gebhart/patrepeval huggingface dataset:
Polystyrene- and Poly(3-vinylpyridine)-Grafted Magnetite Nanoparticles Prepared through Surface-Initiated Nitroxide-Mediated Radical Polymerization (2004)

Polymer-grafted magnetite (Fe3O4) nanoparticles (diameter about 10 nm) were prepared through a direct polymer grafting reaction from their surfaces. The chemisorbed initiator (TEMPO-based alkoxyamine) for nitroxide-mediated radical polymerization with a phosphoric acid group gave controlled polystyrene (PS) and poly(3-vinylpyridine) (P3VP) graft layers on the surface. The graft densities of polymers on the surfaces of magnetite particles were estimated at 0.12−0.20 chains/nm2 by thermogravimetric analysis (TGA). The improvement in the dispersibility of PS-modified magnetite in good solvents was verified by ultraviolet−visible (UV−vis) absorption spectroscopy, transmission electron microscopy (TEM), and dynamic light scattering (DLS). In the case of P3VP-modified magnetite, the particles were stably dispersed in good solvents, by protonation, in acid solution, and by quarternization with iodomethane, in neutral aqueous solution. The magnetic response of the polymer-grafted magnetite against an external magnetic field was confirmed in the stable dispersion.
Molecular and Biochemical Analysis of Calmodulin Interactions with the Calmodulin-Binding Domain of Plant Glutamate Decarboxylase (1995)

We previously provided what to our knowledge is the first evidence that plant glutamate decarboxylase (GAD) is a calmodulin (CaM)-binding protein. Here, we studied the GAD CaM-binding domain in detail. A synthetic peptide of 26 amino acids corresponding to this domain forms a stable complex with Ca2+/CaM with a 1:1 stoichiometry, and amino acid substitutions suggest that tryptophan-485 has an indispensable role in CaM binding. Chemical cross-linking revealed specific CaM/GAD interactions even in the absence of Ca2+. However, increasing KCI concentrations or deletion of two carboxy-terminal lysines abolished these interactions but had a mild effect on CaM/GAD interactions in the presence of Ca2+. We conclude that in the presence of Ca(2+)-hydrophobic interactions involving tryptophan-485 and electrostatic interactions involving the carboxy-terminal lysines mediate CaM/GAD complex formation. By contrast, in the absence of Ca2+, CaM/GAD interactions are essentially electrostatic and involve the carboxy-terminal lysines. In addition, a tryptophan residue and carboxy-terminal lysines are present in the CaM-binding domain of an Arabidopsis GAD. Finally, we demonstrate that petunia GAD activity is stimulated in vitro by Ca2+/CaM. Our study provides a molecular basis for Ca(2+)-dependent CaM/GAD interactions and suggests the possible occurrence of Ca(2+)-independent CaM/GAD interactions.
Vitamin E in the treatment of tardive dyskinesia: a double-blind placebo-controlled study (1992)

The authors compared vitamin E with placebo in a double-blind randomized crossover study of 27 patients with tardive dyskinesia. Each treatment period lasted for 6 weeks. Vitamin E showed no differences from placebo in the treatment of tardive dyskinesia.
The construction of cosmid libraries which can be used to transform eukaryotic cells (1982)

Cosmid vectors have been developed which carry selective markers for growth in bacteria (beta lactamase gene) and animal cells (the Herpes Simplex virus thymidine kinase gene, the transposon Tn-5 aminoglycosyl 3' phosphotransferase gene and the E. coli guanine phosphoribosyltransferase gene). The design of the cosmids allows the exchange of the eukaryotic markers in recombinant cosmids. Human and mouse cosmid libraries containing DNA inserts of about 40kb have been generated by an improved method. Several clones from the human beta-globin locus were isolated. These cosmids transform mouse L cells at high efficiency in both circular and linear form. The newly introduced genes are expressed accurately in L cells.
Efficient Gene Transfer of HIV-1-Specific Short Hairpin RNA into Human Lymphocytic Cells Using Recombinant Adeno-associated Virus Vectors (2004)

The cellular introduction of short, interfering RNA leads to sequence-specific degradation of homologous mRNA, a process termed RNA interference (RNAi). Here, we report that recombinant adeno-associated virus 2 (rAAV-2) can be used to transfer short hairpin (sh) RNA expression cassettes genetically into human cells. HIV-1 replication was suppressed by >95% in H9 cells and primary human lymphocytes that expressed shRNA targeting the first exon of the viral transactivator protein tat compared to control cells. rAAV-2 integrated stably into the host genome, leading to long-term expression of tat shRNA. Our findings demonstrate the utility of rAAV-2 for the genetic transfer of shRNA expression cassettes into human cells, providing an alternative to using retroviral vectors as RNAi delivery systems.
Opsonic Requirements of Staphylococcus Epidermidis (1986)

The opsonic requirements of 18 strains of Staphylococcus epidermidis were compared in pooled normal human serum and in peritoneal dialysate from patients undergoing continuous ambulatory peritoneal dialysis (CAPD). A serum concentration of 2.5% gave optimal opsonisation. The opsonisation of all strains was antibody- and complement-dependent, and there were no significant differences in the pattern of their opsonic requirements. Peritoneal-dialysis effluent from uninfected patients was a poor source of opsonins because of the low levels of immunoglobulin G and of the C3 component of complement it contained. Growth of S. epidermidis in peritoneal-dialysis effluent rather than in broth did not alter its opsonic requirements. Strains from patients undergoing CAPD and suffering from peritonitis were not more resistant to opsonisation and phagocytic killing than those from other sources.
Dielectrophoresis of Submicrometer Latex Spheres. 1. Experimental Results (1998)

A nonuniform electric field exerts a force on a polarizable particle through the Coulomb interaction with the electric dipole induced in the particle, resulting in a motion termed dielectrophoresis. The magnitude of the force depends on the dielectric properties of both the particle and the medium it is suspended in. As a result, measurement of the dielectrophoretic force provides information about the internal and surface dielectric properties of the particle. This paper presents the first detailed measurements of the dielectrophoretic response of submicrometer particles as a function of electrolyte composition and conductivity, applied field frequency, and particle size. Comparisons are made between the experimental results and the classical theory of the dielectrophoretic force derived from Maxwell−Wagner interfacial polarization. For particles of 557 nm diameter, good agreement is obtained between the experimental results and theory of interfacial polarization taking into account the effects of surface conductance. However, the results for smaller sizes of particle (93, 216, and 282 nm diameter) demonstrate that the theory does not adequately explain the dielectric or dielectrophoretic behavior of colloidal particles. The existence of a second low-frequency dispersion is also apparent in the data, attributable to the polarization of the double layer. The data were compared with a theoretical plot generated by modeling the dispersion in terms of a single Debye relaxation.
Assembly of Highly Aligned DNA Strands onto Si Chips (2005)

This paper reports a robust and efficient approach to assemble highly aligned DNA strands onto Si chips. The method combines advantages from molecular combing and microcontact printing to realize controlling both the density and direction of DNA strands on the Si chip. In addition, it also can be utilized to prepare stretched DNA structures on solid surfaces. Compared to approaches that use molecular combing directly on silanated surfaces, the stretched single-chain DNA structures are straighter. Furthermore, by exploiting the hydrophobic property of the intrinsic poly(dimethylsiloxane) stamp, this study also describes a simple way to produce straight bundled DNA arrays on Si and other substrates.
A new and facile synthesis of imidazo[2,1‐b]oxazoles (1997)

Abstract An efficient and clean two step procedure for the synthesis of imidazo[2,1‐ b ]oxazoles has been developed from 2‐aminooxazoles using titanium(IV) chloride assisted cyclization, and a variety of imidazo[2,1‐ b ]oxazoles have been synthesized in good yields. The structure of one of the products was confirmed by X‐ray crystallographic analysis.
MatrixFlow: temporal network visual analytics to track symptom evolution during disease progression. (2012)

MatrixFlow is an interactive visual analytic system that allows users to quickly discover patterns in clinical event sequences. By unearthing the patterns hidden within and displaying them to medical experts, users become empowered to make decisions influenced by historical patterns.
Action of Chondroitinases (1976)

The modes of action of two chondroitinases-AC [EC 4.2.2.5] from Arthrobacter aurescens and Flavobacterium heparinum were examined. By comparison of the increase of viscosity and by analyses of digests using paper chromatography and gel filtration, it was shown that the Arthrobacter enzyme (A-Chase) degrades the substrate by a stepwise attack, while the Flavobacterium enzyme (F-Chase) exhibits a more random attack, though the first attack of both enzymes is of endo-type. Further study was carried out of the initial rate and final extent of the enzymic degradation of various mucopolysaccharides. The order of the initial rates at which the native mucopolysaccharides are degraded was similar for both enzymes. For A-Chase, the initial rate and final extent of degradation of modified chondroitin sulfate C or chondroitin methyl ester, however, were low compared with those of F-Chase. These results also suggested that A-Chase degrades the substrate by stepwise attack and F-Chase by random attack.
In vivo histological evaluation of a novel ablative fractional resurfacing device (2007)

The thermal effects of a novel investigational ablative CO(2) laser system utilizing fractional resurfacing were characterized in human forearm skin. We confirmed our previous ex vivo findings and show for the first time in-vivo, that a controlled array of microscopic treatment zones of ablation and coagulation could be deposited in human skin by varying treatment pulse energy. Immunohistochemical studies of heat shock proteins revealed a persistent collagen remodeling response lasting at least 3 months. We successfully demonstrated the first in-vivo use of ablative fractional resurfacing (AFR) treatment on human skin.
Evaluation campaigns and TRECVid (2006)

The TREC Video Retrieval Evaluation (TRECVid)is an international benchmarking activity to encourage research in video information retrieval by providing a large test collection, uniform scoring procedures, and a forum for organizations 1 interested in comparing their results. TRECVid completed its fifth annual cycle at the end of 2005 and in 2006 TRECVid will involve almost 70 research organizations, universities and other consortia. Throughout its existence, TRECVid has benchmarked both interactive and automatic/manual searching for shots from within a video corpus,automatic detection of a variety of semantic and low-level video features, shot boundary detection and the detection of story boundaries in broadcast TV news. This paper will give an introduction to information retrieval (IR) evaluation from both a user and a system perspective, high-lighting that system evaluation is by far the most prevalent type of evaluation carried out. We also include a summary of TRECVid as an example of a system evaluation bench-marking campaign and this allows us to discuss whether such campaigns are a good thing or a bad thing. There are arguments for and against these campaigns and we present some of them in the paper concluding that on balance they have had a very positive impact on research progress.
Concordance analysis of microbial genomes (1998)

The set of proteins which are conserved across families of microbes contain important targets of new anti-microbial agents. We have developed a simple and efficient computational tool which determines concordances of putative gene products that show sets of proteins conserved across one set of user specified genomes and not present in another set of user specified genomes. The thresholds and the homology scoring criterion are selectable to allow the user to decide the stringency of the homologies. The system uses a relational database to store protein coding regions from different genomes, and to store the results of a complete comparison of all sequences against all sequences using the FASTA program. Using Web technology, the display of all the related proteins for a given sequence and calculation of multiple sequence alignments (using CLUSTALW) can be performed with the click of a button. The current database holds 97 365 sequences from 19 complete or partial genomes and 8798905 FASTA comparison results. A example concordance is presented which demonstrates that the target of the quinolone antibiotics could have been identified using this tool.
Efficient bit allocation for an arbitrary set of quantizers (speech coding) (1988)

A bit allocation algorithm that is capable of efficiently allocating a given quota of bits to an arbitrary set of different quantizers is proposed. This algorithm is useful in any coding scheme which uses bit allocation or, more generally, codebook allocation. It produces an optimal or very nearly optimal allocation, while allowing the set of admissible bit allocation values to be constrained to nonnegative integers. It is particularly useful in cases where the quantizer performance versus rate is irregular and changing in time, a situation that cannot be handled by conventional allocation algorithms.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Surface-Enhanced Raman Spectroscopy (SERS) for Sub-Micromolar Detection of DNA/RNA Mononucleotides (2006)

Surface-enhanced Raman (SER) spectra of all the DNA/RNA mononucleotides have been obtained with high sensitivity using citrate-reduced silver colloids aggregated with MgSO4, rather than the more usual halide ions, which were found to prevent enhancement of these compounds. The SERS spectra of adenine, guanine, thymine, cytosine, and uracil were recorded along with their corresponding nucleosides and 5'-deoxynucleotides. For the cytosine series, all three spectra had similar relative band intensities but the spectra of adenine were different from those of adenosine and dAMP, probably due to differences in orientation on the surface. No enhanced bands from the phosphate or sugar groups were observed. There were general similarities between the SERS spectra of the purine mononucleotides and the pyrimidine mononucleotides, but the spectra were sufficiently different to allow each of them to be distinguished. This method can therefore be used for high sensitivity, label-free identification of mononucleotides.
Expression of the retinoblastoma gene product in bladder carcinoma cells associates with a low frequency of tumor formation. (1992)

Upon inactivation of both alleles of the retinoblastoma gene (RB), individuals develop the intraocular eye tumor, retinoblastoma. The gene encodes a Mr 110,000 phosphorylated nuclear protein that may be involved in regulation of the cell cycle. Besides retinoblastoma, mutations of the gene have been detected in several other types of tumors, including bladder carcinoma. Up to one-third of bladder carcinomas may contain mutations of the RB gene. Introducing the retinoblastoma gene into single retinoblastoma, osteosarcoma, or prostate carcinoma cell lines suppresses their tumorigenicity as assayed in nude mice. We have sought to extend these results by introducing the retinoblastoma gene into multiple bladder carcinoma lines, and analyzing several of the resulting, cloned lines. We have found that inhibition of tumorigenicity, as assayed by tumor growth in nude mice or growth of cells in soft agar, is the only consistent phenotype observed upon re-expression of RB in all bladder carcinoma cells examined. The effect of RB expression on growth and cellular morphology varied depending on the particular parental cell line. We conclude that RB expression generally correlates with reduced tumorigenicity, but not reduced growth rate, in bladder carcinoma cells.
Lipid oligonucleotide conjugates as responsive nanomaterials for drug delivery (2013)

We report Lipid OligoNucleotide conjugates (LONs) bearing either two or three hydrophobic chains. LONs self-assemble into micellar aggregates, which provide a suitable reservoir for hydrophobic drugs such as paclitaxel. Our results demonstrate that the composition of the LONs both in terms of the lipid and the oligonucleotide sequence impacts their ability to host lipophilic molecules. Interestingly, binding of the complementary oligonucleotide selectively induces the release of part of the drug payload of the aggregates. These LON based micelles, which efficiently host hydrophobic drugs, represent an original stimuli-responsive drug delivery system.
Deep Learning for Entity Matching (2018)

Entity matching (EM) finds data instances that refer to the same real-world entity. In this paper we examine applying deep learning (DL) to EM, to understand DL's benefits and limitations. We review many DL solutions that have been developed for related matching tasks in text processing (e.g., entity linking, textual entailment, etc.). We categorize these solutions and define a space of DL solutions for EM, as embodied by four solutions with varying representational power: SIF, RNN, Attention, and Hybrid. Next, we investigate the types of EM problems for which DL can be helpful. We consider three such problem types, which match structured data instances, textual instances, and dirty instances, respectively. We empirically compare the above four DL solutions with Magellan, a state-of-the-art learning-based EM solution. The results show that DL does not outperform current solutions on structured EM, but it can significantly outperform them on textual and dirty EM. For practitioners, this suggests that they should seriously consider using DL for textual and dirty EM problems. Finally, we analyze DL's performance and discuss future research directions.
Study on the Alkylation of p-tert-Butylcalix[8]arene. Partially O-Alkylated Calix[8]arenes (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStudy on the Alkylation of p-tert-Butylcalix[8]arene. Partially O-Alkylated Calix[8]arenesPlacido Neri, Enrico Battocolo, Francesca Cunsolo, Corrada Geraci, and Mario PiattelliCite this: J. Org. Chem. 1994, 59, 14, 3880–3889Publication Date (Print):July 1, 1994Publication History Published online1 May 2002Published inissue 1 July 1994https://pubs.acs.org/doi/10.1021/jo00093a020https://doi.org/10.1021/jo00093a020research-articleACS PublicationsRequest reuse permissionsArticle Views217Altmetric-Citations44LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Normal V(D)J coding junction formation in DNA ligase I deficiency syndromes. (1994)

Bloom syndrome and a clinically related syndrome represented by the cell line 46BR have been associated with reduction in DNA ligase I activity. In these syndromes, DNA ligase I deficiency severely impairs the development and function of the immune system. We undertook analysis of DNA ligase I-deficient cells to determine whether the observed immune deficiency is attributable to a perturbation in the process of V(D)J recombination. V(D)J recombination in Bloom syndrome cell lines and 46BR was examined by a transient transfection assay. No effect on the fidelity of coding and signal junction formation in DNA ligase I-deficient cells was observed. The frequency of V(D)J recombination in DNA ligase I-deficient cells was also examined using recombination substrates modified to function in human cells. Similar recombination frequencies were observed in normal and DNA ligase I-deficient cells, demonstrating that the efficiency of the V(D)J recombination process is unaffected by alterations in DNA ligase I activity. Rearranged immunoglobulin loci from Bloom syndrome cell lines and patient material were molecularly cloned by an inverse polymerase chain reaction strategy which should be applicable to a variety of human immunodeficiency syndromes and were indistinguishable from those found in normal bone marrow samples. Our data argue that the immune system defects associated with DNA ligase I deficiency do not result from perturbation of the V(D)J recombination pathway.
Network information criterion-determining the number of hidden units for an artificial neural network model (1994)

The problem of model selection, or determination of the number of hidden units, can be approached statistically, by generalizing Akaike's information criterion (AIC) to be applicable to unfaithful (i.e., unrealizable) models with general loss criteria including regularization terms. The relation between the training error and the generalization error is studied in terms of the number of the training examples and the complexity of a network which reduces to the number of parameters in the ordinary statistical theory of AIC. This relation leads to a new network information criterion which is useful for selecting the optimal network model based on a given training set.
The Progressive Wave Pump: Numerical Multiphysics Investigation of a Novel Pump Concept With Potential to Ventricular Assist Device Application (2012)

This article describes the numerical fluid-structure interaction (FSI) validation of a new pumping concept and the possibility for application of a further developed type, as an implantable ventricular assist device (VAD). The novel principle of the so-called progressive wave pump is based on the interaction of an elastic membrane actuated by forced excitation with a surrounding fluid and the pump housing. By applying forced vibrations to one end of the membrane, a transversal wave builds up and progresses to the far end generating both a positive pressure gradient and flow rate. Among others, two axisymmetric geometrical configurations are possible, namely the discoidal and the tubular design. The first one has been built as a physical prototype and is experimentally investigated. In addition, a corresponding numerical FSI model is set up and validated against the experimental findings. Based on this validated numerical method, further numerical investigations are conducted focusing on the development of a tubular progressive wave pump concept with regard to its potential for application as a VAD in the future. To address VAD-relevant issues such as size, hydraulic performance, and blood trauma, corresponding numerical simulations involving macroscopic blood trauma models have been performed. Although being still in an early phase of development, the results are promising and indicate that the wave pump concept in its present state is feasible and can be further developed and investigated as a new type of blood pump.