gebhart/patrepeval huggingface dataset:
Intestinal mucus gel and secretory antibody are barriers to Campylobacter jejuni adherence to INT 407 cells (1987)

An in vitro mucus assay was developed to study the role of mucus gel and secretory immunoglobulin A (sIgA) in preventing attachment of Campylobacter jejuni to INT 407 cells. An overlay of rabbit small intestinal mucus was found to impede the attachment of C. jejuni to a monolayer of INT 407 cells. Mucus from rabbits previously colonized with C. jejuni was found to completely inhibit bacterial adherence to the underlying cells. Anti-Campylobacter sIgA was readily detected in mucus samples from previously exposed rabbits and was responsible for eliminating bacterial adherence to the INT 407 cells. This was shown by loss of inhibition after mucus absorption with Campylobacter cells. sIgA-containing mucus caused aggregation of the C. jejuni cells within the mucus layer of the assay system. Nonimmune mucus and sIgA alone were unable to cause bacterial aggregation, suggesting a cooperative role for mucus and sIgA. Antibodies responsible for adhesion inhibition were cross-reactive among several Campylobacter strains and were not directed solely against flagellar antigens.
Wide-field<i>in vivo</i>neocortical calcium dye imaging using a convection-enhanced loading technique combined with simultaneous multiwavelength imaging of voltage-sensitive dyes and hemodynamic signals (2014)

<i>In vivo</i> calcium imaging is an incredibly powerful technique that provides simultaneous information on fast neuronal events, such as action potentials and subthreshold synaptic activity, as well as slower events that occur in the glia and surrounding neuropil. Bulk-loading methods that involve multiple injections can be used for single-cell as well as wide-field imaging studies. However, multiple injections result in inhomogeneous loading as well as multiple sites of potential cortical injury. We used convection-enhanced delivery to create smooth, continuous loading of a large area of the cortical surface through a solitary injection site and demonstrated the efficacy of the technique using confocal microscopy imaging of single cells and physiological responses to single-trial events of spontaneous activity, somatosensory-evoked potentials, and epileptiform events. Combinations of calcium imaging with voltage-sensitive dye and intrinsic signal imaging demonstrate the utility of this technique in neurovascular coupling investigations. Convection-enhanced loading of calcium dyes may be a useful technique to advance the study of cortical processing when widespread loading of a wide-field imaging is required.
A Study on Thermally Induced Microdefects in Czochralski-Grown Silicon Crystals : Dependence on Annealing Temperature and Starting Materials (1980)

Thermally induced microdefects in Czochralski-grown (CZ) silicon crystals have been investigated by both TEM and IR absorption techniques. Dependence of the defect behavior on both the annealing temperature and the starting materials was studied. It was found that the defect nature varies with the temperature, and that the defect density increases exponentially with the decrease of the annealing temperature. The increase in density also has a strong correlation with the initial carbon concentration in the wafer. It is concluded that the oxygen precipitates are heterogeneously formed at sites which have certain correlation with carbon atoms.
Incoming nucleotide binds to Klenow ternary complex leading to stable physical sequestration of preceding dNTP on DNA (2001)

Klenow-DNA complex is known to undergo a rate-limiting, protein conformational transition from an 'open' to 'closed' state, upon binding of the 'correct' dNTP at the active site. In the 'closed' state, Mg(2+) mediates a rapid chemical step involving nucleophilic displacement of pyrophosphate by the 3' hydroxyl of the primer terminus. The enzyme returns to the 'open' state upon the release of PPi and translocation permits the next round of reaction. To determine whether Klenow can translocate to the next site on the addition of the next dNTP, without the preceding chemical step, we studied the ternary complex (Klenow-DNA-dNTP) in the absence of Mg(2+). While the ternary complex is proficient in chemical addition of dNTPs in Mg(2+), as revealed by primer extensions, the same in Mg(2+)-deficient conditions lead to non-covalent (physical) sequestration of first two 'correct' dNTPs in the ternary complex. Moreover, the second dNTP traps the first one in the DNA-helix of the ternary complex. Such a dNTP-DNA complex is found to be stable even after the dissociation of KLENOW: This reveals the novel state of the dNTP-DNA complex where the complementary base is stacked in a DNA-helix non-covalently, without the phosphodiester linkage. Further, shuttling of the DNA between the polymerase and the exonuclease site mediates the release of such a DNA complex. Interestingly, Klenow in such a Mg(2+)-deficient ternary complex exhibits a 'closed' conformation.
A Swarm-Based Volition/Attention Framework for Object Recognition (2006)

Visual attention helps identify the salient parts of a scene and enables efficient object recognition by allocating visual resources to more relevant regions of the scene. In this paper, we present an object recognition framework that combines top-down volitional recognition with attention processes using a swarm of cooperating intelligent agents. Each agent in the swarm is a selfcontained independent classifier that can, given any location in the image, predict the presence of a particular object of interest. Our framework combines bottom-up attention and top-down object classification using Particle Swarm Optimization (PSO) dynamics in a novel architecture that utilizes spatially-modulated evolutionary search to rapidly detect objects of interest in a scene. We use bottom-up maps that are automatically built from saliency, past swarm experience, and constraints on possible object positions to modify the swarm’s behavior and help guide the swarm in locating objects. We present fast object detection/recognition results for a variety of video sequences. Our results show that our framework allows objects to be quickly and accurately located and classified using very sparse sampling of the scene.
Analysis of the tumor-associated antigen TSP-180 (1989)

The tumor-associated antigen complex, TSP-180, was previously defined in carcinoma cell lines and found to be expressed in higher amounts in tumor than in normal tissue. Here, the mouse TSP-180 complex is shown to consist of three related proteins (bands 1, 2, and 3) associated with a distinct protein (band 5) that is probably derived from a precursor protein (band 4). All of these proteins are cell surface glycoproteins, and the largest protein (band 1) can be readily labeled with 32PO4. The mouse TSP-180 complex described here strongly resembles the recently described human integrin alpha 6-beta 4 complex. This homology was confirmed using two distinct rat anti-alpha 6 monoclonal antibodies, each of which recognized both human alpha 6-beta 4 and mouse TSP-180 complexes. Furthermore, the TSP-180 band 5 protein (mouse alpha 6) had an N-terminal sequence identical to that of human alpha 6. Finally, two different monoclonal antibodies are described, 346-11A and 439-9B, which directly recognize the multiple forms of mouse and human beta 4 proteins, respectively.
Properties of <i>Streptomyces fradiae</i> Mutants Blocked in Biosynthesis of the Macrolide Antibiotic Tylosin (1981)

We isolated numerous mutants of Streptomyces fradiae blocked in tylosin biosynthesis after N-methyl-N'-nitro-N-nitrosoguanidine mutagenesis. These mutants were classified into nine groups, based upon the tylosin-like compounds produced and upon cofermentation analyses. More than 80% of the mutants isolated produced no tylosin-like compounds, and the majority of these were blocked only in the formation of tylactone. Four classes of mutants blocked in the biosynthesis or addition of tylosin sugars were isolated; tylA mutants were blocked in the formation of all three tylosin sugars, whereas tylB, tylC, and tylD mutants were blocked specifically in the biosynthesis or the addition of mycaminose, mycarose, and 6-deoxy-d-allose, respectively. Two classes of mutants (tylH and tylI) blocked in specific oxidations of tylactone and two classes (tylE and tylF) blocked in specific O-methylations of demethylmacrocin and macrocin were also characterized. Cofermentation and bioconversion studies with these mutants suggested the following relationships: (i) the tylosin sugars are derived from a common intermediate; (ii) tylactone is the first intermediate which can be excreted in appreciable quantities; (iii) the addition of mycaminose to the C-5 hydroxyl group of tylactone must precede oxidations at C-20 and C-23; (iv) oxidation at C-20 normally precedes the attachment of mycarose to the 4' hydroxyl position of mycaminose; and (v) 6-deoxy-d-allose is added to the C-23 hydroxyl position of the lactone and subsequently O-methylated at 2''' and 3''' positions. The O-methylations appear to be the final two steps in tylosin biosynthesis, and the 2''' O-methylation must occur before the 3''' O-methylation can take place. All of the tyl mutants except the tylG mutants produced relatively high levels of tylosin-like intermediates or shunt products. Mutants blocked in specific steps other than 3''' O-methylation, including a mutant blocked in 2''' O-methylation of demethylmacrocin, produced normal levels of macrocin O-methyltransferase. Mutants apparently containing specific tylosin structural gene mutations produced normal levels of aerial mycelia and spores, produced low levels of tylosin aldehyde reductase, and were resistant to high levels of tylosin. However, three atypical tylG mutants produced no tylosin-like compounds, could not cosynthesize tylosin with any other tyl mutant, could not bioconvert tylactone or macrocin to tylosin, and produced no macrocin O-methyltransferase. These three mutants produced elevated levels of tylosin aldehyde reductase. In addition, one was very succeptible to tylosin and did not produce aerial mycelia or spores.
Oncostatin M: a growth regulator produced by differentiated histiocytic lymphoma cells. (1986)

A polypeptide termed oncostatin M, which inhibits the replication of A375 melanoma and other human tumor cells, but not normal human fibroblasts, has been isolated from serum-free supernatants of U-937 histiocytic lymphoma cells that have been induced to differentiate into macrophage-like cells following treatment with the phorbol ester phorbol 12-myristate 13-acetate. No such growth inhibitory activity is detected in the supernatant of untreated U-937 cells, indicating that the protein is induced or increased in expression in the phorbol ester-induced differentiated cells. Oncostatin M is stable between pH 2 and 11 and after heating for 1 hr at 56 degrees C but is not stable at 90 degrees C. Purification of oncostatin M has been achieved by gel chromatography and reversed-phase HPLC, using sequentially acetonitrile and n-propanol in the presence of aqueous trifluoroacetic acid. The apparent molecular weight of oncostatin M is approximately 18,000, as determined by gel chromatography, and 28,000, as determined by polyacrylamide gel electrophoresis. The amino-terminal amino acid sequence of the purified polypeptide has been determined. No substantial sequence homology between oncostatin M and other proteins was found, including other tumor cell inhibitory proteins produced by mononuclear cells. Oncostatin M, therefore, appears to represent a distinct cell growth regulator.
Imidazo[4,5‐d]pyridazines. III. The Synthesis of 2‐phenylimidazo [4,5‐d]‐pyridazines (1964)

Abstract Based upon an analogy with “Dyrenium”, (6‐phenyl‐2,4,7‐triaminopteridine) (I), 4,7‐diamino‐2‐phenylimidazo[4, 5‐d]pyridazine (II) has been prepared. This compound has been found to possess diuretic activity. In addition a number of other substituted 2‐phenylimidazo[4, 5‐d]pyridazines have been prepared.
Convexification of optimal power flow problem (2010)

The optimal power flow (OPF) problem is nonconvex and generally hard to solve. We provide a sufficient condition under which the OPF problem is equivalent to a convex problem and therefore is efficiently solvable. Specifically, we prove that the dual of OPF is a semidefinite program and our sufficient condition guarantees that the duality gap is zero and a globally optimal solution of OPF is recoverable from a dual optimal solution. This sufficient condition is satisfied by standard IEEE benchmark systems with 14, 30, 57, 118 and 300 buses after small resistance (10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-5</sup> per unit) is added to every transformer that originally assumes zero resistance. We justify why the condition might hold widely in practice from algebraic and geometric perspectives. The main underlying reason is that physical quantities such as resistance, capacitance and inductance, are all positive.
Syndromes of accelerated aging. (1982)

A systematic review of the more than 2,000 genetic loci of man cataloged by McKusick indicated that approximately 7% may play a role in modulating the rates of development of various aspects of the senescent phenotype. Assuming an upper limit of about 100,000 loci in man, numerous alleles at approximately 7,000 loci could be contributing to characteristic patterns of aging in individual human beings. Point mutations or chromosomal aberrations involving such loci may result in various progeroid syndromes. These have been classified into two categories: segmental progeroid syndromes, which involve multiple aspects of the senescent phenotype, and unimodal progeroid syndromes, in which predominantly one aspect of the phenotype is involved. Two different examples of segmental progeroid syndromes were discussed: the Werner syndrome (an autosomal recessive) and the Down syndrome (trisomy 21). Examples of unimodal progeroid syndromes included familial hypercholesterolemia (accelerated atherogenesis), xeroderma pigmentosum (acceleration of skin aging, including age-related neoplasms), and certain forms of intestinal polyposis (acceleration of adenocarcinoma of the colon). It is remarkable and encouraging that the biochemical genetic basis of many progeroid syndromes, including all of those mentioned above, may be amenable to investigation with cultured mesenchymal somatic cells from individual subjects. For example, cells from patients with the Werner's syndrome have a striking limitation of their in vitro replicative life-spans and undergo extensive chromosomal rearrangements. These abnormalities are presumably related to an enzyme deficiency which, in principle, could be identified by biochemical studies of cultured cells.
Biotinylated Glyco-Functionalized Quantum Dots: Synthesis, Characterization, and Cytotoxicity Studies (2009)

Quantum dots (QDs) containing surface carboxylic groups have been successfully modified using biotinylated glycopolymer and carbohydrate/biotin reagents via EDC coupling. The biotinylated glycopolymer was synthesized in controlled dimension via the reversible addition-fragmentation chain transfer (RAFT) polymerization of the three monomers containing biotin, sugar, and amine groups as pendent groups, respectively. The modified QDs were analyzed by dynamic light scattering and fluorescence spectrophotometry, and the data revealed no change in the physical properties of QDs after surface modification. Furthermore, the surface modified QDs showed excellent water solubility and colloidal stability. Subsequently, the availability of the biotin ligand on the surface of functionalized QDs was quantified using 4-hydroxyazobenzene 2-carboxylic acid (HABA)/avidin binding assay. Cell viability studies revealed that the cytotoxicity of QDs after surface functionalization is improved and that the biotinylated glycopolymer modified QDs showed an enhancement in biocompatibility as compared to that of the original QDs. The biotinylated glyco-functionalized quantum dots may act as new suitable fluorescent probes in biomedical applications.
Physicochemical studies of bovine fibrinogen. IV. Ultraviolet absorption and its relation to the structure of the molecule (1968)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPhysicochemical studies of bovine fibrinogen. IV. Ultraviolet absorption and its relation to the structure of the moleculeElemer. MihalyiCite this: Biochemistry 1968, 7, 1, 208–223Publication Date (Print):January 1, 1968Publication History Published online1 May 2002Published inissue 1 January 1968https://doi.org/10.1021/bi00841a026RIGHTS & PERMISSIONSArticle Views221Altmetric-Citations143LEARN 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 InReddit PDF (1 MB) Get e-Alerts Get e-Alerts
Auditory nonlinearities measured with auditory-evoked potentials (1990)

This article describes the use of auditory-evoked potentials (AEPs) as a tool to assess nonlinear processes in the auditory system. Two-tone signals were used as stimuli to obtain AEPs in both animal and human subjects. Frequency analysis of the physiologic waveforms revealed frequencies in the evoked potential that were not present in the acoustic signal. The largest distortion product in the evoked potential corresponded to the difference between the two primary frequencies (f2-f1). This distortion product was present in all subjects tested. Other distortion products at frequencies defined by n(f2-f1), where n less than 5, were also present in some individuals. These frequencies represent distortion components generated from an even-order nonlinear system. Extensive acoustic and electric calibration procedures provided substantial evidence that the distortion products recorded in the AEP were biologic in origin and not the result of acoustic or recording artifact.
Thermo-optically tuned cascaded polymer waveguide taps (1999)

Polymer thermo-optic-waveguide taps have a potential application as light routers for guided-wave optical interconnects involving cascaded fanouts. The taps can guide light from an optical bus bar and direct it into other devices in a switching/modulation network. Thermo-optic waveguide taps are designed and fabricated on silicon wafers using standard very large-scale integrated fabrication techniques. Coupling of light into an adjacent waveguide tap is observed to increase by 12.3% from 38.7% to 51.0% with the application of 34 mW of power.
Protective and Inhibitory Effects of Various Types of Amphipols on the Ca<sup>2+</sup>-ATPase from Sarcoplasmic Reticulum:  A Comparative Study (2006)

Amphipols are amphipathic polymers designed to replace or supplement detergents in membrane protein solution studies. Previous work has suggested both advantages and disadvantages to the use of a polyacrylate-based amphipol, A8-35, for studying the sarcoplasmic reticulum Ca2+-ATPase (SERCA1a). We investigated this issue further using a set of four amphipols with different chemical structures. Previous size exclusion chromatography experiments had shown that A8-35 and SERCA1a/A8-35 complexes aggregate under certain conditions. We show here that aggregation can be prevented by omitting calcium from buffers or by using a sulfonated version of A8-35. A8-35 had previously been shown to protect Ca2+-ATPase from irreversible denaturation, while inhibiting its activity in a reversible manner. We show here that the other three amphipols tested also display these properties and that all four amphipols slow down backward calcium dissociation from the nonphosphorylated solubilized enzyme, a priori an unrelated step. As this calcium dissociation involves the opening up of the bundle of transmembrane ATPase segments, the slowing of this process may indicate that multipoint attachment of the polymers to the hydrophobic transmembrane surface damps protein dynamics ("Gulliver" effect). Damping might be the reason why amphipols also simultaneously protect membrane proteins against irreversible denaturation and may inhibit the activity of those of them that display large rearrangements of their transmembrane surface during their catalytic cycle.
Expression of TrkA confers neuron-like responsiveness to nerve growth factor on an immortalized hypothalamic cell line. (1994)

The result of nerve growth factor (NGF) actions depends upon the cells in which it signals. To define how signaling is influenced by cellular context, it would be useful to examine cells committed to different fates or cells of a single type at different developmental stages. Interest in NGF actions on neurons of the central nervous system led us to examine GT1-1 cells, an immortalized hypothalamic cell line. GT1-1 cells demonstrated neuronal properties but were unresponsive to NGF and other neurotrophins. Through transfection, trkA expression conferred NGF signaling leading to enhanced neuronal differentiation, including dose-dependent induction of neurite outgrowth and a rapid transient increase in c-fos and NGFI-A mRNA. Under serum-free culture conditions, NGF also delayed cell death. These findings suggest that trkA transfection of neurons and neuronal precursors can be used to better define NGF signaling.
Microfluidic 3D Cell Culture: Potential Application For Tissue-Based Bioassays (2012)

Current fundamental investigations of human biology and the development of therapeutic drugs commonly rely on 2D monolayer cell culture systems. However, 2D cell culture systems do not accurately recapitulate the structure, function or physiology of living tissues, nor the highly complex and dynamic 3D environments in vivo. Microfluidic technology can provide microscale complex structures and well-controlled parameters to mimic the in vivo environment of cells. The combination of microfluidic technology with 3D cell culture offers great potential for in vivo-like tissue-based applications, such as the emerging organ-on-a-chip system. This article will review recent advances in the microfluidic technology for 3D cell culture and their biological applications.
Probabilistic Matching of Brain Images (1995)

. Image matching has emerged as an important area of investigation in medical image analysis. In particular, much attention has been focused on the atlas problem, in which a template representing the structural anatomy of the human brain is deformed to match anatomic brain images from a given individual. The problem is made difficult because there are important differences in both the gross and local morphology of the brain among normal individuals. We have formulated the image matching problem under a Bayesian framework. The Bayesian methodology facilitates a principled approach to the development of a matching model. Of special interest is its capacity to deal with uncertainty in the estimates, a potentially important but generally ignored aspect of the solution. In the construction of a reference system for the human brain, the Bayesian approach is well suited to the task of modeling variation in morphology. Statistical information about morphological variability, accumulated over p...