gebhart/patrepeval huggingface dataset:
The inter-database instance identification problem in integrating autonomous systems (2003)

The issue of joining information about the same instance across disparate databases in a composite information system (CIS) environment is discussed. A technique called interdatabase instance identification is presented that is a combination of database management systems and artificial intelligence techniques. Common attributes in the disparate databases are applied first to reduce the number of potential candidates for the same instance. Other attributes in these databases, auxiliary databases, and inferencing rules are utilized next to identify the same instance. A detailed example of the interdatabase instance identification technique is presented using an operational research prototype.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Assessment of the size, position, and optical properties of breast tumors in vivo by noninvasive optical methods (1998)

We present a method for the noninvasive determination of the size, position, and optical properties (absorption and reduced scattering coefficients) of tumors in the human breast. The tumor is first detected by frequency-domain optical mammography. It is then sized, located, and optically characterized by use of diffusion theory as amodel for the propagation of near-infrared light in breast tissue. Our method assumes that the tumor is a spherical inhomogeneity embedded in an otherwise homogeneous tissue. We report the results obtained on a 55-year-old patient with a papillary cancer in the right breast. We found that the tumor absorbs and scatters near-infrared light more strongly than the surrounding healthytissue. Our method has yielded a tumor diameter of 2.1 ? 0.2cm, which is comparable with the actual size of 1.6 cm, determined after surgery. From the tumor absorption coefficients at two wavelengths (690 and 825 nm), we calculated the total hemoglobin concentration (40 ? 10 muM) and saturation (71 ? 9%) of the tumor. These results can provide the clinical examiner with more detailed information about breast lesions detected by frequency-domain optical mammography, thereby enhancing its potential for specificity.
Improved Localized Surface Plasmon Resonance Immunoassay with Gold Bipyramid Substrates (2009)

Gold nanoparticles bound to substrates exhibit localized surface plasmon resonance (LSPR) in their optical extinction spectra at visible and near-infrared wavelengths. The LSPR wavelength is sensitive to the surrounding refractive index, enabling a simple, label-free immunoassay when capture antibodies are bound to the nanoparticles. Gold bipyramids are nanoparticles with a penta-twinned crystal structure, which have a sharp LSPR because of their high monodispersity. Bipyramid substrates were found to have a refractive index sensitivity ranging from 288 to 381 nm/RIU (-0.62 to -0.68 eV/RIU), increasing with the nanoparticle size and aspect ratio. In an immunoassay, the bipyramid substrates yielded higher sensitivity than nanorods and nanospheres. An immunoassay sensitivity constant which depends on both the optical properties of the nanoparticle and conjugation chemistry was found to be K(LSPR) = 0.01 nm x microm(2) for gold bipyramids.
Molecular basis for control of conjugation by bacterial pheromone and inhibitor peptides (2006)

In many bacteria expression of lateral gene transfer and of virulence factors is controlled by cell-cell signalling systems. Molecular interactions of microbial signal molecules with their cognate receptors are not well understood. For the Enterococcus faecalis conjugative plasmid pCF10, the PrgX protein serves as a molecular switch controlling expression of conjugation and virulence genes encoded by the plasmid. The induction state of a pCF10-carrying donor cell is determined by the ratio of two signalling peptides, cCF10 pheromone and iCF10 inhibitor. Recent analysis of PrgX/cCF10 interactions suggests a mechanism for conversion to the induced state. However, the means by which iCF10 peptide antagonizes cCF10 activity is unclear, and it has been suggested that inhibitor peptides block import of pheromone peptides. We now show that both of these peptides interact with the same binding pocket of PrgX, but they differentially alter the conformation of the protein and its oligomerization state, resulting in opposing biological activities.
Novel cell segmentation and online SVM for cell cycle phase identification in automated microscopy (2007)

The software and test datasets are available from the authors.
Coinfection of laboratory rats with Mycoplasma pulmonis and Chlamydia pneumoniae. (2003)

Routine examinations of conventional outbred Wistar rats in our laboratory showed increased serum levels of alkaline phosphatase, aspartate aminotransferase, alanine aminotransferase, and urea. Electron microscopy and specific reactions showed C. pneumoniae and M. pulmonis in lung, liver, spleen, heart, and kidney sections. We could not exclude the fact that other infectious microorganisms detected through routine health surveillance affected the Wistar rat colony; however, we have not identified any of those microorganisms by electron microscopy of the organs listed. Natural coinfection of C. pneumoniae and M. pulmonis can occur in laboratory rats and is associated with histopathological and functional compromise of many organs. Further studies comparing different conventional animals and specific pathogen-free animals are necessary to better understand the present findings and to define whether coinfection influences the results of experimental studies with rats.
Dopamine tone regulates D1 receptor trafficking and delivery in striatal neurons in dopamine transporter-deficient mice (2000)

In vivo, G protein-coupled receptors (GPCR) for neurotransmitters undergo complex intracellular trafficking that contribute to regulate their abundance at the cell surface. Here, we report a previously undescribed alteration in the subcellular localization of D1 dopamine receptor (D1R) that occurs in vivo in striatal dopaminoceptive neurons in response to chronic and constitutive hyperdopaminergia. Indeed, in mice lacking the dopamine transporter, D1R is in abnormally low abundance at the plasma membrane of cell bodies and dendrites and is largely accumulated in rough endoplasmic reticulum and Golgi apparatus. Decrease of striatal extracellular dopamine concentration with 6-hydroxydopamine (6- OHDA) in heterozygous mice restores delivery of the receptor from the cytoplasm to the plasma membrane in cell bodies. These results demonstrate that, in vivo, in the central nervous system, the storage in cytoplasmic compartments involved in synthesis and the membrane delivery contribute to regulate GPCR availability and abundance at the surface of the neurons under control of the neurotransmitter tone. Such regulation may contribute to modulate receptivity of neurons to their endogenous ligands and related exogenous drugs.
Disruption of tight junction structure in salivary glands from Sjögren's syndrome patients is linked to proinflammatory cytokine exposure (2010)

Our findings indicate that local cytokine production in LSGs from SS patients may contribute to the secretory gland dysfunction observed in SS patients by altering tight junction integrity of epithelial cells, thereby decreasing the quality and quantity of saliva.
CONSUMPTION IN LDCS (1999)

AbstractThe following sections are included:INTRODUCTIONOVERVIEWTHE DATASOME NOTES OF CAUTIONMORE ON THE OUTLIERSCOMPARISON WITH OECD CONSUMPTION PATTERNSREFERENCES
Recognition by Elam-1 of the Sialyl-Le x Determinant on Myeloid and Tumor Cells (1990)

Endothelial leukocyte adhesion molecule-1 (ELAM-1) is an endothelial cell adhesion molecule that allows myeloid cells to attach to the walls of blood vessels adjacent to sites of inflammation. ELAM-1 recognizes the sialyl-Lewis X (sialyl-Lex) determinant, NeuAc alpha 2-3Gal beta 1-4(Fuc alpha 1-3)GlcNAc-, a granulocyte carbohydrate also found on the surface of some tumor cell lines. Binding of myeloid cells to soluble ELAM-1 is inhibited by a monoclonal antibody recognizing sialyl-Lex or by proteins bearing sialyl-Lex, some of which may participate in humoral regulation of myeloid cell adhesion. Stimulated granulocytes also release an inhibitor of ELAM-1 binding that can be selectively adsorbed by monoclonal antibody to sialyl-Lex.
Effect of actively transported hexoses on afferent nerve discharge from rat small intestine. (1978)

1. The afferent discharge of mesenteric nerves has been recorded while perfusing salines of different composition through the lumen of rat ileum. The p.d. across the ileum and hexose absorption have also been measured. 2. The ileal mesenteric nerves were sensitive to actively transported hexoses. The discharge recorded increased dramatically on perfusion with 10 or 50 mM-glucose, quietening within 3 min of returning to glucose-free saline. A similar response was obtained with galactose. 3. No change in afferent discharge could be detected on perfusion of mannitol or the slowly transferred hexose, mannose. It is concluded that the response to glucose and galactose is not dependent on the stimulation of non-specific luminal osmoreceptors. 4. Phlorhizin prevented glucose from increasing the afferent nerve discharge. Subsequent perfusion with saline removed the phlorhizin and an afferent nerve response to glucose was restored. It is concluded that this response requires glucose transfer beyond the phlorhizin-sensitive glucose entry mechanism at the luminal side of the mucosal epithelial cell. 5. Very small amounts of glucose or galactose were absorbed under the conditions employed. The time course for the change in p.d. correlated well with that described for the alteration in afferent nerve discharge. 6. Electron micrographs show that ileal nerves consist of bundles of small non-myelinated fibres of approximately 1 micron diameter. 7. The significance of the findings is discussed remembering that carbohydrate absorption is considered to be completed normally in the jejunum.
Psychotropic effects of angiotensin II N-terminal fragments: Asp-Arg-Val-Tyr-Ile-His and Arg-Val-Tyr-Ile-His in rats. (1993)

In this study the effects of angiotensin II (AII) angiotensin II hexapeptide [AII(1-6)] and angiotensin II pentapeptide [AII(2-6)] on the motility, stereotypy, learning of conditioned avoidance responses (CARs) and recall of a passive behavior making it possible to avoid aversive stimulation in rats, were compared. All the peptides were injected into the lateral cerebral ventricle (icv) in a dose of 1 nmol. AII caused a statistically significant increase in the number of crossings, rearings, and bar approaches in an open field whereas [AII(1-6)] and [AII(2-6)] were inactive in this test. The stereotypic behavior induced by an intraperitoneal (ip) injection of apomorphine (1 mg/kg) and amphetamine (7.5 mg/kg) was statistically significantly enhanced only in the rats which received AII icv. The application of AII, but not that of [AII(1-6)] and [AII(2-6)] resulted in a quicker acquisition of the CARs. A better recall of passive avoidance was achieved only by AII, while the fragments [AII(1-6)] and [AII(2-6)] had no effect. These findings indicate that the 1-6 and 2-6 fragments of AII do not possess a psychotropic activity like that of the parent octapeptide.
Assignment of the gene coding for both the β-subunit of prolyl 4-hydroxylase and the enzyme disulfide isomerase to human chromosome region 17p11→qter (1988)

The chromosomal location of the human gene coding for both the beta-subunit of prolyl 4-hydroxylase (P4HB) and the enzyme disulfide isomerase (PDI) was determined using mouse x human somatic cell hybrids and three different methods for identifying either the human P4HB/PDI protein or the respective gene: (1) immunoblotting with species-specific monoclonal antibodies; (2) radioimmunoassay with species-specific polyclonal antibodies; and (3) Southern blotting after cleavage of the DNA with EcoRI, HindIII, or BamHI, followed by hybridization with a mixture of two cDNA probes for human P4HB. All three methods gave identical data, demonstrating complete cosegregation of the human protein or its gene in all 17 cell hybrids tested with human chromosome 17. A cell hybrid lacking an intact chromosome 17 localized the gene to 17p11----qter.
An optical analog-to-digital converter - Design and analysis (1979)

A design for an optical analog-to-digital converter using channel waveguide modulators is described. Optical and electrical power requirements and factors which limit the speed of operation are analyzed, and the implications of signal sampling with a repetitively pulsed light source are discussed.
Comparative bioavailability of three batches of four commercial acetaminophen tablets. (1991)

The aim of this investigation is to evaluate four brands of acetaminophen tablets and three batches of each brand for their in vitro properties and in vivo bioavailabilities using urinary excretion data. All batches dissolved at least 80% of their acetaminophen content within 30 minutes. The differences between the dissolution rates of the batches were not found statistically significant except the batches of brand C. With respect to their dissolution rates, the brands have the following order: A less than B less than C less than D. Statistical analysis of the percent bioavailabilities and the elimination rate constants showed that there was no significant difference between brands and or between the batches. The percent excreted in the first three hours was found to be significantly different between the solution and tablet A, between tablet A and tablet C, and between Tablet A and Tablet D.
Transplanted fetal cardiomyocytes as cardiac pacemaker (2002)

The results constitute the first observation of phenomena indicating electrical and mechanical coupling between allogeneic donor cardiomyocytes and recipient myocardium in-vivo. Further experiments are necessary to evaluate the technique as a potential therapy for atrioventricular block.
Ureido-Substituted Benzenesulfonamides Potently Inhibit Carbonic Anhydrase IX and Show Antimetastatic Activity in a Model of Breast Cancer Metastasis (2011)

A series of ureido-substituted benzenesulfonamides was prepared that showed a very interesting profile for the inhibition of several human carbonic anhydrases (hCAs, EC 4.2.1.1), such as hCAs I and II (cytosolic isoforms) and hCAs IX and XII (transmembrane, tumor-associated enzymes). Excellent inhibition of all these isoforms has been observed with various members of the series, depending on the substitution pattern of the urea moiety. Several low nanomolar CA IX/XII inhibitors also showing good selectivity for the transmembrane over the cytosolic isoforms have been discovered. One of them, 4-{[(3'-nitrophenyl)carbamoyl]amino}benzenesulfonamide, significantly inhibited the formation of metastases by the highly aggressive 4T1 mammary tumor cells at pharmacologic concentrations of 45 mg/kg, constituting an interesting candidate for the development of conceptually novel antimetastatic drugs.
Role of CCR2 in immunobiology and neurobiology (2011)

Abstract Chemokines and their receptors play crucial roles in the trafficking of leukocytes and are of particular interest in the context of the unique inflammatory responses elicited in the central nervous system (CNS). The chemokine receptor CCR2 and its ligand CCL2 have been implicated in a wide range of immunobiological processes and neuropathologies, including recruitment of monocytes and regulation of bone marrow homeostasis, as well as multiple sclerosis, HIV‐associated dementia, Alzheimer’s disease and neuropathic pain. Recently, powerful biological tools (CCR2‐red fluorescent protein [RFP] knock‐in mice) have been developed to analyze the functions of CCR2 in different cell populations, and intriguing results have emerged from those mice. The present review emphasizes CCR2/CCL2 as a key chemokine/chemokine receptor pair that controls the recruitment or retention of a key subset of mononuclear phagocytes in inflammation associated with host defense or disease. (Clin. Exp. Neuroimmunol. doi: 10.1111/j.1759‐1961.2011.00024.x , January 2012)
Crucial Role of IL-4/STAT6 in T Cell-Mediated Hepatitis: Up-Regulating Eotaxins and IL-5 and Recruiting Leukocytes (2003)

T cell-mediated immune responses are implicated in the pathogenesis of a variety of liver disorders; however, the underlying mechanism remains obscure. Con A injection is a widely accepted mouse model to study T cell-mediated liver injury, in which STAT6 is rapidly activated. Disruption of the IL-4 and STAT6 gene by way of genetic knockout abolishes Con A-mediated liver injury without affecting IFN-gamma/STAT1, IL-6/STAT3, or TNF-alpha/NF-kappaB signaling or affecting NKT cell activation. Infiltration of neutrophils and eosinophils in Con A-induced hepatitis is markedly suppressed in IL-4 (-/-) and STAT6(-/-) mice compared with wild-type mice. IL-4 treatment induces expression of eotaxins in hepatocytes and sinusoidal endothelial cells isolated from wild-type mice but not from STAT6(-/-) mice. Con A injection induces expression of eotaxins in the liver and elevates serum levels of IL-5 and eotaxins; such induction is markedly attenuated in IL-4(-/-) and STAT6(-/-) mice. Finally, eotaxin blockade attenuates Con A-induced liver injury and leukocyte infiltration. Taken together, these findings suggest that IL-4/STAT6 plays a critical role in Con A-induced hepatitis, via enhancing expression of eotaxins in hepatocytes and sinusoidal endothelial cells, and induces IL-5 expression, thereby facilitating recruitment of eosinophils and neutrophils into the liver and resulting in hepatitis.
FOXA1, GATA3 and PPARɣ Cooperate to Drive Luminal Subtype in Bladder Cancer: A Molecular Analysis of Established Human Cell Lines (2016)

Discrete bladder cancer molecular subtypes exhibit differential clinical aggressiveness and therapeutic response, which may have significant implications for identifying novel treatments for this common malignancy. However, research is hindered by the lack of suitable models to study each subtype. To address this limitation, we classified bladder cancer cell lines into molecular subtypes using publically available data in the Cancer Cell Line Encyclopedia (CCLE), guided by genomic characterization of bladder cancer by The Cancer Genome Atlas (TCGA). This identified a panel of bladder cancer cell lines which exhibit genetic alterations and gene expression patterns consistent with luminal and basal molecular subtypes of human disease. A subset of bladder cancer cell lines exhibit in vivo histomorphologic patterns consistent with luminal and basal subtypes, including papillary architecture and squamous differentiation. Using the molecular subtype assignments, and our own RNA-seq analysis, we found overexpression of GATA3 and FOXA1 cooperate with PPARɣ activation to drive transdifferentiation of a basal bladder cancer cells to a luminial phenotype. In summary, our analysis identified a set of human cell lines suitable for the study of molecular subtypes in bladder cancer, and furthermore indicates a cooperative regulatory network consisting of GATA3, FOXA1, and PPARɣ drive luminal cell fate.
An Expanded Function for Superoxide Dismutase (1991)

alpha-Hydroxyalkylperoxyl radicals were generated from the primary and secondary alcohols methanol, ethanol and 2-propanol in N2O/O2-saturated aqueous solutions by pulse radiolysis. These radicals reduced a ferric iron porphyrin complex, tetrakis-(4-N-methylpyridyl)porphine, with diffusion-controlled rate constants. The extreme sensitivity of the shift of the Soret absorption band in this reaction was used to determine, by competition kinetics, the reactivity of the peroxyl radicals with different proteins. Only native Cu,Zn-superoxide dismutase and metallothionein showed competitive behavior, with SOD exhibiting rate constants close to the dismutation rate for O2-. Metallothionein was slower by a factor of 30 with hydroxymethylperoxyl radicals. We propose, that SOD has unique properties of the protein surface in addition to the prosthetic copper site, having possibly evolved as a 'general-purpose radical-scavenging protein'.
Signal-to-pump back action and self-oscillation in double-pump Josephson parametric amplifier (2009)

We present the theory of a Josephson parametric amplifier employing two-pump sources. Our calculations are based on input-output theory, and can easily be generalized to any coupled system involving parametric interactions. We analyze the operation of the device, taking into account the feedback introduced by the reaction of the signal and noise on the pump power, and in this framework, compute the response functions of interest---signal and idler gains, internal gain of the amplifier, and self-oscillation signal amplitude. To account for this back action between signal and pump, we adopt a mean-field approach and self-consistently explore the boundary between amplification and self-oscillation. The coincidence of bifurcation and self-oscillation thresholds reveals that the origin of coherent emission of the amplifier lies in the multiwave mixing of the noise components. Incorporation of the back action leads the system to exhibit hysteresis, dependent on parameters such as temperature and detuning from resonance. Our analysis also shows that the resonance condition itself changes in the presence of back action and this can be understood in terms of the change in plasma frequency of the junction. The potential of the double-pump amplifier for quantum-limited measurements and as a squeezer is also discussed.
Efficient and Simplified Parallel Graph Processing over CPU and MIC (2015)

Intel Xeon Phi (MIC architecture) is a relatively new accelerator chip, which combines large-scale shared memory parallelism with wide SIMD lanes. Mapping applications on anode with such an architecture to achieve high parallel efficiency's a major challenge. In this paper, we focus on developing system for heterogeneous graph processing, which is able to utilize both a many-core Xeon Phi and a multi-core CPU ozone node. We propose a simple programming API with unintuitive interface for expressing SIMD parallelism. We develop efficient techniques for supporting our high-level API, focusing on exploiting wide SIMD lanes, massive number of cores, and partitioning of the work across CPU and accelerator, while handling the irregularity of graph applications. The components of our runtime system include a condensed static memory buffer, which supports efficient message insertion and SIMD message reduction while keeping memory requirements low, and specifically formic, a pipelining scheme for efficient message generation by avoiding frequent locking operations. Besides, a hybrid graph partitioning module is able to effectively partition the workload between the CPU and the MIC, ensuring balanced workload and low communication overhead. The main observations from our experimental evaluation using five popular applications are: formic executions, pipelining scheme is up to 3.36x faster than naive approach using locking based message generation, and the speedup over OpenMP ranges from 1.17 to 4.15. Heterogeneous-MIC execution achieves a speedup of up to 1.41 over the better of the CPU-only and MIC-only executions.
Assessing tumor cytoarchitecture using multiecho DSC‐MRI derived measures of the transverse relaxivity at tracer equilibrium (TRATE) (2014)

The assessment of TRATE is clinically feasible and its sensitivity to tissue cytoarchitectural features not present in other imaging methods indicate that it could potentially serve as a unique structural signature or "trait" of cancer.
Moving beyond anti-amyloid therapy for the prevention and treatment of Alzheimer’s disease (2014)

At this juncture it is no longer unreasonable to suggest that further iterations of anti-Aβ therapies should be halted. Clinicians and researchers should instead direct their attention toward greater understanding of the biological function of Aβ both in healthy and demented brains, as well as the involvement of long-term chronic exposure to stress in the etiology of AD.