gebhart/patrepeval huggingface dataset:
Structure shape and stability of nanometric sized particles (2001)

Nanoparticles are a state of matter that has properties different from either molecules or bulk solids. In the present work, we review the shape and structure of nanometer-sized particles; several shapes are discussed, such as the octahedron and truncated octahedron, the icosahedron, the Marks decahedron, the truncated “star-like” decahedron, the rounded decahedron and the regular decahedron. Experimental high-resolution transmission electron microscopy (TEM) images of each type of particle are presented together with the Fast Fourier Transform and a model of the particle. We consider only gold particles grown by vapor deposition or by colloidal methods. High-resolution TEM images of the particles in different orientations are shown. We discuss two basic types of particles uncapped and capped. Data for other metals and semiconductors are reviewed. We have also performed very extensive simulations obtaining the total energy and pair correlation functions for each cluster under study. Furthermore, distributions of single atom energy for every cluster are displayed in order to reveal the effect of surface on the stability of different types and sizes of clusters. We discuss the structure of the particles from ∼1 to ∼100 nm. The mechanisms for stress release as the particles grow larger are reviewed and a mechanism is suggested. Finally, we discuss the parameters that define the shape of a nanoparticle and the possible implications in technological applications.
Acute Endophthalmitis Following Cataract Surgery (2005)

This systematic review indicates that the incidence of endophthalmitis associated with cataract extraction has increased over the last decade. This upward trend in endophthalmitis frequency coincides temporally with the development of sutureless clear corneal incisions.
A General Palladium‐Catalyzed Carbonylative Sonogashira Coupling of Aryl Triflates (2010)

Trifling with triflates: A new protocol for the carbonylative Sonogashira reactions of aryl triflates (see scheme) that provides a significant extension of this interesting methodology is described. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Phase balancing using simulated annealing (1999)

Deregulation eliminates the boundary of the territory of the monopoly power industry. Competition forces utilities to improve power quality as well as to reduce investment and operation costs. Feeder imbalance describes a situation in which the voltages of a three-phase voltage source are not identical in magnitude, or the phase differences between them are not 120 electrical degrees, or both. It affects motors and other devices that depend upon a well-balanced three-phase voltage source. Phase balancing is to make the voltages balanced at each load point of the feeder. Phase swapping is a direct approach for phase balancing with the minimum cost. Phase balancing can enhance utilities' competitive capability by improving reliability, quality, and reducing costs. Therefore, phase balancing optimization is nowadays receiving more attention in the power industry, especially in today's deregulating environments. The nonlinear effects, such as, voltage drops and energy losses, make the problem difficult to solve. This paper introduces simulated annealing as an effective method to solve a power distribution phase balancing problem with its nonlinear effects.
A Torus-Based 4-Way Fault-Tolerant Backbone Network Architecture for Avionic WDM LANs (2011)

In this paper, we leverage the torus topology to design a wavelength division multiplexing (WDM) backbone network for operation in hazardous avionic environments. The proposed WDM local area network offers efficient data delivery and fast fault recovery via establishing four non-overlapping lightpaths for any source–destination pair. First, we describe a torus-based architecture and propose an efficient non-overlapping lightpath setup algorithm: FOLD (Four-way Optimal Disjoint Routing). The algorithm is proved to achieve optimal link utilization. Second, based on the proposed lightpath setup algorithm, a wavelength allocation and reuse (WAR) scheme enforcing wavelength continuity is proposed to minimize the wavelength utilization for all-to-all communication. An analytical calculation on wavelength utilization shows that the proposed WAR performs very close to an ideal wavelength assignment scheme without wavelength continuity being enforced. Lastly, the probabilistic and capacity analysis demonstrates vast reliability improvement via applying the proposed network architecture in terms of network-failure-induced impact on connection reliability and network capacity degradation.
Graph-based modeling of tandem repeats improves global multiple sequence alignment (2013)

Tandem repeats (TRs) are often present in proteins with crucial functions, responsible for resistance, pathogenicity and associated with infectious or neurodegenerative diseases. This motivates numerous studies of TRs and their evolution, requiring accurate multiple sequence alignment. TRs may be lost or inserted at any position of a TR region by replication slippage or recombination, but current methods assume fixed unit boundaries, and yet are of high complexity. We present a new global graph-based alignment method that does not restrict TR unit indels by unit boundaries. TR indels are modeled separately and penalized using the phylogeny-aware alignment algorithm. This ensures enhanced accuracy of reconstructed alignments, disentangling TRs and measuring indel events and rates in a biologically meaningful way. Our method detects not only duplication events but also all changes in TR regions owing to recombination, strand slippage and other events inserting or deleting TR units. We evaluate our method by simulation incorporating TR evolution, by either sampling TRs from a profile hidden Markov model or by mimicking strand slippage with duplications. The new method is illustrated on a family of type III effectors, a pathogenicity determinant in agriculturally important bacteria Ralstonia solanacearum. We show that TR indel rate variation contributes to the diversification of this protein family.
The RACK1 Signaling Scaffold Protein Selectively Interacts with the cAMP-specific Phosphodiesterase PDE4D5 Isoform (1999)

The WD-repeat protein receptor for activated C-kinase (RACK1) was identified by its interaction with the cyclic AMP-specific phosphodiesterase (PDE4) isoform PDE4D5 in a yeast two-hybrid screen. The interaction was confirmed by co-immunoprecipitation of native RACK1 and PDE4D5 from COS7, HEK293, 3T3-F442A, and SK-N-SH cell lines. The interaction was unaffected by stimulation of the cells with the phorbol ester phorbol 2-myristate 3-acetate. PDE4D5 did not interact with two other WD-repeat proteins, beta'-coatomer protein and Gsbeta, in two-hybrid tests. RACK1 did not interact with other PDE4D isoforms or with known PDE4A, PDE4B, and PDE4C isoforms. PDE4D5 and RACK1 interacted with high affinity (Ka approximately 7 nM) [corrected] when they were expressed and purified from Escherichia coli, demonstrating that the interaction does not require intermediate proteins. The binding of the E. coli-expressed proteins did not alter the kinetics of cAMP hydrolysis by PDE4D5 but caused a 3-4-fold change in its sensitivity to inhibition by the PDE4 selective inhibitor rolipram. The subcellular distributions of RACK1 and PDE4D5 were extremely similar, with the major amount of both proteins (70%) in the high speed supernatant (S2) fraction. Analysis of constructs with specific deletions or single amino acid mutations in PDE4D5 demonstrated that a small cluster of amino acids in the unique amino-terminal region of PDE4D5 was necessary for its interaction with RACK1. We suggest that RACK1 may act as a scaffold protein to recruit PDE4D5 and other proteins into a signaling complex.
Acetylpyridinium ion intermediate in pyridine-catalyzed hydrolysis and acyl transfer reactions of acetic anhydride. Observation, kinetics, structure-reactivity correlations, and effects of concentrated salt solutions (1970)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAcetylpyridinium ion intermediate in pyridine-catalyzed hydrolysis and acyl transfer reactions of acetic anhydride. Observation, kinetics, structure-reactivity correlations, and effects of concentrated salt solutionsAlan R. Fersht and William P. JencksCite this: J. Am. Chem. Soc. 1970, 92, 18, 5432–5442Publication Date (Print):September 1, 1970Publication History Published online1 May 2002Published inissue 1 September 1970https://pubs.acs.org/doi/10.1021/ja00721a023https://doi.org/10.1021/ja00721a023research-articleACS PublicationsRequest reuse permissionsArticle Views2156Altmetric-Citations129LEARN 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
Clustering of disease features within 512 multicase rheumatoid arthritis families (2004)

Abstract Objective To determine whether specific rheumatoid arthritis (RA) disease features demonstrate the presence of significant familial clustering. Methods We studied 1,097 individuals with RA from 512 multicase families enrolled in the North American Rheumatoid Arthritis Consortium. All patients were interviewed and examined to collect standardized information about demographic and clinical characteristics. Affected individuals also underwent radiography of the hands and wrists and were genotyped for the HLA–DRB1 shared epitope. Familial clustering of disease features was assessed using contingency table analysis and Pearson correlation coefficients. Multivariate logistic and linear regression analyses were used to account for other characteristics that might influence familial clustering, such as disease duration, sex, and age at diagnosis. Results Several disease characteristics exhibited significant familial clustering, including seropositivity (multivariate odds ratio [OR] 4.3, P &lt; 0.0001), nodules (OR 2.3, P &lt; 0.0001), and age at RA diagnosis (multivariate regression coefficient [β] 0.44, P &lt; 0.0001). Other characteristics demonstrated statistically significant but modest degrees of familial clustering (Joint Alignment and Motion score, Health Assessment Questionnaire score, and year of RA diagnosis) or modest but nonsignificant familial clustering (other extraarticular manifestations, other autoimmune diseases). Conclusion The clustering of certain disease characteristics implicates specific genetic or nongenetic causes. These results highlight the importance of considering disease phenotype in future genetic and epidemiologic studies of RA.
Simultaneous Use of Time-Resolved Fluorescence and Anti-Stokes Photoluminescence in a Bioaffinity Assay (2005)

A bioaffinity assay is described where anti-Stokes photoluminescence of inorganic lanthanide phosphors and time-resolved fluorescence of lanthanide chelates are measured from a single microtitration well without any disturbance from these label technologies to each other. Up-converting phosphor (UPC-phosphor) bioconjugate was produced by grinding the commercial, micrometer-sized UPC-phosphors to colloidal, submicrometer-sized phosphor particles and by attaching these phosphors to biomolecules. Experiments were carried out in standard 96-well microtitration plates to determine detection limits, linearity, and cross-talk of UPC-phosphor and europium chelate. In numbers of molecules the lower limits of detection for UPC-phosphor were roughly 3 x 10(3) particles in solution and 1 x 10(4) particles in solid phase, and for europium label same values were 9 x 10(6) and 9 x 10(7) molecules. Linearity of detection was for UPC-phosphor 5 orders of magnitude in solution and over 4 orders of magnitude in solid phase and for europium label over 5 orders of magnitude in solution and over 4 orders of magnitude in solid phase. The cross-talk between the two labels was practically nonexistent. In this study we show that up-converting anti-Stokes photoluminescent phosphors could be employed in bioaffinity assays as very potential labels with significant advantages either alone or together with long-lifetime lanthanide chelates.
Accounting valuation, market expectation, and cross-sectional stock returns (1998)

This study examines the usefulness of an analyst-based valuation model in predicting cross-sectional stock returns. We estimate firms' fundamental values (V) using I/B/E/S consensus forecasts and a residual income model. We find that V is highly correlated with contemporaneous stock price, and that the V/P ratio is a good predictor of long-term cross-sectional returns. This effect is not explained by a firm's market beta, B/P ratio, or total market capitalization. In addition, we find errors in consensus analyst earnings forecasts are predictable, and that the predictive power of V/P can be improved by incorporating these errors.
The imperative for controlled mechanical stresses in unraveling cellular mechanisms of mechanotransduction (2006)

The results of this study challenge the basic premise of in vitro mechanotransduction studies, i.e. that a controlled flow regime is applied to impart a defined mechanical stimulus to cells. These results also underscore the fact that data from studies in which different chambers are utilized can not be compared, even if the target stress regimes are comparable.
Basic science of HER-2/neu: a review. (1999)

The HER-2/neu (also known as c-erbB-2) oncogene is the second member of the epidermal growth factor receptor family. It is overexpressed in many different types of human cancers, including breast, ovarian, lung, gastric, and oral cancers. Overexpression of HER-2/neu in breast cancer has been associated with poor overall survival and has been shown preclinically to enhance malignancy and the metastatic phenotypes. Although discrepancies exist between different studies, HER-2/ neu overexpression seems to induce chemoresistance in certain experimental conditions. Many studies have convincingly shown that repression of HER-2/neu suppresses the malignant phenotypes of HER-2/neu-overexpressing cancer cells. These findings strongly suggest that HER-2/neu may serve as an excellent target for developing anticancer agents specific for HER-2/neu-overexpressing cancer cells. HER-2/neu-encoded p185 protein is a receptor tyrosine kinase that can be associated with multiple signal transduction pathways. However, it is not yet clear how a specific signal pathway may correspond to a specific biological response. This report reviews basic information on signal transduction of HER-2/neu receptor tyrosine kinase and summarizes our approaches to targeting HER-2/neu-overexpressing cancer cells. The HER-2/neu promoter was targeted using cationic liposomes or an adenovirus vector to deliver the adenovirus-5 EIA gene products and a nontransformed mutant of the SV40 large T antigen into the tumor-bearing mice. This resulted in suppression of the tumor growth and prolongation of survival. For repressing the function of HER-2/neu we used emodin, a tyrosine kinase inhibitor. This agent can inhibit the tyrosine kinase activity of HER-2/neu and preferentially block the growth of the HER-2/neu-overexpressing human breast cancer cells in tissue culture as well as in nude mice.
The acute lymphoblastic leukaemia cell line SEM with t(4;11) chromosomal rearrangement is biphenotypic and responsive to interleukin‐7 (1994)

A cell line, designated SEM, was established from the peripheral blood of a 5-year-old girl in relapse with acute lymphoblastic leukaemia (ALL). Both the lymphoblasts of the patient and the cells of the cell line SEM showed the t(4;11) chromosomal rearrangement. The analysis of the immunophenotype of the SEM cell line revealed the B-cell differentiation antigens CD19, CD22 and CDw75 in the absence of CD20, CD24 and immunoglobulin expression. Besides B-lineage antigens, SEM cells were positive for the myeloid antigens CD13, CD15, CD33 and CDw65. Immunogenotypic analysis of SEM cells showed a monoclonal rearrangement of immunoglobulin heavy-chain (IgH). T-cell receptor (TCR) gamma and delta genes. Addition of interleukin (IL)-7 promoted the growth of the patient's lymphoblasts in culture and enhanced the proliferation of SEM cells. The SEM cells also express messenger RNA (mRNA) for the IL-7 receptor (IL-7R), but no evidence for autocrine production of IL-7 by the cell line was found. Addition of IL-4, tumour necrosis factor (TNF)-alpha, interferon (IFN)-alpha, or IFN-gamma resulted in a profound inhibition of SEM growth. Thus, these cytokines may have important growth regulatory activities for biphenotypic leukaemic ALL cells.
Kinetics of Papain-Catalyzed Hydrolysis of α-N-Benzoyl-L-arginine Ethyl Ester and α-N-Benzoyl-L-argininamide1 (1965)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTKinetics of Papain-Catalyzed Hydrolysis of α-N-Benzoyl-L-arginine Ethyl Ester and α-N-Benzoyl-L-argininamide1John R. Whitaker and Myron L. BenderCite this: J. Am. Chem. Soc. 1965, 87, 12, 2728–2737Publication Date (Print):June 1, 1965Publication History Published online1 May 2002Published inissue 1 June 1965https://pubs.acs.org/doi/10.1021/ja01090a034https://doi.org/10.1021/ja01090a034research-articleACS PublicationsRequest reuse permissionsArticle Views522Altmetric-Citations146LEARN 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
[Serum gamma-glutamyl transpeptidase activity in children with chronic hepatitis B]. (2005)

GGT is suitable serum marker to predict advanced liver fibrosis in children with chronic hepatitis B.
Evaluation of Cartilage Composition and Degradation by High-Resolution Magic-Angle Spinning Nuclear Magnetic Resonance (2004)

Rheumatic diseases are accompanied by a progressive destruction of the cartilage layers of the joints. Although the number of patients suffering from rheumatic diseases is steadily increasing, degradation mechanisms of cartilage are not yet understood, and methods for early diagnosis are not available. Although some information on pathogenesis could be obtained from the nuclear magnetic resonance (NMR) spectra of degradation products in the supernatants of cartilage specimens incubated with degradation-causing agents, the most direct information on degradation processes would come from the native cartilage as such. To obtain highly resolved NMR spectra of cartilage, application of the recently developed high-resolution magic-angle spinning (HR-MAS) NMR technique is advisable to obtain small line-widths of individual cartilage resonances. This technique is nowadays commercially available for most NMR spectrometers and has the considerable advantage that the same pulse sequences as in high-resolution NMR can be applied. Except for a MAS spinning equipment, no solid-state NMR hardware is required. Therefore, this method can be easily implemented. Here, we describe the most important requirements that are necessary to record HR-MAS NMR spectra. The capabilities of the HR-MAS technique are discussed for the 1H and 13C NMR spectra of cartilage.
Synthesis of harringtonine, a Cephalotaxus antitumor alkaloid (1978)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis of harringtonine, a Cephalotaxus antitumor alkaloidKenneth L. Mikolajczak and Cecil R. Smith Jr.Cite this: J. Org. Chem. 1978, 43, 25, 4762–4765Publication Date (Print):December 1, 1978Publication History Published online1 May 2002Published inissue 1 December 1978https://pubs.acs.org/doi/10.1021/jo00419a012https://doi.org/10.1021/jo00419a012research-articleACS PublicationsRequest reuse permissionsArticle Views283Altmetric-Citations18LEARN 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