gebhart/patrepeval huggingface dataset:
Rapid Fine Conformational Epitope Mapping Using Comprehensive Mutagenesis and Deep Sequencing (2015)

Knowledge of the fine location of neutralizing and non-neutralizing epitopes on human pathogens affords a better understanding of the structural basis of antibody efficacy, which will expedite rational design of vaccines, prophylactics, and therapeutics. However, full utilization of the wealth of information from single cell techniques and antibody repertoire sequencing awaits the development of a high throughput, inexpensive method to map the conformational epitopes for antibody-antigen interactions. Here we show such an approach that combines comprehensive mutagenesis, cell surface display, and DNA deep sequencing. We develop analytical equations to identify epitope positions and show the method effectiveness by mapping the fine epitope for different antibodies targeting TNF, pertussis toxin, and the cancer target TROP2. In all three cases, the experimentally determined conformational epitope was consistent with previous experimental datasets, confirming the reliability of the experimental pipeline. Once the comprehensive library is generated, fine conformational epitope maps can be prepared at a rate of four per day.
Blockade of NMDA receptors in the dorsomedial striatum prevents action–outcome learning in instrumental conditioning (2005)

Although there is consensus that instrumental conditioning depends on the encoding of action-outcome associations, it is not known where this learning process is localized in the brain. Recent research suggests that the posterior dorsomedial striatum (pDMS) may be the critical locus of these associations. We tested this hypothesis by examining the contribution of N-methyl-D-aspartate receptors (NMDARs) in the pDMS to action-outcome learning. Rats with bilateral cannulae in the pDMS were first trained to perform two actions (left and right lever presses), for sucrose solution. After the pre-training phase, they were given an infusion of the NMDA antagonist 2-amino-5-phosphonopentanoic acid (APV, 1 mg/mL) or artificial cerebral spinal fluid (ACSF) before a 30-min session in which pressing one lever delivered food pellets and pressing the other delivered fruit punch. Learning during this session was tested the next day by sating the animals on either the pellets or fruit punch before assessing their performance on the two levers in extinction. The ACSF group selectively reduced responding on the lever that, in training, had earned the now devalued outcome, whereas the APV group did not. Experiment 2 replicated the effect of APV during the critical training session but found no effect of APV given after acquisition and before test. Furthermore, Experiment 3 showed that the effect of APV on instrumental learning was restricted to the pDMS; infusion into the dorsolateral striatum did not prevent learning. These experiments provide the first direct evidence that, in instrumental conditioning, NMDARs in the dorsomedial striatum are involved in encoding action-outcome associations.
Review of outcomes after cessation of gonadotropin-releasing hormone agonist treatment of girls with precocious puberty. (2014)

Although gonadotropin-releasing hormone agonists (GnRHa) have been the standard of care of central precocious puberty (CPP) management for many years, there are still questions about the long-term consequences of treatment. With increased utilization of GnRHa treatment, it is now possible to assess posttreatment outcomes in the immediate posttreatment period and into adulthood. This literature review reports on the long-term effects of GnRHa therapy in girls with CPP after therapy has been discontinued. Published reports confirm the reversibility of hypothalamic-pituitary-ovarian axis suppression in females after cessation of GnRHa therapy, with the majority of patients achieving ovulatory menstrual cycles of normal timing and duration. GnRHa therapy does not appear to induce polycystic ovary syndrome or have long-term negative repercussions on either bone mineral density or body composition. Evidence is currently insufficient to identify agent-specific differences in outcomes, reproductive function, and health of offspring.
Viewing transform of image based on vanishing point (2010)

Projective geometry is an effective tool for shape transform of images in computer vision. It contains too many degrees of freedom, and the feature points must be chosen semi-automatically. In order to solve these problems, an improved algorithm of viewing transform with fixed viewpoint based on vanishing point is proposed. First, the relationship model of viewing angle and vanishing point is created. Then, the new method chooses the feature points automatically by detecting vanishing points. Finally, a shape transform based on panning and tilting is made. The test results of two types of images and comparison with other methods demonstrate the applicability and effectiveness of this algorithm.
Ab-Ligity: identifying sequence-dissimilar antibodies that bind to the same epitope (2021)

Solving the structure of an antibody-antigen complex gives atomic level information of the interactions between an antibody and its antigen, but such structures are expensive and hard to obtain. Alternative experimental sources include epitope mapping and binning experiments, which can be used as a surrogate to identify key interacting residues. However, their resolution is usually not sufficient to identify if two antibodies have identical interactions. Computational approaches to this problem have so far been based on the premise that antibodies with similar sequences behave similarly. Such approaches will fail to identify sequence-distant antibodies that target the same epitope. Here, we present Ab-Ligity, a structure-based similarity measure tailored to antibody-antigen interfaces. Using predicted paratopes on model antibody structures, we assessed its ability to identify those antibodies that target highly similar epitopes. Most antibodies adopting similar binding modes can be identified from sequence similarity alone, using methods such as clonotyping. In the challenging subset of antibodies whose sequences differ significantly, Ab-Ligity is still able to predict antibodies that would bind to highly similar epitopes (precision of 0.95 and recall of 0.69). We compared Ab-Ligity's performance to an existing tool for comparing general protein interfaces, InterComp, and showed improved performance on antibody cases achieved in a substantially reduced time. These results suggest that Ab-Ligity will allow the identification of diverse (sequence-dissimilar) antibodies that bind to the same epitopes from large datasets such as immune repertoires. The tool is available at http://opig.stats.ox.ac.uk/resources.
Fast 3D skeleton extraction of airways and applications to virtual bronchoscopy (2014)

In this paper, a novel automatic approach of computing 3D skeletons of airways is introduced, which is based on optimized double distance transform field and endpoints detection. The advanced double distance transform fields are constructed by the fast marching method (FMM). The endpoints are detected automatically combining 3D SUSAN corner detector and the local extreme value of distance from source (DFS). Furthermore, the minimum cost path scheme is used for searching a connected, one voxel thickness flight path of airways in virtual bronchoscopy. Experimental results show that the proposed method is centered, less sensitive to object noisiness, more accurate and more efficient. We have validated the robustness of the proposed method both quantitatively and qualitatively against clinical datasets.
Palladium: Preparation and Catalytic Properties of Particles of Uniform Size (1970)

A method has been developed for the preparation of uniform palladium particles of diameter from 55 to 450 angstroms. Uniform particles of gold layered on palladium were also synthesized. Hydrothermal treatment of aluminum hydroxide sol was used to prepare rods of alumina with uniform cross section from 100 to 500 angstroms and of varying lengths. The palladium was adsorbed as individual particles on alumina rods, both present in aqueous suspension. Then the suspension was dried to give a catalyst containing metal particles of uniform size dispersed in open pores produced by the intermeshing of the alumina rods. This procedure guaranteed the absence of diffusion control in the rate of reactions observed experimentally. All stages of the preparation were monitored with the electron microscope. The kinetics of the ethylene-hydrogen reaction were examined by means of a pulse technique. The number of active sites determined by carbon monoxide titration of the surface was equal to the number of surface atoms as determined by the calculation of the quantities of compounds involved in the synthesis and electron microscope examination. Furthermore, the activity per site depended on the method of preparation, being four times smaller when sodium formate was used as a reducing agent instead of sodium citrate. This may be due to the fact that the shape of particles makes certain crystallographic planes more favorable. Decrease in the size of particles to 56 angstroms produced no effect on catalytic activity beyond that due to the increase in the number of surface atoms. The activity of commercial 5 percent palladium on alumina diluted 100-fold with alumina gave 80.4 percent conversion with propylene and 82.7 percent conversion with ethylene. Thus there was little difference in the behavior of the two olefins.
Fingerprint recognition using neural network (2002)

The authors describe a neural network based approach for automated fingerprint recognition. Minutiae are extracted from the fingerprint image via a multilayer perceptron (MLP) classifier with one hidden layer. The backpropagation learning technique is used for its training. Selected features are represented in a special way such that they are simultaneously invariant under shift, rotation and scaling. Simulation results are obtained with good detection ratio and low failure rate. The proposed method is found to be reliable for a system with a small set of fingerprint data.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Mitotic Effects of a Constitutively Active Mutant of the <i>Xenopus</i> Polo-Like Kinase Plx1 (1999)

During mitosis the Xenopus polo-like kinase 1 (Plx1) plays key roles in the activation of Cdc25C, in spindle assembly, and in cyclin B degradation. Previous work has shown that the activation of Plx1 requires phosphorylation on serine and threonine residues. In the present work, we demonstrate that replacement of Ser-128 or Thr-201 with a negatively charged aspartic acid residue (S128D or T201D) elevates Plx1 activity severalfold and that replacement of both Ser-128 and Thr-201 with Asp residues (S128D/T201D) increases Plx1 activity approximately 40-fold. Microinjection of mRNA encoding S128D/T201D Plx1 into Xenopus oocytes induced directly the activation of both Cdc25C and cyclin B-Cdc2. In egg extracts T201D Plx1 delayed the timing of deactivation of Cdc25C during exit from M phase and accelerated Cdc25C activation during entry into M phase. This supports the concept that Plx1 is a "trigger" kinase for the activation of Cdc25C during the G(2)/M transition. In addition, during anaphase T201D Plx1 reduced preferentially the degradation of cyclin B2 and delayed the reduction in Cdc2 histone H1 kinase activity. In early embryos S128D/T201D Plx1 resulted in arrest of cleavage and formation of multiple interphase nuclei. Consistent with these results, Plx1 was found to be localized on centrosomes at prophase, on spindles at metaphase, and at the midbody during cytokinesis. These results demonstrate that in Xenopus laevis activation of Plx1 is sufficient for the activation of Cdc25C at the initiation of mitosis and that inactivation of Plx1 is required for complete degradation of cyclin B2 after anaphase and completion of cytokinesis.
Decentralized Economic Dispatch in Microgrids via Heterogeneous Wireless Networks (2012)

As essential building blocks of the future smart grid, microgrids can efficiently integrate various types of distributed generation (DG) units to supply the electric loads at the minimum cost based on the economic dispatch. In this paper, we introduce a decentralized economic dispatch approach such that the optimal decision on power generation is made by each DG unit locally without a central controller. The prerequisite power generation and load information for decision making is discovered by each DG unit via a multiagent coordination with guaranteed convergence. To avoid a slow convergence speed which potentially increases the generation cost because of the time-varying nature of DG output, we present a heterogeneous wireless network architecture for microgrids. Low-cost short-range wireless communication devices are used to establish an ad hoc network as a basic information exchange infrastructure, while auxiliary dual-mode devices with cellular communication capabilities are optionally activated to improve the convergence speed. Two multiagent coordination schemes are proposed for the single-stage and hierarchical operation modes, respectively. The optimal number of activated cellular communication devices is obtained based on the tradeoff between communication and generation costs. The performance of the proposed schemes is analyzed and evaluated based on real power generation and load data collected from the Waterloo Region in Canada. Numerical results indicate that our proposed schemes can better utilize the cellular communication links and achieve a desired tradeoff between the communication and generation costs as compared with the existing schemes.
Alternative RISC assembly: Binding and repression of microRNA–mRNA duplexes by human Ago proteins (2012)

MicroRNAs (miRNAs) are small noncoding RNAs that post-transcriptionally regulate protein output from the majority of human mRNAs. In contrast to the consensus view that all miRNAs are associated with Argonaute (Ago) proteins, we determine that miRNAs are expressed in a 13-fold excess relative to Agos in HeLa cells and that miRNAs are bound to mRNAs in a sevenfold excess relative to Agos, implying the existence of miRNA-mRNA duplexes not stoichiometrically bound by Agos. We show that all four human Agos can repress miRNA-mRNA duplexes, but only Ago2 can cleave small interfering RNA-mRNA duplexes in vitro. We visualize direct Ago binding to miRNA-mRNA duplexes in live cells using fluorescence lifetime imaging microscopy. In contrast to the consensus view that Agos bind miRNA duplexes, these data demonstrate that Agos can bind and repress miRNA-mRNA duplexes and support a model of catalytic Ago function in translational repression.
Multiple functions of pro‐parts of aspartic proteinase zymogens (1994)

The importance of aspartic proteinases in human pathophysiology continues to initiate extensive research. With burgeoning information on their biological functions and structures, the traditional view of the role of activation peptides of aspartic proteinases solely as inhibitors of the active site is changing. These peptide segments, or pro-parts, are deemed important for correct folding, targeting, and control of the activation of aspartic proteinase zymogens. Consequently, the primary structures of pro-parts reflect these functions. We discuss guidelines for formation of hypotheses derived from comparing the physiological function of aspartic proteinases and sequences of their pro-parts.
Construction of boundary element models in bioelectromagnetism (2000)

Multisensor electro- and magnetoencephalographic (EEG and MEG) as well as electro- and magnetocardiographic (ECG and MCG) recordings have been proved useful in noninvasively extracting information on bioelectric excitation. The anatomy of the patient needs to be taken into account, when excitation sites are localized by solving the inverse problem. In this work, a methodology has been developed to construct patient specific boundary element models for bioelectromagnetic inverse problems from magnetic resonance (MR) data volumes as well as from two orthogonal X-ray projections. The process consists of three main steps: reconstruction of 3-D geometry, triangulation of reconstructed geometry, and registration of the model with a bioelectromagnetic measurement system. The 3-D geometry is reconstructed from MR data by matching a 3-D deformable boundary element template to images. The deformation is accomplished as an energy minimization process consisting of image and model based terms. The robustness of the matching is improved by multi-resolution and global-to-local approaches as well as using oriented distance maps. A boundary element template is also used when 3-D geometry is reconstructed from X-ray projections. The deformation is first accomplished in 2-D for the contours of simulated, built from the template, and real X-ray projections. The produced 2-D vector field is back-projected and interpolated on the 3-D template surface. A marching cube triangulation is computed for the reconstructed 3-D geometry. Thereafter, a non-iterative mesh-simplification method is applied. The method is based on the Voronoi-Delaunay duality on a 3-D surface with discrete distance measures. Finally, the triangulated surfaces are registered with a bioelectromagnetic measurement utilizing markers. More than fifty boundary element models have been successfully constructed from MR images using the methods developed in this work. A simulation demonstrated the feasibility of X-ray reconstruction; some practical problems of X-ray imaging need to be solved to begin tests with real data.
Stable Isotope Probing with <sup>15</sup> N <sub>2</sub> Reveals Novel Noncultivated Diazotrophs in Soil (2007)

Biological nitrogen fixation is a fundamental component of the nitrogen cycle and is the dominant natural process through which fixed nitrogen is made available to the biosphere. While the process of nitrogen fixation has been studied extensively with a limited set of cultivated isolates, examinations of nifH gene diversity in natural systems reveal the existence of a wide range of noncultivated diazotrophs. These noncultivated diazotrophs remain uncharacterized, as do their contributions to nitrogen fixation in natural systems. We have employed a novel 15N2-DNA stable isotope probing (5N2-DNA-SIP) method to identify free-living diazotrophs in soil that are responsible for nitrogen fixation in situ. Analyses of 16S rRNA genes from 15N-labeled DNA provide evidence for nitrogen fixation by three microbial groups, one of which belongs to the Rhizobiales while the other two represent deeply divergent lineages of noncultivated bacteria within the Betaproteobacteria and Actinobacteria, respectively. Analysis of nifH genes from 15N-labeled DNA also revealed three microbial groups, one of which was associated with Alphaproteobacteria while the others were associated with two noncultivated groups that are deeply divergent within nifH cluster I. These results reveal that noncultivated free-living diazotrophs can mediate nitrogen fixation in soils and that 15N2-DNA-SIP can be used to gain access to DNA from these organisms. In addition, this research provides the first evidence for nitrogen fixation by Actinobacteria outside of the order Actinomycetales.
<title>Argon laser effect on demineralization of human enamel</title> (1992)

Previous studies have recorded the reduction of caries-like lesions in extracted human teeth that have been irradiated with CO<SUB>2</SUB> laser. Other studies have shown a decrease in dissolution rate of enamel that has been irradiated with CO<SUB>2</SUB> laser and acid resistance. This study was conducted to evaluate the effects of Argon laser irradiation on acid resistance and demineralization of dental enamel. Human enamel was laser irradiated with approximately 60 J/cm<SUP>2</SUP> and 120 J/cm<SUP>2</SUP>. The amount of demineralization was determined in a rotating disk assembly (0.1 M acetate buffer, pH-4.5) for 24 hours and the results determined and plotted against the nonlased control using microradiographs and computerized imaging. The amount of dissolution of tooth structure lost to demineralization in 4.5 pH acid bath in a 24 hour period was reduced from approximately 140 micrometers to approximately 70 micrometers . This study show that demineralization is reduced when human enamel is exposed to Argon laser irradiation.
Decolonising HCI and interaction design discourse: some considerations in planning AfriCHI (2016)

Bringing African theorists into the construction of African identity in HCI.
Oxidation of organic compounds with cerium(IV). XVII. Oxidation of 1,2-diarylethanes (1973)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTOxidation of organic compounds with cerium(IV). XVII. Oxidation of 1,2-diarylethanesWalter S. Trahanovsky and Darryl W. BrixiusCite this: J. Am. Chem. Soc. 1973, 95, 20, 6778–6780Publication Date (Print):October 1, 1973Publication History Published online1 May 2002Published inissue 1 October 1973https://pubs.acs.org/doi/10.1021/ja00801a041https://doi.org/10.1021/ja00801a041research-articleACS PublicationsRequest reuse permissionsArticle Views165Altmetric-Citations28LEARN 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
Reorientation in virtual environments using interactive portals (2014)

Real walking is the most natural method of navigation in virtual environments. However, physical space limitations often prevent or complicate its continuous use. Thus, many real walking interfaces, among them redirected walking techniques, depend on a reorientation technique that redirects the user away from physical boundaries when they are reached. However, existing reorientation techniques typically actively interrupt the user, or depend on the application of rotation gain that can lead to simulator sickness. In our approach, the user is reoriented using portals. While one portal is placed automatically to guide the user to a safe position, she controls the target selection and physically walks through the portal herself to perform the reorientation. In a formal user study we show that the method does not cause additional simulator sickness, and participants walk more than with point-and-fly navigation or teleportation, at the expense of longer completion times.
Elements and composition of software-defined data centers (2012)

We have designed and implemented a software stack, "Kumoi" for accelerating cloud middleware research and development. Kumoi first treats cloud resources such as virtual machines (VMs), physical machines and networks as first-class objects. This provides a means for uniform access to various distributed resources while hiding details without compromising functionalities. A scripting environment for making these objects together greatly simplifies the building of a cloud system. Use of this environment should improve efficiency and flexibility in research and development.