gebhart/patrepeval huggingface dataset:
Identification of Foot-and-Mouth Disease Virus-Specific Linear B-Cell Epitopes To Differentiate between Infected and Vaccinated Cattle (2003)

Foot-and-mouth disease (FMD) is a highly contagious viral disease of cloven-hoofed animals. For several years, vaccination of animals, which had proven to be successful for the eradication of the disease, has been forbidden in the United States and the European Community because of the difficulty of differentiating between vaccinated and infected animals. In this study, detailed investigations of the bovine humoral immune response against FMD virus (FMDV) were performed with the aim of identifying viral epitopes recognized specifically by sera derived from FMDV-infected animals. The use of overlapping 15-mer synthetic peptides, covering the whole open reading frame of FMDV strain O(1)K in a peptide enzyme-linked immunosorbent assay, allowed the identification of 12 FMDV strain O(1)K-specific linear B-cell epitopes. Six of these linear B-cell epitopes, located in the nonstructural proteins, were used in further assays to compare the reactivities of sera from vaccinated and infected cattle. Antibodies recognizing these peptides could be detected only in sera derived from infected cattle. In further experiments, the reactivity of the six peptides with sera from animals infected with different strains of FMDV was tested, and strain-independent infection-specific epitopes were identified. Thus, these results clearly demonstrate the ability of a simple peptide-based assay to discriminate between infected and conventionally FMD-vaccinated animals.
Structural Determinants for Protein adsorption/non-adsorption to Silica Surface (2013)

The understanding of the mechanisms involved in the interaction of proteins with inorganic surfaces is of major interest in both fundamental research and applications such as nanotechnology. However, despite intense research, the mechanisms and the structural determinants of protein/surface interactions are still unclear. We developed a strategy consisting in identifying, in a mixture of hundreds of soluble proteins, those proteins that are adsorbed on the surface and those that are not. If the two protein subsets are large enough, their statistical comparative analysis must reveal the physicochemical determinants relevant for adsorption versus non-adsorption. This methodology was tested with silica nanoparticles. We found that the adsorbed proteins contain a higher number of charged amino acids, particularly arginine, which is consistent with involvement of this basic amino acid in electrostatic interactions with silica. The analysis also identified a marked bias toward low aromatic amino acid content (phenylalanine, tryptophan, tyrosine and histidine) in adsorbed proteins. Structural analyses and molecular dynamics simulations of proteins from the two groups indicate that non-adsorbed proteins have twice as many π-π interactions and higher structural rigidity. The data are consistent with the notion that adsorption is correlated with the flexibility of the protein and with its ability to spread on the surface. Our findings led us to propose a refined model of protein adsorption.
Learning Policies for Adaptive Tracking with Deep Feature Cascades (2017)

Visual object tracking is a fundamental and time-critical vision task. Recent years have seen many shallow tracking methods based on real-time pixel-based correlation filters, as well as deep methods that have top performance but need a high-end GPU. In this paper, we learn to improve the speed of deep trackers without losing accuracy. Our fundamental insight is to take an adaptive approach, where easy frames are processed with cheap features (such as pixel values), while challenging frames are processed with invariant but expensive deep features. We formulate the adaptive tracking problem as a decision-making process, and learn an agent to decide whether to locate objects with high confidence on an early layer, or continue processing subsequent layers of a network. This significantly reduces the feed-forward cost for easy frames with distinct or slow-moving objects. We train the agent offline in a reinforcement learning fashion, and further demonstrate that learning all deep layers (so as to provide good features for adaptive tracking) can lead to near real-time average tracking speed of 23 fps on a single CPU while achieving state-of-the-art performance. Perhaps most tellingly, our approach provides a 100X speedup for almost 50% of the time, indicating the power of an adaptive approach.
DNA and RNA enzymes with peroxidase activity An investigation into the mechanism of action (2006)

A DNAhemin complex (PS2.Mhemin), and its RNA counterpart (rPS2.Mhemin), have previously been reported, in the presence of nitrogenous buffers such as HEPES, to show enhanced peroxidative activity relative to both uncomplexed hemin and a control DNAhemin complex (Chem. Biol. 5, 505, 1998). A kinetic analysis of these two hemin-utilizing nucleic acid enzymes provides key insights into the mechanisms for their catalyzed peroxidation reactions. First, control experiments indicate that charge on the added detergent, required for solubility reasons, has little effect on the efficiency of the nucleic-acid-catalyzed reactions. Second, the key functional impact of the two nucleic acid frameworks, either DNA or RNA, appears to be a reduction in the acidity of a water molecule coordinated to the iron atom of the hemin that is bound to the ribozyme and DNAzyme scaffolds. This effect could result from a polar environment and possibly hydrogen bond(s) at the axial position of the hemin, along with favourable hydrophobic interactions for the periphery of the porphyrin ring. Third, the basic component of the buffer enhances the activities; this likely results from a general-base-catalyzed process. Cumulatively, these data supply important clues as to how biopolymers other than a protein can complex with hemin to form productive peroxidase enzymes.Key words: ribozyme, DNAzyme, hemin, peroxidase, mechanism, guanine quadruplex.
Preclinical validation of a repurposed metal chelator as an early-intervention therapeutic for hemotoxic snakebite (2020)

Snakebite envenoming causes 138,000 deaths annually, and ~400,000 victims are left with permanent disabilities. Envenoming by saw-scaled vipers (Viperidae: <i>Echis</i>) leads to systemic hemorrhage and coagulopathy and represents a major cause of snakebite mortality and morbidity in Africa and Asia. The only specific treatment for snakebite, antivenom, has poor specificity and low affordability and must be administered in clinical settings because of its intravenous delivery and high rates of adverse reactions. This requirement results in major treatment delays in resource-poor regions and substantially affects patient outcomes after envenoming. Here, we investigated the value of metal ion chelators as prehospital therapeutics for snakebite. Among the tested chelators, dimercaprol (British anti-Lewisite) and its derivative 2,3-dimercapto-1-propanesulfonic acid (DMPS) were found to potently antagonize the activity of Zn<sup>2+</sup>-dependent snake venom metalloproteinases in vitro. Moreover, DMPS prolonged or conferred complete survival in murine preclinical models of envenoming against a variety of saw-scaled viper venoms. DMPS also considerably extended survival in a "challenge and treat" model, where drug administration was delayed after venom injection and the oral administration of this chelator provided partial protection against envenoming. Last, the potential clinical scenario of early oral DMPS therapy combined with a delayed, intravenous dose of conventional antivenom provided prolonged protection against the lethal effects of envenoming in vivo. Our findings demonstrate that the safe and affordable repurposed metal chelator DMPS can effectively neutralize saw-scaled viper venoms in vitro and in vivo and highlight the promise of this drug as an early, prehospital, therapeutic intervention for hemotoxic snakebite envenoming.
Adenosine-5′-phosphosulfate Kinase from Escherichia coli K12 (1989)

Adenosine-5'-phosphosulfate kinase (ATP:adenylylsulfate 3'-phosphotransferase), the second enzyme in the pathway of sulfate activation, has been purified (approximately 300-fold) to homogeneity from an Escherichia coli K12 strain, which overproduces the enzyme activity (approximately 100-fold). The purified enzyme has a specific activity of 153 mumol of 3'-phosphoadenosine 5'-phosphosulfate (PAPS) formed/min/mg of protein at 25 degrees C. The enzyme is remarkably efficient with a Vmax/Km(APS) of greater than 10(8) M-1 s-1, indicating that at physiologically low substrate concentrations the reaction is essentially diffusion limited. Upon incubation with MgATP a phosphorylated enzyme is formed; the isolated phosphorylated enzyme can transfer its phosphoryl group to adenosine 5'-phosphosulfate (APS) to form PAPS or to ADP to form ATP. The phosphorylated enzyme exists as a dimer of identical 21-kilodalton subunits, while the dephosphorylated form primarily exists as a tetramer. Divalent cations are required for activity with Mg(II), Mn(II), Co(II), and Cd(II) activating. Studies of the divalent metal-dependent stereoselectivity for the alpha- and beta-phosphorothioate derivatives of ATP indicate metal coordination to at least the alpha-phosphoryl group of the nucleotide. Steady state kinetic studies of the reverse reaction indicate a sequential mechanism, with a rapid equilibrium ordered binding of MgADP before PAPS. In the forward direction APS is a potent substrate inhibitor, competitive with ATP, complicating kinetic studies. The primary kinetic mechanism in the forward direction is sequential. Product inhibition studies at high concentrations of APS suggest an ordered kinetic mechanism with MgATP binding before APS. At submicromolar concentrations of APS, product inhibition by both MgADP and PAPS is more complex and is not consistent with a solely ordered sequential mechanism. The formation of a phosphorylated enzyme capable of transferring its phosphoryl group to APS or to MgADP suggests that a ping-pong pathway in which the rate of MgADP dissociation is comparable to the rate of APS binding might contribute at very low concentrations of APS. The substrate inhibition by APS is consistent with APS binding to the enzyme, to form a dead-end E.APS complex.
Niobium-based superconducting nano-device fabrication using all-metal suspended masks (2013)

We report a novel method for the fabrication of superconducting nano-devices based on niobium. The well-known difficulties of lithographic patterning of high-quality niobium are overcome by replacing the usual organic resist mask by a metallic one. The quality of the fabrication procedure is demonstrated by the realization and characterization of long and narrow superconducting lines and niobium-gold-niobium proximity SQUIDs.
Safety analysis of an evolving software architecture (2002)

The safety analysis of an evolving software system has to consider the impact that changes might have on the software components, and to provide confidence that the risk is acceptable. If the impact of a change is not thoroughly analysed, accidents can occur as a result of faulty interactions between components, for example. However, the process of safety analysis can be enhanced if appropriate abstractions are provided for modelling and analysing software components and their interactions. Instead of considering components as the locus of change, the proposed approach assumes that components remain unchanged while their interactions (i.e. connectors) adapt to the different requirements needs. The safety analysis is then performed using model checking to verify whether safe behaviour is maintained when interactions between components change. The feasibility of the approach is demonstrated in terms of a case study that deals with the safety procedures associated with the launching of a sounding rocket.
Catecholamine biosynthetic enzymes are expressed in replicating cells of the peripheral but not the central nervous system. (1980)

We sought to determine whether the precursors of catecholamine-containing neurons in the developing peripheral and central nervous systems of chickens and rats express the biosynthetic enzymes tyrosine hydroxylase [THase; tyrosine 3-monooxygenase; L-tyrosine, tetrahydropteridine: oxygen oxidoreductase (3-hydroxylating), EC 1.14.16.2] or dopamine beta-hydroxylase [DBHase; 3,4-dihydroxyphenylethylamine, ascorbate:oxygen oxidoreductase (beta-hydroxylating), EC 1.14.17.1], prior to the time they withdraw from the cell cycle. Chicken embryos (stages 26-27) were injected with [3H-thymidine and 4 hr later were prepared for the simultaneous demonstration of radioautographically labeled nuclei in immunoreactive THase cells. The brains and sympathetic chains of rat fetuses (days E12-E14), exposed for 2 hr to [3H]thymidine, were treated similarly except that peripheral tissues were stained with a specific antibody to DBHase as well as anti-THase. In the peripheral nervous system of both chicken and rat, nuclei of THase-containing cells were radioautographically labeled. DBHase-containing cells in the peripheral nervous system of rats were also labeled and thus are noradrenergic. THase was localized in cells of the brain of the same rat fetuses beginning on day E12 (no THase was detected on day E11 or E11.5) in the mantle layer of the ventral mesencephalic and rostrolateral rhombocephalic cellular groups; however. THase-containing cells in the central nervous system did not incorporate [3H]thymidine. We conclude that, during development, the adrenergic neuronal precursors of the peripheral nervous system but not of the central, have the capacity to synthesize catecholamines before they withdraw from the cell cycle. Differences in the maturation of peripheral and central neurons may be related to differences in their embryological origin.
Recommender system by grasping individual preference and influence from other users (2013)

We propose a recommendation method that considers the user's individual preference and influence from other users in social media. This method predicts the user's individual preference and influence from other users by applying the probability of divergence from random-selection based on a statistical hypothesis test as a form of modified content-based filtering. We evaluated the proposed method by focusing on the rate at which items that have recommended tags are contained among all items. The proposed method is shown to have higher accuracy than traditional content-based filtering. It is especially effective when some percentage of the items have recommendation tags.
Effect of Subconjunctival and Intraocular Bevacizumab Injections on Corneal Neovascularization in a Mouse Model (2010)

Bevacizumab injections partially inhibit the growth of corneal neovascularization induced by acute chemical injury in a mouse model. The intraocular routes of injection were found to be the most effective, and the subconjunctival route of injection yielded the earliest peak response.
Multicolor super-resolution imaging using spectroscopic single-molecule localization microscopy with optimal spectral dispersion (2019)

We developed transmission diffraction grating-based spectroscopic single-molecule localization microscopy (sSMLM) to collect the spatial and spectral information of single-molecule blinking events concurrently. We characterized the spectral heterogeneities of multiple far-red emitting dyes in a high-throughput manner using sSMLM. We also investigated the influence of spectral dispersion on the single-molecule identification performance of fluorophores with large spectral overlapping. The careful tuning of spectral dispersion in grating-based sSMLM permitted simultaneous three-color super-resolution imaging in fixed cells with a single objective lens at a relatively low photon budget. Our sSMLM has a compact optical design and can be integrated with conventional localization microscopy to provide add-on spectroscopic analysis capability.
De verzorging van centraal veneuze catheters: de ontwikkeling van een richtlijn (2003)

In dit artikel worden 12 evidence based aanbevelingen gedaan ten aanzien van de verzorging van centraal veneuze catheters (CVCs). Het artikel geeft een overzicht van de meest recente wetenschappelijke literatuur over dit onderwerp en heeft gediend als achtergrondinformatie bij de ontwikkeling van een richtlijn voor de verzorging van niet-getunnelde CVCs die in de vena subclavia zijn ingebracht
Notes- Fluorocarbon Sulfides I. Synthesis of Bis(perfluoropropyl) Sulfide and Bis(perfluoroheptyl) Disulfide (1961)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTNotes- Fluorocarbon Sulfides I. Synthesis of Bis(perfluoropropyl) Sulfide and Bis(perfluoroheptyl) DisulfideGeorge TiersCite this: J. Org. Chem. 1961, 26, 9, 3515–3516Publication Date (Print):September 1, 1961Publication History Published online6 March 2003Published inissue 1 September 1961https://pubs.acs.org/doi/10.1021/jo01067a607https://doi.org/10.1021/jo01067a607research-articleACS PublicationsRequest reuse permissionsArticle Views49Altmetric-Citations6LEARN 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
Improved Procedure for the Synthesis of Enamine <i>N</i>-Oxides (2008)

An improved procedure for the preparation of enamine N-oxides involving aminolysis of epoxides, chlorination, N-oxidation, and dehydrochlorination is described. Although isolated beta-chloroamine N-oxides are prone to rearrangements when isolated, these side reactions can be slowed by the presence of stabilizing organic acids. The scope and limitations of this strategy are discussed.
The Canadian Archives Summit, 2014 (2014)

Canadian archives are the foundation of Canadian studies, and the development of Canadian studies will depend in large
The role of type-1 plasminogen activator inhibitor in failure of thrombolytic therapy with recombinant tissue plasminogen activator. (1993)

We investigated the possible role of type-1 plasminogen activator inhibitor (PAI-1) on success or failure of thrombolytic therapy with recombinant tissue plasminogen activator (rt-PA) in 10 responders and 10 non-responders with acute myocardial infarction and early initiation of therapy within 2 h of onset using the common infusion scheme (100 mg rt-PA over 3 h). We determined plasma levels of t-PA (activity and antigen) as well as PAI-1 (activity and antigen) in samples obtained before, during and after thrombolytic treatment and compared the course of each of those parameters between responders and non-responders to therapy. Success or failure of treatment was determined by a combination of noninvasive methods and proven by coronary angiography within 5 days of initiation of thrombolysis. Thirty, 60, 90, and 120 min after initiation of rt-PA infusion, specific t-PA activities in plasma of responders were 0.62, 0.63, 0.62, and 0.57 (IU/ng/ml), respectively, as compared to 0.42, 0.42, 0.40, and 0.32 (IU/ng/ml) in nonresponders (p < 0.001). Between 4 and 8 h after initiation of therapy, a time span known to be critical for thrombotic reocclusion, specific activities were still significantly elevated in responders as compared to non-responders (p < 0.01). PAI-1 activity levels, which were not detectable during rt-PA infusion in either group, recovered to pre-treatment values 2 h earlier in non-responders.(ABSTRACT TRUNCATED AT 250 WORDS)
Optimal diagonal precoder for multiantenna communication systems (2005)

In this paper, we examine a multiantenna single-user wireless communication system fitted with a QR-based successive cancellation receiver (QR receiver). Initially, our consideration is confined to uncoded binary phase shift keying (BPSK) signals transmitted through independent and identically distributed (IID) Rayleigh fading channels and to the design of an optimum precoder for the transmitter. For minimum feeding back of the channel state information (CSI) to the transmitter from the receiver, we stipulate the precoder to be in the form of a power loading square diagonal matrix. We proceed to develop the theory for the design of this diagonal matrix based on the minimization of the lower bound of the average bit error rate (BER) of transmission. The design obtained provides substantially lower error rates than most of other existing schemes under the same environment. The corresponding gain in signal-to-noise ratio (SNR) can be several decibels. To further improve the performance, we extend the design to include an optimal detection order of the received bits using an iterative approach. This iterative process proves to have fast convergence and results in a design providing significant SNR gain. We also propose a subchannel dropping scheme for cases in which SNR is low, and when the minimum BER precoder is equipped with this scheme, its average performance can be substantially superior to the Vertical Bell Laboratories Layered Space-Time (V-BLAST) detection. We extend our design of the optimum precoder to quadrature amplitude modulation (QAM) modulation scheme and similar performance gain has been observed.
A Study on the Influence of Korea Internet Shopping Mall's Customer Satisfaction Factor to Chinese Internet Shoppers (2006)

Multiple regression is used to examine the relationship between a set of two or more independent variables and one dependent variable. It provides the information necessary to make predictions of the dependent variables based on several independent variables. To do so, the multiple regression equation is extended to: y= y=attractiveness a=the value of the intercept =the slope(weighting) of the first variable = the slope(weighting) of the second variable =the slope of the th variable The resulting regression equation of this research is y= y=3.233+0.374(site's system)+0.268(customer satisfaction)+0.17(products)+0.077(delivery)
A hygrometer comprising a porous silicon humidity sensor with phase-detection electronics (2003)

A novel hygrometer is presented, comprising a capacitive humidity sensor with a porous silicon (PS) dielectric and electronics. The adsorption of water vapor by the PS layer leading to change of its effective dielectric constant is modeled with an effective medium approximation (EMA). A simple, but precise, phase-sensitive electronic circuit has been developed. This detects any change of phase of a sinusoidal signal transmitted through the PS dielectric and correlates to ambient humidity. It is outlined how the nonlinear response of the sensor is compensated through piecewise linearization. The sensor is tested in combination with the phase detection circuitry. Excellent linearity over the entire range of relative humidity is achieved. Experimental results show a resolution better than 0.1% and an accuracy of 2% (near the transition region) and better than 0.1% (otherwise). The response time is less than 10 s with good stability.