gebhart/patrepeval huggingface dataset:
Novel Fold and Carbohydrate Specificity of the Potent Anti-HIV Cyanobacterial Lectin from Oscillatoria agardhii (2010)

Oscillatoria agardhii agglutinin (OAA) is a recently discovered cyanobacterial lectin that exhibits potent anti-HIV activity. Up to now, only its primary structure and carbohydrate binding data have been available. To elucidate the structural basis for the antiviral mechanism of OAA, we determined the structure of this lectin by x-ray crystallography at 1.2 Å resolution and mapped the specific carbohydrate recognition sites of OAA by NMR spectroscopy. The overall architecture of OAA comprises 10 β-strands that fold into a single, compact, β-barrel-like domain, creating a unique topology compared with all known protein structures in the Protein Data Bank. OAA sugar binding was tested against Man-9 and various disaccharide components of Man-9. Two symmetric carbohydrate-binding sites were located on the protein, and a preference for Manα(1-6)Man-linked sugars was found. Altogether, our structural results explain the antiviral activity OAA and add to the growing body of knowledge about antiviral lectins.
A <scp>cladistic analysis of chloroplast</scp> DNA <scp>restriction site variation and morphology for the genera of the</scp> J<scp>uglandaceae</scp> (1995)

The phylogenetic relationships of the genera of the Juglandaceae are examined with cladistic analyses of chloroplast DNA (cpDNA) restriction site variation and morphology. Rates of evolution of the chloroplast genome are slower than in many other groups of plants, enabling the entire genome to be utilized at the intergeneric level. The trees resulting from the two independent analyses were completely congruent. The combined analysis of the two data sets produced a tree completely congruent with the cladogram from the two data sets analyzed independently. The cladogram is compared with previous classifications, cladistic analyses, and fossil history for the family. Although the topology resulting from the cladistic analyses of this study was strongly congruent with previous estimates of relationships within the family, the fossil record indicates that the basal‐most lineages in the cladistic trees arose later than the more terminal lineages. This reversed order of origin indicates that perhaps the rooting of the trees is erroneous.
PREDBALB/c: a system for the prediction of peptide binding to H2d molecules, a haplotype of the BALB/c mouse (2005)

PRED(BALB/c) is a computational system that predicts peptides binding to the major histocompatibility complex-2 (H2(d)) of the BALB/c mouse, an important laboratory model organism. The predictions include the complete set of H2(d) class I (H2-K(d), H2-L(d) and H2-D(d)) and class II (I-E(d) and I-A(d)) molecules. The prediction system utilizes quantitative matrices, which were rigorously validated using experimentally determined binders and non-binders and also by in vivo studies using viral proteins. The prediction performance of PRED(BALB/c) is of very high accuracy. To our knowledge, this is the first online server for the prediction of peptides binding to a complete set of major histocompatibility complex molecules in a model organism (H2(d) haplotype). PRED(BALB/c) is available at http://antigen.i2r.a-star.edu.sg/predBalbc/.
Knee surgery (1990)

The Hospital for Special Surgery, New York Hospital-Cornell University Medical College, New York, New York, USA Current Opinion in Rheumatology 1990, 2:160-162
THE PHOSPHODIESTERASE III INHIBITOR AMRINONE MODULATES CYTOKINE AND NITRIC OXIDE PRODUCTION IN IMMUNOSTIMULATED MACROPHAGES (1998)

Society of Critical Care Medicine; 27th Educational and Scientific Symposium; San Antonio, Texas, USA; February 4-8, 1998: Poster Hall: Thursday, February 5, 1998 5: 45-7: 15 pm; Friday, February 6, 1998 11: 40 am-1: 00 pm; Saturday, February 7, 1998 11: 40 am-1: 00 pm: Poster Presentations: Immunology
Assessing potential health risks from microcystin toxins in blue-green algae dietary supplements. (2000)

The presence of blue-green algae (BGA) toxins in surface waters used for drinking water sources and recreation is receiving increasing attention around the world as a public health concern. However, potential risks from exposure to these toxins in contaminated health food products that contain BGA have been largely ignored. BGA products are commonly consumed in the United States, Canada, and Europe for their putative beneficial effects, including increased energy and elevated mood. Many of these products contain Aphanizomenon flos-aquae, a BGA that is harvested from Upper Klamath Lake (UKL) in southern Oregon, where the growth of a toxic BGA, Microcystis aeruginosa, is a regular occurrence. M. aeruginosa produces compounds called microcystins, which are potent hepatotoxins and probable tumor promoters. Because M. aeruginosa coexists with A. flos-aquae, it can be collected inadvertently during the harvesting process, resulting in microcystin contamination of BGA products. In fall 1996, the Oregon Health Division learned that UKL was experiencing an extensive M. aeruginosa bloom, and an advisory was issued recommending against water contact. The advisory prompted calls from consumers of BGA products, who expressed concern about possible contamination of these products with microcystins. In response, the Oregon Health Division and the Oregon Department of Agriculture established a regulatory limit of 1 microg/g for microcystins in BGA-containing products and tested BGA products for the presence of microcystins. Microcystins were detected in 85 of 87 samples tested, with 63 samples (72%) containing concentrations > 1 microg/g. HPLC and ELISA tentatively identified microcystin-LR, the most toxic microcystin variant, as the predominant congener.
Array of cobalt nanoparticles in silica: Synthesis and effects of thermal annealing (2006)

The synthesis, characterization, and the effects of isochronal annealing of nearly monodispersive three-dimensional arrays of Co nanoparticles are presented. Samples were obtained by alternating electron beam evaporation of Co and SiO2 layers 0.5 and 20nm thick, respectively, onto fused silica. Transmission electron microscopy (TEM) revealed the presence of 3.2nm diameter Co particles with a size dispersion standard deviation of 16%. Annealing at temperatures up to 800°C was carried out in vacuum for 5min. Field and zero-field cooled measurements of the magnetic susceptibility monitored the effects of annealing on the magnetic behavior. Two temperature regimes were observed. One, up to 700°C with an activation energy of 0.062eV where no significant particle size change was observed, was tentatively related to bonding ordering within the particles. The other regime, with an activation energy of 0.67eV, was attributed to Co diffusion and reflected particle growth as observed by TEM. These results were supported by exchange bias anisotropy and x-ray photoelectron spectroscopy measurements.
Involvement of caspase activation through release of cytochrome<i>c</i>from mitochondria in apoptotic cell death of macrophages infected with<i>Actinobacillus actinomycetemcomitans</i> (2004)

We previously reported that infection with the periodontopathic bacterium Actinobacillus actinomycetemcomitans induced apoptosis in a mouse macrophage cell line J774.1. In the present study, we examined the involvement of cytochrome c and caspases in the induction of apoptosis in A. actinomycetemcomitans-infected J774.1 cells. Following infection, the expression levels of cytochrome c, and cleaved forms of caspase-3 and caspase-9 in the cells were examined using immunoblot analysis. Cytochrome c was released from mitochondria into the cytoplasm after A. actinomycetemcomitans-infected J774.1 cells were cultured for 6 h, and caspase-3 and caspase-9 were found to be cleaved forms in the cells. Further, caspase-9 activity was markedly increased, and phosphorylated p53 was detected in the cells 30 h following infection. These results suggest that apoptosis in A. actinomycetemcomitans-infected J774.1 cells is regulated by the release of cytochrome c from mitochondria into cytoplasm and the subsequent activation of caspases through phosphorylation of p53.
General, Label-Free Method for Determining <i>K</i><sub>d</sub> and Ligand Concentration Simultaneously (2015)

Some of the most commonly used affinity reagents (e.g., antibodies) are often developed and used in conditions where their input concentrations ([L]0) and affinities (K(d)) are not known. Here, we have developed a general approach to determine both [L]0 and K(d) values simultaneously for affinity reagents (small molecules, proteins, and antibodies). To do this, we perform quantitative equilibrium exclusion immunoassays with two different concentrations of target and fit the data simultaneously to determine K(d) and [L]0. The results give accurate and reproducible measures of both values compared to established methods. By performing detailed error analysis, we demonstrate that our fitting gives unique solutions and indicates where K(d) and [L]0 measures are reliable. Furthermore, we found that a divalent model of antibody binding gives accurate K(d) and [L]0 values in both the forward (antibody immobilized) and the reverse (target immobilized) assays-addressing the long-term problem of obtaining quantitative data from reverse assays.
Wideband monopulse tracking feed (2002)

This paper presents a compact monopulse tracking feed using a single corrugated horn and a TM/sub 01/ mode tracking coupler for wideband operation. The demo feed system is such that the communication channel operates from 12 to 30 GHz and the tracking channel operates from 24 to 28 GHz. The feed was designed to have a 10 dB beamwidth of 30 /spl deg/ to achieve the maximum efficiency for a Cassegrain antenna. The coupler is designed by a longitudinal traveling wave mechanism and utilizes the circular TE/sub 11/ and TM/sub 01/ modes that provide the sum and the difference channels, respectively, to achieve monopulse tracking.
Compiler techniques for enhancing data locality (1999)

Many applications are memory intensive and thus are bounded by memory latency and bandwidth. While improving memory performance is an important problem for uniprocessor machines, it is even more important for shared memory multiprocessors such as CC-NUMA (cache-coherent non-uniform memory access) machines. An architectural solution to the long memory latencies problem is to adopt a hierarchical memory system, where the higher levels (e.g., caches) are expensive, small, and fast whereas the lower levels (e.g., memories, secondary and tertiary storages) are cheaper, larger, and slower. Since the access latency varies from level to level, it is very important to utilize this memory hierarchy fully by having the majority of data accesses satisfied from the higher levels, i.e., caches. This dissertation first proposes a data transformation framework to improve cache locality. Instead of modifying the execution order of loop iterations as done by most of the current compiler techniques, the data transformations modify the memory layouts of large arrays. We illustrate the cases where data (memory layout) transformations are preferable to loop transformations and show how to generate code after a data layout transformation. Later we present a unified data locality optimization framework where both loop and data transformations are used in concert to improve cache locality. We demonstrate that such a unified framework achieves better results than frameworks based on pure loop or pure data transformations. We also quantify the benefits by giving performance numbers obtained on a single processor as well as multiple processors of SGI/Cray Origin 2000, a CC-NUMA machine. Our performance results on a uniprocessor as well as multiprocessors show marked improvements in cache misses and overall execution times. This unified technique can also be used for main memory-secondary storage hierarchy. We also briefly discuss how our approach can be made to work in an inter-procedural setting.
Corrections to “A Software-Defined Ultrasonic Networking Framework for Wearable Devices” (2019)

In Section VI of the above paper <xref ref-type="bibr" rid="ref1" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">[1]</xref> , incorrectly numbered reference citations were introduced during the editing of the paper. The citations should be as follows.
Sensitivity analysis of scattering parameters with electromagnetic time-domain simulators (2006)

We propose an efficient adjoint-variable approach to the sensitivity analysis of S-parameters obtained from full-wave electromagnetic (EM) time-domain simulations. It allows the computation of the S-parameter derivatives with respect to the design variables with negligible overhead. No solutions of adjoint EM problems are needed. The computation is done as an independent post-process outside the solver. The sole requirement is the ability of the solver to export the field solution at user-defined points. Most commercial solvers have this ability, which makes our approach readily applicable to practical design problems. The approach is verified through the analysis of waveguide and antenna structures using commercial simulators.
Replication genes of plasmid pE194-cop and repF: transcripts and encoded proteins (1990)

In vivo transcription of the replication region of plasmid pE194 yeidls two classes of mRNAs that encode Cop and RepF proteins, respectively. These transcripts are oriented 5' to 3' exclusively in the clockwise direction on the standard map. The cop region contains an open reading frame capable of encoding a 55-amino-acid protein that was demonstrated electrophoretically as a 6-kilodalton product synthesized in Bacillus subtilis minicells and chemically by N-terminal sequencing of a 116-kilodalton fusion protein with Escherichia coli beta-galactosidase. Four transcripts derived from the repF region were found, of which the longest, approximately 720 nucleotides, had the length, orientation, and transcription start site necessary to code for the full-length RepF protein (216 amino acid residues), deduced from the DNA sequence. The 5' ends of the shorter repF transcripts fall within the repF open reading frame. We propose that (i) cop specifies a protein rather than an RNA countertranscript, (ii) the Cop protein functions as a negative-acting element in pE194 replication by regulating synthesis of both RepF and of itself, and (iii) increased plasmid copy number can be explained in terms of cop region mutations that either reduce the intrinsic activity of Cop protein or the rate of its synthesis.
Mechanism of the Water Gas Shift Reaction on Pt:  First Principles, Experiments, and Microkinetic Modeling (2008)

We present a microkinetic model as well as experimental data for the low-temperature water gas shift (WGS) reaction catalyzed by Pt at temperatures from 523 to 573 K and for various gas compositions at a pressure of 1 atm. Thermodynamic and kinetic parameters for the model are derived from periodic, self-consistent density functional theory (DFT-GGA) calculations on Pt(111). The destabilizing effect of high CO surface coverage on the binding energies of surface species is quantified through DFT calculations and accounted for in the microkinetic model. Deviations of specific fitted model parameters from DFT calculated parameters on Pt(111) point to the possible role of steps/defects in this reaction. Our model predicts reaction rates and reaction orders in good agreement with our experiments. The calculated and experimental apparent activation energies are 67.8 kJ/mol and 71.4 kJ/mol, respectively. The model shows that the most significant reaction channel proceeds via a carboxyl (COOH) intermediate. Formate (HCOO), which has been experimentally observed and thought to be the key WGS intermediate in the literature, is shown to act only as a spectator species.
Synthesis and transilience of a 1,3-diazabiphenylene (1983)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis and transilience of a 1,3-diazabiphenyleneMarc d'Alarcao and Nelson J. LeonardCite this: J. Am. Chem. Soc. 1983, 105, 18, 5958–5960Publication Date (Print):September 1, 1983Publication History Published online1 May 2002Published inissue 1 September 1983https://doi.org/10.1021/ja00356a063RIGHTS & PERMISSIONSArticle Views115Altmetric-Citations9LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (441 KB) Get e-AlertsSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
SEROLOGY OF <i>NEISSERIA GONORRHOEAE.</i> CHARACTERIZATION OF RABBIT HYPERIMMUNE ANTISERA BY LINE‐ROCKET IMMUNOELECTROPHORESIS FOR USE IN COAGGLUTINATION (1980)

The co-agglutination (COA) and line-rocket immunoelectrophoresis (L-RIE) techniques were investigated for the serological classification of Neisseria gonorrhoeae. COA with absorbed sera was found to demonstrate "strain-specific" as well as cross-reacting antigens. The results were dependent on the immunizing, absorbing and agglutinating properties of a particular strain. Heated (100 degrees C) whole cells were found to be more reactive in the COA tests than untreated or formalin-fixed organisms. It was possible by L-RIE to compare the antigenic relationship between at least 20 strains in a single test run. This technique was applied on the 16 major outer membrane protein (MOMP) reference strains, which could then be divided into two separate groups with regard to cross-reacting antigens. Based on the findings by the L-RIE tests, selective absorptions of antibodies were performed for use in preparation of COA reagents. It was found that the reactions of these reagents with the MOMP reference strains could be assigned to three different antigenic classes. Reagents prepared for these classes are proposed as a basis for serological classification of Neisseria gonorrhoeae.
21001 Molecular Dynamics Study on the Effect of Interaction between Hg and Fe on the Strength of Fe (2009)

First principle calculations were conducted to elucidate the primary mechanism of Liquid Metal Embrittlement (LME) on Fe-Hg system. The calculational results were compared with Fe-Sb and Cu-Hg systems, in both of which LME is observed. Our computational results show that the extent of the fluctuation on charge density distributions caused by the liquid metal atom negatively correlates with the probability of LME. Although the distributions of the total energy with respect to the distance between the solid and liquid atoms and to lattice size tangential to the solid surface are strongly dependent on the liquid metal materials, they are not seen to relate with the probability of LME.
T-cadherin is present on endothelial microparticles and is elevated in plasma in early atherosclerosis (2010)

Our findings reveal a novel mechanism of T-cad-dependent signalling in the vascular endothelium. We identify T-cad as an endothelial MP antigen in vivo and demonstrate that its level in plasma is increased in early atherosclerosis and correlates with endothelial dysfunction.
Complex Histories of Genes Encoding 3-Hydroxy-3-methylglutaryl-CoenzymeA Reductase (2005)

The mevalonate pathway for the synthesis of isoprenoids can be found in organisms from all domains of life. It has been previously demonstrated that the first gene specific to that pathway, which encodes the enzyme 3-hydroxy-3-methylglutaryl-CoenzymeA reductase (HMGR), has been transferred between domains by lateral gene transfer on several occasions. Here we look within the domain Bacteria at lateral acquisition of HMGR, whether as a single gene or as part of a mevalonate pathway cluster. We observe a complex history of multiple transfer events probably reflecting the fact that HMGR could be beneficial in a variety of physiological and genetic contexts. We demonstrate that even in Vibrio species, where HMGR is not clustered with other genes to form an operon or a metabolic cluster, it is under strong purifying selection.
Status and developments of animal cell technology using suspension culture techniques (1982)

Abstract In this review the state of the art in animal cell technology, using suspension culture techniques is updated as far as the end of 1980. We have tried to discuss, on a broad basis, the current status and potential developments of both, the purely biological and the biochemical engineering aspects which may be important to improve the performance and design of animal cell technologies. The process economics could be considerably improved by the use of transformed animal cell substrates, the use of cheaper cultivation media and by methodological and engineering means. Most of these aspects are in the state of realization. Nevertheless, for a great variety of biological active substances which do not require so – or posttranslational processing, recombinant DNA‐techniques (e.g. genetic engineering) are a promising alternative for the production of animal cell derived substances.
Review on space robotics: Toward top-level science through space exploration (2017)

Robotics and autonomous systems have been instrumental to space exploration by enabling scientific breakthroughs and by fulfilling human curiosity and ambition to conquer new worlds. We provide an overview of space robotics as a rapidly emerging field, covering basic concepts, definitions, historical context, and evolution. We further present a technical road map of the field for the coming decades, taking into account major challenges and priorities recognized by the international space community. Space robotics represents several key enablers to a wide range of future robotic and crewed space missions as well as opportunities for knowledge and technology transfer to many terrestrial sectors. In the greater humanitarian context, space robotics inspires both current and future generations to exploration and critical study of science, technology, engineering, and mathematics.
Radiation efficiency of printed slot antennas backed by a ground reflector (2002)

Although in the literature the back-reflector technique has been extensively used as a means of rendering the slot patterns unidirectional, there is no quantitative information on the effectiveness of this approach. In this work, the use of a back reflector as a means of increasing the efficiency and antenna gain of printed slot antennas is evaluated. For this purpose, the radiation efficiency of reflector-backed printed slot antennas on either electrically thin or thick substrates is thoroughly characterized; both single and twin slot elements are considered. Twin slot elements have been previously proposed for the reduction of the coupling to the dominant surface-wave mode in the case of electrically thick substrates. In this article, twin slot elements are explored as a means of enhancing the radiation efficiency of printed slots backed by a ground reflector. It is shown that in the case of thick substrates, simultaneous partial cancellation of the surface-wave and the parallel-plate TEM modes can be achieved. On the other hand, in the case of thin substrates where the back radiation is severe, the twin slot element can be utilized for the drastic reduction of the parallel-plate TEM mode.