gebhart/patrepeval huggingface dataset:
Monitoring tat peptide binding to TAR RNA by solid-state 31P-19F REDOR NMR (2005)

Complexes of the HIV transactivation response element (TAR) RNA with the viral regulatory protein tat are of special interest due in particular to the plasticity of the RNA at this binding site and to the potential for therapeutic targeting of the interaction. We performed REDOR solid-state NMR experiments on lyophilized samples of a 29 nt HIV-1 TAR construct to measure conformational changes in the tat-binding site concomitant with binding of a short peptide comprising the residues of the tat basic binding domain. Peptide binding was observed to produce a nearly 4 A decrease in the separation between phosphorothioate and 2'F labels incorporated at A27 in the upper helix and U23 in the bulge, respectively, consistent with distance changes observed in previous solution NMR studies, and with models showing significant rearrangement in position of bulge residue U23 in the bound-form RNA. In addition to providing long-range constraints on free TAR and the TAR-tat complex, these results suggest that in RNAs known to undergo large deformations upon ligand binding, 31P-19F REDOR measurements can also serve as an assay for complex formation in solid-state samples. To our knowledge, these experiments provide the first example of a solid-state NMR distance measurement in an RNA-peptide complex.
Etch Stop Techniques for Micromachining (1997)

A presentation of etch stop engineering is presented with a review of the present state of the art in etch stop micro‐machining. This review assumes a global definition for an etch stop and focuses on salient examples of common etch stop techniques, as well as unique and/or novel etch stop methods. A table of representative etch stops is also presented as a summary.
Multiple cyclic AMP receptors are linked to adenylyl cyclase in Dictyostelium. (1992)

cAMP receptor 1 and G-protein alpha-subunit 2 null cell lines (car1- and g alpha 2-) were examined to assess the roles that these two proteins play in cAMP stimulated adenylyl cyclase activation in Dictyostelium. In intact wild-type cells, cAMP stimulation elicited a rapid activation of adenylyl cyclase that peaked in 1-2 min and subsided within 5 min; in g alpha 2- cells, this activation did not occur; in car1- cells an activation occurred but it rose and subsided more slowly. cAMP also induced a persistent activation of adenylyl cyclase in growth stage cells that contain only low levels of cAMP receptor 1 (cAR1). In lysates of untreated wild-type, car1-, or g alpha 2- cells, guanosine 5'-O-'(3-thiotriphosphate) (GTP gamma S) produced a similar 20-fold increase in adenylyl cyclase activity. Brief treatment of intact cells with cAMP reduced this activity by 75% in control and g alpha 2- cells but by only 8% in the car1- cells. These observations suggest several conclusions regarding the cAMP signal transduction system. 1) cAR1 and another cAMP receptor are linked to activation of adenylyl cyclase in intact cells. Both excitation signals require G alpha 2. 2) cAR1 is required for normal adaptation of adenylyl cyclase. The adaptation reaction caused by cAR1 is not mediated via G alpha 2. 3) Neither cAR1 nor G alpha 2 is required for GTP gamma S-stimulation of adenylyl cyclase in cell lysates. The adenylyl cyclase is directly coupled to an as yet unidentified G-protein.
An energy-based model for electrowetting-induced droplet actuation (2006)

Electrowetting (EW) induced droplet motion has been explored in the past decade in view of its promising applications in the field of microfluidics. This paper demonstrates the potential of energy-based analyses for modeling the performance of EW-based fluid actuation systems. Analyses based on system energy minimization offer simplified modeling tools to predict the overall performance of EW systems while circumventing the need to model the numerous complexities in the system. An analytical model is developed to estimate the actuation force on a droplet moving between two electrodes. The origins and contributions of various components of the actuation force are analyzed. The effects of dielectric parameters, electrode layout, droplet geometry and shape are discussed with the objective of maximizing the actuation force. The actuation force model is combined with semi-analytical models for predicting the forces opposing droplet motion to develop a model that predicts transient EW-induced droplet motion. Parametric results are obtained to evaluate the importance of operating voltage, fluid properties and droplet geometry on droplet motion.
A rapid and sensitive method for detection and quantification of calcineurin and calmodulin-binding proteins using biotinylated calmodulin. (1985)

Purified bovine brain calmodulin was biotinylated with biotinyl-epsilon-aminocaproic acid N-hydroxysuccinimide. Biotinylated calmodulin was used to detect and quantify calmodulin-binding proteins following both protein blotting and slot-blot procedures by using alkaline phosphatase or peroxidase coupled to avidin. When purified bovine brain calcineurin, a calmodulin-dependent protein phosphatase, was immobilized on nitrocellulose slot blots, biotinylated calmodulin bound in a calcium-dependent saturable manner; these blots were then quantified by densitometry. Biotinylated calmodulin was able to detect as little as 10 ng of calcineurin, and the binding was competitively inhibited by addition of either native calmodulin or trifluoperazine. When biotinylated calmodulin was used to probe protein blots of crude brain cytosol and membrane preparations after gel electrophoresis, only protein bands characteristic of known calmodulin-binding proteins (i.e., calmodulin-dependent protein kinase, calcineurin, spectrin) were detected with avidin-peroxidase or avidin-alkaline phosphatase procedures. Purified calcineurin was subjected to one- and two-dimensional gel electrophoresis and protein blotting; as expected, only the 61-kDa calmodulin-binding subunit was detected. When the two-dimensional protein blot was incubated with biotinylated calmodulin and detected with avidin-alkaline phosphatase, several apparent forms of the 61-kDa catalytic subunit were detected, consistent with isozymic species of the enzyme. The results of these studies suggest that biotinylated calmodulin can be used as a simple, sensitive, and quantifiable probe for the study of calmodulin-binding proteins.
A hybrid neural model for type classification of entity mentions (2015)

The semantic class (i.e., type) of an entity plays a vital role in many natural language processing tasks, such as question answering. However, most of existing type classification systems extensively rely on hand-crafted features. This paper introduces a hybrid neural model which classifies entity mentions to a wide-coverage set of 22 types derived from DBpedia. It consists of two parts. The mention model uses recurrent neural networks to recursively obtain the vector representation of an entity mention from the words it contains. The context model, on the other hand, employs multilayer perceptrons to obtain the hidden representation for contextual information of a mention. Representations obtained by the two parts are used together to predict the type distribution. Using automatically generated data, these two parts are jointly learned. Experimental studies illustrate that the proposed approach outperforms baseline methods. Moreover, when type information provided by our method is used in a question answering system, we observe a 14.7% relative improvement for the top-1 accuracy of answers.
Sources of autoantigens in systemic lupus erythematosus (2005)

Several factors may contribute to the generation of systemic lupus erythematosus-specific autoantigens. Determining the underlying causes of autoantibody production may provide important insight into the etiology and pathogenesis of this disease.
Which Yeast Species Shall I Choose? Saccharomyces cerevisiae Versus Pichia pastoris (Review) (2012)

Having decided on yeast as a production host, the choice of species is often the first question any researcher new to the field will ask. With over 500 known species of yeast to date, this could pose a significant challenge. However, in reality, only very few species of yeast have been employed as host organisms for the production of recombinant proteins. The two most widely used, Saccharomyces cerevisiae and Pichia pastoris, are compared and contrasted here.
DESIGN AND EVALUATION OF A NOVEL PULSATILE BIOREACTOR FOR BIOLOGICALLY ACTIVE HEART VALVES (2004)

Biologically active replacement heart valves (tissue engineered, recellularized xenograft) offer enhanced function compared to current valve therapies by possessing the capacity for remodeling and growth to meet the hemodynamic needs of the patient and eliminating the need for chronic medication. However, many fundamental questions remain as to how these valves will function in vivo, and new in vitro tools need to be created to address these questions. Traditional in vitro heart valve testing devices (mock flow loops) are designed to subject valves to physiologic and pathologic hemodynamic conditions. These devices offer a heart valve designer a useful tool with which to evaluate the mechanical functioning of their device in a variety of well-controlled hemodynamic situations. Unfortunately, these devices have not been designed for testing valves built of biologically active materials which require proper nutrient and waste exchange, pH, temperature, and freedom from attacks by microbial organisms in order to function. Pulsatile bioreactors have been developed to provide the aforementioned biological requirements to developing tissue engineered valves [1, 2], but these systems offer very limited hemodynamic control in comparison to mock flow loops. Therefore, in order to better understand the role of hemodynamics in the function of biologically active heart valves (BAHV), and to thereby create better BAHV designs, a new type of pulsatile bioreactor should be created that also incorporates more of the hemodynamic control found in mock circulatory loops. This thesis details the both the development of such a device and evaluating its functionality.
Conformational Analysis of Oligomers of (<i>R</i>)-3-Hydroxybutanoic Acid in Solutions by 1H NMR Spectroscopy (1998)

Abstract Oligomers of (R)-3-hydroxybutanoic acid (3-HB) with different end groups and chain lengths have been prepared as model compounds of bacterial poly[(R)-3-hydroxybutanoate] [P(3-HB)]. They were studied in terms of their conformational behavior generated by rotation about CH2–CH bond of 3-HB units in solutions. The conformational behaviors of 3-HB oligomers were investigated in various solvents by analysis of vicinal coupling in the 500-MHz 1H NMR spectra. For all 3-HB oligomers studied in this work, 3-HB units without hydroxy group were found, in every solvent, to adopt similar conformational distributions to those of P(3-HB) polymer backbone in solutions, in which trans and gauche conformers are preferable, while the other gauche conformer is strongly disfavored. On the other hand, 3-HB units adjacent to hydroxy terminal group in 3-HB oligomers show different conformational behaviors relative to those of other 3-HB units. In non-polar organic solvents, only gauche conformer is predominant, due to the formation of an intramolecular hydrogen bond between hydroxy and carbonyl groups, while in polar organic solvents, the conformer distributions are similar to those of 3-HB units without hydroxy groups. In aqueous solution, for 3-HB units adjacent to hydroxy terminal group, the fractions of gauche conformer are still higher than those of trans conformer due to the formation of an intramolecular hydrogen bond.
Multi-quantum-path interference in high harmonic generation driven by a chirped laser pulse (2009)

We theoretically investigate the quantum-path interference during the high harmonic generation in argon and observe the multi-quantum- path-interference (MQPI) effect related to the chirp of driving laser pulse. We successfully identify the interference originated from four significantly contributing quantum paths in the interaction of "isolated" atom with the driving laser field. Moreover, the MQPI effect is further demonstrated beyond the single atom response by spatial filtering which is used for angle-selective detection of transmitted light when three-dimensional propagation is considered. It implies that the role of high-order electron returning trajectories during high harmonic generation can be observed in the experiment.
Paint and Coating Testing Manual: 15th. Edition of the Gardner-Sward Handbook (2012)

Description "Having been in the coatings industry for over 30 years, I know how useful the Gardner-Sward Manual can be. For years I have relied on the 14th edition of this fine book to answer many of my paint-testing questions, but a lot has changed in the industry since it was published in 1995. I know a lot of hard work has gone into preparing the new and updated 15th edition, and I am really looking forward to it." Dwight Weldon, President, Weldon Laboratories 79 comprehensive chapters, written by experts in their various fields, reflect the new and updated technologies within the paint and coating industry in the 16 years since the last edition was published. This heavily updated new manual describes briefly and critically most ASTM test methods that are significant in the world of paint technology. New and updated topics include This edition is a valuable guide to the topics, test methods, procedures, and standards of ASTM and other national and international organizations.
Demethylation of the <i>FOXP3</i> gene in human melanoma cells precludes the use of this epigenetic mark for quantification of Tregs in unseparated melanoma samples (2011)

The human suppressive T cells that stably express transcription factor FOXP3, or regulatory T cells (Tregs), are thought to suppress antitumor immune responses. The most specific marker for human Tregs is the demethylation of CpG dinucleotides located in the first intron of FOXP3 (FOXP3i1). FOXP3i1 is completely methylated in other hematopoietic cells, including nonsuppressive T cells that transiently express FOXP3 after activation. Previously, we and others reported estimations of the frequency of Tregs in the blood of melanoma patients using a FOXP3i1 methylation-specific qPCR assay. Here, we attempted to quantify Tregs inside tumor samples using this assay. However, we found demethylated FOXP3i1 sequences in the melanoma cells themselves. This demethylation was not associated with substantial FOXP3 mRNA or protein expression, even though the demethylation extended to the promoter and terminal regions of the gene in some melanoma cells. Our results imply that analyzing Treg frequencies by quantification of demethylated FOXP3i1 will require that tumor-infiltrating T cells be separated from melanoma cells.
Quasidirect products of quasigroups (1975)

(1975). Quasidirect products of quasigroups. Communications in Algebra: Vol. 3, No. 9, pp. 835-850.
A Concise, Asymmetric Synthesis of Tetramic Acid Derivatives (2002)

[reaction: see text] A simple, asymmetric synthesis of tetramic acid derivatives is described in this paper. The key step is a carbonyl transfer from carbonyldiimidazole (CDI) to alpha-diimines (I) to form N-alkyl-4-alkylamino-5-methylenepyrrol-2-ones (II). In turn, these compounds can be easily transformed into tetramic acid derivatives (III) in two additional steps.
N-Terminal Pro–B-Type Natriuretic Peptide Testing Improves the Management of Patients With Suspected Acute Heart Failure (2007)

In a universal health coverage system mandating judicious use of healthcare resources, inclusion of NT-proBNP testing improves the management of patients presenting to emergency departments with dyspnea through improved diagnosis, cost savings, and improvement in selected outcomes.
The Numerical Solution of Some Important Transmission-Line Problems (1965)

The generalized numerical solution of Laplace's equation in two dimensions is dealt with, subject to boundary conditions imposed by conducting surfaces and dielectrics which are permitted a limited amount of inhomogeneity. It is shown how this solution may be applied in the determination of the properties of TEM-mode transmission lines including the equivalent circuits of simple obstacles in these lines. The theory is illustrated with a number of examples, certain of which do not appear to have been previously treated theoretically in the literature. While certain of the examples serve mainly to show the power of the technique, others are given very detailed treatment with the production of much new design data.
Recognition of tumor cells by Dectin-1 orchestrates innate immune cells for anti-tumor responses (2014)

The eradication of tumor cells requires communication to and signaling by cells of the immune system. Natural killer (NK) cells are essential tumor-killing effector cells of the innate immune system; however, little is known about whether or how other immune cells recognize tumor cells to assist NK cells. Here, we show that the innate immune receptor Dectin-1 expressed on dendritic cells and macrophages is critical to NK-mediated killing of tumor cells that express N-glycan structures at high levels. Receptor recognition of these tumor cells causes the activation of the IRF5 transcription factor and downstream gene induction for the full-blown tumoricidal activity of NK cells. Consistent with this, we show exacerbated in vivo tumor growth in mice genetically deficient in either Dectin-1 or IRF5. The critical contribution of Dectin-1 in the recognition of and signaling by tumor cells may offer new insight into the anti-tumor immune system with therapeutic implications.
<title>Recent developments in the VACIS gamma radiography systems</title> (1998)

The VACIS-I prototype system, which has been used at U.S.- Mexico POEs for cargo truck and railroad freight-car inspections, has served as a seedbed for other vehicle inspection systems that are cost-effective, transportable, high- speed, reliable, and utilize very low level radiation exposure. The STAR (stolen automobile recovery) system has been developed and successfully tested at Miami, Florida. Its status and further developmental possibilities are discussed. VACIS-II, the high-resolution (0.5 inches versus 2 inches for VACIS-I) system that scans the entire cargo truck, including the van, is capable of conducting normal as well as oblique scans in 1 1/2 minutes. Railroad VACIS, dubbed SENTINEL, which will scan railroad cars entering the U.S. at about 5 mph is now under development. It has the option of utilizing a Co-60 source for inspecting heavier cargoes. In addition, MOBILE VACIS is in the planning stage. As presently envisioned, it will be mounted on a small vehicle with an extendable detector tower and deployable gamma-ray source to scan a suspect vehicle, either a passenger car or cargo truck, for contraband. The state of development of these systems, as well as some of the options and concerns, are presented.
The Effect of TGF-beta Delivered Through a Collagen Scaffold on Wound Healing (1999)

In this preliminary study, the wound healing response of full-thickness skin defects to transforming growth factor beta (TGF-beta) incorporated in a collagen scaffold was evaluated. The objectives of this study were (1) to compare the effects of TGF-beta on the cellular and tissue response and mechanical properties and (2) to determine the effects of a collagen scaffold on wound healing when compared to control. Three 3 x 3 cm, full-thickness defects were created on the dorsi of 15 New Zealand White rabbits. Each rabbit had a control (no treatment), collagen scaffold, and collagen scaffold with TGF-beta (2 microg/cm2). All the wounds were covered with a transparent polyurethane dressing. There were three periods of study (1, 2, and 3 weeks) with five rabbits in each period. The volume fraction of the tissue and cells was histomorphometrically determined for each wound. A greater inflammatory response was found in the collagen scaffold-treated group, but the fastest epithelialization and contraction rates were associated with TGF-beta and collagen. No significant differences in the mechanical strength between the different treatment groups were seen. Overall, TGF-beta delivered through a collagen scaffold enhanced the healing process and showed promise for future clinical applications.
Minimal resonator loss for circuit quantum electrodynamics (2010)

Single photon level quality factors of 500x10^3 are shown in NbTiN superconducting resonators at millikelvin temperatures. This result originates from the intrinsic low dielectric loss of NbTiN, as demonstrated by comparison with Ta, and by removing unnecessary parts of the dielectric substrate.
K-Nearest-Neighbours with a novel similarity measure for intrusion detection (2013)

K-Nearest-Neighbours is one of the simplest yet effective classification methods. The core computation behind it is to calculate the distance from a query point to all of its neighbours and to choose the closest one. The Euclidean distance is the most frequent choice, although other distances are sometimes required. This paper explores a simple yet effective similarity definition within Nearest Neighbours for intrusion detection applications. This novel similarity rule is fast to compute and achieves a very satisfactory performance on the intrusion detection benchmark data sets tested.
Reaction of Some Substituted Phenanthrenes with n-Butyllithium (1940)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTReaction of Some Substituted Phenanthrenes with n-ButyllithiumHenry Gilman and Thomas H. CookCite this: J. Am. Chem. Soc. 1940, 62, 10, 2813–2817Publication Date (Print):October 1, 1940Publication History Published online1 May 2002Published inissue 1 October 1940https://pubs.acs.org/doi/10.1021/ja01867a054https://doi.org/10.1021/ja01867a054research-articleACS PublicationsRequest reuse permissionsArticle Views199Altmetric-Citations19LEARN 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
Probability mapping images in dynamic speckle classification (2013)

We propose the use of a learning procedure to identify regions of similar dynamics in speckle image sequences that includes more than one descriptor. This procedure is based on the application of a naïve Bayes statistical classifier comprising the use of several descriptors. The class frontiers can be depicted so that the proportion of identified regions may be measured. To demonstrate the results, assembly of an RGB image, where each plane (R, G, and B) is associated with a particular region (class), was labeled according to its biospeckle dynamics. A high brightness in one color means a high probability of the pixel belonging to the corresponding class, and vice versa.