacts between clay particles are therefore more compliant in shear than in compression.
Characterization and cloning of a novel glycoprotein expressed by stromal cells in T-dependent areas of peripheral lymphoid tissues. (1992)

A novel glycoprotein (gp) expressed by stromal cells of peripheral lymphoid tissue has been characterized immunohistochemically, biochemically, and at the molecular level. This molecule, gp38, was identified with a monoclonal antibody (mAb) (clone 8.1.1) previously shown to react with a subpopulation of thymic epithelium. This mAb generated a reticular labeling pattern in medullary and paracortical areas of lymph nodes and in splenic white pulp. At the ultrastructural level, labeling by the 8.1.1 mAb was restricted to fibroblastic reticular stromal cells. Serial sections of lymph node and spleen labeled with anti-CD3, anti-B220, and 8.1.1 mAbs clearly showed that the 8.1.1+ cells were associated with T cell-dependent areas. In severe combined immunodeficiency (SCID) or Nu/Nu mice, splenic white pulp also exhibited reticular labeling with the 8.1.1 mAb in the absence of detectable numbers of T cells, indicating that the appearance of 8.1.1-reactive stromal cells in discrete areas of peripheral lymphoid tissue was T cell independent. The cDNA encoding this stromal cell molecule was cloned by direct expression in COS cells and found to encode a 172 amino acid sequence with the typical features of a type I integral membrane protein. COS cells transfected with the gp38 clone direct the expression of an approximately 38-kD protein that reacts with the 8.1.1 mAb but not with isotype-matched controls. Comparison of the predicted amino acid sequence of 8.1.1 mAb but not with isotype-matched controls. Comparison of the predicted amino acid sequence of 8.1.1 with proteins in the National Biomedical Research Foundation (NBRF) data base showed that gp38 is very closely related to the early response protein OTS-8 obtained from a cDNA library of tumor promoting agent (TPA)-induced murine osteoblastic cell line, MC3T3-E1.
Nonparametric Econometrics: A Primer (2008)

This review is a primer for those who wish to familiarize themselves with nonparametric econometrics. Though the underlying theory for many of these methods can be daunting for some practitioners, this article will demonstrate how a range of nonparametric methods can in fact be deployed in a fairly straightforward manner. Rather than aiming for encyclopedic coverage of the field, we shall restrict attention to a set of touchstone topics while making liberal use of examples for illustrative purposes. We will emphasize settings in which the user may wish to model a dataset comprised of continuous, discrete, or categorical data (nominal or ordinal), or any combination thereof. We shall also consider recent developments in which some of the variables involved may in fact be irrelevant, which alters the behavior of the estimators and optimal bandwidths in a manner that deviates substantially from conventional approaches.
Scanning superconducting quantum interference device microscope in a dilution refrigerator (2001)

We report on a scanning superconducting quantum interference device microscope operating at temperatures down to 20 mK in a dilution refrigerator. The instrument is designed for studying quantum mechanical coherence effects in mesoscopic systems and investigating magnetic effects on a mesoscopic length scale in novel materials. We have demonstrated the low-temperature operating capabilities of the instrument by studying superconducting tin disks and the superconducting transition of a thin-film tungsten sample and vortices in the same film. Looking forward, we discuss the applicability of the instrument to measurements of persistent currents in normal-metal rings.
Wavelength scanning achieves pixel super-resolution in holographic on-chip microscopy (2016)

Lensfree holographic on-chip imaging is a potent solution for high-resolution and field-portable bright-field imaging over a wide field-of-view. Previous lensfree imaging approaches utilize a pixel super-resolution technique, which relies on sub-pixel lateral displacements between the lensfree diffraction patterns and the image sensor’s pixel-array, to achieve sub-micron resolution under unit magnification using state-of-the-art CMOS imager chips, commonly used in e.g., mobile-phones. Here we report, for the first time, a wavelength scanning based pixel super-resolution technique in lensfree holographic imaging. We developed an iterative super-resolution algorithm, which generates high-resolution reconstructions of the specimen from low-resolution (i.e., under-sampled) diffraction patterns recorded at multiple wavelengths within a narrow spectral range (e.g., 10-30 nm). Compared with lateral shift-based pixel super-resolution, this wavelength scanning approach does not require any physical shifts in the imaging setup, and the resolution improvement is uniform in all directions across the sensor-array. Our wavelength scanning super-resolution approach can also be integrated with multi-height and/or multi-angle on-chip imaging techniques to obtain even higher resolution reconstructions. For example, using wavelength scanning together with multi-angle illumination, we achieved a halfpitch resolution of 250 nm, corresponding to a numerical aperture of 1. In addition to pixel super-resolution, the small scanning steps in wavelength also enable us to robustly unwrap phase, revealing the specimen’s optical path length in our reconstructed images. We believe that this new wavelength scanning based pixel super-resolution approach can provide competitive microscopy solutions for high-resolution and field-portable imaging needs, potentially impacting tele-pathology applications in resource-limited-settings.
Quantum Theory of the Optical and Electronic Properties of Semiconductors (1990)

This revised second edition on the Quantum Theory of the Optical and Electronic Properties of Semiconductors presents the basic elements needed to understand and engage in research in semiconductor physics. In this revised second edition misprints are corrected and some new and more detailed material is added. In order to treat the valence-band structure of semiconductors, an introduction to the k.p. theory and the related description in terms of the Luttinger Hamiltonian is included. An introductory chapter on mesoscopic semiconductor structures discussing the modifications of the envelope function approximation caused by the spatial quantum confinement is also included. Many results are developed in parallel first for bulk material, and then for quasi-two-dimensional quantum wells, and for quasi-one-dimensional quantum wires. Semiconductor quantum dots are treated in a separate chapter. The discussion of time-dependent and coherent phenomena in semiconductors has been considerably extended by including a section dealing with the theoretical description of photon echoes in semiconductors. A new chapter on magneto-absorption has been added, in which magneto-excitons and magneto-plasmas in two-dimensional systems are discussed. The chapter on electron kinetics due to the interaction with longitudinal-optical phonons has been extended. The material is presented in sufficient detail for graduate students and researchers who have a general background in quantum mechanics, and is aimed at solid state physicists, engineers, materials and optical scientists.
The isopropyl ester of methionine hydroxy-analogueis absorbed through the rumen wall in the cow (2004)

A new form of methionine, the isopropyl ester of methionine hydroxy analog (HMBi), has been proven to be available for milk protein synthesis in dairy cows. Studies have also shown that HMBi can be degraded by rumen micro-organisms. By two different experimental approaches (emptied and washed rumen; catheterization of the ruminal vein), we have demonstrated that HMBi ability to be rapidly absorbed by the rumen wall can explain its partial protection from microbial degradations. The high effi ciency of HMBi to pass through biological membranes seems to be due to the molecule's isopropyl ester radical.
A Mobile-Based Service for Building Social Networks for Mobile Users (2012)

Nowadays, social networks become popular with the emerging of web-based social networking services. Recently, several mobile services are developed to connect users to their favourite social networks such as Face book, Twitter, Flickr, etc. However, these services depends upon the existing web based social networks. In this paper, we present a mobile service called Mobilink for joining groups across communities. The originality of the work is that the framework of the service allows creating and joining social networks that are self contained for mobile company servers. The service consists of several sub-services such as users invitation, group finding and others. Users can use Mobil ink and its sub-services without the need to create their own accounts on social web sites and thus their own groups.
Acoustic Radiation Force Impulse-Induced Peak Displacements Reflect Degree of Anisotropy in Transversely Isotropic Elastic Materials (2017)

In transversely isotropic (TI) materials, mechanical properties (Young's modulus, shear modulus, and Poisson's ratio) are different along versus across the axis of symmetry (AoS). In this work, the feasibility of interrogating such directional mechanical property differences using acoustic radiation force impulse (ARFI) imaging is investigated. We herein test the hypotheses that 1) ARFI-induced peak displacements (PDs) vary with TI material orientations when an asymmetrical ARFI excitation point spread function (PSF) is used, but not when a symmetrical ARFI PSF is employed; and 2) the ratio of PDs induced with the long axis of an asymmetrical ARFI PSF oriented along versus across the material's AoS is related to the degree of anisotropy of the material. These hypotheses were tested in silico using finite element method (FEM) models and Field II. ARFI excitations had F/1.5, 3, 4, or 5 focal configurations, with the F/1.5 and F/5 cases having the most asymmetrical and symmetrical PSFs at the focal depth, respectively. These excitations were implemented for ARFI imaging in 52 different simulated TI materials with varying degrees of anisotropy, and the ratio of ARFI-induced PDs was calculated. The change in the ratio of PDs with respect to the anisotropy of the materials was highest for the F/1.5, indicating that PD was most strongly impacted by the material orientation when the ARFI excitation was the most asymmetrical. On the contrary, the ratio of PDs did not depend on the anisotropy of the material for the F/5 ARFI excitation, suggesting that PD did not depend on material orientation when the ARFI excitation was symmetrical. Finally, the ratio of PDs achieved using asymmetrical ARFI PSF reflected the degree of anisotropy in TI materials. These results support that symmetrical ARFI focal configurations are desirable when the orientation of the ARFI excitation to the AoS is not specifically known and measurement standardization is important, such as for longitudinal or cross-sectional studies of anisotropic organs. However, asymmetrical focal configurations are useful for exploiting anisotropy, which may be diagnostically relevant. Feasibility for future experimental implementation is demonstrated by simulating ultrasonic displacement tracking and by varying the ARF duration.
Signal Transduction by MAP Kinases: Regulation by Phosphorylation-Dependent Switches (1999)

The kinases of mitogen-activated protein (MAP) kinase cascades transmit signals through sequential phosphorylation and activation of the enzymes. However, recent evidence indicates that protein-protein interactions between the kinases themselves or with substrates or other components are also a critical means of regulation. Whitmarsh and Davis summarize these findings with emphasis on new evidence from yeast that, when phosphorylated, a MAP kinase kinase actually switches from a negative regulator that binds to and inhibits its target MAP kinase to a positive regulator of that same enzyme.
More than 100-wavelength-channel picosecond optical pulse generation from single laser source using supercontinuum in optical fibres (1993)

A novel method for generating multiwavelength-channel picosecond optical pulses from a single laser source is proposed using supercontinuum in optical fibres combined with an all-fibre birefringent periodic filter. More than 100-wavelength-channel, 10 ps optical pulses are generated simultaneously over a 1.224–1.394 μm spectral range with a 1.9 nm spacing using a 7.6 ps Nd : YLF laser pulse source.
Van der Waals forces and zero-point energy for dielectric and permeable materials (1974)

It is pointed out that symmetries of Maxwell's equations under interchange of electric and magnetic fields can be exploited to convert calculations of van der Waals forces between electrically polarizable particles and dielectric materials into results for magnetically polarizable particles and permeable materials. In particular, the forces between perfectly conducting materials calculated from ideas of zero-point radiation are the same as the forces between infinitely permeable materials. Combinations of dielectric materials and permeable materials can lead to repulsive van der Waals forces. For example, two infinitely permeable parallel plates are attracted together with exactly the same force as obtained by Casimir for the van der Waals attraction between two perfectly conducting plates. On the other hand, two parallel plates of area $A$ and separation $d$, one of which is a perfect conductor and one of which is infinitely permeable, are repelled by a force $F=\frac{7}{8}\frac{{\ensuremath{\pi}}^{2}\ensuremath{\hbar}cA}{240{d}^{4}}$, differing in magnitude by a factor of $\frac{7}{8}$ from Casimir's attractive force. A calculation of the repulsive force is given based on ideas of classical electromagnetic zero-point radiation.