gebhart/patrepeval huggingface dataset:
Differential structural requirements of heparin and heparan sulfate proteoglycans that promote binding of basic fibroblast growth factor to its receptor. (1994)

Heparan sulfate proteoglycans (HSPG) are obligatory for receptor binding and mitogenic activity of basic fibroblast growth factor (bFGF). The capacity of various species of heparin and heparan sulfate (HS) to promote bFGF receptor binding was investigated using both Chinese hamster ovary mutant cells deficient in cell surface HSPG and a soluble bFGF receptor-alkaline phosphatase fusion protein. Highly sulfated oligosaccharides were more effective than medium and low sulfate fractions of the same size oligosaccharide. O-Sulfation in heparin was found to be critical for its capacity to promote binding of bFGF to its receptors. The highest level of bFGF-receptor binding was achieved in the presence of over-sulfated heparin fragments (% sulfur > 14) regardless of whether the N-position was sulfated or acetylated. Unlike receptor binding of bFGF which requires oligosaccharides containing at least 8-10 sugar units, displacement of heparin- or HS-bound bFGF was obtained by oligosaccharides containing as little as four sugar units and by an N-sulfated, O-desulfated heparin fragment (% sulfur = 5.3). A preparation of total cell surface-derived HS induced bFGF receptor binding. A preliminary survey of several defined and affinity purified species of cell surface HSPG, including syndecan, fibroglycan, and glypican failed to identify natural HSPG that promote high affinity receptor binding of bFGF. A similar lack of activity was observed with species of HS isolated from bovine arterial tissue and characterized for their effect on vascular smooth muscle cell proliferation. Moreover, most of these species of HS inhibited in a dose-dependent manner the restoration of bFGF-receptor binding induced by heparin or by total HSPG. These results suggest the involvement of defined heparin-like oligosaccharide sequences and unique species of cell surface and extracellular matrix HS in the regulation of bFGF receptor binding and biological activity.
Immunomodulatory β-Glucan from Lentinus edodes Activates Mitogen-activated Protein Kinases and Nuclear Factor-κB in Murine RAW 264.7 Macrophages (2011)

Lentinan, a cell wall β-glucan from the fruiting bodies of Lentinus edodes, is well known to be a biological defense modifier, but the signal transduction pathway(s) induced by Lentinan have not been elucidated. In this study, we extracted Lentinan (LNT-S) by ultrasonication from Lentinus edodes and report that, in murine RAW 264.7 macrophages, LNT-S glucan activated NF-κB p65 and triggered its nuclear translocation as determined by Western blotting. Moreover, LNT-S enhanced NF-κB-luciferase activity in the Dual-Luciferase gene system assay. Its upstream signaling molecules, MAPKs such as ERK1/2 and JNK1/2, were shown to be activated by assessing the level of phosphorylation in a time- and concentration-dependent manner, but its downstream proinflammatory enzyme, inducible NOS, was not observed. The data evaluated using a TNF-α ELISA kit and Griess reagent further demonstrated that no proinflammatory mediators such as TNF-α and NO were produced by LNT-S stimulation in RAW 264.7 cells. In contrast, LPS significantly induced inducible NOS expression and increased NO and TNF-α production, which are associated with activation of the NF-κB p65/p50 heterodimer complex. It is possible that LNT-S did not activate NF-κB p65/p50, and the activation of NF-κB p65 was not sufficient to stimulate cytokine production. These data demonstrate that LNT-S glucan carries out its immunomodulating activity by activating MAPK signaling pathways without secretion of TNF-α and NO.
Tomoregulin-1 (TMEFF1) inhibits nodal signaling through direct binding to the nodal coreceptor Cripto (2003)

Transforming growth factor beta (TGF-beta) signals regulate multiple processes during development and in adult. We recently showed that tomoregulin-1 (TMEFF1), a transmembrane protein, selectively inhibits nodal but not activin in early Xenopus embryos. Here we report that TMEFF1 binds to the nodal coreceptor Cripto, but does not associate with either nodal or the type I ALK (activin receptor-like kinase) 4 receptor in coimmunoprecipitation assays. The inhibition of the nodal signaling by TMEFF1 in Xenopus ectodermal explants is rescued with wild-type but not mutant forms of Cripto. Furthermore, we show that the Cripto-FRL1-Cryptic (CFC) domain in Cripto, which is essential for its binding to ALK4, is also important for its interaction with TMEFF1. Our results demonstrate for the first time that nodal signaling can be regulated by a novel mechanism of blocking the Cripto coreceptor.
O-GlcNAc and neurodegeneration: biochemical mechanisms and potential roles in Alzheimer's disease and beyond (2014)

Alzheimer disease (AD) is a growing problem for aging populations worldwide. Despite significant efforts, no therapeutics are available that stop or slow progression of AD, which has driven interest in the basic causes of AD and the search for new therapeutic strategies. Longitudinal studies have clarified that defects in glucose metabolism occur in patients exhibiting Mild Cognitive Impairment (MCI) and glucose hypometabolism is an early pathological change within AD brain. Further, type 2 diabetes mellitus (T2DM) is a strong risk factor for the development of AD. These findings have stimulated interest in the possibility that disrupted glucose regulated signaling within the brain could contribute to the progression of AD. One such process of interest is the addition of O-linked N-acetylglucosamine (O-GlcNAc) residues onto nuclear and cytoplasmic proteins within mammals. O-GlcNAc is notably abundant within brain and is present on hundreds of proteins including several, such as tau and the amyloid precursor protein, which are involved in the pathophysiology AD. The cellular levels of O-GlcNAc are coupled to nutrient availability through the action of just two enzymes. O-GlcNAc transferase (OGT) is the glycosyltransferase that acts to install O-GlcNAc onto proteins and O-GlcNAcase (OGA) is the glycoside hydrolase that acts to remove O-GlcNAc from proteins. Uridine 5'-diphosphate-N-acetylglucosamine (UDP-GlcNAc) is the donor sugar substrate for OGT and its levels vary with cellular glucose availability because it is generated from glucose through the hexosamine biosynthetic pathway (HBSP). Within the brains of AD patients O-GlcNAc levels have been found to be decreased and aggregates of tau appear to lack O-GlcNAc entirely. Accordingly, glucose hypometabolism within the brain may result in disruption of the normal functions of O-GlcNAc within the brain and thereby contribute to downstream neurodegeneration. While this hypothesis remains largely speculative, recent studies using different mouse models of AD have demonstrated the protective benefit of pharmacologically increased brain O-GlcNAc levels. In this review we summarize the state of knowledge in the area of O-GlcNAc as it pertains to AD while also addressing some of the basic biochemical roles of O-GlcNAc and how these might contribute to protecting against AD and other neurodegenerative diseases.
Chromatin loops are selectively anchored using scaffold/matrix-attachment regions (2004)

The biological significance of nuclear scaffold/matrix-attachment regions (S/MARs) remains a topic of long-standing interest. The key to understanding S/MAR behavior relies on determining the physical attributes of in vivo S/MARs and whether they serve as rigid or flexible chromatin loop anchors. To analyze S/MAR behavior, single and multiple copies of the S/MAR-containing constructs were introduced into various host genomes of transgenic mice and transfected cell lines. These in vivo integration events provided a system to study the association and integration patterns of each introduced S/MAR. By utilizing FISH to visualize directly the localization of S/MARs on the nuclear matrix or chromatin loop, we were able to assign specific attributes to the S/MAR. Surprisingly, when multiple-copy S/MARs were introduced they were selected and used as nuclear matrix anchors in a discriminatory manner, even though they all contained identical primary sequences. This selection process was probably mediated by S/MAR availability including binding strength and copy number, as reflected by the expression profiles and association of multi-copy tandem inserted constructs. Whereas S/MARs functioned as the mediators of loop attachment, they were used in a selective and dynamic fashion. Consequently, S/MAR anchors were necessary but not sufficient for chromatin loops to form. These observations reconcile many seemingly contradictory attributes previously associated with S/MARs.
Polymer-bound oxime esters as supports for solid-phase peptide synthesis. The preparation of protected peptide fragments (1980)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPolymer-bound oxime esters as supports for solid-phase peptide synthesis. The preparation of protected peptide fragmentsWilliam F. DeGrado and Emil Thomas KaiserCite this: J. Org. Chem. 1980, 45, 7, 1295–1300Publication Date (Print):March 1, 1980Publication History Published online1 May 2002Published inissue 1 March 1980https://pubs.acs.org/doi/10.1021/jo01295a026https://doi.org/10.1021/jo01295a026research-articleACS PublicationsRequest reuse permissionsArticle Views1399Altmetric-Citations225LEARN 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
Learning a Convolutional Neural Network for Image Compact-Resolution (2018)

We study the dual problem of image super-resolution (SR), which we term image compact-resolution (CR). Opposite to image SR that hallucinates a visually plausible high-resolution image given a low-resolution input, image CR provides a low-resolution version of a high-resolution image, such that the low-resolution version is both visually pleasing and as informative as possible compared to the high-resolution image. We propose a convolutional neural network (CNN) for image CR, namely, CNN-CR, inspired by the great success of CNN for image SR. Specifically, we translate the requirements of image CR into operable optimization targets for training CNN-CR: the visual quality of the compact resolved image is ensured by constraining its difference from a naively downsampled version and the information loss of image CR is measured by upsampling/super-resolving the compact-resolved image and comparing that to the original image. Accordingly, CNN-CR can be trained either separately or jointly with a CNN for image SR. We explore different training strategies as well as different network structures for CNN-CR. Our experimental results show that the proposed CNN-CR clearly outperforms simple bicubic downsampling and achieves on average 2.25 dB improvement in terms of the reconstruction quality on a large collection of natural images. We further investigate two applications of image CR, i.e., low-bit-rate image compression and image retargeting. Experimental results show that the proposed CNN-CR helps achieve significant bits saving than High Efficiency Video Coding when applied to image compression and produce visually pleasing results when applied to image retargeting.
Overview of Drug Discovery and Development (2006)

This overview unit describes the core activities involved in the drug discovery and development process, from target identification - including preclinical biology, medicinal and process chemistry - to pharmacokinetics and metabolism (ADME), and also activities related to the to the drug approval process. The latter include the activities related to the filing of an IND (Investigational New Drug) application and also Phases I - III of clinical trials that form the basis of an NDA (New Drug Application) submission, as well as post-marketing Phase IV activities as required by the U.S. Food and Drug Administration (FDA) and the European and Japanese counterparts.
Implosion dynamics measurements at the National Ignition Facility (2012)

Measurements have been made of the in-flight dynamics of imploding capsules indirectly driven by laser energies of 1–1.7 MJ at the National Ignition Facility [Miller et al., Nucl. Fusion 44, 228 (2004)]. These experiments were part of the National Ignition Campaign [Landen et al., Phys. Plasmas 18, 051002 (2011)] to iteratively optimize the inputs required to achieve thermonuclear ignition in the laboratory. Using gated or streaked hard x-ray radiography, a suite of ablator performance parameters, including the time-resolved radius, velocity, mass, and thickness, have been determined throughout the acceleration history of surrogate gas-filled implosions. These measurements have been used to establish a dynamically consistent model of the ablative drive history and shell compressibility throughout the implosion trajectory. First results showed that the peak velocity of the original 1.3-MJ Ge-doped polymer (CH) point design using Au hohlraums reached only 75% of the required ignition velocity. Several capsule, hohlraum, and laser pulse changes were then implemented to improve this and other aspects of implosion performance and a dedicated effort was undertaken to test the sensitivity of the ablative drive to the rise time and length of the main laser pulse. Changing to Si rather than Ge-doped inner ablator layers and increasing the pulse length together raised peak velocity to 93% ± 5% of the ignition goal using a 1.5 MJ, 420 TW pulse. Further lengthening the pulse so that the laser remained on until the capsule reached 30% (rather than 60%–70%) of its initial radius, reduced the shell thickness and improved the final fuel ρR on companion shots with a cryogenic hydrogen fuel layer. Improved drive efficiency was observed using U rather than Au hohlraums, which was expected, and by slowing the rise time of laser pulse, which was not. The effect of changing the Si-dopant concentration and distribution, as well as the effect of using a larger initial shell thickness were also examined, both of which indicated that instabilities seeded at the ablation front are a significant source of hydrodynamic mix into the central hot spot. Additionally, a direct test of the surrogacy of cryogenic fuel layered versus gas-filled targets was performed. Together all these measurements have established the fundamental ablative-rocket relationship describing the dependence of implosion velocity on fractional ablator mass remaining. This curve shows a lower-than-expected ablator mass at a given velocity, making the capsule more susceptible to feedthrough of instabilities from the ablation front into the fuel and hot spot. This combination of low velocity and low ablator mass indicates that reaching ignition on the NIF will require &amp;gt;20 μm (∼10%) thicker targets and laser powers at or beyond facility limits.
Hypoxia-inducible factor 1α is up-regulated by oncostatin M and participates in oncostatin M signaling # (2009)

HIF1alpha levels increase significantly after treatment of hepatocytes and hepatoma cells with OSM, and HIF1alpha contributes to OSM downstream signaling events, pointing to a cross-talk between cytokine and hypoxia signaling in processes such as liver development and regeneration.
Surface‐enhanced Raman scattering of CO2 dissolved in aqueous colloidal solutions of silver and gold (1995)

Abstract The observation of surface‐enhanced Raman scatterings (SERS) from CO 2 molecules dissolved in aqueous solutions of silver and gold colloids measured with 850 nm near‐IR excitation is reported. Different types of surface enhancement and surface‐enhanced Raman spectra were observed. The SERS spectrum of CO 2 on colloidal gold is in good agreement with the spectrum of CO 2 dissolved in water. Two different types of SERS spectra were found for CO 2 on colloidal silver. They can be assigned to physisorbed and/or weakly chemisorbed CO 2 molecules and to strongly bonded CO 2 ‐ negatively charged surface radicals, respectively. The enhancement factor for the stretching mode of carbon dioxide is estimated to be of the order of 10 2 −10 4 , depending on the kinds of metal and types of adsorption, which demonstrates that SERS on colloidal silver or gold particles in solution offers possibilities for detecting CO 2 dissolved in liquids at low concentrations.
Normal Anatomy and Imaging of the Hip: Emphasis on Impingement Assessment (2013)

A comprehensive knowledge of normal hip anatomy and imaging techniques is essential in the evaluation and assessment of the patient with hip pain. This article reviews the osseous, soft tissue, and vascular components of the hip and the normal anatomical variants encountered in routine hip imaging. Basic and advanced hip imaging is discussed with particular emphasis on radiographic and computed tomography measurements and their utility in evaluating patients with developmental hip dysplasia and femoroacetabular impingement syndrome.
Entity Disambiguation for Knowledge Base Population (2010)

The integration of facts derived from information extraction systems into existing knowledge bases requires a system to disambiguate entity mentions in the text. This is challenging due to issues such as non-uniform variations in entity names, mention ambiguity, and entities absent from a knowledge base. We present a state of the art system for entity disambiguation that not only addresses these challenges but also scales to knowledge bases with several million entries using very little resources. Further, our approach achieves performance of up to 95% on entities mentioned from newswire and 80% on a public test set that was designed to include challenging queries.
Investigation into an Alternating Multilayer Film of Poly(4-Vinylpyridine) and Poly(acrylic acid) Based on Hydrogen Bonding (1999)

A new approach for the fabrication of a multilayer film assembly is explored, which is based on the alternating assembling of poly(4-vinylpyridine) and poly(acrylic acid) via hydrogen bonding. The homogeneous multilayer films were characterized by UV−vis and X-ray diffraction measurements. The control of layer thickness was studied in detail via adjustment of the molecular weight and concentration of poly(4-vinylpyridine) solution. The nature of the interaction between the two polymers was identified as hydrogen bonding by IR spectroscopy.
Photoluminescent Arrays of Nanopatterned Monolayer MoS2 (2017)

Abstract Monolayer 2D MoS 2 grown by chemical vapor deposition is nanopatterned into nanodots, nanorods, and hexagonal nanomesh using block copolymer (BCP) lithography. The detailed atomic structure and nanoscale geometry of the nanopatterned MoS 2 show features down to 4 nm with nonfaceted etching profiles defined by the BCP mask. Atomic resolution annular dark field scanning transmission electron microscopy reveals the nanopatterned MoS 2 has minimal large‐scale crystalline defects and enables the edge density to be measured for each nanoscale pattern geometry. Photoluminescence spectroscopy of nanodots, nanorods, and nanomesh areas shows strain‐dependent spectral shifts up to 15 nm, as well as reduction in the PL efficiency as the edge density increases. Raman spectroscopy shows mode stiffening, confirming the release of strain when it is nanopatterned by BCP lithography. These results show that small nanodots (≈19 nm) of MoS 2 2D monolayers still exhibit strong direct band gap photoluminescence (PL), but have PL quenching compared to pristine material from the edge states. This information provides important insights into the structure–PL property correlations of sub‐20 nm MoS 2 structures that have potential in future applications of 2D electronics, optoelectronics, and photonics.
Olefin homologation with titanium methylene compounds (1978)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTOlefin homologation with titanium methylene compoundsF. N. Tebbe, G. W. Parshall, and G. S. ReddyCite this: J. Am. Chem. Soc. 1978, 100, 11, 3611–3613Publication Date (Print):May 1, 1978Publication History Published online1 May 2002Published inissue 1 May 1978https://doi.org/10.1021/ja00479a061RIGHTS & PERMISSIONSArticle Views7742Altmetric-Citations888LEARN 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 InReddit PDF (389 KB) Get e-Alerts Get e-Alerts
Chaos control by using Motor Maps (2002)

In this paper a new method for chaos control is proposed, consisting of an unsupervised neural network, namely a Motor Map. In particular a feedback entrainment scheme is adopted: a chaotic system with a given parameter set generates the reference trajectory for another chaotic system with different parameters to be controlled: the Motor Map is required to provide the appropriate time-varying gain value for the feedback signal. The state of the controlled system is considered as input to the Motor Map. Particular efforts have been paid to the feasibility of the implementation. Indeed, the simulations performed have been oriented to design a Motor Map suitable for an hardware realization, thus some restrictive hypotheses, such as for example a low number of neurons, have been assumed. A huge number of simulations has been carried out by considering as system to be controlled a Double Scroll Chua Attractor as well as other chaotic attractors. Several reference trajectories have also been considered: a limit cycle generated by a Chua's circuit with different parameters values, a double scroll Chua attractor, a chaotic attractor of the family of the Chua's circuit attractors. In all the simulations instead of controlling the whole state space, only two state variables have been fed back. Good results in terms of settling time (namely, the period in which the map learns the control task) and steady state errors have been obtained with a few neurons. The Motor Map based adaptive controller offers high performances, specially in the case when the reference trajectory is switched into another one. In this case, a specialization of the neurons constituting the Motor Map is observed: while a group of neurons learns the appropriate control law for a reference trajectory, another group specializes itself to control the system when the other trajectory is used as a reference. A discrete components electronic realization of the Motor Map is presented and experimental results confirming the simulation results are shown. (c) 2002 American Institute of Physics.