gebhart/patrepeval huggingface dataset:
Toward “metalloMOFzymes”: Metal–Organic Frameworks with Single-Site Metal Catalysts for Small-Molecule Transformations (2016)

Metal-organic frameworks (MOFs) are being increasingly studied as scaffolds and supports for catalysis. The solid-state structures of MOFs, combined with their high porosity, suggest that MOFs may possess advantages shared by both heterogeneous and homogeneous catalysts, with few of the shortcomings of either. Herein, efforts to create single-site catalytic metal centers appended to the organic ligand struts of MOFs will be discussed. Reactions important for advanced energy applications, such as H2 production and CO2 reduction, will be highlighted. Examining how these active sites can be introduced, their performance, and their existing limitations should provide direction for design of the next generation of MOF-based catalysts for energy-relevant, small-molecule transformations. Finally, the introduction of second-sphere interactions (e.g., hydrogen bonding via squaramide groups) as a possible route to enhancing the activity of these metal centers is reported.
Does IC design have a future in the clouds? (2010)

Cloud computing is used to describe a collection of (remote) data centers (the hardware and the software) and applications delivered from them as a service (SaaS, Software as a Service). Its success is driven by the cost-effective on-demand availability of large, scalable amounts of computing resources. The cloud has become an established paradigm for many enterprise and consumer applications such as email, web servers, productivity applications, customer relationship management, etc. However, in IC design its success is still limited.
Transport Mechanisms Underlying Ionic Conductivity in Nanoparticle-Based Single-Ion Electrolytes (2020)

Recent studies have demonstrated the potential of nanoparticle-based single-ion conductors as battery electrolytes. In this work, we introduce a coarse-grained multiscale simulation approach to identify the mechanisms underlying the ion mobilities in such systems and to clarify the influence of key design parameters on conductivity. Our results suggest that for the experimentally studied electrolyte systems, the dominant pathway for cation transport is along the surface of nanoparticles, in the vicinity of nanoparticle-tethered anions. At low nanoparticle concentrations, the connectivity of cationic surface transport pathways and conductivity increase with nanoparticle loading. However, cation mobilities are reduced when nanoparticles are in close vicinity, causing conductivity to decrease for sufficiently high particle loadings. We discuss the impacts of cation and anion choice as well as solvent polarity within this picture and suggest means to enhance ionic conductivities in single-ion conducting electrolytes based on nanoparticle salts.
The Influence of Immune Complex-Bearing Follicular Dendritic Cells on the IgM Response, Ig Class Switching, and Production of High Affinity IgG (2005)

It is believed that Ag in immune complexes (ICs) on follicular dendritic cells (FDCs) selects high affinity B cells and promotes affinity maturation. However, selection has been documented in the absence of readily detectable ICs on FDCs, suggesting that FDC-ICs may not be important. These results prompted experiments to test the hypothesis that IC-bearing murine FDCs can promote high affinity IgG responses by selecting B cells after stimulating naive IgM(+) cells to mature and class switch. Coculturing naive lambda(+) B cells, FDCs, (4-hydroxy-3-nitrophenyl)acetyl-chicken gamma-globulin (CGG) + anti-CGG ICs, and CGG-primed T cells resulted in FDC-lymphocyte clusters and production of anti-4-hydroxy-5-iodo-3-nitrophenyl acetyl. Class switching was indicated by a shift from IgM to IgG, and affinity maturation was indicated by a change from mostly low affinity IgM and IgG in the first week to virtually all high affinity IgG anti-4-hydroxy-5-iodo-3-nitrophenyl acetyl in the second week. Class switching and affinity maturation were easily detectable in the presence of FDCs bearing appropriate ICs, but not in the absence of FDCs. Free Ag plus FDCs resulted in low affinity IgG, but affinity maturation was only apparent when FDCs bore ICs. Class switching is activation-induced cytidine deaminase (AID) dependent, and blocking FDC-CD21 ligand-B cell CD21 interactions inhibited FDC-IC-mediated enhancement of AID production and the IgG response. In short, these data support the concept that ICs on FDCs can promote AID production, class switching, and maturation of naive IgM(+) B cells, and further suggest that the IC-bearing FDCs help select high affinity B cells that produce high affinity IgG.
An RNA polymerase from the ocean improves in vitro RNA synthesis (560.1) (2014)

Phages in the ocean harbor the greatest diversity of protein on the earth. Since a large portion of these proteins must play roles in nucleic acids metabolism, one would expect numerous novel mechanisms underlying the fundamental processes including transcription, DNA replication, and recombination and thus abundant molecular reagents therein. We recently characterized the single subunit RNA polymerase from marine cyanophage Syn5 and identified its promoter sequence. This marine enzyme catalyzes RNA synthesis over a wide range of temperature and salinity. Its processivity is greater than 30,000 nt without any significant intermediate products. Most important, Syn5 RNA polymerase produces precise run‐off transcripts with homogeneous 3’ termini. The enzyme predominantly used for in vitro run‐off RNA synthesis‐T7 RNA polymerase synthesizes, in addition to run‐off products of precise length, transcripts with an additional non‐base‐paired nucleotide at the 3’‐terminus (N+1 product). Therefore, the enzyme is advantageous for the production of RNAs that require precise 3’‐termini, such as tRNAs and RNA fragments that are used for subsequent assembly.
Particle Swarm Optimization and Image Analysis (2009)

Particle Swarm Optimization (PSO) is a simple but powerful optimization algorithm, introduced by Kennedy and Eberhart (Kennedy 1995). Its search for function optima is inspired by the behavior of flocks of birds looking for food. Similarly to birds, a set (swarm) of agents (particles) fly over the search space, which is coincident with the function domain, looking for the points where the function value is maximum (or minimum). In doing so, each particle’s motion obeys two very simple difference equations which describe the particle’s position and velocity update. A particle’s motion has a strong random component (exploration) and is mostly independent from the others’; in fact, the only piece of information which is shared among all members of the swarm, or of a large neighborhood of each particle, is the point where the best value for the function has been found so far. Therefore, the search behavior of the swarm can be defined as emergent, since no particle is specifically programmed to achieve the final collective behavior or to play a specific role within the swarm, but just to perform a much simpler local task. This chapter introduces the basics of the algorithm and describes the main features which make it particularly efficient in solving a large number of problems, with particular regard to image analysis and to the modifications that must be applied to the basic algorithm, in order to exploit its most attractive features in a domain which is different from function optimization.
Measuring Coronary Artery Capillary Resistance with Variable Inflow Conditions (2021)

A better understanding of the effects of variable inflow velocities on coronary capillary resistance is essential to creating a predictive model for personalized coronary flow. This paper proposes an experimental setup and presents measurement results for coronary artery capillary resistance with variable inflow conditions. A peristaltic pump with a programmable controller is used to pump fluid into distal coronary artery branches of cadaveric porcine hearts. The resulting pressures are recorded using transduced continuous pressure monitoring. The paper analyses the transient resistive pressure in coronary arteries and shows the capillary resistive pressures as a function of variable inflow conditions.
A Comment on the Weiss–Weinstein Bound for Constrained Parameter Sets (2008)

The Weiss-Weinstein bound (WWB) provides a lower limit on the mean-squared error (MSE) achievable by an estimator of an unknown random parameter. In this correspondence, it is shown that some previously proposed simplified versions of the bound do not always hold for constrained parameters, i.e., parameters whose distribution has finite support. These simplifications can produce results which are no longer lower bounds on the MSE. Sufficient conditions are provided for the reductions to be valid.
Computer‐Aided Design and Synthesis of 1‐{4‐[(3,4‐Dihydroxybenzylidene)amino]phenyl}‐5‐oxopyrrolidine‐3‐carboxylic Acid as an Nrf2 Enhancer (2018)

Invited for this month's cover is Prof. Arie Gruzman (Bar-Ilan University) and collaborators who have developed an Nrf2 enhancer. This compound activated the Nrf2 transduction pathway and because of this the translation of dozens of antioxidant cytoprotective proteins in a dose- and time-dependent manner and protected PC-12 cells against oxidative stress. Considering the imbalance between production and elimination of oxidative species involved in the pathophysiology of many human diseases, this compound is a promising starting point for the development of novel therapeutics for the treatment of oxidative-stress-related diseases. Read the full text of the article at 10.1002/cplu.201700539.
Optical properties and laser characteristics of highly Nd3+-doped Y3Al5O12 ceramics (2000)

Diode-pumped laser oscillation in highly Nd3+-doped polycrystalline Y3Al5O12 (YAG) ceramics has been demonstrated. The Nd:YAG ceramics are highly transparent; the loss of a 2.3 at. % neodymium-doped ceramic is as low as that of a 0.9 at. % Nd:YAG single crystal. The high doping of Nd3+ ions realizes large pump absorption; a 6.6 at. %-doped ceramic has an absorption coefficient of 60.4 cm−1 at 808 nm. The same concentration quenching parameter is obtained between the Nd:YAG ceramics and Nd:YAG single crystals. A laser using an 847-μm-thick 3.4 at. % Nd:YAG ceramic as a gain medium operates at 2.3 times higher output power than the same laser with a 719-μm-thick 0.9 at. % Nd:YAG single-crystal gain medium.
Open and Closed Radicals: Local Geometry around Unpaired Electrons Governs Magic-Angle Spinning Dynamic Nuclear Polarization Performance (2020)

The development of magic-angle spinning dynamic nuclear polarization (MAS DNP) has allowed atomic-level characterization of materials for which conventional solid-state NMR is impractical due to the lack of sensitivity. The rapid progress of MAS DNP has been largely enabled through the understanding of rational design concepts for more efficient polarizing agents (PAs). Here, we identify a new design principle which has so far been overlooked. We find that the local geometry around the unpaired electron can change the DNP enhancement by an order of magnitude for two otherwise identical conformers. We present a set of 13 new stable mono- and dinitroxide PAs for MAS DNP NMR where this principle is demonstrated. The radicals are divided into two groups of isomers, named open (O-) and closed (C-), based on the ring conformations in the vicinity of the N-O bond. In all cases, the open conformers exhibit dramatically improved DNP performance as compared to the closed counterparts. In particular, a new urea-based biradical named HydrOPol and a mononitroxide O-MbPyTol yield enhancements of 330 ± 60 and 119 ± 25, respectively, at 9.4 T and 100 K, which are the highest enhancements reported so far in the aqueous solvents used here. We find that while the conformational changes do not significantly affect electron spin-spin distances, they do affect the distribution of the exchange couplings in these biradicals. Electron spin echo envelope modulation (ESEEM) experiments suggest that the improved performance of the open conformers is correlated with higher solvent accessibility.
Electrophoretic deposition of bioactive silica‐calcium phosphate nanocomposite on Ti‐6Al‐4V orthopedic implant (2011)

Bioactive silica-calcium phosphate nanocomposite (SCPC) has been coated on Ti-6Al-4V implant employing an electrophoretic deposition (EPD) technique. The effects of composition and pH of the suspending medium on the zeta potential of three different SCPC formulations; SCPC25, SCPC50 and SCPC75 were analyzed. The average zeta potential of SCPC50 in pure ethanol was more negative than that of SCPC25 or SCPC75; however, the difference was not statistically significant. Discs of Ti-6Al-4V were passivated, coated with SCPC50 (200 nm-10 μm) and thermally treated at 600-800°C to produce a coating thickness in the range of 43.1 ± 5.7 to 30.1 ± 4.6 μm. After treatment at 600, 700, and 800°C, the adhesion strength at the SCPC50/Ti-6Al-4V interface was 42.6 ± 3.6, 44.7 ± 8.7, and 47.2 ± 4.3 MPa, respectively. SEM-EDX analyses of SCPC50-coated Ti-6Al-4V preimmersed in PBS for 7 days showed the formation of a Ca-deficient hydroxyapatite surface layer. ICP-OES analyses of the immersing solution (n = 6) showed an increase in the ionic concentration of Si from 3.3 ± 0.9 to 5.0 ± 1.2 ppm between days 1 and 4; after which no significant change in the Si concentration was measured. Bone marrow mesenchymal stem cells attached to the SCPC50-coated implants expressed significantly higher (p < 0.05) alkaline phosphatase activity (82.4 ± 25.6 nmoles p-NP/mg protein/min) than that expressed by cells attached to HA-coated or uncoated implants. Results of the study suggest that bioactive SCPC50 can efficiently be coated on Ti-6Al-4V using EPD. The SCPC50 coating has the potential to enhance bone integration with the orthopedic implant.
Prolonged exercise to fatigue in humans impairs skeletal muscle Na+-K+-ATPase activity, sarcoplasmic reticulum Ca2+release, and Ca2+uptake (2004)

Prolonged exhaustive submaximal exercise in humans induces marked metabolic changes, but little is known about effects on muscle Na+-K+-ATPase activity and sarcoplasmic reticulum Ca2+ regulation. We therefore investigated whether these processes were impaired during cycling exercise at 74.3 +/- 1.2% maximal O2 uptake (mean +/- SE) continued until fatigue in eight healthy subjects (maximal O2 uptake of 3.93 +/- 0.69 l/min). A vastus lateralis muscle biopsy was taken at rest, at 10 and 45 min of exercise, and at fatigue. Muscle was analyzed for in vitro Na+-K+-ATPase activity [maximal K+-stimulated 3-O-methylfluorescein phosphatase (3-O-MFPase) activity], Na+-K+-ATPase content ([3H]ouabain binding sites), sarcoplasmic reticulum Ca2+ release rate induced by 4 chloro-m-cresol, and Ca2+ uptake rate. Cycling time to fatigue was 72.18 +/- 6.46 min. Muscle 3-O-MFPase activity (nmol.min(-1).g protein(-1)) fell from rest by 6.6 +/- 2.1% at 10 min (P <0.05), by 10.7 +/- 2.3% at 45 min (P <0.01), and by 12.6 +/- 1.6% at fatigue (P <0.01), whereas 3[H]ouabain binding site content was unchanged. Ca2+ release (mmol.min(-1).g protein(-1)) declined from rest by 10.0 +/- 3.8% at 45 min (P <0.05) and by 17.9 +/- 4.1% at fatigue (P < 0.01), whereas Ca2+ uptake rate fell from rest by 23.8 +/- 12.2% at fatigue (P=0.05). However, the decline in muscle 3-O-MFPase activity, Ca2+ uptake, and Ca2+ release were variable and not significantly correlated with time to fatigue. Thus prolonged exhaustive exercise impaired each of the maximal in vitro Na+-K+-ATPase activity, Ca2+ release, and Ca2+ uptake rates. This suggests that acutely downregulated muscle Na+, K+, and Ca2+ transport processes may be important factors in fatigue during prolonged exercise in humans.
Orally active .beta.-lactam inhibitors of human leukocyte elastase-1. Activity of 3,3-diethyl-2-azetidinones (1992)

A thorough analysis of the mechanism of inhibition of human leukocyte elastase (HLE) by a monocyclic beta-lactam and the mechanism of beta-lactam hydrolysis led to the preparation of potent and highly stable inhibitors of HLE. This work led to the identification of 4-[(4-carboxyphenyl)-oxy]-3,3-diethyl-1- [[(phenylmethyl)amino]carbonyl]-2-azetidinone (2) as the first orally active inhibitor of human leukocyte elastase (HLE). Analogs of 2 with different substituents on the urea N were synthesized and evaluated for their activity in vitro against HLE as well as in vivo in a hamster lung hemorrhage model. Compounds with a methyl or a methoxy group in the para position of the benzene ring were very potent in both assays. The results are discussed on the basis of the proposed model for the binding of this class of inhibitors to HLE and a possible mechanism of inhibition is presented.
Document image segmentation as selection of Voronoi edges (2002)

This paper presents a method of document image segmentation for pages with document components of arbitrary shape as well as any skew angles. The characteristics of the proposed method are as follows: the Voronoi diagram is constructed based on the connected components to obtain the candidates of boundaries of document components; and the candidates are utilized to estimate the inter-character, inter-line and inter-column gaps without the use of domain specific parameters so as to select the boundaries. From the experimental results for 80 images with non-Manhattan layout and the skews of 0/spl deg//spl sim/450. We have confirmed that the method is effective for extraction of column regions and as efficient as other methods based on connected component analysis.
Synthesis and in vitro Evaluation of 9-Anilino-3,6-diaminoacridines Active Against a Multidrug-Resistant Strain of the Malaria Parasite Plasmodium falciparum (1994)

A series of 9-anilinoacridines have been prepared and evaluated for their activity against a multidrug-resistant K1 strain of the malaria parasite Plasmodium falciparum in erythrocyte suspensions. 3,6-Diamino substitution on the acridine ring resulted in lower mammalian cell cytotoxicity and higher antiparasitic activity than other substitution patterns, providing compounds with the highest in vitro therapeutic indices. A new synthesis of 3,6-diamino-9-anilinoacridines, via reduction of the corresponding diazides, gives much higher yields than traditional methods. Within the subset of 3,6-diamino-9-anilinoacridines, there was considerable tolerance to substitution at the 1'-anilino position. In a sharp divergence with structure-activity relationships for high mammalian cell toxicity and anticancer effects, derivatives bearing electron-withdrawing 1'-substituents (e.g., SO2-NHR and CONHR) showed the most potent antimalarial activity (IC50 values of 10-20 nM). Representative compounds were shown to be potent inhibitors of the DNA strand-passing activity of human topoisomerase II and of the DNA decatenation activity of the corresponding parasite enzyme. The 1'-SO2NH2derivative 7n completely inhibited strand passage by Jurkat topoisomerase II at 20 microM, and an increase in linear DNA (indicative of inhibition of religation) was seen at or above 1 microM. It also inhibited the decatenating activity of the parasite topoisomerase II at 6 microM and above. In contrast, the analogous compound without the 3,6-diamino substituent was inactive in both assays up to 100 microM. Overall, there was a positive relationship between the ability of the drugs to inhibit parasite growth in culture and their ability to inhibit parasite topoisomerase II activity in an isolated enzyme assay. The 1'-SO2NH2 derivative 7n showed a high IVTI (1000) and was a potent inhibitor of both P. falciparum in vitro (IC50 20 nM) and P. falciparum-derived topoisomerase II. However, the compound was inactive against Plasmodium berghei in mice; reasons may include rapid metabolic inactivation (possibly by N-acetylation) and/or poor distribution.
ChemInform Abstract: Homolytic Alkylation of Heteroaromatic Bases: The Problem of Monoalkylation. (1990)

Abstract The silver‐catalyzed decarboxylation of carboxylic acids such as (II) by persulfate leads to alkyl radicals, which are utilized for the selective alkylation of bases such as (I).
Survey of Engineering Models for Systems Biology (2016)

In recent years, the field of systems biology has emerged from a confluence of an increase both in molecular biotechnology and in computing storage and power. As a discipline, systems biology shares many characteristics with engineering. However, before the benefits of engineering-based modeling formalisms and analysis tools can be applied to systems biology, the engineering discipline(s) most related to systems biology must be identified. In this paper, we identify the cell as an embedded computing system and, as such, demonstrate that systems biology shares many aspects in common with computer systems engineering, electrical engineering, and chemical engineering. This realization solidifies the grounds for using modeling formalisms from these engineering subdisciplines to be applied to biological systems. While we document several examples where this is already happening, our goal is that identifying the cell as an embedded computing system would motivate and facilitate further discovery through more widespread use of the modeling formalisms described here.
VISION (2012)

We argue that for computers to do more for us, we need to show the cloud what we see and embrace cloud-powered sight for mobile users. We present sample applications that will be empowered by this vision, discuss why the timing is right to tackle it, and offer our initial thoughts on some of the important research challenges.
ChemInform Abstract: Antimalarially Potent, Easily Prepared, Fluorinated Endoperoxides. (1997)

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.
Use of Spin Echo Magic Angle Spinning 1H NMR in Reaction Monitoring in Combinatorial Organic Synthesis (1996)

ADVERTISEMENT RETURN TO ISSUEPREVAddition/CorrectionNEXTUse of Spin Echo Magic Angle Spinning 1H NMR in Reaction Monitoring in Combinatorial Organic SynthesisRavi S. Garigipati, Bruce Adams, Jerry L. Adams, and Susanta K. SarkarCite this: J. Org. Chem. 1996, 61, 15, 5190Publication Date (Web):July 26, 1996Publication History Published online26 July 1996Published inissue 1 January 1996https://pubs.acs.org/doi/10.1021/jo964011fhttps://doi.org/10.1021/jo964011fcorrectionACS PublicationsCopyright © 1996 American Chemical Society. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views328Altmetric-Citations10LEARN 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 Get e-Alertsclose Get e-Alerts