gebhart/patrepeval huggingface dataset:
A Dynamic Defect Generation Strategy for Efficient Enzyme Immobilization in Robust Metal‐Organic Frameworks for Catalytic Hydrolysis and Chiral Resolution (2023)

Abstract Enzyme immobilization has been demonstrated to be a favorable protocol for promoting the industrialization of bioactive molecules, but still with formidable challenge. Addressing this challenge, we create a dynamic defect generation strategy for enzyme immobilization by using the dissociation equilibrium of metal‐organic frameworks (MOFs) mediated by enzymes. Enzymes can act as “macro ligands” to generate competitive coordination against original ligands, along with the release of metal clusters of MOFs to generate defects, hence promoting the gradual transport of enzymes from the surface to inside. Various enzymes can be efficiently immobilized in MOFs to afford composites with good enzymatic activities, protective performances and exceptional reusabilities. Moreover, multienzyme bioreactors capable of efficient cascade reactions can also be generated. This study provides new opportunities to construct highly efficient biocatalysts incorporating different types of enzymes.
Using Antibodies and Mutants To Localize the Presumptive gH/gL Binding Site on Herpes Simplex Virus gD (2018)

HSV virus-cell and cell-cell fusion requires multiple interactions between four essential virion envelope glycoproteins, gD, gB, gH, and gL, and between gD and a cellular receptor, nectin-1 or herpesvirus entry mediator (HVEM). Current models suggest that binding of gD to receptors induces a conformational change that leads to activation of gH/gL and consequent triggering of the prefusion form of gB to promote membrane fusion. Since protein-protein interactions guide each step of fusion, identifying the sites of interaction may lead to the identification of potential therapeutic targets that block this process. We have previously identified two "faces" on gD: one for receptor binding and the other for its presumed interaction with gH/gL. We previously separated the gD monoclonal antibodies (MAbs) into five competition communities. MAbs from two communities (MC2 and MC5) neutralize virus infection and block cell-cell fusion but do not block receptor binding, suggesting that they block binding of gD to gH/gL. Using a combination of classical epitope mapping of gD mutants with fusion and entry assays, we identified two residues (R67 and P54) on the presumed gH/gL interaction face of gD that allowed for fusion and viral entry but were no longer sensitive to inhibition by MC2 or MC5, yet both were blocked by other MAbs. As neutralizing antibodies interfere with essential steps in the fusion pathway, our studies strongly suggest that these key residues block the interaction of gD with gH/gL.<b>IMPORTANCE</b> Virus entry and cell-cell fusion mediated by HSV require gD, gH/gL, gB, and a gD receptor. Neutralizing antibodies directed against any of these proteins bind to residues within key functional sites and interfere with an essential step in the fusion pathway. Thus, the epitopes of these MAbs identify critical, functional sites on their target proteins. Unlike many anti-gD MAbs, which block binding of gD to a cellular receptor, two, MC2 and MC5, block a separate, downstream step in the fusion pathway which is presumed to be the activation of the modulator of fusion, gH/gL. By combining epitope mapping of a panel of gD mutants with fusion and virus entry assays, we have identified residues that are critical in the binding and function of these two MAbs. This new information helps to define the site of the presumptive interaction of gD with gH/gL, of which we have limited knowledge.
A Proteomics Study of Brassinosteroid Response in Arabidopsis (2007)

The plant steroid hormones brassinosteroids (BRs) play an important role in a wide range of developmental and physiological processes. How BR signaling regulates diverse processes remains unclear. To understand the molecular details of BR responses, we performed a proteomics study of BR-regulated proteins in Arabidopsis using two-dimensional DIGE coupled with LC-MS/MS. We identified 42 BR-regulated proteins, which are predicted to play potential roles in BR regulation of specific cellular processes, such as signaling, cytoskeleton rearrangement, vesicle trafficking, and biosynthesis of hormones and vitamins. Analyses of the BR-insensitive mutant bri1-116 and BR-hypersensitive mutant bzr1-1D identified five proteins (PATL1, PATL2, THI1, AtMDAR3, and NADP-ME2) affected both by BR treatment and in the mutants, suggesting their importance in BR action. Selected proteins were further studied using insertion knock-out mutants or immunoblotting. Interestingly about 80% of the BR-responsive proteins were not identified in previous microarray studies, and direct comparison between protein and RNA changes in BR mutants revealed a very weak correlation. RT-PCR analysis of selected genes revealed gene-specific kinetic relationships between RNA and protein responses. Furthermore BR-regulated posttranslational modification of BiP2 protein was detected as spot shifts in two-dimensional DIGE. This study provides novel insights into the molecular networks that link BR signaling to specific cellular and physiological responses.
Artificial lateral line systems for feedback control of underwater robots (2012)

A lateral line system, consisting of arrays of flow-sensing neuromasts, allows fish and amphibians to probe their ambient environment and plays a vital role in their behaviors spanning predator/prey detection, schooling, rheotaxis, courtship and communication. The feats of biological lateral lines have inspired an increasing interest in engineering a similar sensing module for underwater robots and vehicles. Often known as artificial lateral lines, these sensors could potentially enable an underwater robot to detect and identify moving or stationary objects, and exploit ambient flow energy for efficient locomotion. Despite the advances made in this area, realizing a practical artificial lateral line still faces significant challenges in both signal processing and flow sensor fabrication. 
In this dissertation we describe our effort in developing signal processing methods for hydrodynamic object localization and tracking using an artificial lateral line (ALL). We consider two types of objects, a vibrating sphere and a non-vibrating cylinder, both of which are of interest in underwater applications. A vibrating sphere, known as a dipole source, is widely used in the study of biological lateral lines and it emulates the rhythmic body or fin movement. A non-vibrating cylinder (with unknown cross-section shape), on the other hand, represents a general moving or stationary object underwater with a 2D flow profile. 
First, a novel bio-inspired artificial lateral line system is proposed for underwater robots and vehicles by exploiting the inherent sensing capability of ionic polymer-metal composites (IPMCs). Analogous to its biological counterpart, the IPMC-based lateral line processes the sensor signals through a neural network, and we demonstrate the performance of this approach in the localization of a dipole source. 
Second, with an assumption of potential flows, we formulate nonlinear estimation problems for the localization and tracking of a dipole source based on analytical flow models, and propose and compare several algorithms for solving the problem. For the case of a moving cylinder, we use conformal mapping to represent a general cross-section profile, and explore the use of Kalman-filtering-type techniques in the tracking and size/shape estimation of the object. 
We have conducted extensive experiments to validate the developed algorithms with an artificial lateral line prototype made of millimeter-scale IPMC sensors, with sensor-to-sensor separation of 2 cm, which is determined through an optimization process based on the Cramer-Rao bound (CRB) analysis. 
Finally, we experimentally explore the use of IPMC sensors for estimating the hydrodynamic parameters involved in a Karman vortex street that is created by a stationary cylinder in a flow. We validate that the vortex shedding frequency, which can be extracted from the sensor signal, shows clear correlation with the flow speed and the obstacle size.
Discovering the link between nutrition and skin aging (2012)

Skin has been reported to reflect the general inner-health status and aging. Nutrition and its reflection on skin has always been an interesting topic for scientists and physicians throughout the centuries worldwide. Vitamins, carotenoids, tocopherols, flavonoids and a variety of plant extracts have been reported to possess potent anti-oxidant properties and have been widely used in the skin care industry either as topically applied agents or oral supplements in an attempt to prolong youthful skin appearance. This review will provide an overview of the current literature "linking" nutrition with skin aging.
Synthesis of (3S,4S)-4-amino-3-hydroxy-6-methylheptanoic acid derivatives. Analysis of diastereomeric purity (1978)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis of (3S,4S)-4-amino-3-hydroxy-6-methylheptanoic acid derivatives. Analysis of diastereomeric purityDaniel H. Rich, Eric T. Sun, and Amrit S. BoparaiCite this: J. Org. Chem. 1978, 43, 18, 3624–3626Publication Date (Print):September 1, 1978Publication History Published online1 May 2002Published inissue 1 September 1978https://pubs.acs.org/doi/10.1021/jo00412a053https://doi.org/10.1021/jo00412a053research-articleACS PublicationsRequest reuse permissionsArticle Views468Altmetric-Citations94LEARN 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
Electrical and Electromagnetic Monitoring of a Salt Water Injection Experiment (1993)

PreviousNext No AccessSymposium on the Application of Geophysics to Engineering and Environmental Problems 1993Electrical and Electromagnetic Monitoring of a Salt Water Injection ExperimentAuthors: David L. AlumbaughH. F. MorrisonDavid L. AlumbaughLawrence Berkeley Laboratory and University of California at Berkeley and H. F. MorrisonLawrence Berkeley Laboratory and University of California at Berkeleyhttps://doi.org/10.4133/1.2922039 SectionsAboutPDF/ePub ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinked InRedditEmail Abstract Introductory paragraph for this paper is available only in the PDF and GZipped PS filesPermalink: https://doi.org/10.4133/1.2922039FiguresReferencesRelatedDetails Symposium on the Application of Geophysics to Engineering and Environmental Problems 1993ISSN (online):1554-8015Copyright: 1993 Pages: 694 publication data© 1993 Copyright © 1993 The Environmental and Engineering Geophysical SocietyPublisher:Environmental & Engineering Geophysical Society HistoryPublished: 30 Sep 2008 CITATION INFORMATION David L. Alumbaugh and H. F. Morrison, (1993), "Electrical and Electromagnetic Monitoring of a Salt Water Injection Experiment," Symposium on the Application of Geophysics to Engineering and Environmental Problems Proceedings : 597-598. https://doi.org/10.4133/1.2922039 Plain-Language Summary PDF DownloadLoading ...
Effects of Anion Proximity in Peptide Primary Sequence on the Rate and Mechanism of Leucine Oxidation (2006)

Hydroxyl radical surface mapping is a useful tool for investigating protein structure and folding. The rate of protein side-chain oxidation by the hydroxyl radical is known to be affected primarily by the chemical reactivity of the side chain and the accessibility of the reactive site to the radical. Efforts have been made to determine the inherent rate of stable product formation of each amino acid side chain, so that the rate of oxidation of an amino acid can be used to accurately estimate the average solvent accessibility of the amino acid side chain in the folded protein. However, the effects of nearby primary sequence on peptide oxidation have not been studied. Here, we examine the amounts of various oxidation products of a small peptide consisting of one leucine and one aspartic acid separated by zero to five glycine residues, as well as with modification of the N- and C-terminus. We find that the relative amounts of certain oxidation products can be heavily influenced by the primary structure of the surrounding peptide. The formation of many products, including hydroxylation, is inhibited by proximity to negative charges, while the formation of other products showed more complicated responses to changing primary sequence.
Potential responders to FOLFOX therapy for colorectal cancer by Random Forests analysis (2011)

Random Forests on gene-expression data for CRC patients was effectively able to stratify responders to FOLFOX therapy with high accuracy, and use of pharmacogenomics in anticancer therapy is the first step in planning personalised therapy.
Relaxation of Proton Conductivity and Stress in Proton Exchange Membranes Under Strain (2006)

The stress relaxation and proton conductivity of Nafion 117 membrane (N117-H) and sulfonated poly(arylene ether sulfone) copolymer membrane with 35% sulfonation (BPSH35) in acid forms were investigated under uniaxial loading conditions. The results showed that when the membranes were stretched, their proton conductivities in the direction of the strain initially increased compared to the unstretched films. The absolute increases in proton conductivities were larger at higher temperatures. It was also observed that proton conductivities relaxed exponentially with time at 30°C. In addition, the stress relaxation of N117-H and BPSH35 films under both atmospheric and an immersed (in deionized water) condition was measured. The stresses were found to relax more rapidly than the proton conductivity at the same strains. An explanation for the above phenomena is developed based on speculated changes in the channel connectivity and length of proton conduction pathway in the hydrophilic channels, accompanied by the rotation, reorientation, and disentanglements of the polymer chains in the hydrophobic domains.
β‐adrenoceptor subtypes mediating the airways response to BRL 35135 in man (1993)

1 The purpose of the study was to assess the bronchorelaxant effects of the beta3-adrenoceptor agonist BRL 35135 in normal human airways. 2 Eight healthy male subjects were studied, having previously demonstrated airways responsiveness to inhaled salbutamol 200 microg, with a group mean (+/- s.e. mean) fall in airways resistance (Raw), from baseline, of 37 +/- 5%. 3 Subjects attended the laboratory on 3 separate days, having fasted and taken placebo (PL) or nadolol 20 mg (N20), 2 h previously. 4 After 30 min rest, baseline measurements of Raw, serum potassium, glucose and free fatty acid were performed before subjects were given single oral doses of BRL 35135 8 mg (BRL) or placebo BRL. Measurements were repeated 60 min after the BRL or placebo BRL were given. 5 There was a significant (P < 0.05) fall in Raw (% change from baseline, as means and 95% CI) with PL/BRL: -32(-18, -46), compared with either PL/PL: -8(5, -21), or N20/BRL: -11(2, -24). There was no significant difference between PL/PL and N20/BRL. 6 A similar pattern to Raw was observed for both of the beta2-mediated metabolic responses which were also antagonised by nadolol. For the potassium response (mmol l(-1)), there was a significant (P < 0.05) difference between PL/BRL: -0.50(-0.31, -0.69), in comparison with either PL/PL: 0.08(-0.11, 0.27) or N20/BRL: 0.09(-0.10, 0.28), but values for PL/PL and N20/BRL were not significantly different. In contrast, with the free fatty acid response (nmol 1(-1)), the increase seen with N20/BRL: 85(1.0, 171.0) was significantly (P < 0.05) different from PL/PL: 3.7(-82.3, 89.8), but was not different from PL/BRL: 132.5(46.5, 218.5). 7 In conclusion, BRL 35135 produced airways, potassium and glucose responses which were antagonised by nadolol, whereas the lipolysis response was not. This suggests that there are not functional beta3-adrenoceptors in human airways.
Ray tracing animated scenes using coherent grid traversal (2006)

We present a new approach to interactive ray tracing of moderate-sized animated scenes based on traversing frustum-bounded packets of coherent rays through uniform grids. By incrementally computing the overlap of the frustum with a slice of grid cells, we accelerate grid traversal by more than a factor of 10, and achieve ray tracing performance competitive with the fastest known packet-based kd-tree ray tracers. The ability to efficiently rebuild the grid on every frame enables this performance even for fully dynamic scenes that typically challenge interactive ray tracing systems.
Explicit expressions for totally symmetric spherical functions and symmetry-dependent properties of multipoles (2014)

Closed expressions for matrix elements 〈 lm' | A (G)| lm 〉, where | lm 〉 are spherical functions and A (G) is the average of all symmetry operators of point group G, are derived for all point groups (PGs) and then used to obtain linear combinations of spherical functions that are totally symmetric under all symmetry operations of G. In the derivation, we exploit the product structure of the groups. The obtained expressions are used to explore properties of multipoles of symmetric charge distributions. We produce complete lists of selection rules for multipoles Q l and their moments Q lm , as well as of numbers of independent moments in a multipole, for any l and m and for all PGs. Periodicities and other trends in these properties are revealed.
ChemInform Abstract: Inhibition of Neutral Metalloendopeptidase and Angiotesin‐Converting Enzyme by Selected Naturally Occurring Chromone Derivatives. (1999)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
SYNTHESIS, STRUCTURE AND REACTIVITY OF SalanH2-METAL COMPLEXES (1996)

Abstract The present work is an exploration into synthesis of complexes of general formula LH2M (where M = Mn, Fe, Cu, and Al). The results obtained for L = Salophan (M = Fe (1), Cu (2)); Salomphan (M = Mn (3), Fe(4), Cu(5); Salpan (M = Fe(6), Cu(7)) and L = Salean (M = AlCl) (8) are reported. When 8 is dissolved in MeOH, [SaleanH2AlOMe]2 (9) is formed. In MeOH, and in the presence of air, 1 and 4 undergo oxidation of both the ligand and metal (Fe(II) to Fe(III) to form the "half" Schiff base complexes, [SalophanHFeOMe]2 (10) and [SalomphanHFeOMe]2 (11). Compounds 9–11 were structurally characterized. Crystal Data: (9) C36H46Al2N4O7, Space Group P-1 (no. 2) with a = 7.536(1) Å, b = 10.513(2)Å, c = 11.997(2) Å, α = 97.72(1), β = 94.040(10)°, γ = 102.73(1), V = 914.8(3) Å3 and Z = 2. With 226 parameters refined on 1226 reflections having F>6.0[sgrave](F), the final R values were R = 0.0540 and Rw = 0.0565; (10), C46H46Fe2N4O8, Space Group P-1 (no. 2) with a = 9.400(2) Å, b = 10.718(4) Å, c = 12.354(3) Å, α = 76.28(3), β = 67.89(2)°, γ = 86.63(3), V = 1119.7(7) Å3 and Z = 2. With 289 parameters refined on 1327 reflections having F>6.0[sgrave](F), the final R values were R = 0.0672 and Rw = 0.0749; (11), C48H54Fe2N4O8, Space Group P-1 (no. 2) with a = 9.047(2) Å, b = 11.723(2) Å, c = 12.419(3) Å, α = 80.14(2), β = 68.68(3)°, γ = 85.88(2), V = 1208.8(4) Å3 and Z = 2. With 307 parameters refined on 2171 reflections having F>4.0[sgrave](F), the final R values were R = 0.0546 and Rw = 0.0573. Key Words: SalanH4 SalenH2 ironaluminiumX-ray structure
Annexin B1 fromTaenia soliummetacestodes is a newly characterized member of the annexin family (2007)

Abstract We previously reported cloning of the Taenia solium annexin B1 gene from a metacestode cDNA expression library and demonstrated that it acts as a protective antigen for effective vaccine development against cysticercosis. In the present study we produced recombinant annexin B1 and antiserum against the protein to investigate its structural and functional properties. Western blotting of metacestode fractions indicated that T. solium annexin B1, similar to vertebrate annexins, associates with acid phospholipids in the presence of Ca 2+ . This property was confirmed by the recognition of apoptotic cells by labeled annexin B1. CD spectroscopy results demonstrated that α-helices are the main secondary structures of the protein. Ca 2+ binding increases the α-helix content and causes significant thermal stabilization with a melting temperature increase of approximately 10°C. Functional Ca 2+ -dependent phospholipid binding sites of annexin B1 were investigated using mutant proteins. By changing a conserved acidic amino acid residue that putatively combines Ca 2+ in each domain of annexin B1 singly or in combination, we found that Ca 2+ binding in the first domain is more important than that at the other Ca 2+ binding sites. Annexin B1 is a metacestode stage-specific antigen, with the protein being mainly localized in the teguments and surrounding cyst wall of T. solium metacestodes, suggesting a role in the parasite-host interaction.