gebhart/patrepeval huggingface dataset:
Salmonellae activate tumor necrosis factor alpha production in a human promonocytic cell line via a released polypeptide (1997)

Invasive strains of Salmonella spp. cause both systemic and localized infections in humans. The ability to resist infection and some aspects of the tissue pathology associated with the presence of Salmonella in the gastrointestinal tract have been shown to be mediated in part by the induction of tumor necrosis factor alpha (TNF-alpha), a proinflammatory cytokine produced by activated macrophages and lymphocytes. Recent reports indicate that TNF-alpha is involved in the induction of human immunodeficiency virus replication by Salmonella in the latently infected human promonocytic cell line U1. In the present study, we investigated the effects of Salmonella on TNF-alpha production in U1 cells and a related cell line, U38. Unlike Escherichia coli or Yersinia enterocolitica, salmonellae rapidly induce TNF-alpha expression in these cells through a released factor(s). Time course experiments show that the kinetics of TNF-alpha production by U38 cells stimulated with Salmonella conditioned medium closely resemble those observed in response to live Salmonella. The observation that TNF-alpha levels are elevated by 60 min after exposure to either bacteria or their conditioned medium suggests that the soluble inducer is continuously released or shed by the bacteria and that the signal acts rapidly to increase TNF-alpha production. Furthermore, the ability to produce the TNF-alpha inducer is shared by at least four Salmonella serotypes and does not correlate with the abilities to invade and to survive within phagocytes. Treatment of active conditioned medium with trypsin, but not low pH, high temperature, or urea, significantly inhibits its TNF-alpha-inducing effect on U38 cells, a finding which points to a polypeptide product of Salmonella as the mediator of TNF-alpha production. Gel filtration chromatography of Salmonella conditioned medium reveals two peaks of activity, consistent with molecular masses of approximately 150 and 110 kDa.
Chromatic framework for vision in bad weather (2002)

Conventional vision systems are designed to perform in clear weather. However, any outdoor vision system is incomplete without mechanisms that guarantee satisfactory performance under poor weather conditions. It is known that the atmosphere can significantly alter light energy reaching an observer. Therefore, atmospheric scattering models must be used to make vision systems robust in bad weather. In this paper, we develop a geometric framework for analyzing the chromatic effects of atmospheric scattering. First, we study a simple color model for atmospheric scattering and verify it for fog and haze. Then, based on the physics of scattering, we derive several geometric constraints on scene color changes, caused by varying atmospheric conditions. Finally, using these constraints we develop algorithms for computing fog or haze color depth segmentation, extracting three dimensional structure, and recovering "true" scene colors, from two or more images taken under different but unknown weather conditions.
Asymmetric Aminocatalysis (2001)

This account focuses on novel amine-catalyzed reactions recently discovered in our laboratories. Among the newly developed transformations are efficient proline-catalyzed intermolecular aldol, Mannich, Michael reactions and a novel three-component reaction. 9 Conclusions
Mechanism of Thermal Decomposition of Lignin (1984)

Differential thermal analysis studies of milled wood lignin and lignin carbohydrate complex at different heating rates showed three exothermic peaks. The heating rate is the factor that affects their sharpness and position. The peaks are sharp at low heating rates. Infrared spectra and scanning electron micrographs of the pyrolyzed lignin residues show that aliphatic scission of the lignin molecule at the onset of pyrolysis and progressive carbonization of the surface are the principal features of degradation; there is no intermediate compound formed during the pyrolysis.
Highly Ordered MWNT-Based Matrixes:  Topography at the Nanoscale Conceived for Tissue Engineering (2006)

A method based on the conventional lithographic technique combined with the layer-by-layer (LBL) assembly process is applied to the construction of free-standing micro- and nanostructured matrixes. The method enables controlled shaping and considerable chemical and mechanical stability of the self-assembled monolayers, allowing for high reproducibility in manufacturing. The matrixes are characterized by controlled geometry, surface topography, and chemical composition. The complete architecture is made up of successive layers of intercrossed carbon nanotubes that self-assemble into orderly structures. In particular, the present method aims to create architectures and topographies that mimic those occurring naturally (native tissue structures). In addition, nanoindentation and nanoscratch techniques were used to evaluate the mechanical properties of the carbon nanotube-based matrixes.
Voltage Tunable Electroluminescence of CdTe Nanoparticle Light-Emitting Diodes (2002)

Strong electroluminescence was observed in a CdTe nanoparticle light-emitting diode that was fabricated by layer-by-layer assembly of poly(p-phenylenevinylene) and CdTe nanoparticles. The turn-on voltage for the electroluminescence is 4.0 V. The electroluminescence is exclusively from CdTe nanoparticles, with a 30 nm red shift in emission wavelength from the photoluminescence and shifts to longer wavelengths at higher applied voltages. Possible mechanisms for this red shift are discussed, and it is concluded that the de-trapping of surface states and trap centers due to electric excitation, the involvement of traps in the electroluminescence, and the quantum confined Stark effect are the major reasons for the red shift.
An intelligent load shedding (ILS) system application in a large industrial facility (2005)

Conventional methods of system load shedding are too slow and do not effectively calculate the correct amount of load to be shed. This results in either excessive or insufficient load reduction. In recent years, load shedding systems have been repackaged using conventional under-frequency relay and/or breaker interlocks schemes integrated with programmable logic controllers to give a new look to an antiquated load preservation methodology. A truly modern and intelligent load shedding system with a computerized power management system should provide fast and optimal load management by utilizing system topology and actual operating conditions tempered with knowledge of past system disturbances. This paper demonstrates the need for a modern load shedding scheme and introduces the new technology of intelligent load shedding. Comparisons of intelligent load shedding with conventional load shedding methods are made from perspectives of system design, system engineering, project implementation, and system operation. A case study of the application of an intelligent load shedding scheme in a large industrial facility is provided.
Emerging Evidences of Mesoscopic-Scale Complexity in Neat Ionic Liquids and Their Mixtures (2017)

Ionic liquids (ILs) represent a blooming class of continuously developing advanced materials, with the aiming of a green chemical industry. Their appealing physical and chemical properties are largely influenced by their micro- and mesoscopic structure that is known to possess a high degree of hierarchical organization. High-impact application fields are largely affected by the complex morphology of neat ionic liquids and their mixtures. This Perspective highlights new arising research directions that point to an enhanced level of structural complexity in several IL-based systems, including mixtures. The latter represent a change in paradigm in the approach to formulate new, task-specific IL-based media, and the reported phenomenology has the potential to further expand their range of applications by calling for a revisitation of the nature of interactions in these exciting media.
Genome-Wide Location and Function of DNA Binding Proteins (2000)

Understanding how DNA binding proteins control global gene expression and chromosomal maintenance requires knowledge of the chromosomal locations at which these proteins function in vivo. We developed a microarray method that reveals the genome-wide location of DNA-bound proteins and used this method to monitor binding of gene-specific transcription activators in yeast. A combination of location and expression profiles was used to identify genes whose expression is directly controlled by Gal4 and Ste12 as cells respond to changes in carbon source and mating pheromone, respectively. The results identify pathways that are coordinately regulated by each of the two activators and reveal previously unknown functions for Gal4 and Ste12. Genome-wide location analysis will facilitate investigation of gene regulatory networks, gene function, and genome maintenance.
CD40-CD154 interaction in experimental and human disease (review). (1999)

Cell-to-cell signals between T lymphocytes and antigen-presenting cells strictly regulate the development of the immune response. It has clearly emerged that among these signals few cell surface receptor-ligand pairs, such as CD40 and its ligand, CD154, are mandatory for the induction of lymphocyte activation. The early observation that mutations of CD154 gene are responsible for a human severe immunodeficiency primed an impressive number of studies aimed to functionally characterize this receptorial system in view of therapeutically exploiting its properties. Indeed, various approaches aimed to disrupt natural CD40-CD154 interaction were highly effective in the prevention and treatment of several experimental models of autoimmune disease and transplant rejection. In parallel, abnormalities of this pathway were constantly found in several immunologically-mediated human diseases. Furthermore, a number of studies have dissected the role of CD40 and its ligand in the immune response against various microbial and viral pathogens. Since these molecules are often expressed by tumor cells, it is not surprising that great efforts have been made to address their function also in the development of cancer. Most recent data strongly suggest an involvement of endothelial CD40 in the vascular processes that lead to atherogenesis. This review focuses on the most significant advances in the understanding of the molecular regulatory events involving CD40 and its ligand in experimental and human disease.
A Novel Class of GABAA Receptor Subunit in Tissues of the Reproductive System (1997)

A novel subunit of the gamma-aminobutyrate, type A (GABAA) receptor family has been identified in human and rat tissues. The subunit displays 30-40% amino acid identity with known family members and represents a distinct subunit class (termed pi). Transcripts of the pi subunit were detected in several human tissues and were particularly abundant in the uterus. The pi subunit protein can assemble with known GABAA receptor subunits and confer unique ligand binding properties to the recombinant receptors in which it combines. Most notably, the presence of the pi subunit alters the sensitivity of recombinant receptors to the endogenous steroid, pregnanolone. Identification of the pi subunit indicates a new target for pharmacological manipulation of GABAA receptors that are located outside of the central nervous system.
Fibers from a low dielectric constant fluorinated polyimide: Solution spinning and morphology control (1997)

Control of the internal morphology of wet-spun fibers from a fluorinated polyimide has been achieved by varying the rate of polymer coagulation through adjustments in nonsolvent/solvent miscibility and precipitation strength of the coagulation bath. Filament internal morphologies ranged from very porous or sponge-like to fully solid. Intermediate structures included fibers containing a spongy core with a nonporous skin, sponge-like fibers containing large voids, and a relatively solid material containing randomly spaced small voids. The cross-sectional shape of the fiber is dependent upon the coagulation process as well as the volume contraction of the initial extrudate. Drawn fibers (3×) retained the original asspun cross-sectional shape and also lost porosity. Mechanical properties of poly(6FDA-4BDAF) fibers have an inverse relationship to filament porosity. Maximum modulus and break strength for drawn fibers is approximately 6 CPa and 200 MPa, respectively. Asspun mechanical properties were dependent upon the processing conditions and have moduli between 0.4–3.0 Gpa and break strengths of 10–160 MPa. A dielectric constant of 2.50 for nonporous films was measured over a frequency range between 1.0 MHz to 1.8 GHz, showing little dispersion. © 1997 John Wiley & Sons, Inc.
Preliminary findings in the neurophysiological assessment of intercostal nerve injury during thoracotomy (2002)

This study demonstrates for the first time that intercostal nerve injury occurs routinely due to rib retraction during thoracotomy. We believe that it may be an important step toward understanding the cause of post-thoracotomy neuralgia.
The Role of Oleic Acid: From Synthesis to Assembly of Perovskite Nanocuboid Two-Dimensional Arrays (2014)

Oleic acid, an 18-carbon chain fatty acid, has been widely used as a surfactant to fabricate colloidal nanocrystals. In previous work, we discovered a lamellar microemulsion strategy to fabricate sub-20 nm SrTiO(3) nanocuboids using oleic acid and oleate species. Here, we demonstrate (i) the general synthesis with lamellar microemulsions of a family of compositionally varied BaxSr(1-x)TiO(3) crystalline nanocuboids with uniform size, and (ii) subsequent assembly into two-dimensional arrays by nanoparticle-bound oleate in a nonpolar solvent. The measured interparticle distance (2.4 nm) of adjacent nanoparticles in an array is less than the length of a double oleate layer (∼4 nm). On the basis of calculations of the interfacial free energy, we propose the hydrophobic, hydrocarbon-terminated groups of oleate from adjacent nanocuboids are situated closely but do not overlap. Lower aspect ratio nanocuboids are bordered by four adjacent nanocuboids which results in a uniform direction self-assembly array, whereas higher aspect ratio nanocuboids are bordered by five or six adjacent nanocuboids and can develop an arced local coordination.
Macrophage colony-stimulating factor receptor c-fms is a novel target of imatinib (2005)

Imatinib is a tyrosine kinase inhibitor that suppresses the growth of bcr-abl-expressing chronic myeloid leukemia (CML) progenitor cells by blockade of the adenosine triphosphate (ATP)-binding site of the kinase domain of bcr-abl. Imatinib also inhibits the c-abl, platelet-derived growth factor (PDGF) receptor, abl-related gene (ARG) and stem-cell factor (SCF) receptor tyrosine kinases, and has been used clinically to inhibit the growth of malignant cells in patients with CML and gastrointestinal stromal tumors (GISTs). Although initially considered to have minimal effects of normal hematopoiesis, recent studies show that imatinib also inhibits the growth of some nonmalignant hematopoietic cells, including monocyte/macrophages. This inhibition could not be attributed to the known activity profile of imatinib. Here, we demonstrate for the first time that imatinib targets the macrophage colony-stimulating factor (M-CSF) receptor c-fms. Phosphorylation of c-fms was inhibited by therapeutic concentrations of imatinib, and this was not due to down-regulation in c-fms expression. Imatinib was also found to inhibit M-CSF-induced proliferation of a cytokine-dependent cell line, further supporting the hypothesis that imatinib affects the growth and development of monocyte and/or macrophages through inhibition of c-fms signaling. Importantly, these results identify an additional biologic target to those already defined for imatinib. Imatinib should now be assessed for activity in diseases where c-fms activation is implicated, including breast and ovarian cancer and inflammatory conditions.
P3‐188: Noninvasive optical imaging of retinal amyloid plaques in mice model of Alzheimer's disease: Early detection and treatment assessment (2010)

A definite diagnosis of Alzheimer's disease (AD) is determined following brain autopsy by detection of hallmark pathologies of the disease: an extracellular aggregates of amyloid-β (Aβ) peptides, termed as Aβ plaques, and an intracellular neurofibrillary tangles. Presently, noninvasive monitoring of Aβ plaques in the brains of living patients is, however, inadequate due to restricted resolution and specificity. We, thus, hypothesized that the eyes can serve as a window to the brain for direct and noninvasive imaging of AD. To this end, we used APPswe/PS1dE9 double-transgenic AD mice, which faithfully represent some of the key pathologies found in the human disease. We investigated presence and formation of amyloid plaques in retinas from these AD mice, as well as estimated the correlation between retinal amyloid plaques and the plaque pathology in the brain. Lastly, we evaluated responsiveness of retinal plaques to an immune-based therapy and the ability to image them in live mice. Here, we detected Aβ plaques in retinal samples of AD mice, and found that Aβ plaques appear in the retina significantly earlier than in the brain. Retinal plaques accumulated during disease progression, and in good correlation with brain pathology. Moreover, retinal Aβ plaque number and size were significantly reduced following an immune-based therapy, which we found to be effective in reducing plaques in the brain. Systemic administration of a natural compound that binds and labels Aβ plaques, allowed in vivo noninvasive visualization of retinal Aβ plaques in live AD mice, with high resolution and specificity. These studies establish the potential of direct retinal Aβ plaque imaging in live subjects as a promising tool for early AD diagnosis, prognosis and assessment of therapies.
Effects of Small Molecules on Chaperone-Mediated Autophagy (2005)

Autophagy, including macroautophagy (MA), chaperone-mediated autophagy (CMA), crinophagy, pexophagy and microautophagy, are processes by which cells select internal components such as proteins, secretory vesicles, organelles, or foreign bodies, and deliver them to lysosomes for degradation. MA and CMA are activated during conditions of serum withdrawal in cell culture and during short-term and prolonged starvation in organisms, respectively. Although MA and CMA are activated under similar conditions, they are regulated by different mechanisms. We used pulse/chase analysis under conditions in which most intracellular proteolysis is due to CMA to test a variety of compounds for effects on this process. We show that inhibitors of MA such as 3-methyladenine, wortmannin, and LY294002 have no effect on CMA. Protein degradation by MA is sensitive to microtubule inhibitors such as colcemide and vinblastine, but protein degradation by CMA is not. Activators of MA such as rapamycin also have no effect on CMA. We demonstrate that CMA, like MA, is inhibited by protein synthesis inhibitors anisomycin and cycloheximide. CMA is also partially inhibited when the p38 mitogen activated protein kinase is blocked. Finally we demonstrate that the glucose-6-phophate dehydrogenase inhibitor, 6-aminonicotinamide, and heat shock protein of 90 kilodaltons inhibitor, geldanamycin, have the ability to activate CMA.
Support vector machines for histogram-based image classification (1999)

Traditional classification approaches generalize poorly on image classification tasks, because of the high dimensionality of the feature space. This paper shows that support vector machines (SVM's) can generalize well on difficult image classification problems where the only features are high dimensional histograms. Heavy-tailed RBF kernels of the form K(x, y) = e(-rho)Sigma(i)/xia-yia/b with a < or = 1 and b < or = 2 are evaluated on the classification of images extracted from the Corel stock photo collection and shown to far outperform traditional polynomial or Gaussian radial basis function (RBF) kernels. Moreover, we observed that a simple remapping of the input x(i)-->x(i)(a) improves the performance of linear SVM's to such an extend that it makes them, for this problem, a valid alternative to RBF kernels.
Enhanced thermoelectric figure of merit in nanostructured n-type silicon germanium bulk alloy (2008)

The dimensionless thermoelectric figure of merit (ZT) of the n-type silicon germanium (SiGe) bulk alloy at high temperature has remained at about one for a few decades. Here we report that by using a nanostructure approach, a peak ZT of about 1.3 at 900 °C in an n-type nanostructured SiGe bulk alloy has been achieved. The enhancement of ZT comes mainly from a significant reduction in the thermal conductivity caused by the enhanced phonon scattering off the increased density of nanograin boundaries. The enhanced ZT will make such materials attractive in many applications such as solar, thermal, and waste heat conversion into electricity.
Purification and renaturation of recombinant human interleukin-2 (1987)

Recombinant human interleukin-2 (IL-2) expressed as Escherichia coli was isolated as insoluble aggregates of protein (inclusion bodies) after cell breakage. IL-2 and contaminants were dissolved in 6 M-guanidinium chloride/10 mM-dithiothreitol, pH 8.5, and further purified in reduced and denatured form by gel-permeation chromatography in the same solvent. Renaturation was effected by dilution and autoxidation; IL-2 of native specific activity was isolated at over 95% purity by reversed-phase h.p.l.c.; an additional peak of reduced protein was also observed. Most losses of native IL-2 occurred on refolding, probably because of an aggregation process; concentrations around 1 microgram/ml were necessary to achieve 30% recovery. It was essential to maintain the denatured protein in reduced form before renaturation and autoxidation, which was most efficient at pH 8.5 with 1.5 microM-CuSO4. A procedure based on these observations has been used to prepare IL-2 on the 50 micrograms scale.
Molecular Basis of the Time-Dependent Inhibition of Cyclooxygenases by Indomethacin (2004)

Cyclooxygenases (COXs) are the therapeutic targets of nonsteroidal antiinflammatory drugs. Indomethacin (INDO) was one of the first nonsteroidal antiinflammatory drugs to be characterized as a time-dependent, functionally irreversible inhibitor, but the molecular basis of this phenomenon is uncertain. In the crystal structure of INDO bound to COX-2, a small hydrophobic pocket was identified that surrounds the 2'-methyl group of INDO. The pocket is formed by the residues Ala-527, Val-349, Ser-530, and Leu-531. The contribution of this pocket to inhibition was evaluated by altering its volume by mutagenesis of Val-349. The V349A mutation expanded the pocket and increased the potency of INDO, whereas the V349L mutation reduced the size of the pocket and decreased the potency of INDO. Particularly striking was the reversibility of INDO inhibition of the V349L mutant. The 2'-des-methyl analogue of INDO (DM-INDO) was synthesized and tested against wild-type COX-1 and COX-2, as well as the Val-349 mutants. DM-INDO bound to all enzymes tested, but only inhibited wt mCOX-2 and the V349I enzyme. Without the 2'-methyl group anchoring DM-INDO in the active site, the compound was readily competed off of the enzyme by arachidonic acid. The kinetics of inhibition were comparable to the kinetics of binding as evaluated by fluorescence quenching. These results highlight binding of the 2'-methyl of INDO in the hydrophobic pocket as an important determinant of its time-dependent inhibition of COX enzymes.