gebhart/patrepeval huggingface dataset:
Synthesis, Physicochemical Properties, and Hydrogen Bonding of 4(5)‐Substituted 1‐H‐Imidazole‐2‐carboxamide, a Potential Universal Reader for DNA Sequencing by Recognition Tunneling (2012)

We have developed a chemical reagent that recognizes all naturally occurring DNA bases, a so called universal reader, for DNA sequencing by recognition tunneling in nanopores.1 The primary requirements for this type of molecules are the ability to form non-covalent complexes with individual DNA bases and to generate recognizable electronic signatures under an electrical bias. 1-H-imidazole-2-carboxamide was designed as such a recognition moiety to interact with the DNA bases through hydrogen bonding. In the present study, we first furnished a synthetic route to 1-H-imidazole-2-carboxamide containing a short ω-functionalized alkyl chain at its 4(5) position for its attachment to metal and carbon electrodes. The acid dissociation constants of the imidazole-2-carboxamide were then determined by UV spectroscopy. The data show that the 1-H-imidazole-2-carboxamide exists in a neutral form between pH 6-10. Density functional theory (DFT) and NMR studies indicate that the imidazole ring exists in prototropic tautomers. We propose an intramolecular mechanism for tautomerization of 1-H-imidazole-2-carboxamide. In addition, the imidazole-2-carboxamide can self-associate to form hydrogen bonded dimers. NMR titration found that naturally occurring nucleosides interacted with 1-H-imidazole-2-carboxamide through hydrogen bonding in a tendency of dG>dC≫dT>dA. These studies are indispensable to assisting us in understanding the molecular recognition that takes place in the nanopore where routinely used analytical tools such as NMR and FTIR cannot be conveniently applied.
Electron-beam-tunable interference filter spatial light modulator (1988)

A new type of electron-beam-addressed spatial light modulator has been demonstrated. It is based on the local tuning of an optothermal nonlinear interference filter by the scanned electron beam. Such an e-beam-tunable interference filter device should find applications in both display technology and optical data processing.
Regional creatine kinase, adenylate kinase, and lactate dehydrogenase in normal canine brain. (1988)

Following acute stroke, creatine kinase and other enzymes are released into the cerebrospinal fluid and blood from injured brain tissue. To determine whether regional differences in brain enzyme activity might exist and therefore affect the amount of enzyme released, we quantified the levels of creatine kinase, adenylate kinase, and lactate dehydrogenase in 12 regions of normal canine brain (n = 4). Adenylate kinase activity varied the least among regions (49 +/- 7 units/g), followed by lactate dehydrogenase activity (122 +/- 28 units/g). The pattern for both adenylate kinase and lactate dehydrogenase was higher activity in predominantly gray matter areas, lower activity in white matter, and intermediate activity in mixed regions. The distribution of creatine kinase brain isoenzyme and mitochondrial creatine kinase in canine brain was less predictable, showing wider variations among regions (isoenzyme, 462 +/- 116 units/g; mitochondrial, 42 +/- 20 units/g). Even cerebral gray matter demonstrated substantial regional variations in creatine kinase brain isoenzyme, ranging from 606 units/g in the parietal cortex to 329 units/g in the temporal cortex. We conclude that the content of creatine kinase brain isoenzyme varies more than twofold among areas of brain. This regional variation may be important in the interpretation of creatine kinase brain isoenzyme measurements in cerebrospinal fluid and serum used to assess neurologic injury following stroke.
NEOL: Toward Never-Ending Object Learning for robots (2016)

Learning to recognize objects based on names is a crucial capability for personal robots. Recent recognition methods successfully learn to recognize objects in a train-once-then-test setting. Yet, these methods do not apply readily to robotic settings, where a robot might continuously encounter new objects and new names. In this work, we present a framework for Never-Ending Object Learning (NEOL). Our framework automatically learns to organize object names into a semantic hierarchy using crowdsourcing and background knowledge bases. It then uses the hierarchy to improve the consistency and efficiency of annotating objects. It also adapts information from additional image datasets to learn object classifiers from a very small number of training examples. We present experiments to test the performance of the adaptation method and demonstrate the full system in a never-ending object learning experiment.
The downstream box: an efficient and independent translation initiation signal in Escherichia coli. (1996)

The downstream box (DB) was originally described as a translational enhancer of several Escherichia coli and bacteriophage mRNAs located just downstream of the initiation codon. Here, we introduced nucleotide substitutions into the DB and Shine-Dalgarno (SD) region of the highly active bacteriophage T7 gene 10 ribosome binding site (RBS) to examine the possibility that the DB has an independent and functionally important role. Eradication of the SD sequence in the absence of a DB abolished the translational activity of RBS fragments that were fused to a dihydrofolate reductase reporter gene. In contrast, an optimized DB at various positions downstream of the initiation codon promoted highly efficient protein synthesis despite the lack of a SD region. The DB was not functional when shifted upstream of the initiation codon to the position of the SD sequence. Nucleotides 1469-1483 of 16S rRNA ('anti-downstream box') are complementary to the DB, and optimizing this complementarity strongly enhanced translation in the absence and presence of a SD region. We propose that the stimulatory interaction between the DB and the anti-DB places the start codon in close contact with the decoding region of 16S rRNA, thereby mediating independent and efficient initiation of translation.
Preparation of Polymer Particles in Nonaqueous Direct and Inverse Miniemulsions (2000)

Polymerizable miniemulsions were formulated in nonaqueous media, and it is shown that these systems exhibit characteristics similar to those of aqueous miniemulsions. Depending on the polarity of the continuous medium and the dispersed phase, the formulation of direct and inverse miniemulsions is possible. Direct miniemulsions in nonaqueous media are exemplified by dispersing styrene in formamide or glycol. Inverse miniemulsions were generated with the polar monomer hydroxyethyl methacrylate, acrylamide, or acrylic acid in cyclohexane or hexadecane as the unpolar continuous phase, and the miniemulsions were polymerized to latexes. For both the direct and inverse miniemulsions, it was shown that during high shear dispersion a steady state of droplet size is reached and that addition of a strong lipophobe (for inverse systems) or ultrahydrophobe (for regular systems) is required to stabilize the resulting miniemulsion for sufficient times. With surface tension measurements, the coverage of the particles with surfactant was determined to be incomplete. These facts are typical for the miniemulsion state; i.e., it is proven that organic miniemulsions indeed can be made and polymerized.
Exhaled Nitric Oxide Levels during Acute Asthma Exacerbation (2005)

FE(NO) measurements in ED patients with acute asthma exacerbations were poorly reproducible and did not correlate with standard measures of asthma severity. These results suggest that using existing technology, FE(NO) is not a useful marker for assessing severity, response to treatment, or disposition of acute asthmatic patients in the ED.
Amorphous silicon alloy photovoltaic research?present and future (2000)

Amorphous silicon alloy has received a great deal of attention as a low-cost material for solar cells and modules. The disorder inherent in the material creates many defect states that impede carrier transport, and the major challenge has been to improve the light-to-electricity conversion efficiency. The most successful method of growing high quality material is by the use of hydrogen dilution in deposition gas mixture which results in a material with improved order. We discuss here the various approaches taken to improve material and device quality that have resulted in stable cell and module efficiencies of 13% and 10·5%, respectively. We also discuss future directions of research. Copyright © 2000 John Wiley & Sons, Ltd.
Ambient mass spectrometry using desorption electrospray ionization (DESI): instrumentation, mechanisms and applications in forensics, chemistry, and biology (2005)

Analytical characteristics of DESI are summarized. Examples of applications to small and large molecules, to in situ analysis, and to high-throughput analyses are presented. Evidence is provided for both a heterogeneous charge-transfer mechanism and a droplet pick-up mechanism of ionization. The speed, lack of the need for sample preparation, selectivity, and sensitivity of DESI are all demonstrated and discussed. Instrumentation is also discussed. Forensic applications as well as emerging areas of application including tissue imaging are given emphasis.
Digital Audio Watermarking (2005)

This chapter provides a comprehensive survey and summary of the technical achievements in the research area of digital audio watermarking. In order to give a big picture of the current status of this area, this chapter covers the research aspects of performance evaluation for audio watermarking, human auditory system, digital watermarking for PCM audio, digital watermarking for wav-table synthesis audio, and digital watermarking for compressed audio. Based on the current technology used in digital audio watermarking and the demand from real-world applications, future promising directions are identified.
Sorting of mannose 6-phosphate receptors and lysosomal membrane proteins in endocytic vesicles. (1988)

The intracellular distributions of the cation-independent mannose 6-phosphate receptor (MPR) and a 120-kD lysosomal membrane glycoprotein (lgp120) were studied in rat hepatoma cells. Using quantitative immunogold cytochemistry we found 10% of the cell's MPR located at the cell surface. In contrast, lgp120 was not detectable at the plasma membrane. Intracellularly, MPR mainly occurred in the trans-Golgi reticulum (TGR) and endosomes. lgp120, on the other hand, was confined to endosomes and lysosomes. MPR was present in both endosomal tubules and vacuoles, whereas lgp120 was confined to the endosomal vacuoles. In cells incubated for 5-60 min with the endocytic tracer cationized ferritin, four categories of endocytic vacuoles could be discerned, i.e., vacuoles designated MPR+/lgp120-, MPR+/lgp120+, MPR-/lgp120+, and vacuoles nonimmunolabeled for MPR and lgp120. Tracer first reached MPR+/lgp120-, then MPR+/lgp120+, and finally MPR-/lgp120+ vacuoles, which are assumed to represent lysosomes. To study the kinetics of appearance of endocytic tracers in MPR-and/or lgp120-containing pools in greater detail, cells were allowed to endocytose horse-radish peroxidase (HRP) for 5-90 min. The reduction in detectability of MPR and lgp120 antigenicity on Western blots, due to treatment of cell homogenates with 3'3-diaminobenzidine, was followed in time. We found that HRP reached the entire accessible pool of MPR almost immediately after internalization of the tracer, while prolonged periods of time were required for HRP to maximally access lgp120. The combined data suggest that MPR+/lgp120+ vacuoles are endocytic vacuoles, intermediate between MPR+/lgp120-endosomes and MPR-/lgp120+ lysosomes, and represent the site where MPR is sorted from lgp120 destined for lysosomes. We propose that MPR is sorted from lgp120 by selective lateral distribution of the receptor into the tubules of this compartment, resulting in the retention of lgp120 in the vacuoles and the net transport of lgp120 to lysosomes.
Mouse LYVE-1 Is an Endocytic Receptor for Hyaluronan in Lymphatic Endothelium (2001)

The glycosaminoglycan hyaluronan is a key substrate for cell migration in tissues during inflammation, wound healing, and neoplasia. Unlike other matrix components, hyaluronan (HA) is turned over rapidly, yet most degradation occurs not locally but within distant lymph nodes, through mechanisms that are not yet understood. While it is not clear which receptors are involved in binding and uptake of hyaluronan within the lymphatics, one likely candidate is the lymphatic endothelial hyaluronan receptor LYVE-1 recently described in our laboratory (Banerji, S., Ni, J., Wang, S., Clasper, S., Su, J., Tammi, R., Jones, M., and Jackson, D.G. (1999) J. Cell Biol. 144, 789-801). Here we present evidence that LYVE-1 is involved in the uptake of hyaluronan by lymphatic endothelial cells using a new murine LYVE-1 orthologue identified from the EST data base. We show that mouse LYVE-1 both binds and internalizes hyaluronan in transfected 293T fibroblasts in vitro and demonstrate using immunoelectron microscopy that it is distributed equally among the luminal and abluminal surfaces of lymphatic vessels in vivo. In addition, we show by means of specific antisera that expression of mouse LYVE-1 remains restricted to the lymphatics in homozygous knockout mice lacking a functional gene for CD44, the closest homologue of LYVE-1 and the only other Link superfamily HA receptor known to date. Together these results suggest a role for LYVE-1 in the transport of HA from tissue to lymph and imply that further novel hyaluronan receptors must exist that can compensate for the loss of CD44 function.
Decision analysis comes of age. (1983)

Ten years ago, decision analysis was still an experimental management technique. But even then supporters claimed that eventually it would become for the manager what calculus is to the engineer. According to the authors of this article, decision analysis that incorporates personal judgment has not yet become what some expected, but it has, nonetheless, gained acceptance in many large corporations and government departments. One of the reasons for this acceptance is the greater flexibility and sensitivity of decision analysis to managers' needs than earlier forms had. In other words, today's decision analysis techniques can better take into account the people, the politics, the time pressures, and all the messy but critical factors that managers have to contend with. In this article, the authors describe three major forms of decision analysis and show how real managers have used decision tree analysis, probabilistic forecasting, and multiattribute analysis to solve real business problems.
Clustering and Mechanics in Dense Depletion and Thermal Gels (2005)

We report on the microstructure and mechanical properties (elastic modulus) of concentrated depletion and thermal gels of octadecyl-coated silica particles for different values of the strength of interaction--polymer concentration for depletion gels and temperature for thermal gels. The depletion gels are composed of dense clusters and voids, while the thermal gels are devoid of clusters. Shear breaks up clusters in depletion gels while it induces clustering in the thermal gels. In both of these gels, the microstructure recovers to the presheared state upon cessation of shear. The recovery of the elastic modulus mimics the microstructure in the sense that the elastic modulus recovers to the presheared sheared state after shearing is stopped. Calculations of the gel boundary by modeling the interactions with an effective one-component square-well model reveals that suspensions with similar ranges of attraction gel at the same volume fraction at a fixed strength of attraction. Calculations of the elastic modulus using the naïve mode coupling theory for depletion gels are in good agreement with experimental measurements provided clustering is taken into account and have the same magnitude as the elastic moduli of thermal gels with similar strengths of attraction. These calculations, in addition to the experimental observations reinforce the point that the microscopic parameter determining the elastic modulus of dense gels and its recovery is the localization length which is only a fraction of the particle diameter and not the structure on the length scale of the particle diameter and larger.
Cytogenetics and oncogenes in leukemia (1992)

Cytogenetic and molecular studies have assumed an increasing role in the evaluation and management of patients with leukemia. Many cytogenetic findings have become well established as important independent indicators of prognosis in the acute leukemias. There has been a recent explosion of knowledge about the genes involved in leukemogenesis and the manner in which their structure or expression is altered by chromosomal translocations or point mutations. Application of newer techniques such as the polymerase chain reaction and in situ hybridization has begun to allow quantitation of residual leukemia cells after therapy. Cytogenetic and molecular findings should allow us to use more individualized therapy in treating leukemia, as well as therapy targeting leukemia-specific abnormal gene products.
Mapping of biologically relevant sites on human IL-1 beta using monoclonal antibodies. (1988)

mAb have been raised that recognize human IL-1 beta. Using overlapping peptide fragments expressed in yeast and bacteria, we have mapped the regions of the protein to which these antibodies bind. To assess the relevance of the different regions of IL-1 beta for the expression of its biologic activity, the ability of the antibodies to block IL-1 activity was assayed. Antibodies recognizing the regions 133-148 and 251-269 of human IL-1 beta could inhibit the activity of IL-1 beta, but not of IL-1 alpha, in two different biologic assays, the murine thymocyte proliferation and PGE2 release from human fibroblasts. Conversely, antibodies that recognize the region 218-243 have only a moderate inhibitory effect on the IL-1 beta biologic activity in both assays. Finally, an antibody mapping to the region 148-192 did not inhibit IL-1 beta activity either on thymocytes or on fibroblasts. It is suggested that IL-1 beta-induced cell activation involves different regions of the protein and that both N-terminal and C-terminal fragments are involved in the correct functioning of the IL-1 beta molecule.
The glycine-rich domain of nucleolin has an unusual supersecondary structure responsible for its RNA-helix-destabilizing properties. (1992)

Nucleolin, a major nucleolar protein implicated in preribosome assembly and transcriptional regulation, possesses a C-terminal domain unusually rich in glycine, arginine, and phenylalanine residues. A polypeptide (p10), corresponding to this domain, has been synthesized by means of an Escherichia coli expression system and purified to homogeneity. Nitrocellulose binding assays have clearly shown that this domain of nucleolin is capable of interacting with RNA, and indeed all nucleic acids tested, in an efficient but nonspecific manner. A combination of circular dichroism and infrared spectroscopy provide strong evidence that repeated beta-turns are a major structural component of this polypeptide, which is entirely consistent with its amino acid composition and above all the presence of repeat motifs such as RGGF. Circular dichroism technique also shows that the interaction of p10 with RNA involves an unstacking of the nucleotide bases and an unfolding of the RNA secondary structure. While the role of the C-terminal domain of nucleolin in vivo has yet to be established, our findings suggest that it may act to unfold regions of ribosomal RNA so that a second domain of nucleolin has access to its specific binding site.
Synthesis of isotopically labelled [3‐14C]‐ and [3,3‐2H2]‐5‐fluoro‐1,3‐dihydro‐1‐hydroxy‐2,1‐benzoxaborole (AN2690), a new antifungal agent for the potential treatment of onychomycosis (2007)

Abstract 5‐Fluoro‐1,3‐dihydro‐1‐hydroxy‐2,1‐benzoxaborole (AN2690) is a new antifungal agent for the potential treatment of onychomycosis. During the preclinical development phase, it was necessary to synthesize the radioisotope [3‐ 14 C]‐5‐fluoro‐1,3‐dihydro‐1‐hydroxy‐2,1‐benzoxaborole and the deuterium isotope [3,3‐ 2 H 2 ]‐5‐fluoro‐1,3‐dihydro‐1‐hydroxy‐2,1‐benzoxaborole for in vitro studies. We report the synthesis of these two isotopically labelled derivatives. Copyright © 2007 John Wiley &amp; Sons, Ltd.
Viscosity of Glycerol and Its Aqueous Solutions (1951)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTViscosity of Glycerol and Its Aqueous SolutionsJ. B. Segur and Helen E. OberstarCite this: Ind. Eng. Chem. 1951, 43, 9, 2117–2120Publication Date (Print):September 1, 1951Publication History Published online1 May 2002Published inissue 1 September 1951https://pubs.acs.org/doi/10.1021/ie50501a040https://doi.org/10.1021/ie50501a040research-articleACS PublicationsRequest reuse permissionsArticle Views14875Altmetric-Citations608LEARN 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 options Get e-Alerts
Review article: biological activity markers in inflammatory bowel disease (2007)

Acute phase reactants and faecal markers are useful to assess the disease activity in clinical practice. More data are required on cytokines and adhesion molecules. C-reactive protein, erythrocyte sedimentation rate, interleukins and faecal markers may be useful in predicting a relapse.
Citrobacter rodentium of mice and man (2005)

The major classes of enteric bacteria harbour a conserved core genomic structure, common to both commensal and pathogenic strains, that is most likely optimized to a life style involving colonization of the host intestine and transmission via the environment. In pathogenic bacteria this core genome framework is decorated with novel genetic islands that are often associated with adaptive phenotypes such as virulence. This classical genome organization is well illustrated by a group of extracellular enteric pathogens, which includes enteropathogenic Escherichia coli (EPEC), enterohaemorrhagic E. coli (EHEC) and Citrobacter rodentium, all of which use attaching and effacing (A/E) lesion formation as a major mechanism of tissue targeting and infection. Both EHEC and EPEC are poorly pathogenic in mice but infect humans and domestic animals. In contrast, C. rodentium is a natural mouse pathogen that is related to E. coli, hence providing an excellent in vivo model for A/E lesion forming pathogens. C. rodentium also provides a model of infections that are mainly restricted to the lumen of the intestine. The mechanism's by which the immune system deals with such infections has become a topic of great interest in recent years. Here we review the literature of C. rodentium from its emergence in the mid-1960s to the most contemporary reports of colonization, pathogenesis, transmission and immunity.