gebhart/patrepeval huggingface dataset:
16-channel optical add/drop multiplexer usingsilica-based arrayed-waveguide gratings (1995)

An optical add/drop multiplexer (ADM) that enables full access to 16 individual wavelength channels has been fabricated on a planar lightwave circuit (PLC). The device consists of three arrayed-waveguide gratings which are connected by 16 thermo-optic switches. The on-off crosstalk for the main input to the main output port is less than –24 dB and that for the main input to the drop port is about –13 dB. The fibre-to-fibre insertion losses are 7–8 dB and 3–4 dB when signals are coupled to the main input port and to the add port, respectively.
Wavelet denoising of multiframe optical coherence tomography data (2012)

We introduce a novel speckle noise reduction algorithm for OCT images. Contrary to present approaches, the algorithm does not rely on simple averaging of multiple image frames or denoising on the final averaged image. Instead it uses wavelet decompositions of the single frames for a local noise and structure estimation. Based on this analysis, the wavelet detail coefficients are weighted, averaged and reconstructed. At a signal-to-noise gain at about 100% we observe only a minor sharpness decrease, as measured by a full-width-half-maximum reduction of 10.5%. While a similar signal-to-noise gain would require averaging of 29 frames, we achieve this result using only 8 frames as input to the algorithm. A possible application of the proposed algorithm is preprocessing in retinal structure segmentation algorithms, to allow a better differentiation between real tissue information and unwanted speckle noise.
An Experiment in Enhancing Information Access by Natural Language Processing (1997)

We explore the hypothesis that lexical disambiguation could be applied to provide useful information access services. Specifically, we refined a lexical disambiguation method, and used it in a fully automatic categorization algorithm we developed. We also used this method more directly, to implement a service that retrieves documents by word sense. &lt;p&gt;To test these algorithms, we developed an experimental system, IAGO!, in which we applied these algorithms to accessing the World Wide Web. IAGO! comprises both an Web directory (i.e., a classification of articles by topic) and a Web search service. Unlike most other Web directories, IAGO!'s directory was generated by a fully automatic process. One experiment shows a cataloging accuracy of 97%. &lt;p&gt;To improve net searching, IAGO! enables users to refine their queries by first detecting lexical ambiguities, and then allowing users to select specific word senses by which to search. IAGO! returns only Web pages in which a given keyword occurs in the specified sense. To help evaluate these results, we derive some performance thresholds that a disambiguation algorithm needs to operate within in order to be useful for retrieval. Our experimental results suggest that the implemented algorithm is performing well above these needs
Structure and promoter characterization of the gene encoding the large subunit (R1 protein) of mouse ribonucleotide reductase. (1993)

Mammalian ribonucleotide reductase (EC 1.17.4.1) is composed of two nonidentical subunits, proteins R1 and R2, both required for enzyme activity. The structure of the genomic mouse ribonucleotide reductase R1 gene was compiled from a number of overlapping lambda clones isolated from a Charon 4A mouse sperm genomic library. The R1-encoding gene covers 26 kb and consists of 19 exons. All exon-intron boundaries were located by dideoxynucleotide sequencing, showing that intron 7 starts with the variant GC instead of GT. About 3.5 kb of DNA from the 5'-flanking region of the R1-encoding gene were cloned and sequenced, and the transcriptional start site was determined by nuclease S1 mapping of RNA. DNase I footprinting assays on the R1 promoter identified two nearly identical 23-bp-long protein-binding regions. Three protein complexes binding to one of the 23-mer regions were resolved and partially identified by using gel-retardation mobility-shift assays and UV crosslinking. One complex most likely contained Sp1, and another complex showed S-phase-specific binding, suggesting a direct role in the cell-cycle-dependent R1 gene expression.
Dendritic Silver Nanostructure Growth and Evolution in Replacement Reaction (2007)

In this study, a well-defined dendritic silver nanostructure can be large-scale synthesized in AgNO3 (aqueous) at room temperature. The nonequilibrium and anisotropic growth at different silver ion concentrations result in controllable morphologies and morphological evolution. At high silver ion concentrations, a strong anisotropic growth contributes to a fine single crystalline silver dendrite. As the reaction proceeds, the dendritic structure transforms into a thermodynamically stable hexagonal structure. At a relatively low silver ion concentration, a particle-aggregated fractal pattern can be obtained due to relatively small anisotropy. As the reaction time increases, the transition from polycrystalline aggregates to a single crystal during silver dendritic growth can be observed. An oriented attachment mechanism can be used to explain the structural and morphological evolution of silver nanostructures. Silver nanostructures with various morphologies are expected to have significant potential applications in superhydrophobic surfaces, surface-enhanced Raman scattering, and others.
Different subcellular locations of secretome components of Gram-positive bacteria (2006)

Gram-positive bacteria contain different types of secretion systems for the transport of proteins into or across the cytoplasmic membrane. Recent studies on subcellular localization of specific components of these secretion systems and their substrates have shown that they can be present at various locations in the cell. The translocons of the general Sec secretion system in the rod-shaped bacterium Bacillus subtilis have been shown to localize in spirals along the cytoplasmic membrane, whereas the translocons in the coccoid Streptococcus pyogenes are located in a microdomain near the septum. In both bacteria the Sec translocons appear to be located near the sites of cell wall synthesis. The Tat secretion system, which is used for the transport of folded proteins, probably localizes in the cytoplasmic membrane and at the cell poles of B. subtilis. In Lactococcus lactis the ABC transporter dedicated to the transport of a small antimicrobial peptide is distributed throughout the membrane. Possible mechanisms for maintaining the localization of these secretion machineries involve their interaction with proteins of the cytoskeleton or components of the cell wall synthesis machinery, or the presence of lipid subdomains surrounding the transport systems.
Hyperbranched Aliphatic Polyesters (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTHyperbranched Aliphatic PolyestersE. Malmstroem, M. Johansson, and A. HultCite this: Macromolecules 1995, 28, 5, 1698–1703Publication Date (Print):February 1, 1995Publication History Published online1 May 2002Published inissue 1 February 1995https://pubs.acs.org/doi/10.1021/ma00109a049https://doi.org/10.1021/ma00109a049research-articleACS PublicationsRequest reuse permissionsArticle Views2921Altmetric-Citations460LEARN 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
Cubic convolution interpolation for digital image processing (1981)

Cubic convolution interpolation is a new technique for resampling discrete data. It has a number of desirable features which make it useful for image processing. The technique can be performed efficiently on a digital computer. The cubic convolution interpolation function converges uniformly to the function being interpolated as the sampling increment approaches zero. With the appropriate boundary conditions and constraints on the interpolation kernel, it can be shown that the order of accuracy of the cubic convolution method is between that of linear interpolation and that of cubic splines. A one-dimensional interpolation function is derived in this paper. A separable extension of this algorithm to two dimensions is applied to image data.
Cytotoxic quaternary alkaloids from the flowers of Narcissus tazetta. (2001)

Intensive chromatographic separation of the polar fraction of an ethanolic extract of the fresh flowers of Narcissus tazetta L. (Amaryllidaceae) yielded two new quaternary alkaloids with a phenanthrene skeleton, N-methyl-8,9-methylenedioxy-phenantridinium methylsulfate (1) and N-methyl-8,9-methylenedioxy-phenantridinium malate (2). The structure determination of the alkaloids was based on one- and two-dimensional NMR studies including HMQC, and HMBC studies, and mass spectroscopic analysis. The existence, in 1, of the methylsulfate group was confirmed by X-ray diffraction analysis. Cytotoxic activities for 1 and 2 against a panel of cancer cell lines are also reported.
ChemInform Abstract: Mechanisms of Ligand Recognition in Myoglobin. (1995)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Nanosized Building Blocks for Customizing Novel Antibiofilm Approaches (2016)

Recent advances in nanotechnology provide unparalleled flexibility to control the composition, size, shape, surface chemistry, and functionality of materials. Currently available engineering approaches allow precise synthesis of nanocompounds (e.g., nanoparticles, nanostructures, nanocrystals) with both top-down and bottom-up design principles at the submicron level. In this context, these "nanoelements" (NEs) or "nanosized building blocks" can 1) generate new nanocomposites with antibiofilm properties or 2) be used to coat existing surfaces (e.g., teeth) and exogenously introduced surfaces (e.g., restorative or implant materials) for prevention of bacterial adhesion and biofilm formation. Furthermore, functionalized NEs 3) can be conceived as nanoparticles to carry and selectively release antimicrobial agents after attachment or within oral biofilms, resulting in their disruption. The latter mechanism includes "smart release" of agents when triggered by pathogenic microenvironments (e.g., acidic pH or low oxygen levels) for localized and controlled drug delivery to simultaneously kill bacteria and dismantle the biofilm matrix. Here we discuss inorganic, metallic, polymeric, and carbon-based NEs for their outstanding chemical flexibility, stability, and antibiofilm properties manifested when converted into bioactive materials, assembled on-site or delivered at biofilm-surface interfaces. Details are provided on the emerging concept of the rational design of NEs and recent technological breakthroughs for the development of a new generation of nanocoatings or functional nanoparticles for biofilm control in the oral cavity.
Quantitative Microarray Profiling of DNA-Binding Molecules (2007)

A high-throughput Cognate Site Identity (CSI) microarray platform interrogating all 524 800 10-base pair variable sites is correlated to quantitative DNase I footprinting data of DNA binding pyrrole-imidazole polyamides. An eight-ring hairpin polyamide programmed to target the 5 bp sequence 5'-TACGT-3' within the hypoxia response element (HRE) yielded a CSI microarray-derived sequence motif of 5'-WWACGT-3' (W = A,T). A linear beta-linked polyamide programmed to target a (GAA)3 repeat yielded a CSI microarray-derived sequence motif of 5'-AARAARWWG-3' (R = G,A). Quantitative DNase I footprinting of selected sequences from each microarray experiment enabled quantitative prediction of Ka values across the microarray intensity spectrum.
Impact of siRNA Overhangs for Dendrimer-Mediated siRNA Delivery and Gene Silencing (2013)

Small interfering RNA (siRNA) have attracted considerable attention, as compelling therapeutics providing safe and competent delivery systems are available. Dendrimers are emerging as appealing siRNA delivery vectors thanks to their unique, well-defined architecture and the resulting cooperativity and multivalency confined within a nanostructure. We have recently disclosed the structurally flexible fifth-generation TEA-core PAMAM dendrimer (G5) as an effective nanocarrier for delivery of sticky siRNA bearing long complementary sequence overhangs (dA)n/(dT)n (n = 5 or 7). Here, using combined experimental/computational approaches, we successfully clarified (i) the underlying mechanisms of interaction between the dendrimer nanovector G5 and siRNA molecules bearing either complementary or noncomplementary sequence overhangs of different length and chemistry and (ii) the impact of siRNA overhangs contributing toward the improved delivery potency. Using siRNA with complementary overhangs offer the best action in term of gene silencing through the formation of concatemers, that is, supramolecular structures resulting from synergistic and cooperative binding via (dA)n/(dT)n bridges (n = 5 or 7). On the other hand, although siRNA bearing long, noncomplementary overhangs (dA)n/(dA)n or (dT)n/(dT)n (n = 5 or 7) are endowed with considerably higher gene silencing potency than normal siRNA with (dT)2/(dT)2, they remain less effective than their sticky siRNA counterparts. The observed gene silencing potency depends on length, nature, and flexibility of the overhangs, which behave as a sort of clamps that hold and interact with the dendrimer nanovectors, thus impacting siRNA delivery performance and, ultimately, gene silencing. Our findings can be instrumental in designing siRNA entities with enhanced capability to achieve effective RNA interference for therapeutic applications.
Prevention of Oxidative Rancidity in Rice Bran during Storage (1999)

The effect of microwave heat on lipoxygenase (LOX) activity in rice bran under various storage conditions was examined. Raw rice bran from the long-grain variety Lemont was adjusted to 21% moisture content and heated in a microwave oven at 850 W for 3 min. Raw and microwave-heated rice bran samples were packed in zipper-top bags or vacuum packs and stored at room temperature (25 degrees C) or in the refrigerator (4-5 degrees C) for 16 weeks. Samples were analyzed for LOX activity at 4-week intervals. LOX activity did not significantly change from its initial value at week 0 for zipper-top and vacuum-packed samples while stored at 4-5 degrees C for 12 weeks, but decreased at week 16. Vacuum packing did not show a significant impact on LOX activity during 16 weeks of storage. Microwave-heated samples stored in the refrigerator did not show significant change in LOX activity for up to 12 weeks but showed a significant (p < 0. 05) decrease at 16 weeks. Results showed that oxidative rancidity of rice bran could be prevented by microwave heating the samples, packing in zipper-top bags, and storing at 4-5 degrees C for up to 16 weeks.
The Presenilin 1 Protein Is a Component of a High Molecular Weight Intracellular Complex That Contains β-Catenin (1998)

The presenilin (PS) genes associated with Alzheimer disease encode polytopic transmembrane proteins which undergo physiologic endoproteolytic cleavage to generate stable NH2- and COOH-terminal fragments (NTF or CTF) which co-localize in intracellular membranes, but are tightly regulated in their stoichiometry and abundance. We have used linear glycerol velocity and discontinuous sucrose gradient analysis to investigate the distribution and native conformation of PS1 and PS2 during this regulated processing in cultured cells and in brain. The PS1 NTF and CTF co-localize in the endoplasmic reticulum (ER) and in the Golgi apparatus, where they are components of a approximately 250-kDa complex. This complex also contains beta-catenin but not beta-amyloid precursor protein (APP). In contrast, the PS1 holoprotein precursor is predominantly localized to the rough ER and smooth ER, where it is a component of a approximately 180-kDa native complex. PS2 forms similar but independent complexes. Restricted incorporation of the presenilin NTF and CTF along with a potentially functional ligand (beta-catenin) into a multimeric complex in the ER and Golgi apparatus may provide an explanation for the regulated accumulation of the NTF and CTF.
Solution Structure of Kistrin, a Potent Platelet Aggregation Inhibitor and GP IIb-IIIa Antagonist (1991)

The structure of kistrin, which is a member of a homologous family of glycoprotein IIb-IIIa (GP IIb-IIIa) antagonists and potent protein inhibitors of platelet aggregation, has been determined by two-dimensional nuclear magnetic resonance (NMR) spectroscopy. The 68-residue protein consists of a series of tightly packed loops held together by six disulfide bonds and has almost no regular secondary structure. Kistrin has an Arg-Gly-Asp (RGD) adhesion site recognition sequence important for binding to GP IIb-IIIa that is located at the apex of a long loop across the surface of the protein.
Formulation and Evaluation of a Vitamin C Multiple Emulsion (2006)

Multiple phase emulsions are increasingly used as alternatives to simple emulsions in personal care products. One of the major advantages of these emulsions over simple emulsions is slow and controlled release of their ingredients. Other favorite cosmetic characteristics of multiple emulsions include occlusivity (in O/W/O emulsions), esthetics and consumer acceptance. Vitamin C (ascorbic acid) has been widely used in formulations of skin care products. Due to its effects on collagen biosynthesis, it is considered as moisturizing and anti-aging active ingredient. Instability problems such as oxidation susceptibility have made incorporating vitamin C in topical formulations a challenging issue. The O/W/O emulsions have been formulated using two-step procedure, to investigate vitamin C stability and its release profile. By using different surfactant types and ratios, volume ratio of phases, multiple emulsions containing vitamin C were prepared. Different parameters and formulation factors such as temperature of phases, duration and speed of mixing were evaluated. Based on our results, more stable emulsions were prepared from non-ionic siliconized surfactants, sorbitan derivatives and co-surfactants such as polyglyceryl derivatives. Physical stability was determined by microscopic examination, centrifugation and incubating emulsions in different temperatures. Vitamin C in vitro release studies from O/W and O/W/O emulsions were conducted using Franz diffusion cell (at room temperature) and UV spectrophotometry. The results showed that in the first four-hour period, about 14% of vitamin C released from O/W/O emulsions. It appears that in multiple emulsions the profile of release follows zero-order kinetics. Our data indicate that incorporating vitamin C in multiple emulsions significantly increased its stability possibly attributed to the formation of reverse micelles of surfactants (and/or co-surfactants), which entrapped vitamin C inside the micelles surrounded by hydrophilic heads of surfactant. Moreover, vitamin C was released from multiple emulsions in a zero order slow and controlled release manner.
Characterization of C3dg Binding to a Recess Formed Between Short Consensus Repeats 1 and 2 of Complement Receptor Type 2 (CR2; CD21) (1998)

To allow for a better characterization of the ligand binding structures of human complement receptor type 2 (CR2; CD21), we have established an IgG1 kappa mouse mAb, FE8, that interferes efficiently with binding of C3dg and EBV to CR2. In contrast to mAb OKB7, the only well-characterized mAb with similar specificity, mAb FE8 blocked binding of soluble C3dg or particles carrying multiple copies of surface-bound C3dg to CR2 or induced complete removal of these ligands from the receptor. In vitro EBV infection of B lymphocytes, on the other hand, was abrogated by mAbs FE8 and OKB7 with similar dose-response characteristics. As FE8 was shown to recognize a discontinuous epitope, a series of overlapping peptides derived from SCR1 and -2 and immobilized on cellulose was screened with FE8. The results suggest that up to five discontinuous sequences contributed to the epitope. The sequence 63-EYFNKYS-69, located between the two SCR units, reacted most intensively. Two other sequences, 16-YYSTPI-21 and 105-NGNKSVWCQANN-116, are located between Cys1 and Cys2 of SCR1 and around Cys3 of SCR2, respectively. Based on the solution structure for two factor H SCRs, a three-dimensional model of SCR1 and -2 was generated. The FE8 binding peptide sequences were located in relative proximity to each other, bounding the recess formed between SCR1 and -2. This potential of mAb FE8 is currently unique and may be exploited for interfering with conditions of unwanted recognition of C3dg-coated structures by the immune system.
Anti-idiotype as antibody against the formyl peptide chemotaxis receptor of the neutrophil. (1982)

Anti-idiotypic antibodies have been produced in mice, guinea pigs, and goat against rabbit antibodies to the chemoattractant f Met-Leu-Phe. The anti-idiotypic antibodies were demonstrated by their capacity in the presence of preimmune rabbit serum to block the binding of 125I anti-f Met-Leu-Phe to f Met-Leu-Phe-human transferrin absorbed to microtiter plates. Goat anti-idiotypic antibodies were further demonstrated by their ability, when absorbed to Staphylococcus aureus, to selectively bind 125I anti-f Met-Leu-Phe. In addition, some of the goat anti-idiotypic IgG was able to bind nearly all rabbit and rat anti-f Met-Leu-Phe antibodies examined. This was shown by 1) the ability of antibodies produced in rabbits immunized with either f Met-Leu-Phe conjugated to goat IgG or f Met-Leu-Phe conjugated to keyhole limpet hemocyanin (KLH) when adsorbed to S. aureus to bind the 125I F(ab')2 goat anti-idiotype, and 2) the ability of various rat anti-f Met-Leu-Phe antibodies to block the binding of 125I rabbit anti-f Met-Leu-Phe to goat anti-idiotype absorbed to S. aureus. Finally, goat anti-idiotypic antibodies can also cross-react with the receptor on the rabbit neutrophil for the formyl peptides as evidenced by 1) the direct binding of goat anti-idiotypic IgG to the PMN, 2) the ability of F(ab')2 fragments to goat anti-idiotype to partially inhibit the binding of f Met-Leu-(3H)Phe to rabbit PMN, and 3) loss of anti-idiotype and anti-PMN receptor activity after passage over an anti-f Met-Leu-Phe column. These data support Jerne's hypothesis of "internal image" and suggest a feasible experimental approach for producing anti-cell receptor antibody without purifying the receptor.