gebhart/patrepeval huggingface dataset:
Wavelength Dependence of Metal-Enhanced Fluorescence (2009)

In this paper, metal-enhanced fluorescence (MEF) from 6-propionyl-2-dimethylaminonaphthalene (Prodan) in different solvents when placed in close proximity to silver island films (SIFs), surface-deposited nanoparticles, is studied. We observe that MEF is wavelength dependent: the enhanced emission of Prodan on SIFs in different solvents changes from 1.5- to 3-fold as compared to a glass control sample containing no silver nanoparticles. Our findings strongly suggest that MEF of Prodan in different solvents is correlated with the scattering portion of the extinction spectrum for metallic particles, i.e., the fluorophore couples and radiates through that scattering mode, which further confirms our laboratories current interpretation of the MEF effect.
Low-loss planar optical waveguides fabricated in SIMOX material (1992)

Planar optical waveguides have been formed in SIMOX structures, and the effect of the thickness of the buried oxide layer on propagation loss hs been studied. Waveguides with a guiding layer thickness of approximately 6 mu m have been measured, and the lowest loss, which is on the order of that of pure silicon, was observed for a buried oxide thickness of 0.4 mu m, at a measurement wavelength of 1.523 mu m.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Activation of the TGF- β /Activin-Smad2 Pathway during Allergic Airway Inflammation (2001)

Changes in the levels of transforming growth factor (TGF)-beta cytokines or receptors observed during the progression of several inflammatory and fibrotic disorders have been used to implicate these cytokines in the pathophysiology of these diseases. Although correlative, these studies were inconclusive because they were unable to demonstrate actual continuous TGF-beta-mediated signaling in the involved tissues. We reasoned that the phosphorylation state and subcellular localization of Smad2, the intracellular effector of TGF-beta/activin-mediated signaling, could be used as a marker of active signaling mediated by these cytokines in situ. We therefore used an experimental model of ovalbumin-induced allergic airway inflammation and were able to demonstrate a dramatic increase in the numbers of bronchial epithelial, alveolar, and infiltrating inflammatory cells expressing nuclear phosphorylated Smad2 within the allergen-challenged lungs. This was accompanied by strong upregulation of the activin receptor ALK-4/ActR-IB and redistribution of the TGF-beta responsive ALK-5/TbetaR-I. Although levels of TGF-beta1, TGF-beta2, and TGF-beta3 messenger RNA (mRNA) were marginally altered, the level of activin mRNA was strongly upregulated during the inflammatory response. Our data illustrate the usefulness of antiphosphorylated Smad antibodies in demonstrating active TGF- beta/activin-mediated signaling in vivo and strongly suggest that activin/Smad-mediated signaling could be a critical contributor in the pathophysiology of allergic pulmonary diseases.
The Fixation of Tetanus Toxin by Ganglioside (1961)

SUMMARY: The fixation of tetanus toxin by brain ganglioside has been confirmed. A method has been developed for assaying the toxin-fixing capacity of ganglioside in the analytical ultracentrifuge. Under appropriate conditions ganglioside will fix many times its own weight of toxin. Ganglioside preparations from brain contain at least three gangliosides; at least two of these differ in their sialic acid contents and toxinfixing capacities. The sialic acid residues (and their free carboxyl groups) are essential for toxin-fixation. Tetanus toxin does not appear (so far) to bring about any change in the ganglioside molecule.
Tactile discrimination in children: the tactile assessment kit (1998)

In this article, a tool for the assessment of tactile discrimination in children is described and research that aimed to investigate the ability of the test to differentiate across age and between children with and without coordination difficulties is reported. The results indicated that this test, the tactile assessment kit, will be useful as a clinical tool for differentiating dysfunction and any change in the children's functional ability due to maturation.
Enhancement of human monocyte function against Candida albicans by the colony-stimulating factors (CSF): IL-3, granulocyte-macrophage-CSF, and macrophage-CSF. (1989)

The effect of IL-3, granulocyte-macrophage (GM)-CSF and macrophage (M)-CSF on Candida albicans growth inhibition by human peripheral blood monocytes was investigated. By using a radiolabel microassay developed in our laboratory that makes use of the incorporation of [3H]glucose into residual C. albicans, we demonstrated that rGM-CSF and rIL-3 effectively enhanced human monocyte-mediated anticandidal activity. Incubation for 24 h with either GM-CSF or IL-3 significantly enhanced monocyte antifungal responses down to 0.01 U/ml. M-CSF, at higher concentrations of 10 U/ml, could also enhance monocyte function but to a smaller degree. None of the CSF interfered directly with fungal growth, even up to 1000 U/ml. Because IFN-gamma is also a known monocyte activator, its effect on monocytes was also assessed. Monocytes were first cultured in medium for several days and then further incubated with each of the cytokines. Monocytes aged in medium were found to lose their spontaneous anticandidal activity. Such aged monocytes did not develop anticandidal activity in response to IFN-gamma but did in response to GM-CSF or IL-3. To further elucidate this difference, fresh monocytes were continuously cultured with or without cytokines for 1 to 5 days before assessing their anticandidal activity. Monocytes cultured in IFN-gamma progressively lost their activity by 2 days but monocytes in GM-CSF or IL-3 maintained their high level of anticandidal activity throughout the whole length of culture. Therefore, GM-CSF and IL-3 not only enhanced fresh monocyte anticandidal activity, but maintained monocyte function for a longer period. These results suggest that GM-CSF and IL-3 may act on monocytes via a different pathway than does IFN-gamma.
A Phase I/IB trial of murine monoclonal anti-GD2 antibody 14.G2a plus interleukin-2 in children with refractory neuroblastoma (1997)

The murine MoAb 14.G2a was well tolerated at the MTD and appeared to have some antitumor activity. Further development of this approach will involve additional engineered forms of the antibody as well as testing in the adjuvant and minimal residual disease setting.
44-kd Oncofetal Transplantation Antigen in Rodent and Human Fetal Cells: Implications of Recrudescence in Human and Rodent Cancers (1993)

Shared 44-kd oncofetal antigen OFA offers promise as a tumor detection marker in human squamous cell carcinoma and other human carcinoma development, and syngeneic mouse tumors are good model systems to explore oncofetal antigen antigenicity.
Formation and Propagation of Tau Oligomeric Seeds (2013)

Tau misfolding and aggregation leads to the formation of neurofibrillary tangles (NFTs), which have long been considered one of the main pathological hallmarks for numerous neurodegenerative diseases known as tauopathies, including Alzheimer's Disease (AD) and Parkinson's Disease (PD). However, recent studies completed both in vitro and in vivo suggest that intermediate forms of tau, known as tau oligomers, between the monomeric form and NFTs are the true toxic species in disease and the best targets for anti-tau therapies. However, the exact mechanism by which the spread of pathology occurs is unknown. Evidence suggests that tau oligomers may act as templates for the misfolding of native tau, thereby seeding the spread of the toxic forms of the protein. Recently, researchers have reported the ability of tau oligomers to enter and exit cells, propagating from disease-affected regions to unaffected areas. While the mechanism by which the spreading of misfolded tau occurs has yet to be elucidated, there are a few different models which have been proposed, including cell membrane stress and pore-formation, endocytosis and exocytosis, and non-traditional secretion of protein not enclosed by a membrane. Coming to an understanding of how toxic tau species seed and spread through the brain will be crucial to finding effective treatments for neurodegenerative tauopathies.
Characterization of Flow‐Induced Compositional Structure in Electrodeposited NiFe Composition‐Modulated Alloys (1998)

Flow‐induced NiFe composition‐modulated alloys (CMAs) are plated onto the disk of a rotating ring‐disk electrode (RRDE) by oscillating the RRDE rotation rate during galvanostatic deposition. The relationships between processing and compositional structure in the electrodeposited CMAs are explored using an optimized potentiostatic stripping voltammetry technique, scanning electron microscopy, and energy‐dispersive X‐ray spectroscopy. Results show that the CMA wavelength scales as the inverse of the flow oscillation frequency and the composition modulation amplitude are strongly affected by variations in both electrolyte flow oscillation frequency and amplitude. Fast Fourier transform analysis is used to probe the dynamic time scales of NiFe electrodeposition and to investigate the sensitivity of NiFe deposition to the oscillating electrolyte flow field. Results indicate that critical deposition chemistries occur over time scales much slower than those governing typical mass‐transfer processes.
A Review of Acousto-Optic Signal Correlators (1977)

Many techniques have been proposed in the past for using acousto-optic devices to perform signal correlation. This paper reviews these techniques and discusses the design tradeoffs involved in choosing a particular configuration for a given application. Configurations are classed as two major types. The first type, spatial integrating correlators, perform correlation by integrating light diffracted by all parts of the signal(s) which are simultaneously present in the acoustic device. This type of correlator has a large range window, but the time bandwidth product is limited by device parameters. The second type, time integrating correlators, use a detector array or vidicon to perform an integration in time for each point within the cell. This provides a limited range window but a large time bandwidth product. Results obtained with both types of systems are shown, along with pictures of fabricated hardware. Acousto-optic device parameters are also summarized for comparison with competitive technologies.
Optical design of a free-space photonic switching system (1997)

The optical design of a photonic switching system is described in detail. The system is a 4-f imaging system with one lens design based on a Petzval lens and the second lens design based on a double Gauss lens. The assembled system is 60 mm x 70 mm x 370 mm and features a single imaging stage, pupil division for beam combination, and a single fiber bundle for both input and output. A brief description of the system requirements is provided, and the implication of some of these requirements for the paraxial design is explained. The choice of design forms for the lenses is explained, the design process is outlined, and the final lens designs are provided. Lens tolerancing is outlined and the final lens tolerances are provided. Finally, the assembly and the alignment processes are described.
Conditional expression of the vesicular stomatitis virus glycoprotein gene in Escherichia coli. (1981)

Bacterial plasmids that directed expression of the vesicular stomatitis virus glycoprotein (G-protein) gene under control of the tryptophan operon regulatory region were constructed. A plasmid directing the synthesis of a G-protein-like protein (containing the NH2-terminal segment of seven amino acids encoded by the trpE gene fused to the complete G-protein sequence lacking only its NH2-terminal methionine) could be transformed into trpR+ (repressed) but not into trpR- (derepressed) cells. This result suggested initially that derepressed synthesis of the G-protein-like protein encoded by this plasmid was lethal in Escherichia coli. Deletion of the sequence encoding the large hydrophobic segment near the COOH terminus of G-protein did not overcome this lethality. Lethality of derepressed synthesis was overcome by deletion of the G-protein gene region encoding 10 amino acids in the hydrophobic NH2-terminal domain (signal peptide). Tryptic peptide mapping demonstrated that the G-protein-like protein and some truncated proteins encoded by the plasmid contained G-protein protein sequences. Antisera to vesicular stomatitis virus precipitated the G-protein-like protein, showing that it shares antigenic determinants with the authentic G-protein protein.
Proxemic interactions in ubiquitous computing ecologies (2011)

An important challenge in ubiquitous computing (ubicomp) is to create techniques that allow people to seamlessly and naturally connect to and interact with the increasing number of digital devices. I propose to leverage the knowledge of people's and devices' spatial relationships - called proxemics - in ubicomp interaction design. I introduce my work of proxemic interactions that consider fine-grained information of proxemics to mediate people's interactions with digital devices, such as large digital surfaces or portable personal devices. This research includes the design of development tools for programmers creating proxemic-aware systems, and the design and evaluation of such interactive ubicomp systems.
Photonic bandgaps with defects and the enhancement of Faraday rotation (2000)

We investigate enhancement of magnetooptical rotation in periodic magnetic garnet thin-film stacks with defects using a combination of coupled-mode theory and matrix calculations. We prove that a combination of high rotation per unit length and high output is unattainable for a symmetric grating with a single central defect. We demonstrate that the addition of a second defect introduces sufficient degrees of freedom to allow high transmission for a much larger range of rotation angles than was previously possible. We present a number of designs with emphasis an achieving 45/spl deg/ rotation in very short propagation lengths.
Pax9-deficient mice lack pharyngeal pouch derivatives and teeth and exhibit craniofacial and limb abnormalities (1998)

Pax genes have been shown to play important roles in mammalian development and organogenesis. Pax9, a member of this transcription factor family, is expressed in somites, pharyngeal pouches, mesenchyme involved in craniofacial, tooth, and limb development, as well as other sites during mouse embryogenesis. To analyze its function in vivo, we generated Pax9 deficient mice and show that Pax9 is essential for the development of a variety of organs and skeletal elements. Homozygous Pax9-mutant mice die shortly after birth, most likely as a consequence of a cleft secondary palate. They lack a thymus, parathyroid glands, and ultimobranchial bodies, organs which are derived from the pharyngeal pouches. In all limbs, a supernumerary preaxial digit is formed, but the flexor of the hindlimb toes is missing. Furthermore, craniofacial and visceral skeletogenesis is disturbed, and all teeth are absent. In Pax9-deficient embryos tooth development is arrested at the bud stage. At this stage, Pax9 is required for the mesenchymal expression of Bmp4, Msx1, and Lef1, suggesting a role for Pax9 in the establishment of the inductive capacity of the tooth mesenchyme. In summary, our analysis shows that Pax9 is a key regulator during the development of a wide range of organ primordia.
A family of transketolases that directs isoprenoid biosynthesis via a mevalonate-independent pathway (1998)

Isopentenyl diphosphate, the common precursor of all isoprenoids, has been widely assumed to be synthesized by the acetate/mevalonate pathway in all organisms. However, based on in vivo feeding experiments, isopentenyl diphosphate formation in several eubacteria, a green alga, and plant chloroplasts has been demonstrated very recently to originate via a mevalonate-independent route from pyruvate and glyceraldehyde 3-phosphate as precursors. Here we describe the cloning from peppermint (Mentha x piperita) and heterologous expression in Escherichia coli of 1-deoxy-D-xylulose-5-phosphate synthase, the enzyme that catalyzes the first reaction of this pyruvate/glyceraldehyde 3-phosphate pathway. This synthase gene contains an ORF of 2,172 base pairs. When the proposed plastid targeting sequence is excluded, the deduced amino acid sequence indicates the peppermint synthase to be about 650 residues in length, corresponding to a native size of roughly 71 kDa. The enzyme appears to represent a novel class of highly conserved transketolases and likely plays a key role in the biosynthesis of plastid-derived isoprenoids essential for growth, development, and defense in plants.
Rice Hemoglobins (Gene Cloning, Analysis, and O2-Binding Kinetics of a Recombinant Protein Synthesized in Escherichia coli) (1997)

Although nonsymbiotic hemoglobins (Hbs) are found in different tissues of dicots and monocots, very little is known about hb genes in monocots and the function of Hbs in nonsymbiotic tissues. We report the cloning and analysis of two rice (Oryza sativa L.) hb genes, hb1 and hb2, that code for plant Hbs. Rice hb1 and hb2 genes contain four exons and three introns, as with all of the known plant hb genes. At least three copies of the hb gene were detected in rice DNA, and analysis of gene expression shows that hb1 and hb2 are expressed in leaves but only hb1 is expressed in roots. A cDNA for rice Hb1 was expressed in Escherichia coli, and the recombinant Hb (rHb1) shows an unusually high affinity for O2 because of a very low dissociation constant. The absorbance spectra of the ferric and deoxyferrous rHb1 indicate that, in contrast to symbiotic Hbs, a distal ligand is coordinated to the ligand-binding site. Mutation of the distal His demonstrates that this residue coordinates the heme Fe of ferric and deoxyferrous rHb1 and stabilizes O2 in oxy-rHb1. The biochemical properties of rice rHb1 suggest that this protein probably does not function to facilitate the diffusion of O2.
A miniature digital current sensor with differential Hall probes using enhanced chopping techniques and mechanical stress compensation (2012)

A 10kHz bandwidth 50Amax current sensor using a Hall effect gradiometer without magnetic core provides 80kHz update rate with a digital interface. Very low un-calibrated offset of 30mA (1σ) and after calibration typical 10mA over temperature is accomplished by a chopped multi-bit feedback continuous-time 3rd order ΔΣ-ADC. This also realizes low noise of 13mA <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">rms</sub> in 1kHz signal bandwidth. The ADC uses enhanced chopping techniques and additional digital feedback loops to avoid chopper ripple. New analog and digital stress-compensation circuits with lateral and vertical n-doped resistors achieve lifetime gain drifts below 1% and temperature compensation. Auto-zeroing ping-pong comparators offer a fast over-current detection of 1...2μs on a dedicated output pin. The monolithic integrated sensor chip and the 4kV galvanic isolated current rail fit into a very small 7×7×1mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> package.
Overexpression of an enzymically inactive interleukin-1-receptor-associated kinase activates nuclear factor-kappaB. (1999)

Upon interleukin 1 (IL-1) stimulation, the IL-1-receptor (IL-1R)-associated kinase (IRAK) is rapidly recruited to the IL-1R complex and undergoes phosphorylation. Here we demonstrate that recombinant wild-type IRAK (IRAK-WT), but not a kinase-defective mutant with Asp340 replaced by an asparagine residue (IRAK-Asp340Asn), is highly phosphorylated and is capable of auto-phosphorylation in vitro. Overexpression of both IRAK-WT and IRAK-Asp340Asn caused activation of nuclear factor kappaB, suggesting that the kinase activity of IRAK is not required outside of the IL-1R complex.
Structure and function correlation in histone H2A peptide-mediated gene transfer (2002)

Histone H2A has been found to be efficient in DNA delivery into a number of cell lines. We have reasoned that this DNA-delivery activity is mediated by two mechanisms: (i) electrostatically driven DNA binding and condensation by histone and (ii) nuclear import of these histone H2A.DNA polyplexes via nuclear localization signals in the protein. We have identified a 37-aa N-terminal peptide of histone H2A that is active in in vitro gene transfer. This peptide can function as a nuclear localization signal and can bind DNA. Amino acid substitutions that replace positively charged residues and/or DNA-binding residues of this peptide obliterate transfection activity. The introduction of a proline in the first turn of an alpha-helix of this 37-mer obliterates transfection activity, suggesting that the integrity of the alpha-helical structure of the N-terminal region of histone H2A is related to its transfection activity.
Sphingosine-1-phosphate is a ligand for the G protein-coupled receptor EDG-6 (2000)

EDG-6 is a recently cloned member of the endothelial differentiation gene (EDG) G protein-coupled receptor family that is expressed in lymphoid and hematopoietic tissue and in the lung. Homology of EDG-6 to the known sphingosine-1-phosphate (SPP) receptors EDG-1, EDG-3, and EDG-5 and lysophosphatidic acid (LPA) receptors EDG-2 and EDG-4 suggested that its ligand may be a lysophospholipid or lysosphingolipid. We examined the binding of [(32)P]SPP to HEK293 cells, transiently transfected with cDNA encoding EDG-6. Binding of [(32)P]SPP was saturable, demonstrating high affinity (K(D) = 63 nmol/L). Binding was also specific for SPP, as only unlabeled SPP and sphinganine-1-phosphate, which lacks the trans double bond at the 4 position, potently displaced radiolabeled SPP. LPA did not compete for binding of SPP at any concentration tested, whereas sphingosylphosphorylcholine competed for binding to EDG-6, but only at very high concentrations. In addition, SPP activated extracellular signal-regulated kinase (Erk) in EDG-6 transfected cells in a pertussis toxin-sensitive manner. These results indicate that EDG-6 is a high affinity receptor for SPP, which couples to a G(i/o) protein, resulting in the activation of growth-related signaling pathways. (Blood. 2000;95:2624-2629)
Coloring a Family of Circular Arcs (1975)

This paper presents a collection of results about coloring a family of circular arcs. We prove that the strong perfect graph conjecture is valid for circular-arc graphs. We give some upper bounds on the number of colors needed to color various families of arcs. Finally, we convert the problem of determining whether a family of arcs can be q-colored into a multicommodity flow problem.
Development of Neonatal Th1/Th2 Function (2000)

Newborn animals generally mount poor T cell-mediated immune responses in vivo. As a result, neonates fall prey to infectious agents and diseases which have little impact on immunocompetent adult animals. For some time, it was believed that this phenomenon was due to an intrinsic inability of newborns to mount developmentally mature Th1 responses. Recent studies in mice have challenged that view; under certain conditions, adult-level Th1 function has been achieved in newborns. More often, however, neonates develop Th2-dominant responses. A major challenge in the field of developmental immunology is to understand why the 'default' response for neonates is Th2 function. Cell intrinsic as well as environmental influences may contribute to Th2 skewing in neonates.
Enhanced excretion of urinary leukotriene E4 in coronary artery disease and after coronary artery bypass surgery (1993)

Levels of cysteinyl leukotrienes are raised in coronary artery disease patients both before and after coronary artery bypass surgery. As these mediators are capable of inducing potent vasoconstrictive effects on atherosclerotic coronary arteries and the saphenous vein, our results could have important clinical and possibly therapeutic implications.