gebhart/patrepeval huggingface dataset:
Molecular Genetic Approaches II: Expression–Interaction Cloning (2003)

Expression-interaction cloning provides a powerful tool for the identificationx of proteins that interact with each other. The method described here is based on the overlay procedure, which was originally developed to identify proteins that interact with protein kinase C (PKC) (1). A number of variations of this method have been developed (2,3) and used successfully to clone and identify proteins that interact with PKC by expression library screening (4,5). The principle of this method is the immobilizing of potential binding proteins on nitrocellulose and overlaying PKC in the presence or absence of PKC activators, and the detection of any interaction using anti-PKC antibodies in immunological detection assays. This procedure can identify receptors for activated C kinase (RACKs) and/or PKC substrates. The method could easily be adapted to allow interaction cloning using a protein of interest other than PKC, provided a good source of purified protein or epitope tagged peptides and antibodies (as a means of detection) are available.
NMR structure and peptide hormone binding site of the first extracellular domain of a type B1 G protein-coupled receptor (2004)

The corticotropin-releasing factor (CRF) ligand family has diverse effects on the CNS, including the modulation of the stress response. The ligands' effects are mediated by binding to CRF G protein-coupled receptors. We have determined the 3D NMR structure of the N-terminal extracellular domain (ECD1) of the mouse CRF receptor 2beta, which is the major ligand recognition domain, and identified its ligand binding site by chemical-shift perturbation experiments. The fold is identified as a short consensus repeat (SCR), a common protein interaction module. Mutagenesis reveals the integrity of the hormone-binding site in the full-length receptor. This study proposes that the ECD1 captures the C-terminal segment of the ligand, whose N terminus then penetrates into the transmembrane region of the receptor to initiate signaling. Key residues of SCR in the ECD1 are conserved in the G protein-coupled receptor subfamily, suggesting the SCR fold in all of the ECD1s of this subfamily.
Compressive ghost imaging (2009)

We describe an advanced image reconstruction algorithm for pseudothermal ghost imaging, reducing the number of measurements required for image recovery by an order of magnitude. The algorithm is based on compressed sensing, a technique that enables the reconstruction of an N-pixel image from much less than N measurements. We demonstrate the algorithm using experimental data from a pseudothermal ghost-imaging setup. The algorithm can be applied to data taken from past pseudothermal ghost-imaging experiments, improving the reconstruction’s quality.
Identifying link farm spam pages (2005)

With the increasing importance of search in guiding today's web traffic, more and more effort has been spent to create search engine spam. Since link analysis is one of the most important factors in current commercial search engines' ranking systems, new kinds of spam aiming at links have appeared. Building link farms is one technique that can deteriorate link-based ranking algorithms. In this paper, we present algorithms for detecting these link farms automatically by first generating a seed set based on the common link set between incoming and outgoing links of Web pages and then expanding it. Links between identified pages are re-weighted, providing a modified web graph to use in ranking page importance. Experimental results show that we can identify most link farm spam pages and the final ranking results are improved for almost all tested queries.
Chromophore-Functionalized Gold Nanoparticles (2003)

We report in this Account the design of chromophore-functionalized metal nanoparticles and the detailed investigation of the ground- and excited-state interactions between the metal nanoparticles and the photoactive molecules. The methodologies adopted for organizing chromophore-functionalized gold nanoparticles on two-dimensional surfaces and the mechanistic details of various deactivation channels of the photoexcited chromophores, such as energy and electron transfer to the metal nanoparticle, are presented. The possible applications of such chromophore-functionalized gold nanoparticles in photovoltaics, light-mediated binding and release of biologically important molecules such as amino acid derivatives, and fluorescent display devices are described.
Word sense disambiguation for free-text indexing using a massive semantic network (1993)

Semantics-free, word-based information retrieval is thwarted by two complementary problems. First, search for relevant documents returns irrelevant items when all meanings of a search term are used, rather than just the meaning intended. This causes low precision. Second, relevant items are missed when they are indexed not under the actual search terms, but rather under related terms. This causes low recall. With semantics-free approaches there is generally no way to improve both precision and recall at the same time. Word sense disambiguation during document indexing should improve precision. We have investigated using the massive Word Net semantic network for disambigu at ion during indexing. With the unconstrained text of the SMART ret rieval environment, we have had to derive our own content description from the input text, given only part-ofspeech tagging of the input. We employ the notion of semantic distance between network nodes. Input text terms with multiple senses are disambiguated by finding the combination of senses from a set of contiguous terms which minimizes total pairwise dist ante between senses. Results so far have been encouraging. Improvement in disamblguation compared with chance is clear
Atrial natriuretic peptide regulates release of Na+-K+-ATPase inhibitor from rat brain (1988)

Tissue culture media from incubations of fragments of rat brain were collected and partially purified. These supernatants were effective in inhibiting the Na+-K+ pump as indicated by a 77% reduction of ouabain-sensitive 86Rb+ uptake into human erythrocytes. Release of the Na+-K+-ATPase inhibitor depended on the amount of tissue, the temperature, and the length of incubation. Atrial natriuretic peptide (ANP) injected intravenously, or included (10(-8) M) in the in vitro incubation of brain tissue, decreased the release of the Na+-K+-ATPase inhibitor by 74 and 42%, respectively. Control experiments using the neuropeptide arginine vasopressin showed no effect on release of the inhibitor. These studies indicate that ANP is capable of regulating the release from brain of a Na+-K+-ATPase inhibitor with similar chromatographic characteristics to the one previously obtained from extraction of bovine hypothalamus and raise the possibility that the two factors are interrelated in the regulation of fluid and electrolyte balance.
Theory of the<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mi>π</mml:mi></mml:math>-electron spin density due to the<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msup><mml:mrow><mml:mi mathvariant="normal">Cr</mml:mi></mml:mrow><mml:mrow><mml:mn>3</mml:mn><mml:mo>+</mml:mo></mml:mrow></mml:msup></mml:mrow></mml:math>ion and<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msup><mml:mrow><mml:mi mathvariant="normal">Cr</mml:mi></mml:mrow><mml:mrow><mml:mn>3</mml:mn><mml:mo>+</mml:mo></mml:mrow></mml:msup></mml:mrow></mml:math>ion pair in a cubic fluoride lattice (1979)

The theory of the $\ensuremath{\pi}$-electron spin density of the ${\mathrm{F}}^{\ensuremath{-}}$-ion site in the neighborhood of the ${\mathrm{Cr}}^{3+}$ ion, as in the octahedron ${\mathrm{Cr}}^{3+}$${\mathrm{F}}_{6}^{\ensuremath{-}}$, and the ${\mathrm{Cr}}^{3+}$-ion pair, ${\mathrm{Cr}}^{3+}$${\mathrm{F}}^{\ensuremath{-}}$${\mathrm{Cr}}^{3+}$, is developed from first principles by considering the transfer of $\ensuremath{\pi}$ electrons from the occupied orbitals of the ${\mathrm{F}}^{\ensuremath{-}}$ ion to the empty orbits on the ${\mathrm{Cr}}^{3+}$ ion. All the Hartree-Fock integrals of the kinetic energy and the Coulomb interactions are calculated as a function of interatomic separation. The ${\mathrm{F}}^{\ensuremath{-}}$ spin density is predicted in the case of one magnetic-ion ${\mathrm{Cr}}^{3+}$ neighbor as well as in the case of the ${\mathrm{Cr}}^{3+}$${\mathrm{F}}^{\ensuremath{-}}$${\mathrm{Cr}}^{3+}$ linear system. There is a returning hyperfine field as a result of a charge-redistribution effect. It is found that the spin density of the ${\mathrm{F}}^{\ensuremath{-}}$ site in the one-ion case is larger and varies as ${R}^{\ensuremath{-}6}$, as compared with the case of ion pair in which it is found to vary as ${R}^{\ensuremath{-}7}$ in the neighborhood of a ${\mathrm{Cr}}^{3+}$-${\mathrm{F}}^{\ensuremath{-}}$ separation varying from $R=2$ \AA{} to $R=2.1$ \AA{}.
Efficient Hybrid Security Mechanisms for Heterogeneous Sensor Networks (2007)

Many applications that make use of sensor networks require secure communication. Because asymmetric-key solutions are difficult to implement in such a resource-constrained environment, symmetric-key methods coupled with a priori key distribution schemes have been proposed to achieve the goals of data secrecy and integrity. These approaches typically assume that all nodes are similar in terms of capabilities and, hence, deploy the same number of keys in all sensors in a network to provide the aforementioned protections. In this paper, we demonstrate that a probabilistic unbalanced distribution of keys throughout the network that leverages the existence of a small percentage of more capable sensor nodes can not only provide an equal level of security, but also reduce the consequences of node compromise. To fully characterize the effects of the unbalanced key management system, we design, implement, and measure the performance of a complementary suite of key establishment protocols known as LIGER. Using their predeployed keys, nodes operating in isolation from external networks can securely and efficiently establish keys with each other. Should resources such as a backhaul link to a key distribution center (KDC) become available, networks implementing LIGER automatically incorporate and benefit from such facilities. Detailed experiments demonstrate that the unbalanced distribution in combination with the multimodal LIGER suite offers a robust and practical solution to the security needs in sensor networks
In vitro Activity of Rifaximin, Metronidazole and Vancomycin against &lt;i&gt;Clostridium difficile&lt;/i&gt; and the Rate of Selection of Spontaneously Resistant Mutants against Representative Anaerobic and Aerobic Bacteria, Including Ammonia-Producing Species (2000)

The low toxicity, broad antibacterial activity and very poor absorption from the gastrointestinal tract of rifaximin suggest a potential therapeutic use for this drug in gastrointestinal diseases, as well as in the management of patients with cirrhosis and chronic portal-systemic encephalopathy.
DC offset and IM2 removal in direct conversion receivers (2002)

DC offsets cause interference in homodyne receivers, caused by nonlinearity and imbalances in the receiving amplifier and mixing circuits, as well as local oscillator (LO) leakage into the RF input port and RF leakage into the LO port. The latter causes a squaring action (hence, second order intermodulation distortion (IM2)) in the mixer which generates a DC offset (low frequency) that varies with the amplitude of any high power RF interfering (jamming) signal, whatever its applied frequency. A method for removing this DC offset is described. The signal immediately after the mixer is squared to obtain a distortion estimate of the jamming signal, and then subtracted from the main signal path to remove the interference from the desired signal. The experimental results indicate an 11.5 dB improvement in jamming margin for systems with 30 kHz RF bandwidth. In the experiment an adaptive equaliser is used to equalise the two paths and improve the dynamic response.
Lycopene is a more potent inhibitor of human cancer cell proliferation than either α‐carotene or β‐carotene (1995)

The antiproliferative properties of lycopene, the major tomato carotenoid, were compared with those of alpha- and beta-carotene. Lycopene, delivered in cell culture medium from stock solutions in tetrahydrofuran, strongly inhibited proliferation of endometrial (Ishikawa), mammary (MCF-7), and lung (NCI-H226) human cancer cells with half-maximal inhibitory concentration of 1-2 microM; alpha- and beta-carotene were far less effective inhibitors. For example, in Ishikawa cells, a 4-fold higher concentration of alpha-carotene or a 10-fold higher concentration of beta-carotene was needed for the same order of growth suppression. The inhibitory effect of lycopene was detected after 24 hours of incubation, and it was maintained for at least three days. In contrast to cancer cells, human fibroblasts were less sensitive to lycopene, and the cells gradually escaped growth inhibition over time. In addition to its inhibitory effect on basal endometrial cancer cell proliferation, lycopene also suppressed insulin-like growth factor-I-stimulated growth. Insulin-like growth factors are major autocrine/paracrine regulators of mammary and endometrial cancer cell growth. Therefore, lycopene interference in this major autocrine/paracrine system may open new avenues for research on the role of lycopene in the regulation of endometrial cancer and other tumors.
Super-smooth x-ray reflection grating fabrication (1997)

Blazed, grazing incidence x-ray reflection gratings are an important component of modern high resolution spectrometers and related x-ray optics. These have traditionally been fabricated by diamond scribing in a ruling engine, or more recently by interferometric lithography followed by ion etching. These traditional methods result in gratings which suffer from a number of deficiencies, including high surface roughness and poor control of the groove profile. These deficiencies lead to poor diffraction efficiency and high levels of scattered light. We have developed a novel fabrication method for fabricating blazed x-ray reflection gratings which utilizes silicon wafers that are cut 0.7° off of the (111) plane. In solutions such as potassium hydroxide (KOH), silicon is etched in 〈111〉 directions orders of magnitude slower than in other directions, resulting in extremely smooth {111} facets. The gratings are patterned using interferometric lithography with 351.1 nm wavelength and transferred into the substrate using tri-level resist processing, reactive-ion etching (RIE), and silicon nitride masking during the KOH etch. The narrow (&amp;lt;0.1 μm) ridge of silicon which supports the nitride mask is removed using a chromium lift-off step followed by a CF4 RIE trench etch. The result is a grating with extremely smooth blaze facets which is suitable for x-ray reflection after evaporative coating with thin Cr/Au. Atomic force microscope images confirm that fabricated gratings have less than a 0.4 nm rms roughness—much smoother than conventional gratings which have over ∼1 nm roughness. Theory predicts that reduced blaze facet roughness increases diffraction efficiency. Experiments and simulations performed at the Lawrence Berkeley Laboratory and Columbia University confirm that efficiency is increased; in fact, measured peak efficiencies reach ∼80% of calculated theoretical limits. Peak grating efficiencies were achieved that are ∼35% greater than that of the best available ruled masters of comparable design.
Adaptive-optics ultrahigh-resolution optical coherence tomography (2004)

Merging of ultrahigh-resolution optical coherence tomography (UHR OCT) and adaptive optics (AO), resulting in high axial (3 microm) and improved transverse resolution (5-10 microm) is demonstrated for the first time to our knowledge in in vivo retinal imaging. A compact (300 mm x 300 mm) closed-loop AO system, based on a real-time Hartmann-Shack wave-front sensor operating at 30 Hz and a 37-actuator membrane deformable mirror, is interfaced to an UHR OCT system, based on a commercial OCT instrument, employing a compact Ti:sapphire laser with 130-nm bandwidth. Closed-loop correction of both ocular and system aberrations results in a residual uncorrected wave-front rms of 0.1 microm for a 3.68-mm pupil diameter. When this level of correction is achieved, OCT images are obtained under a static mirror configuration. By use of AO, an improvement of the transverse resolution of two to three times, compared with UHR OCT systems used so far, is obtained. A significant signal-to-noise ratio improvement of up to 9 dB in corrected compared with uncorrected OCT tomograms is also achieved.
Design of Self-Delegation for Mobile Terminals (2005)

In this paper, we propose a new authentication mechanism for the mobile environments, called Self-Delegation. In the mechanism, a user stores information that relates to strict authentication in a tamper-resistant module that can be kept securely at home. Time-limited authority is delegated to the mobile terminal by communicating with the tamper-resistant module on a local basis. After the delegation, a remote service can authenticate the user for a limited time. We propose two self-delegation schemes, and analyze the security of the proposed scheme based on a security model that we define. Furthermore, we have implemented the self-delegation and authentication protocols on a PDA and a Java card, both of which have ISO14443 I/F, and show the feasibility of the implemented protocols.
Learning to Skim Text (2017)

Recurrent Neural Networks are showing much promise in many sub-areas of natural language processing, ranging from document classification to machine translation to automatic question answering. Despite their promise, many recurrent models have to read the whole text word by word, making it slow to handle long documents. For example, it is difficult to use a recurrent network to read a book and answer questions about it. In this paper, we present an approach of reading text while skipping irrelevant information if needed. The underlying model is a recurrent network that learns how far to jump after reading a few words of the input text. We employ a standard policy gradient method to train the model to make discrete jumping decisions. In our benchmarks on four different tasks, including number prediction, sentiment analysis, news article classification and automatic Q&A, our proposed model, a modified LSTM with jumping, is up to 6 times faster than the standard sequential LSTM, while maintaining the same or even better accuracy.
Fast Single-image Defogging (2014)

Bad weather conditions such as fog, haze, and dust often reduce the performance of outdoor cameras. To improve the effectiveness of surveillance and in-vehicle cameras under such conditions, we propose a method based on a dark channel prior for quickly defogging images. It first estimates the intensity of the atmospheric light by searching the sky area in the foggy image. Then it estimates the transmission map by refining a coarse map from a fine map. Finally, it produces a clearer image from the foggy image by using the estimated intensity and the transmission map. When implemented on a notebook PC with a graphics processing unit (GPU), it was able to process 50 images (720 × 480 pixels) per second. It can thus be used for real-time processing of surveillance and in-vehicle system images.
Evidence-based approach to acute exacerbations of COPD (2003)

Chronic obstructive pulmonary disease (COPD) is the fourth leading cause of death in the United States, and it accounts for approximately 500,000 hospitalizations for exacerbations each year. New definitions of acute COPD exacerbation have been suggested, but the one used by Anthonisen et al. is still widely accepted. It requires the presence of one or more of the following findings: increase in sputum purulence, increase in sputum volume, and worsening of dyspnea. Patients with COPD typically present with acute decompensation of their disease one to three times a year, and 3% to 16% of these will require hospital admission. Hospital mortality of these admissions ranges from 3% to 10% in severe COPD patients, and it is much higher for patients requiring ICU admission. The etiology of the exacerbations is mainly infectious (up to 80%). Other conditions such as heart failure, pulmonary embolism, nonpulmonary infections, and pneumothorax can mimic an acute exacerbation or possibly act as "triggers." Baseline chest radiography and arterial blood gas analysis during an exacerbation are recommended. Oxygen administration through a venturi mask seems to be appropriate and safe, and the oxygen saturation should be kept just above 90%. Either a short acting beta 2-agonist or an anticholinergic is the preferred bronchodilator agent. The choice between the two depends largely on potential undesirable side effects and the patient's coexistent conditions. Adding a second bronchodilator to the first one does not seem to offer much benefit. The evidence suggests similar benefit of MDIs when compared with nebulized treatment for bronchodilator delivery. If MDIs are to be used, spacer devices are recommended. Steroids do improve several outcomes during an acute COPD exacerbation, and a 10- to 14-day course seems appropriate. Antibiotic use has been shown to be beneficial, especially for patients with severe exacerbation. Changes in bacteria strains have been documented during exacerbations, and newer generations of antibiotics might offer a better response rate. There is no role for mucolytic agents or chest physiotherapy in the acute exacerbation setting. Noninvasive positive pressure ventilation might benefit a group of patients with rapid decline in respiratory function and gas exchange. It has the potential to decrease the need for intubation and invasive mechanical ventilation and possibly decrease in-hospital mortality.
Effects of Aerobic Exercise on Lipid Profiles and High Molecular Weight Adiponectin in Japanese Workers (2011)

Aerobic exercise led to an improvement in body composition and lipid profiles. High molecular weight adiponectin concentrations tended to improve compared with pre-aerobic exercise levels.
Synthesis and antitumor activity of cyclophosphamide analogs. 2. Preparation, hydrolytic studies, and anticancer screening of 5-bromocyclophosphamide, 3,5-dehydrocyclophosphamide, and related systems (1979)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis and antitumor activity of cyclophosphamide analogs. 2. Preparation, hydrolytic studies, and anticancer screening of 5-bromocyclophosphamide, 3,5-dehydrocyclophosphamide, and related systemsSusan Marie Ludeman, Gerald Zon, and William EganCite this: J. Med. Chem. 1979, 22, 2, 151–158Publication Date (Print):February 1, 1979Publication History Published online1 May 2002Published inissue 1 February 1979https://pubs.acs.org/doi/10.1021/jm00188a006https://doi.org/10.1021/jm00188a006research-articleACS PublicationsRequest reuse permissionsArticle Views233Altmetric-Citations22LEARN 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