gebhart/patrepeval huggingface dataset:
High-Frequency, ICCD Diffuse Optical Tomography System for Separation of Optical Properties in Small Tissue Volumes (2006)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text S. V. Patwardhan and J. P. Culver., "High-Frequency, ICCD Diffuse Optical Tomography System for Separation of Optical Properties in Small Tissue Volumes," in Biomedical Optics, Technical Digest (CD) (Optica Publishing Group, 2006), paper WD5. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Truncated staphylococcal nuclease is compact but disordered. (1992)

Deletion of 13 amino acids from the carboxyl terminus of the 149-amino acid staphylococcal nuclease molecule results in a denatured, partly unfolded molecule that lacks persistent secondary structure but is compact under physiological conditions. Since the modification is a carboxyl-terminal deletion, it is argued that the state resembles a peptide emerging from the ribosome just before the complete folding pathway is initiated. In this paper, we characterize the molecule by nuclear magnetic resonance, circular dichroism, and small-angle x-ray scattering measurements. The truncated nuclease shows wild-type levels of activity in the presence of calcium and is found to fold into a native-like conformation in the presence of 3',5'-bisphospho-2'-deoxythymidine, a potent inhibitor. Thus, the truncated molecule retains the capacity to fold. Our results suggest that extensive solvent exclusion generates a compact polypeptide chain prior to the development of persistent secondary structural features as a protein folds during biosynthesis.
Amide Isosteres of Oroidin: Assessment of Antibiofilm Activity and C. elegans Toxicity (2009)

The synthesis and antibiofilm activities of sulfonamide, urea, and thiourea oroidin analogues are described. The most active derivative was able to selectively inhibit P. aeruginosa biofilm development and is also shown to be nontoxic upward of 1 mM to the development of C. elegans in comparison to other similar isosteric analogues and the natural product oroidin.
Genetic Analysis of Histone H4: Essential Role of Lysines Subject to Reversible Acetylation (1990)

The nucleosome is the fundamental unit of assembly of the chromosome and reversible modifications of the histones have been suggested to be important in many aspects of nucleosome function. The structure-function relations of the amino-terminal domain of yeast histone H4 were examined by the creation of directed point mutations. The four lysines subject to reversible acetylation were essential for histone function as the substitution of arginine or asparagine at these four positions was lethal. No single lysine residue was completely essential since arginine substitutions at each position were viable, although several of these mutants were slower in completing DNA replication. The simultaneous substitution of glutamine for the four lysine residues was viable but conferred several phenotypes including mating sterility, slow progression through the G2/M period of the division cycle, and temperature-sensitive growth, as well as a prolonged period of DNA replication. These results provide genetic proof for the roles of the H4 amino-terminal domain lysines in gene expression, replication, and nuclear division.
Cell Culture Modeling to Test Therapies Against Hyperglycemia-Mediated Oxidative Stress and Injury (2005)

The concept that oxidative stress is a key mediator of nerve injury in diabetes has led us to design therapies that target oxidative stress mechanisms. Using an in vitro model of glucose-treated dorsal root ganglion (DRG) neurons in culture, we can examine both free radical generation, using fluorimetric probes for reactive oxygen species, and cell death via the TUNEL assay. The cell culture system is scaled down to a 96-well plate format, and so is well suited to high-throughput screening. In the present study, we test the ability of three drugs, nicotinamide, allopurinol, and alpha-lipoic acid, alone and in combination to prevent DRG neuron oxidative stress and cell death. This combination of drugs is currently in clinical trial in type 1 diabetic patients. We demonstrate independent effects on oxidative stress and neuronal survival for the three drugs, and neuronal protection using the three drugs in combination. The data strengthen the rationale for the current clinical trial. In addition, we describe an effective tool for rapid preclinical testing of novel therapies against diabetic neuropathy.
Conformation and Optical Activity of all‐trans, mono‐cis, and di‐cis Carotenoids: Temperature Dependent Circular Dichroism (1979)

Abstract The CD. spectra of carotenoids with an asymmetric centre at C(3) have the following unusual features: (1) All‐ trans and di‐ cis compounds with two end‐rings, at least one of which possesses an asymmetric C‐atom, have very similar CD. spectra, whereas the corresponding mono‐ cis compounds give mirror‐image CD. spectra; (2) In carotenoids or apocarotenoids with only one end‐ring all‐ trans and mono‐ cis compounds have the same CD. spectra; (3) The CD. spectra of such carotenoids are strongly temperature dependent either increasing in magnitude or completely changing in sign upon cooling. These properties have been rationalized with the aid of a model with takes the total chromophore of the carotenoid as being intrinsically chiral with symmetry C 2 . It seems that the chirality arises not only from the presence of the hydroxyl group of an asymmetric carbon atom, C(3), which occupies an equatorial position thereby locking the conformation of the end‐ring, but also from the steric hindrance across the formal single bond C(6), C(7), linking the end‐ring to the chain and thus creating a chiral π‐system. (The twist about the C(6), C(7)‐bond acquires a handedness because of the predominance of one conformational form of the end‐ring. In this way, the double bonds of the end‐ring become twisted out of the plane of the chain with one hand predominating. Thus the whole conjugated system becomes chiral). The reversal of sign between the trans (and di‐ cis ) and mono‐ cis compounds is due to a tilt of the 2‐fold symmetry axis and thereby a change of chirality. The temperature dependence stems from the varying population of forms of different twist of the end‐group relative to the chain. Compounds with 7, 8‐triple bonds also show distinct CD. spectra and a sign change between all‐ trans and mono‐ cis isomers in addition to temperature dependence. The latter property demonstrates that some steric hindrance between the end‐ring and the main chain is present in these compounds. Some suggestions for the origins of the sign patterns and band intensities of the CD. and absorption spectra are included.
Latent semantic space (2000)

We present a novel algorithm that creates document vectors with reduced dimensionality. This work was motivated by an application characterizing relationships among documents in a collection. Our algorithm yielded inter-document similarities with an average precision up to 17.8% higher than that of singular value decomposition (SVD) used for Latent Semantic Indexing. The best performance was achieved with dimensional reduction rates that were 43% higher than SVD on average. Our algorithm creates basis vectors for a reduced space by iteratively “scaling” vectors and computing eigenvectors. Unlike SVD, it breaks the symmetry of documents and terms to capture information more evenly across documents. We also discuss correlation with a probabilistic model and evaluate a method for selecting the dimensionality using log-likelihood estimation.
Signaling Lymphocytic Activation Molecule (CDw150) Is Homophilic but Self-associates with Very Low Affinity (2000)

Signaling lymphocytic activating molecule ((SLAM) CDw150) is a glycoprotein that belongs to the CD2 subset of the immunoglobulin superfamily and is expressed on the surface of activated T- and B-cells. It has been proposed that SLAM is homophilic and required for bidirectional signaling during T- and B-cell activation. Previous work has suggested that the affinity of SLAM self-association might be unusually high, undermining the concept that protein interactions mediating transient cell-cell contacts, such as those involving leukocytes, have to be weak in order that such contacts are readily reversible. Using surface plasmon resonance-based methods and analytical ultracentrifugation (AUC), we confirm that SLAM is homophilic. However, we also establish a new theoretical treatment of surface plasmon resonance-derived homophilic binding data, which indicates that SLAM-SLAM interactions (solution K(d) approximately 200 micrometer) are in fact considerably weaker than most other well characterized protein-protein interactions at the cell surface (solution K(d) approximately 0.4-20 micrometer), a conclusion that is supported by the AUC analysis. Whereas further analysis of the AUC data imply that SLAM could form "head to head" dimers spanning adjacent cells, the very low affinity raises important questions regarding the physiological role and/or properties of such interactions.
Substituent and solvent effects on the thermal isomerisation of 7H-pyrazolo[5,1-c]-1,2,4-triazole azomethine dyes (1991)

Activation parameters for the thermal syn–anti isomerisation of 25 pyrazolotriazole azomethine dyes in ethanol have been obtained, and the effect of solvent on the rate of isomerisation examined for two of these compounds. Substituent and solvent variations have only a minor influence upon the rate constants, and steric crowding about the CN bond is the major factor in determining the isomerisation rate. For substituent variations in the 3-position there is a reasonable Hammett correlation between rate constants and σp substituent constants and an isokinetic relationship, with an ill-defined isokinetic temperature, at ca. 520–1200 K. These data are discussed in terms of the inversion, rotation and biradical mechanisms for isomerisation.
Mapping the Substrate Binding Site of the Prostaglandin Transporter PGT by Cysteine Scanning Mutagenesis (1999)

We have identified a cDNA, PGT, that encodes a widely expressed transporter for prostaglandin (PG) E(2), PGF(2alpha), PGD(2), 8-iso-PGF(2alpha), and thromboxane B(2). To begin to understand the molecular mechanisms of transporter function, we have initiated a structure-function analysis of PGT to identify its substrate-binding region. We have found that by introducing the small, water-soluble, thiol-reactive anion Na(2-sulfonatoethyl)methanethiosulfonate (MTSES) into the substrate pathway, we were able to cause inhibition of transport that could be reversed with dithiothreitol. Importantly, co-incubation with PGE(2) protected PGT from this inhibition, suggesting that MTSES gains access to the aqueous pore pathway of PGT to form a mixed disulfide near the substrate-binding site. To identify the susceptible cysteine, we mutated, one at a time, all six of the putative transmembrane cysteines to serine. Only the mutation of Cys-530 to serine within putative transmembrane 10 became resistant to inhibition by MTSES. Thus, Cys-530 is the substrate-protectable, MTSES-inhibitable residue. To identify other residues that may be lining the substrate-binding site, we initiated cysteine-scanning mutagenesis of transmembrane 10 using Cys-530 as an entry point. On a C530S, MTSES-resistant background, residues in the N- and C-terminal directions were individually mutated to cysteine (Ala-513 to His-536), one at a time, and then analyzed for MTSES inhibition. Of the 24 cysteine-substituted mutants generated, 6 were MTSES-sensitive and, among these, 4 were substrate-protectable. The pattern of sensitivity to MTSES places these residues on the same face of an alpha-helix. The results of cysteine-scanning mutagenesis and molecular modeling of putative transmembrane 10 indicate that the substrate binding of PGT is formed among its membrane-spanning segments, with 4 residues along the cytoplasmic end of helix 10 contributing to one surface of the binding site.
Assessment of cartilage volume in the femorotibial joint with magnetic resonance imaging and 3D computer reconstruction. (1994)

Our goal was the development of an accurate and objective technique to depict and quantitate articular cartilage using magnetic resonance imaging (MRI) and 3D data processing.A method of 3D image analysis has been developed that provides a noninvasive technique of measuring cartilage volume from standard diagnostic MR images.Using a computer workstation, cartilage from Fast Field Echo (FFE) MR images was reconstructed into 3 dimensions (3D). The accuracy and reproducibility of both thickness and volume measurements obtained from the existing computer software was tested using calibration test objects. We describe the sources of error we encountered when attempting to quantitate cartilage using the existing computer software, the methods developed to reduce these errors, and a preliminary cartilage volume study using healthy human volunteers.We have identified errors involved in attempting cartilage volume estimations using the existing 3D computer software and have developed a data processing technique that minimizes these errors. With these objective data processing techniques we have improved the reproducibility of the technique to +/- 10-15% error. This modified technique provides a promising new method for viewing and quantifying cartilage volume from standard diagnostic MR images.
Role of multiple gene copies in particulate methane monooxygenase activity in the methane-oxidizing bacterium Methylococcus capsulatus Bath (1999)

Genes for the subunits of particulate methane monooxygenase, PmoABC, have been sequenced from the gamma-proteobacterial methanotroph Methylococcus capsulatus Bath. M. capsulatus Bath contains two complete copies of pmoCAB, as well as a third copy of pmoC. The two pmoCAB regions were almost identical at the nucleotide sequence level, differing in only 13 positions in 3183 bp. At the amino acid level, each translated gene product contained only one differing residue in each copy. However, the pmoC3 sequence was more divergent from the two other pmoC copies at both the far N-terminus and far C-terminus. Chromosomal insertion mutations were generated in all seven genes. Null mutants could not be obtained for pmoC3, suggesting that it may play an essential role in growth on methane. Null mutants were obtained for pmoC1, pmoC2, pmoA1, pmoA2, pmoB1 and pmoB2. All of these mutants grew on methane, demonstrating that both gene copies were functional. Copy 1 mutants showed about two-thirds of the wild-type whole-cell methane oxidation rate, while copy 2 mutants showed only about one-third of the wild-type rate, indicating that both gene copies were necessary for wild-type particulate methane monooxygenase activity. It was not possible to obtain double null mutants that were defective in both pmo copies, which may indicate that some expression of pMMO is important for growth.
Origin of electrophosphorescence from a doped polymer light emitting diode (2001)

The origin of electrophosphorescence from a doped polymer light emitting diode (LED) has been investigated. A luminescent polymer host, poly(9,9-dioctylfluorene) (PFO), was doped with a red phosphorescent dye, 2,3,7,8,12,13,17,18-octaethyl-21H,23H-porphyrin platinum(II) (PtOEP). The maximum external quantum efficiency of $3.5%$ was obtained at a concentration of $4%$ PtOEP by weight. Energy transfer mechanisms between PFO and PtOEP were studied by absorption, photoluminescence, and photoinduced absorption spectroscopy. Even though electroluminescence spectra were dominated by PtOEP at a concentration of only $0.2 \mathrm{wt}%$ PtOEP, F\"orster transfer of singlet excitons was weak and there was no evidence for Dexter transfer of triplet excitons. We conclude that the dominant emission mechanism in doped LED's is charge trapping followed by recombination on PtOEP molecules.
Low-cost, low-loss microlens arrays fabricated by soft-lithography replication process (2003)

This letter describes a soft lithographic approach for fabricating low-cost, low-loss microlens arrays. An accurate negative reproduction (stamp) of an existing high-quality lens surface (master) is made by thermally curing a prepolymer to a silicone elastomer against the master. Fabricating the stamp on a rigid backing plate minimizes distortion of its surface relief. Dispensing a liquid photocurable epoxy loaded to high weight percent with functionalized silica nanoparticles into the features of relief on the mold and then curing this material with UV radiation against a quartz substrate generates a replica lens array. The physical and optical characteristics of the resulting lenses suggest that the approach will be suitable for a range of applications in micro and integrated optics.
Metal- and Anion-Binding Supramolecular Gels (2009)

ADVERTISEMENT RETURN TO ISSUEPREVReviewNEXTMetal- and Anion-Binding Supramolecular GelsMarc-Oliver M. Piepenbrock, Gareth O. Lloyd, Nigel Clarke*, and Jonathan W. Steed*View Author Information Durham University, Department of Chemistry, South Road, Durham DH1 3LE, United Kingdom* To whom correspondence should be addressed. E-mail: [email protected]Cite this: Chem. Rev. 2010, 110, 4, 1960–2004Publication Date (Web):December 22, 2009Publication History Received9 September 2009Published online22 December 2009Published inissue 14 April 2010https://pubs.acs.org/doi/10.1021/cr9003067https://doi.org/10.1021/cr9003067review-articleACS PublicationsCopyright © 2009 American Chemical SocietyRequest reuse permissionsArticle Views19697Altmetric-Citations1121LEARN 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 SUBJECTS:Anions,Gelation,Gels,Ligands,Metals Get e-Alerts
The Art of Manufacturing Gold Catalysts (2011)

Gold has been considered as an active catalyst only when suitable techniques of preparation provided high metal dispersion. A comprehensive survey of the different methods now available for preparing active gold catalysts is reported with particular attention to the role of the supporting material in determining catalyst characteristics.
Pathogenesis of herpes simplex labialis: correlation of vesicle fluid interferon with lesion age and virus titer (1982)

Of 51 patients with herpes simplex labialis, 50 had detectable interferon (IFN) in samples of lesion vesicle fluid. The median titer of vesicle fluid IFN was 8,200 U. and the range of values was 400 to 63,600 U. The amount of vesicle fluid IFN was correlated with lesion age (r = 0.32, P = 0.024) and vesicle fluid virus titer (r = 0.59, P = 0.00004), but not with the clinical severity of the disease. The presence of vesicle fluid IFN (1,500 to 28,600 U) in 15 lesions less than 12 h old emphasizes the need for early treatment in studies of antiviral agents for herpes simplex labialis.
New direct observations of asphalts and asphalt binders by scanning electron microscopy and atomic force microscopy (1996)

Observations made using AFM and SEM have been combined in order to study the structure of asphalts. Fluorescence microscopy was used to aid in understanding the structural changes occurring when polymer is added to the asphalts. With the atomic force microscope we are able to study the structure of the asphalts without any pre‐preparation. Despite very low resolution, our study reveal ed a network of asphaltene molecules with regard to asphalt gel. The same result is obtained by SEM observation but with a much better resolution. SEM observation, however, needs an adequate preparation method. In the presence of polymer we observed a rearrangement of the initial asphaltene association which leads to the assumption that polymer can aggregate the asphaltene phase.
Interaction between Prostatic Fibroblast and Epithelial Cells in Culture: Role of Androgen* (1989)

We have established and characterized two cell lines from the ventral prostate gland of normal Nb rats: NbE-1 (prostatic epithelial) and NbF-1 (prostatic fibroblast) cell lines. To identify the direct mitogenic action of dihydrotestosterone (DHT), we incubated these cell lines alone and together (in the presence and absence of cell contact) with various concentrations of DHT (0.1-10,000 ng/ml) for 24-72 h and assayed for the rate of DNA synthesis and the total number of cells in tissue culture at specified time periods. Results demonstrate that the primary target for DHT mitogenic action is the prostatic fibroblasts. DHT inhibited the growth of prostatic epithelial cells by themselves, but stimulated prostatic epithelial cell growth when the epithelial cells were cocultured with prostatic fibroblasts. Furthermore, the cell-conditioned medium obtained from either the fibroblast or the epithelial cells stimulated in an autocrine or a paracrine manner the growth of prostatic cells in culture. These results are consistent with the concept that DHT stimulates the growth of prostatic epithelial cells indirectly via its direct mitogenic action on the prostatic fibroblasts. Because epithelial cells are the cell type principally responsible for converting testosterone to DHT, and the fibroblasts respond to the mitogenic action of DHT, our results support the concept that tight metabolic cooperation exists between prostatic epithelial and fibroblast cells. These data are in agreement with previous in vivo studies in which we have demonstrated that androgen receptors in the mesenchyme are obligatory for androgen-induced prostate growth and development.
Structural identification of autoinducer of Photobacterium fischeri luciferase (1981)

Synthesis of bacterial luciferase in some strains of luminous bacteria requires a threshold concentration of an autoinducer synthesized by the bacteria and excreted into the medium. Autoinducer excreted by Photobacterium fischeri strain MJ-1 was isolated from the cell-free medium by extraction with ethyl acetate, evaporation of solvent, workup with ethanol-water mixtures, and silica gel chromatography, followed by normal-phase and then reverse-phase high-performance liquid chromatography. The final product was greater than 99% pure. The structure of the autoinducer as determined by high-resolution 1H nuclear magnetic resonance spectroscopy, infrared spectroscopy, and high-resolution mass spectrometry was N-(3-oxohexanoly)-3-aminodihydro-2(3H)-furanone [or N-(beta-ketocaproyl)homoserine lactone]. The formation of homoserine by hydrolysis of the autoinducer was consistent with this structure. Synthetic autoinducer, obtained as a racemate, was prepared by coupling homoserine lactone to the ethylene glycol ketal of sodium 3-oxohexanoate, followed by mildly acidic removal of the protecting group; this synthetic material showed the appropriate biological activity.