gebhart/patrepeval huggingface dataset:
Demonstration and analysis of bridging regioselectivity operative during di-.pi.-methane photorearrangement of ortho-substituted benzonorbornadienes and anti-7,8-benzotricyclo[4.2.2.02,5]deca-3,7,9-trienes (1977)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDemonstration and analysis of bridging regioselectivity operative during di-.pi.-methane photorearrangement of ortho-substituted benzonorbornadienes and anti-7,8-benzotricyclo[4.2.2.02,5]deca-3,7,9-trienesRobert A. Snow, Denise M. Cottrell, and Leo A. PaquetteCite this: J. Am. Chem. Soc. 1977, 99, 11, 3734–3744Publication Date (Print):May 1, 1977Publication History Published online1 May 2002Published inissue 1 May 1977https://pubs.acs.org/doi/10.1021/ja00453a036https://doi.org/10.1021/ja00453a036research-articleACS PublicationsRequest reuse permissionsArticle Views419Altmetric-Citations21LEARN 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
Use of Polymerase Chain Reaction-Amplified Ribosomal Intergenic Sequences for the Diagnosis of<i>Verticillium tricorpus</i> (1994)

Verticillium dahliae, V. albo-atrum, and V. tricorpus are common pathogens of potato. Currently, polymerase chain reaction (PCR) assays based on sequence differences in their ribosomal RNA genes are available for the specific diagnosis of the first two species. Using the same principles, we developed an analogous assay to detect V. tricorpus. The 18-28S rDNA intragenic region of V. tricorpus was obtained by PCR amplification of genomic DNA from the fungus. Sequence analyses indicated that the 5.8S rDNA sequences were conserved among all three Verticillium species but the internal transcribed spacer regions of V. tricorpus clearly were divergent. These sequence differences were used to synthesize a specific primer set for the diagnosis of V. tricorpus [...]
<i>Pseudomonas aeruginosa</i>PqsA Is an Anthranilate-Coenzyme A Ligase (2007)

Pseudomonas aeruginosa is an opportunistic human pathogen which relies on several intercellular signaling systems for optimum population density-dependent regulation of virulence genes. The Pseudomonas quinolone signal (PQS) is a 3-hydroxy-4-quinolone with a 2-alkyl substitution which is synthesized by the condensation of anthranilic acid with a 3-keto-fatty acid. The pqsABCDE operon has been identified as being necessary for PQS production, and the pqsA gene encodes a predicted protein with homology to acyl coenzyme A (acyl-CoA) ligases. In order to elucidate the first step of the 4-quinolone synthesis pathway in P. aeruginosa, we have characterized the function of the pqsA gene product. Extracts prepared from Escherichia coli expressing PqsA were shown to catalyze the formation of anthraniloyl-CoA from anthranilate, ATP, and CoA. The PqsA protein was purified as a recombinant His-tagged polypeptide, and this protein was shown to have anthranilate-CoA ligase activity. The enzyme was active on a variety of aromatic substrates, including benzoate and chloro and fluoro derivatives of anthranilate. Inhibition of PQS formation in vivo was observed for the chloro- and fluoroanthranilate derivatives, as well as for several analogs which were not PqsA enzymatic substrates. These results indicate that the PqsA protein is responsible for priming anthranilate for entry into the PQS biosynthetic pathway and that this enzyme may serve as a useful in vitro indicator for potential agents to disrupt quinolone signaling in P. aeruginosa.
A study on the use of 8-directional features for online handwritten Chinese character recognition (2005)

This paper presents a study of using 8-directional features for online handwritten Chinese character recognition. Given an online handwritten character sample, a series of processing steps, including linear size normalization, adding imaginary strokes, nonlinear shape normalization, equidistance resampling, and smoothing, are performed to derive a 64/spl times/64 normalized online character sample. Then, 8-directional features are extracted from each online trajectory point, and 8 directional pattern images are generated accordingly, from which blurred directional features are extracted at 8/spl times/8 uniformly sampled locations using a filter derived from the Gaussian envelope of a Gabor filter. Finally, a 512-dimensional vector of raw features is formed. Extensive experiments on the task of recognizing 3755 level-1 Chinese characters in GB2312-80 standard are performed to compare and discern the best setting for several algorithmic choices and control parameters. The effectiveness of the studied approach is confirmed.
Invited Article: Autonomous assembly of atomically perfect nanostructures using a scanning tunneling microscope (2014)

A major goal of nanotechnology is to develop the capability to arrange matter at will by placing individual atoms at desired locations in a predetermined configuration to build a nanostructure with specific properties or function. The scanning tunneling microscope has demonstrated the ability to arrange the basic building blocks of matter, single atoms, in two-dimensional configurations. An array of various nanostructures has been assembled, which display the quantum mechanics of quantum confined geometries. The level of human interaction needed to physically locate the atom and bring it to the desired location limits this atom assembly technology. Here we report the use of autonomous atom assembly via path planning technology; this allows atomically perfect nanostructures to be assembled without the need for human intervention, resulting in precise constructions in shorter times. We demonstrate autonomous assembly by assembling various quantum confinement geometries using atoms and molecules and describe the benefits of this approach.
Regulation of in vitro gene expression using antisense oligonucleotides or antisense expression plasmids transfected using starburst PAMAM dendrimers (1996)

Starburst polyamidoamine (PAMAM) dendrimers are a new type of synthetic polymer characterized by a branched spherical shape and a high density surface charge. We have investigated the ability of these dendrimers to function as an effective delivery system for antisense oligonucleotides and ‘antisense expression plasmids’ for the targeted modulation of gene expression. Dendrimers bind to various forms of nucleic acids on the basis of electrostatic interactions, and the ability of DNA-dendrimer complexes to transfer oligonucleotides and plasmid DNA to mediate antisense inhibition was assessed in an in vitro cell culture system. Cell lines that permanently express luciferase gene were developed using dendrimer mediated transfection. Transfections of antisense oligonucleotides or antisense cDNA plasmids into these cell lines using dendrimers resulted in a specific and dose dependent inhibition of luciferase expression. This inhibition caused ∼25–50% reduction of baseline luciferase activity. Binding of the phosphodiester oligonucleotides to dendrimers also extended their intracellular survival. While dendrimers were not cytotoxic at the concentrations effective for DNA transfer, some non-specific suppression of luciferase expression was observed. Our results indicate that Starburst dendrimers can be effective carriers for the introduction of regulatory nucleic acids and facilitate the suppression of the specific gene expression.
Development Perspectives Of The Biobased Economy: A Review (2010)

ABSTRACT This paper provides an outline of the biobased economy, its perspectives for agriculture and, more particularly, for development purposes. Possibilities of development of biobased products, advanced biofuels, and viable and efficient biorefinery concepts are explored. The paper lists non‐fuel bioproducts (e.g., chemicals, pharmaceuticals, biopolymers) and presents basic principles and development options for biorefineries that can be used to generate them alongside biofuels, power, and by‐products. One of the main challenges is to capture more value from existing crops without compromising the needs and possibilities of small‐scale, less endowed farmers. Biobased products offer the most development perspectives, combining large market volumes with medium to high price levels. Consequently, the most can be expected from products like fine chemicals, lubricants, and solvents. In addition, biosolar cells can help to relax pressures on biomass production systems while decentralized production chains can serve local needs for energy, materials, and nutrients as their requirement for viable economic development are linked to larger markets. Research challenges include development of such production and market chains, and of biosolar cells and selection of model crops that offer perspectives for less favored producers and underdeveloped rural areas.
A novel method for the detection of necrotic lesions in human cancers. (1988)

Data are presented in support of the hypothesis that malignant tumors, containing abnormally permeable, degenerating cells, can be selectively detected using monoclonal antibodies to intracellular antigens. Biodistribution, imaging, and autoradiographic studies were performed in nude mice transplanted with four different human tumor cell lines to demonstrate the binding of radiolabeled antinuclear monoclonal antibodies within bulky tumors containing necrotic lesions. For these studies, two monoclonal antibodies, designated TNT-1 (IgG2a) and TNT-2 (IgM) were chosen since they were found to bind to abundant nuclear antigens which are retained in permeable, dying cells. F(ab')2 fragments prepared by pepsin digestion were radiolabeled with iodine-125 or iodine-131 by the iodogen method for i.v. administration. Biodistribution studies in nontumor-bearing BALB/c mice at various time intervals revealed normal patterns of antibody excretion with no accumulation of antibody in healthy organs. In contrast, biodistribution studies performed on Day 3 in tumor-bearing nude mice showed high tumor to organ ratios in those animals bearing necrotic tumors. Necrotic regions dissected at necropsy gave tumor to blood ratios as high as 131:1. Transplants having little demonstrable necrosis were found to have low tumor to blood ratios (0.4:1). Sequential imaging studies confirmed the high tumor-to-organ ratios and showed positive tumor imaging as early as 4 h. Autoradiographic studies of excised tumors showed the presence of label selectively in necrotic areas with preferential labeling over the nuclei of degenerating cells. Because of the universal presence of these nuclear antigens and the known prevalence of necrosis in tumors, this approach may be of value for the imaging and treatment of a wide variety of cancers in humans.
Chromosomal Deficiencies and the Embryonic Development of Drosophila Melanogaster (1937)

Chromosome aberrations have marked effects upon the development of an organism.Many such aberrations are lethal.In Drosophila this is particularly true of chromosomal deficiencies, as first described by Bridges.2A more detailed study of the effects of such aberrations made by Li' shows that in all the cases he investigated deficiencies are lethal in the homozygous condition-the organisms dying in the egg or larval stages.Heterozygous deficiencies result in death in later stages, although many are not lethal.A few exceptional cases of viable homozygous deficiencies have been de- scribed.4'5In such instances the deficiencies are among the smallest known, probably for very few genes.These facts emphasize the importance of the chromosomes in the develop- mental processes.Just what the chromosomal functions may be, how- ever, is by no means clear; nor is the r6le of the individual gene evident.An ideal approach, such as the removal of one gene at a time, then of com- binations of genes, to determine the part played by each and its interac- tions with others, presents many practical difficulties.The existence of numerous deficiencies, however, makes an approximation to this approach possible by the study of the effects of larger or smaller blocks of genes.The present study is concerned with the effects of certain deficiencies upon the embryonic development of D. melanogaster.The deficiencies used involved greater or lesser portions of the X-chromosome, ranging from the total absence of the X to a small deficiency involving relatively few "bands" as seen in the salivary gland chromosome.The technique of Huettner and Rabinowitz6 was used, in a somewhat modified form, for the observation of living eggs, and details of internal structure were studied by means of sectioned material.'Only timed eggs were used.Usually fe- males were allowed to lay for half an hour and the eggs allowed to develop to the desired stage at a temperature of 22-23C.
[Nephrotoxicity of anti-CD3 monoclonal antibodies]. (1991)

The OKT3 monoclonal antibody entails a transient acute nephrotoxicity when used either to prevent or to treat renal allograft rejection. This nephrotoxicity was reproduced experimentally in mice injected with 145-2C11, an anti-CD3 monoclonal antibody which shares many properties with OKT3. Both clinical and experimental data suggest that the renal lesions are due to the systemic release of cytokines that occurs prior to the immunosuppression. Pre-treatment with corticosteroids before the injection of anti-CD3 monoclonal antibody mitigates both the release of cytokines and the nephrotoxicity, in a dose-dependent manner. Experimental data suggest that very high doses of methylprednisolone (50 mg/kg) administered 2 to 3 hours before the monoclonal antibody are necessary to obtain an optimal protection.
Redistribution Reactions of Methylsiloxanes Catalyzed by Transition Metal Complexes. (1982)

Redistribution reactions of a variety of hydrogen-substituted siloxanes are catalyzed by various transition metal complexes of iridium and rhodium. The products arise from breaking and remaking of Si-C, Si-H, and Si-O bonds. Siloxanes not possessing a Si-H bond are inert under the conditions studied. The most favored reaction pathway appears to preferentially scramble the groups directly attached to the silicon bearing the hydrogen atom. A new cyclo-iridiadisiloxane, L2(CO)(H)-Ir(SiMeROSiMeR) (L = Ph3P, R = Me3SiO) is reported. This compound exists in three isomeric forms as a consequence of the spatial arrangements of the R and Me groups on the ring. (Author)
Ramsey interference in strongly driven Rydberg systems (1993)

We have studied the evolution of regular and ``dark'' radial wave packets under the influence of two coherent, temporally separated 100 fs laser pulses. The atomic states are probed by ramped-field ionization. The final state populations exhibit Ramsey oscillations with periods ranging from 2.6--1000 fs as a function of the delay between the two pulses. This time-domain bound-state interferometry reveals several new aspects of the dynamic evolution of wave packets in the presence of strong laser fields. Lowest order perturbation theory is inadequate to describe wave packet formations, even at the lowest intensities studied.
Engineered proteins detect spontaneous DNA breakage in human and bacterial cells (2013)

Spontaneous DNA breaks instigate genomic changes that fuel cancer and evolution, yet direct quantification of double-strand breaks (DSBs) has been limited. Predominant sources of spontaneous DSBs remain elusive. We report synthetic technology for quantifying DSBs using fluorescent-protein fusions of double-strand DNA end-binding protein, Gam of bacteriophage Mu. In Escherichia coli GamGFP forms foci at chromosomal DSBs and pinpoints their subgenomic locations. Spontaneous DSBs occur mostly one per cell, and correspond with generations, supporting replicative models for spontaneous breakage, and providing the first true breakage rates. In mammalian cells GamGFP-labels laser-induced DSBs antagonized by end-binding protein Ku; co-localizes incompletely with DSB marker 53BP1 suggesting superior DSB-specificity; blocks resection; and demonstrates DNA breakage via APOBEC3A cytosine deaminase. We demonstrate directly that some spontaneous DSBs occur outside of S phase. The data illuminate spontaneous DNA breakage in E. coli and human cells and illustrate the versatility of fluorescent-Gam for interrogation of DSBs in living cells. DOI:http://dx.doi.org/10.7554/eLife.01222.001.
Long-range surface-plasmon modes in silver and aluminum films (1983)

We report the first observation to our knowledge of a sharp minimum in the attenuated total reflectivity of a thin metal film between index-matching layers. The resonance is due to the excitation of the long-range surface-plasmon mode on both sides of the thin metal films, as originally discussed by Sarid [Phys. Rev. Lett. 47, 1927 (1981)]. The angular widths of the observed resonance in silver and aluminum films are both reduced by over an order of magnitude relative to that associated with the Kretschmann excited mode.
Randomized Double-Blind Study of Potassium Citrate in Idiopathic Hypocitraturic Calcium Nephrolithiasis (1993)

In an attempt to document the efficacy of potassium citrate in stone formation, 57 patients with active lithiasis (2 or more stones during the preceding 2 years) and hypocitraturia were randomly allocated into 2 groups, with 1 group taking 30 to 60 mEq. potassium citrate daily in wax matrix tablet formation and the other group receiving placebo. In 18 patients receiving potassium citrate for 3 years stone formation significantly declined after treatment from 1.2 +/- 0.6 to 0.1 +/- 0.2 per patient year (p < 0.0001), in 13 patients (72%) the disease was in remission and all patients showed a reduced stone formation rate individually. In contrast, 20 patients taking placebo medication for 3 years showed no significant change in stone formation rate (1.1 +/- 0.4 to 1.1 +/- 0.3 per patient year) and in only 4 patients (20%) was the disease in remission. The stone formation rate during potassium citrate treatment was significantly lower than during the placebo treatment (0.1 +/- 0.2 versus 1.1 +/- 0.3 per patient year, p < 0.001). Potassium citrate therapy caused a significant increase in urinary citrate, pH and potassium, whereas placebo did not. Adverse reactions to potassium citrate were mild causing only 2 patients in the potassium citrate group and 1 in the placebo group to withdraw from the study. In summary, our randomized trial showed the efficacy of potassium citrate in preventing new stone formation in idiopathic hypocitraturic calcium nephrolithiasis.
Dynamic single cell culture array (2006)

It is important to quantify the distribution of behavior amongst a population of individual cells to reach a more complete quantitative understanding of cellular processes. Improved high-throughput analysis of single cell behavior requires uniform conditions for individual cells with controllable cell-cell interactions, including diffusible and contact elements. Uniform cell arrays for static culture of adherent cells have previously been constructed using protein micropatterning techniques but lack the ability to control diffusible secretions. Here we present a microfluidic-based dynamic single cell culture array that allows both arrayed culture of individual adherent cells and dynamic control of fluid perfusion with uniform environments for individual cells. In our device no surface modification is required and cell loading is done in less than 30 seconds. The device consists of arrays of physical U-shaped hydrodynamic trapping structures with geometries that are biased to trap only single cells. HeLa cells were shown to adhere at a similar rate in the trapping array as on a control glass substrate. Additionally, rates of cell death and division were comparable to the control experiment. Approximately 100 individual isolated cells were observed growing and adhering in a field of view spanning approximately 1 mm(2) with greater than 85% of cells maintained within the primary trapping site after 24 hours. Also, greater than 90% of cells were adherent and only 5% had undergone apoptosis after 24 hours of perfusion culture within the trapping array. We anticipate uses in single cell analysis of drug toxicity with physiologically relevant perfused dosages as well as investigation of cell signaling pathways and systems biology.
Immunochemical studies of serum, urine and calculus proteins in urolithiasis. (1985)

Total serum protein levels in 70 patients with urolithiasis were not significantly different from those in 20 control subjects, although certain variations were detected in individual protein patterns. In contrast, total urinary protein was significantly higher in patients with urolithiasis. 4-6 different components, i.e., albumin, alpha 1-acidic glycoprotein, alpha 1-antitrypsin, Gc-globulin, fibrinogen and immunoglobulin G, were found in the matrices of calculi and in urine, suggesting that proteinuria may play a role in the formation of stones in patients with urolithiasis.
The influence of the framework core residues on the biophysical properties of immunoglobulin heavy chain variable domains (2009)

Antibody variable domains differ considerably in stability. Single-chain Fv (scFv) fragments derived from natural repertoires frequently lack the high stability needed for therapeutic application, necessitating reengineering not only to humanize their sequence, but also to improve their biophysical properties. The human V(H)3 domain has been identified as having the best biophysical properties among human subtypes. However, complementarity determining region (CDR) grafts from highly divergent V(H) domains to huV(H)3 frequently fail to reach its superior stability. In previous experiments involving a CDR graft from a murine V(H)9 domain of very poor stability to huV(H)3, a hybrid V(H) framework was obtained which combines the lower core residues of muV(H)9 with the surface residues of huV(H)3. It resulted in a scFv with far better biophysical properties than the corresponding grafts to the consensus huV(H)3 framework. To better understand the origin of the superior properties of the hybrid framework, we constructed further hybrids, but now in the context of the consensus CDR-H1 and -H2 of the original human V(H)3 domain. The new hybrids included elements from either murine V(H)9, human V(H)1 or human V(H)5 domains. From guanidinium chloride-induced equilibrium denaturation measurements, kinetic denaturation experiments, measurements of heat-induced aggregation and comparison of soluble expression yield in Escherichia coli, we conclude that the optimal V(H) framework is CDR-dependent. The present work pinpoints structural features responsible for this dependency and helps to explain why the immune system uses more than one framework with different structural subtypes in framework 1 to optimally support widely different CDRs.
Effect of an 8‐month treatment with omega‐3 fatty acids (eicosapentaenoic and docosahexaenoic) in patients with cystic fibrosis (2003)

Long-term eicosapentaenoic plus docosahexanoic acid supplementation (8 months) has positive effects, such as decreasing inflammation, in cystic fibrosis.