gebhart/patrepeval huggingface dataset:
Silicon thermooptical micromodulator with 700-kHz -3-dB bandwidth (1995)

A silicon Fabry-Perot waveguide modulator, operating at the fiber optic communication wavelengths of 1.3 and 1.55 μm, has been entirely fabricated using microelectronic techniques. The planar optical cavity has been defined by plasma etching and has a length of 100 μm. The device, based on the thermooptic effect, is electrically driven and exhibits a maximum modulation depths of 60%. The measured -3 dB bandwidth is 700 kHz, which is by far the best result ever reported, to our knowledge, for thermooptic effect based modulators.
Tangible interaction + graphical interpretation (2000)

Construction toys are a superb medium for geometric models. We argue that such toys, suitably instrumented or sensed, could be the inspiration for a new generation of easy-to-use, tangible modeling systems—especially if the tangible modeling is combined with graphical-interpretation techniques for enhancing nascent models automatically. The three key technologies needed to realize this idea are embedded computation, vision-based acquisition, and graphical interpretation. We sample these technologies in the context of two novel modeling systems: physical building blocks that self-describe, interpret, and decorate the structures into which they are assembled; and a system for scanning, interpreting, and animating clay figures.
Sequence of a cDNA clone encoding the zinc metalloproteinase hemorrhagic toxin e from Crotalus atrox: evidence for signal, zymogen and disintegrin-like structures (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSequence of a cDNA clone encoding the zinc metalloproteinase hemorrhagic toxin e from Crotalus atrox: evidence for signal, zymogen and disintegrin-like structuresLawrence A. Hite, John D. Shannon, Jon B. Bjarnason, and Jay W. FoxCite this: Biochemistry 1992, 31, 27, 6203–6211Publication Date (Print):July 1, 1992Publication History Published online1 May 2002Published inissue 1 July 1992https://pubs.acs.org/doi/10.1021/bi00142a005https://doi.org/10.1021/bi00142a005research-articleACS PublicationsRequest reuse permissionsArticle Views156Altmetric-Citations119LEARN 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
A loop-free extended Bellman-Ford routing protocol without bouncing effect (1989)

Distributed algorithms for shortest-path problems are important in the context of routing in computer communication networks. We present a protocol that maintains the shortest-path routes in a dynamic topology, that is, in an environment where links and nodes can fail and recover at arbitrary times. The novelty of this protocol is that it avoids the bouncing effect and the looping problem that occur in the previous approaches of the distributed implementation of Bellman-Ford algorithm. The bouncing effect refers to the very long duration for convergence when failures happen or weights increase, and the nonterminating exchanges of messages, or counting-to-infinity behavior, in disconnected components of the network resulting from failures. The looping problems cause data packets to circulate and, thus, waste bandwidth. These undesirable effects are avoided without any increase in the overall message complexity of previous approaches required in the connected part of the network. The time complexity is better than the distributed Bellman-Ford algorithm encountering failures. The key idea in the implementation is to maintain only loop-free paths, and search for the shortest path only from this set.
Influence of structural variation on nuclear localization of DNA-binding polyamide-fluorophore conjugates (2004)

A pivotal step forward in chemical approaches to controlling gene expression is the development of sequence-specific DNA-binding molecules that can enter live cells and traffic to nuclei unaided. DNA-binding polyamides are a class of programmable, sequence-specific small molecules that have been shown to influence a wide variety of protein-DNA interactions. We have synthesized over 100 polyamide-fluorophore conjugates and assayed their nuclear uptake profiles in 13 mammalian cell lines. The compiled dataset, comprising 1300 entries, establishes a benchmark for the nuclear localization of polyamide-dye conjugates. Compounds in this series were chosen to provide systematic variation in several structural variables, including dye composition and placement, molecular weight, charge, ordering of the aromatic and aliphatic amino-acid building blocks and overall shape. Nuclear uptake does not appear to be correlated with polyamide molecular weight or with the number of imidazole residues, although the positions of imidazole residues affect nuclear access properties significantly. Generally negative determinants for nuclear access include the presence of a beta-Ala-tail residue and the lack of a cationic alkyl amine moiety, whereas the presence of an acetylated 2,4-diaminobutyric acid-turn is a positive factor for nuclear localization. We discuss implications of these data on the design of polyamide-dye conjugates for use in biological systems.
Characterization of the progressive growth of columns by excimer laser irradiation of silicon (1999)

The growth mechanism of columns produced by excimer laser irradiation of a silicon target is investigated. The micrometric columns are formed by a cumulative process with well-defined steps. The first steps lead to silicon hillocks, which evolve to columns through a little-understood mechanism. To investigate it, we irradiated a Si(100) single crystal in air with the necessary pulses of an excimer laser beam to obtain two samples, one with a partially and one with a fully developed column structure. Then we alternated scanning electron microscopy observations with irradiation pulses on the same target area. The progressive evolution of the laser-generated structures is presented. Columns grow at notably high rates, from around 0.5 μm/pulse during the early stages to 0.2 μm/pulse on average for 10–20 μm tall columns. The experimental results lead us to suggest a hydrodynamic growth mechanism.
Anatomical Changes and Immunolocalization of Cellulase during Abscission as Observed on Nitrocellulose Tissue Prints (1990)

A fundamental event in abscission is the breakdown of cell wall material in a discrete zone of cells known as the separation layer. Three dimensional images produced by viewing tissue prints of abscission zones on nitrocellulose (NC) membranes with incident illumination showed changes in the tissue integrity taking place in the separation layer as the process of abscission proceeded. The cell softening which occurs due to the dissolution of the cell wall appeared in the tissue prints as a diffuse line at the anatomical transition between the pulvinus and petiole and was easily observed on NC tissue prints of either longitudinal or serial cross-sections through abscission zones. In bean leaf abscission the dissolution of cell walls has been correlated with the appearance of a form of cellulase with an isoelectric point of pH 9.5. Antibodies specific for this enzyme were used to study the localization of 9.5 cellulase in the distal abscission zone of Phaseolus vulgaris L., cv Red Kidney after tissue printing on NC. It was found that 9.5 cellulase was localized in the separation layer but also occurred in the vascular tissue of the adjacent pulvinus. No antibody binding was observed in nonabscising tissue or preimmune controls. These results confirm previous biochemical studies and demonstrate that immunostaining of nitrocellulose tissue prints is a fast and reliable method to localize proteins or enzymes in plant tissue.
Complex genetic contribution of the Apo AI-CIII-AIV gene cluster to familial combined hyperlipidemia. Identification of different susceptibility haplotypes. (1997)

Familial combined hyperlipidemia (FCH) is a common genetic lipid disorder in Western societies. In a recent report (Dallinga-Thie, G.M., X.D. Bu, M. van Linde-Sibenius Trip, J.I. Rotter, A.J. Lusis, and T.W.A. de Bruin. J. Lipid Res., 1996, 36:136-147) we have studied three restriction enzyme polymorphisms: XmnI, and MspI sites 5' of the apo AI gene and SstI site in the 3' untranslated region of exon 4 of the apo CIII gene in 18 FCH pedigrees, including 18 probands, 178 hyperlipidemic relatives, 210 normolipidemic relatives, and 176 spouses. DNA variations in the apo AI-CIII-AIV gene cluster had a modifying effect on plasma triglycerides, LDL cholesterol, and apolipoprotein CIII levels. In this study, combinations of haplotypes were analyzed to further characterize their interactions and effect on the expression of severe hyperlipidemia in FCH subjects. A specific combination of haplotypes with one chromosome carrying the X1M1S2 (1-1-2) haplotype and the other the X2M2S1 haplotype (2-2-1) was significantly more frequent in hyperlipidemic relatives (6%) than in normolipidemic relatives (3%) and spouses (0.5%). Associated with this combination of haplotypes were significantly elevated plasma cholesterol (P < 0.0001), triglycerides (P < 0.0001), and apo CIII (P < 0.001) levels when compared to the wild type combination of haplotypes 1-1-1/1-1-1. The only spouse with this specific combination of haplotypes showed a severe hyperlipidemic phenotype, similar to FCH. Furthermore, nonparametric sibpair linkage analysis revealed significant linkage between these markers in the gene cluster and the FCH phenotype (MspI P = 0.0088, SstI P = 0.044, and XMS haplotype P = 0.037). The present findings confirm that the apo AI-CIII-IV gene cluster contributes to the FCH phenotype, but this contribution is genetically complex. An epistatic interaction between different haplotypes of the gene cluster was demonstrated. The S2 allele on one haplotype was synergistic to the X2M2 allele on the other haplotype in its hyperlipidemic effect. Therefore, two different susceptibility loci exist in the gene cluster, demonstrating the paradigm of complex genetic contribution to FCH.
phyA dominates in transduction of red‐light signals to rapidly responding genes at the initiation of Arabidopsis seedling de‐etiolation (2006)

Contrary to expectations based on the visible phenotypic behavior of seedlings undergoing de-etiolation in response to continuous red light (Rc), previous gene expression profiling showed that one or more of the five-membered phytochrome (phy) family of Arabidopsis, other than phyB, is predominantly responsible for transducing the Rc signals to light-responsive genes. To begin to identify which phys are involved, and to define potential primary targets of phy signaling, we have examined the genome-wide expression profiles of genes responding to Rc within 1 h (early response genes) of initial exposure of dark-grown wild-type, phyA, phyB and phyAphyB double mutant seedlings to the light signal. The data show that phyA has a quantitatively dominant role in Rc-induced expression of these early response genes, that phyB has minimal detectable regulatory activity in the presence of phyA, but assumes a quantitatively larger role in its absence, and that phyA and phyB combined are responsible for the full extent of Rc responsiveness of 96% of these genes. No evidence was obtained of a significant role for the remaining family members, phyC, phyD or phyE, in this process. In striking contrast, Rc-imposed repression of early response gene expression remains quantitatively strong in the phyAphyB double mutant, as well as the monogenic mutants, suggesting a significant role for one or more of the other three phys in this response. Examination of the established or predicted functional roles of the early response genes indicates that genes encoding transcription factors represent the largest single category, at a frequency three times their prevalence genome-wide. This dominance is particularly striking among those genes responding most robustly to the Rc signal, where >50% are classified as involved in transcriptional regulation, suggesting that these may have potentially primary regulatory roles at the interface between phy signaling and the light-responsive transcriptional network. Integration of the present data with those of a previous genome-scale transcriptional analysis of a pif3 mutant, suggests a complex network involving perception and transduction of inductive Rc signals by both phyA and phyB through both PIF3 and other undefined signaling partners to early response genes.
Synthesis, Phase Behavior, and Curing Studies of Bisacetylene Rigid-Rod Thermosets (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis, Phase Behavior, and Curing Studies of Bisacetylene Rigid-Rod ThermosetsElliot P. Douglas, David A. Langlois, and Brian C. BenicewiczCite this: Chem. Mater. 1994, 6, 11, 1925–1933Publication Date (Print):November 1, 1994Publication History Published online1 May 2002Published inissue 1 November 1994https://pubs.acs.org/doi/10.1021/cm00047a007https://doi.org/10.1021/cm00047a007research-articleACS PublicationsRequest reuse permissionsArticle Views220Altmetric-Citations50LEARN 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
Carbon supply for storage-product synthesis in developing seeds of oilseed rape (2000)

The aim of this work was to find out how the sugars in the endosperm of oilseed rape contribute to the flux of oil synthesis. While the hexose content of the liquid endosperm decreased during development the sucrose content increased. It is important to understand the relative rates of use of the endosperm sugars for two reasons. Firstly we need to know which sugars are used, and at what stages in development, in order to understand the roles of enzymes involved in their metabolism. Secondly, changes in sugar concentration have been implicated in the regulation of expression of genes determining storage-product synthesis [see Weber, Borisjuk and Wobus (1997) Trends Plant Sci. 2, 169–174, for review]. The rate of consumption of sugar is one factor governing its concentration. We present data showing both the concentration-dependence of conversion of sugar to oil, and the in vivo concentrations of sugars; we relate these data sets to each other and discuss the effects of the intracellular pool of sucrose. Glucose, fructose and sucrose are all substrates for oil synthesis, but the rates of their use (particularly sucrose) are underestimated because of dilution by sucrose from the intracellular pool.
Benzyloxazolidine-2,4-diones as potent hypoglycemic agents (1991)

A series of benzyloxazolidine-2,4-diones, containing oxazole-based side chains, were found to lower blood glucose levels in the genetically obese ob/ob mouse. Incorporation of a benzofuran structural element in these compounds provides greatly enhanced in vivo potency. The syntheses and structure-activity relationships for this series are detailed.
Methods for sequence and structural analysis of B and T cell receptor repertoires (2020)

B cell receptors (BCRs) and T cell receptors (TCRs) make up an essential network of defense molecules that, collectively, can distinguish self from non-self and facilitate destruction of antigen-bearing cells such as pathogens or tumors. The analysis of BCR and TCR repertoires plays an important role in both basic immunology as well as in biotechnology. Because the repertoires are highly diverse, specialized software methods are needed to extract meaningful information from BCR and TCR sequence data. Here, we review recent developments in bioinformatics tools for analysis of BCR and TCR repertoires, with an emphasis on those that incorporate structural features. After describing the recent sequencing technologies for immune receptor repertoires, we survey structural modeling methods for BCR and TCRs, along with methods for clustering such models. We review downstream analyses, including BCR and TCR epitope prediction, antibody-antigen docking and TCR-peptide-MHC Modeling. We also briefly discuss molecular dynamics in this context.
Scattering reduction at near-infrared frequencies using plasmonic nanostructures (2013)

Novel fabrication, detection and analysis approaches were employed to experimentally demonstrate scattering reduction by a plasmonic nanostructure operating at 1550 nm. The nanostructure consisted of a silicon nanorod surrounded by a plasmonic metamaterial cover comprised of eight gold nanowires and was fabricated by a combination of electron beam lithography, focused ion beam milling and dry and wet etching. The optical standing wave pattern of the device in the near-field was obtained using heterodyne near-field scanning optical microscopy. It was found that the spatial curvature of the interference fringes of the optical standing wave pattern was directly related to the scattering reduction of the device. The experiments were in excellent agreement with the theoretical predictions and suggested that the device reduced the scattering by 9.5 dB when compared to a bare silicon nanorod of diameter 240 nm and by 6 dB when compared to a bare silicon nanorod of diameter 160 nm.
<title>Holographic optical element (HOE) imaging in DuPont holographic photopolymers</title> (1994)

DuPont holographic photopolymers have been used to fabricate high quality holographic optical elements. The wide spectral sensitivity possible in these materials allows imaging near the desired HOE playback conditions. Multicolor imaging with ion and dye lasers using these materials is discussed. Mastering materials and methods are described for reflection and transmission HOE replication. HOE performance is compared to performance predicted by coupled- wave theory and HOE applications using these materials are described.
SOME REACTIONS OF ATOMIC HYDROGEN (1929)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSOME REACTIONS OF ATOMIC HYDROGENH. C. Urey and G. I. LavinCite this: J. Am. Chem. Soc. 1929, 51, 11, 3286–3290Publication Date (Print):November 1, 1929Publication History Published online1 May 2002Published inissue 1 November 1929https://pubs.acs.org/doi/10.1021/ja01386a016https://doi.org/10.1021/ja01386a016research-articleACS PublicationsRequest reuse permissionsArticle Views71Altmetric-Citations7LEARN 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
The Transcriptional Specificity of NF-κB Dimers Is Coded within the κB DNA Response Elements (2012)

Nuclear factor κB (NF-κB) regulates gene expression by binding to specific DNA elements, known collectively as κB sites, that are contained within the promoters/enhancers of target genes. We found that the identity of the central base pair (bp) of κB sites profoundly affects the transcriptional activity of NF-κB dimers. RelA dimers prefer an A/T bp at this position for optimal transcriptional activation (A/T-centric) and discriminate against G/C-centric κB sites. The p52 homodimer, in contrast, activates transcription from G/C-centric κB sites in complex with Bcl3 but represses transcription from the A/T-centric sites. The p52:Bcl3 complex binds to these two classes of κB sites in distinct modes, permitting the recruitment of coactivator, corepressor, or both coactivator and corepressor complexes in promoters that contain G/C-, A/T-, or both G/C- and A/T-centric sites. Therefore, through sensing of bp differences within κB sites, NF-κB dimers modulate biological programs by activating, repressing, and altering the expression of effector genes.
Glycosylation Using a Thioglycoside and Methyl Trifluoro-Methanesulfonate. A New and Efficient Method for CIS and Trans Glycoside Formation (1987)

Abstract For the synthesis of large oligosaccharides and biologically active oligosaccharide derivatives it is often desirable to use a block synthesis, that is to link an oligosaccharide residue to another or to a non-carbohydrate aglycon. It is sometimes difficult to prepare glycosyl halide derivatives of the oligosaccharides in good yields, and there is a need for glycosylating agents which can be prepared under mild conditions and in good yields.