gebhart/patrepeval huggingface dataset:
Relationship between IL-4 and IL-5 mRNA Expression and Disease Severity in Atopic Asthma (1997)

Atopic asthma is characterized by chronic inflammation of the bronchial mucosa in which eosinophil- and immunoglobulin E (IgE)-dependent mechanisms are believed to be prominent. Therefore, specific proeosinophilic mediators such as interleukin (IL)-5 and essential cofactors for IgE switching in B-lymphocytes such as IL-4 could play a pivotal role in asthma. However, the exact role that individual inflammatory mediators play in the development of the disease in humans is still unknown. Using semiquantitative reverse transcriptase-polymerase chain reaction amplification in bronchial biopsies from 10 atopic asthmatics, we have tested the hypothesis that IL-4 and IL-5 mRNA expression relative to beta-actin mRNA correlates with validated indicators of disease severity. IL-4 and IL-5 mRNA copies relative to beta-actin mRNA were detected in bronchial biopsies from atopic asthmatics. The numbers of IL-5 mRNA copies relative to beta-actin mRNA correlated with disease severity assessed by the Aas asthma score (r = 0.70, p = 0.01), baseline FEV1 (r = -0.94, p = 0.001), baseline peak expiratory flow rate (r = -0.77, p = 0.01), peak expiratory flow rate variability over 2 wk (r = 0.69, p = 0.028), and the histamine PC20 (r = -0.72, p = 0.018). Conversely, the numbers of IL-4 mRNA copies relative to beta-actin mRNA did not correlate with asthma severity, but they positively correlated with total serum IgE concentrations (r = -0.90, p = 0.001). Our present results support the concept that IL-5 may determine asthma clinical expression and severity, and by inference they support the development of IL-5 targeted therapies.
Kinetic Modeling of Surface-Initiated Photoiniferter-Mediated Photopolymerization in Presence of Tetraethylthiuram Disulfide (2008)

A rate equation-based kinetic model is developed to investigate the effect of important reaction parameters on surface-initiated photoiniferter-mediated photopolymerization (SI-PMP) of methyl methacrylate. In particular, the effect of incident light intensity and concentration of added deactivating species, tetraethylthiuram disulfide (TED), on the growth kinetics of surface-tethered poly(methyl methacrylate) (PMMA) layers was studied in detail. In accord with experimental results, model predictions suggest that maximum rates of PMMA layer growth observed during initial stages of SI-PMP increase as TED concentration ([TED]) is decreased and as light intensity is increased. Conversely, the maximum thickness of the PMMA layers, which is defined as the thickness at which 99% of the surface-tethered polymer chains are irreversibly terminated, increases as [TED] increases and as light intensity decreases. As light intensity and added deactivator affect the number of propagating surface-tethered radicals, findings from this study delineate strategies for optimizing the formation of surface-tethered PMMA brushes by SI-PMP and creating block copolymer brushes.
Virus-like particle-induced fusion from without in tissue culture cells: role of outer-layer proteins VP4 and VP7 (1997)

We recently described an assay that measures fusion from without induced in tissue culture cells by rotavirus, a nonenveloped, triple-protein-layered member of the Reoviridae family (M. M. Falconer, J. M. Gilbert, A. M. Roper, H. B. Greenberg, and J. S. Gavora, J. Virol. 69:5582-5591, 1995). The conditions required for syncytium formation are similar to those for viral penetration of the plasma membrane during the course of viral infection of host cells, as the presence of the outer-layer proteins VP4 and VP7 and the cleavage of VP4 are required. Here we present evidence that virus-like particles (VLPs) produced in Spodoptera frugiperda Sf-9 cells from recombinant baculoviruses expressing the four structural proteins of rotavirus can induce cell-cell fusion to the same extent as native rotavirus. This VLP-mediated fusion activity was dependent on trypsinization of VP4, and the strain-specific phenotype of individual VP4 molecules was retained in the syncytium assay similar to what has been seen with reassortant rotaviruses. We show that intact rotavirus and VLPs induce syncytia with cells that are permissive to rotavirus infection whereas nonpermissive cells are refractory to syncytium formation. This finding further supports our hypothesis that the syncytium assay accurately reflects very early events involved in viral infection and specifically the events related to viral entry into the cell. Our results also demonstrate that neither viral replication nor rotavirus proteins other than VP2, VP6, VP4, and VP7 are required for fusion and that both VP4 and VP7 are essential. The combination of a cell-cell fusion assay and the availability of recombinant VLPs will permit us to dissect the mechanisms of rotavirus penetration into host cells.
Modeling and Representation (2004)

This chapter contains sections titled: Modeling to Enable Interoperation Integration versus Interoperation Common Ontologies Knowledge Representations Elementary Algebra: Relations Hierarchies Modeling Fundamentals UML as an Ontology Language Alternative Terminology Notes Exercises
Detailed Structural Analysis of <i>N</i>-Glycans Released From Glycoproteins in SDS-PAGE Gel Bands Using HPLC Combined With Exoglycosidase Array Digestions (2006)

In contrast to the linear sequences of protein and DNA, oligosaccharides are branched structures. In addition, almost all glycoproteins consist of a heterogeneous collection of differently glycosylated variants. Glycan analysis therefore requires high-resolution separation techniques that can provide detailed structural analysis, including both monosaccharide sequence and linkage information. This chapter describes how a combination of high-performance liquid chromatography (HPLC) and exoglycosidase enzyme array digestions can deliver quantitative glycan analysis of sugars released from glycoproteins in sodium dodecyl sulfate-polyacrylamide gel electrophoresis gel bands by matching HPLC elution positions with a database of standard glycans.
Effects of porosity and clay content on wave velocities in sandstones (1986)

Abstract The ultrasonic compressional (V p ) and shear (V s ) velocities and first-arrival peak amplitude (A p ) were measured as functions of differential pressure to 50 MPa and to a state of saturation on 75 different sandstone samples, with porosities phi ranging from 2 to 30 percent and volume clay content C ranging from 0 to 50 percent, respectively. Both V p and V s were found to correlate linearly with porosity and clay content in shaly sandstones. At confining pressure of 40 MPa and pore pressure of 1.0 MPa, the best least-squares fits to the velocity data areEquationandEquationDeviations from these equations are less than 3 percent and 5 percent for V p and V s , respectively.The velocities of clean sandstones are significantly higher than those predicted by the above linear fits (about 7 percent for V p and 11 percent for V s ), which indicates that a very small amount of clay (1 or a few percent of volume fraction) significantly reduces the elastic moduli of sandstones.For shaly sandstones we conclude that, to first order, more sensitive to the porosity and clay content than is V p . Consequently, velocity ratios V p /V s and their differences between fully saturated (s) and dry (d) samples also show clear correlation with the clay content and porosity.For shaly sandstones we conclude that, to first order, clay content is the next most important parameter to porosity in reducing velocities, with an effect which is about 0.31 for V p to 0.38 for V s that of the effect of porosity.
Digital confocal microscopy through a multimode fiber (2015)

Acquiring high-contrast optical images deep inside biological tissues is still a challenging problem. Confocal microscopy is an important tool for biomedical imaging since it improves image quality by rejecting background signals. However, it suffers from low sensitivity in deep tissues due to light scattering. Recently, multimode fibers have provided a new paradigm for minimally invasive endoscopic imaging by controlling light propagation through them. Here we introduce a combined imaging technique where confocal images are acquired through a multimode fiber. We achieve this by digitally engineering the excitation wavefront and then applying a virtual digital pinhole on the collected signal. In this way, we are able to acquire images through the fiber with significantly increased contrast. With a fiber of numerical aperture 0.22, we achieve a lateral resolution of 1.5µm, and an axial resolution of 12.7µm. The point-scanning rate is currently limited by our spatial light modulator (20Hz).
Deficiency in NOD Antigen-Presenting Cell Function May Be Responsible for Suboptimal CD4+CD25+ T-Cell–Mediated Regulation and Type 1 Diabetes Development in NOD Mice (2006)

Various defects in antigen-presenting cells (APCs) and T-cells, including regulatory cells, have been associated with type 1 diabetes development in NOD mice. CD4(+)CD25(+) regulatory cells play a crucial role in controlling various autoimmune diseases, and a deficiency in their number or function could be involved in disease development. The current study shows that NOD mice had fewer CD4(+)CD25(+) regulatory cells, which expressed normal levels of glucocorticoid-induced tumor necrosis factor receptor and cytotoxic T-lymphocyte-associated antigen-4. We have also found that NOD CD4(+)CD25(+) cells regulate poorly in vitro after stimulation with anti-CD3 and NOD APCs in comparison with B6 CD4(+)CD25(+) cells stimulated with B6 APCs. Surprisingly, stimulation of NOD CD4(+)CD25(+) cells with B6 APCs restored regulation, whereas with the reciprocal combination, NOD APCs failed to activate B6 CD4(+)CD25(+) cells properly. Interestingly, APCs from disease-free (>30 weeks of age), but not diabetic, NOD mice were able to activate CD4(+)CD25(+) regulatory function in vitro and apparently in vivo because only spleens of disease-free NOD mice contained potent CD4(+)CD25(+) regulatory cells that prevented disease development when transferred into young NOD recipients. These data suggest that the failure of NOD APCs to activate CD4(+)CD25(+) regulatory cells may play an important role in controlling type 1 diabetes development in NOD mice.
A 4-Bit Double SONOS Memory (DSM) with 4 Storage Nodes per Cell for Ultimate Multi-Bit Operation (2006)

We proposed a 4-bit double SONOS memory with two ONO layers, 4 storage nodes, for ultimate multi-bit operation and firstly demonstrate 4-bit operation using the physically separated 4 storage nodes. By using CHEI/HHI program/erase, each node was easily programmed and erased without any detrimental interference among the nodes. In the gate length of 120nm, the read/write margins of ~0.8V for front side (FS) and ~1.1V for back side (BS) at V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">DS</sub> =1.2V was obtained. The V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">TH </sub> shifts of ~1.5V for both program/erase (P/E) were observed with the P/E conditions, V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">D</sub> /V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">FG</sub> =3/5V, 3/-4V for FS and VD/VBG=3.2/7V, 3.2/-5V for BS, respectively, with the duration of 1 ms. The V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">TH</sub> windows of ~0.9V for FS and ~1.1V for BS were achieved even after 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sup> P/E cycles
Precision printing and optical modeling of ultrathin SWCNT/C60 heterojunction solar cells (2015)

Semiconducting single-walled carbon nanotubes (s-SWCNTs) are promising candidates as the active layer in photovoltaics (PV), particularly for niche applications where high infrared absorbance and/or semi-transparent solar cells are desirable. Most current fabrication strategies for SWCNT PV devices suffer from relatively high surface roughness and lack nanometer-scale deposition precision, both of which may hamper the reproducible production of ultrathin devices. Additionally, detailed optical models of SWCNT PV devices are lacking, due in part to a lack of well-defined optical constants for high-purity s-SWCNT thin films. Here, we present an optical model that accurately reconstructs the shape and magnitude of spectrally resolved external quantum efficiencies for ultrathin (7,5) s-SWCNT/C60 solar cells that are deposited by ultrasonic spraying. The ultrasonic spraying technique enables thickness tuning of the s-SWCNT layer with nanometer-scale precision, and consistently produces devices with low s-SWCNT film average surface roughness (Rq of <5 nm). Our optical model, based entirely on measured optical constants of each layer within the device stack, enables quantitative predictions of thickness-dependent relative photocurrent contributions of SWCNTs and C60 and enables estimates of the exciton diffusion lengths within each layer. These results establish routes towards rational performance improvements and scalable fabrication processes for ultra-thin SWCNT-based solar cells.
Facial dystonia, essential blepharospasm and hemifacial spasm. (1991)

Movement disorders, or dyskinesias, in the facial region may be categorized in several ways. Dystonic movement disorders in the cranial-cervical region, including essential blepharospasm, Meige syndrome and spasmodic torticollis, are characterized by uncontrollable squeezing movements in the face and neck. These disorders typically present in the fifth and sixth decades of life. Essential blepharospasm is particularly debilitating, as the involuntary eyelid closure that accompanies this condition may result in functional blindness with an otherwise normal visual pathway. Hemifacial spasm is an intermittent, unilateral, spasmodic contraction of the muscles innervated by the facial nerve. This disorder usually presents in the third or fourth decade and has a different underlying pathophysiology than the dystonias. Botulinum A toxin therapy has largely supplanted surgical intervention in the treatment of essential blepharospasm and hemifacial spasm.
A histochemical study of the rheumatoid synovium: focus on nitric oxide, nerve growth factor high affinity receptor, and innervation. (2000)

We suggest that all elements involved in the transduction pathway that is activated by NGF and that proceeds through NO and tumor suppressor p53 are present in the synovium during RA, controlling cell cycle arrest, cell differentiation, and apoptosis.
Patterned Supported Bilayers on Self-Assembled Monolayers:  Confinement of Adjacent Mobile Bilayers (2001)

10.1021/la010776t
Influenza virus hemagglutinin and neuraminidase glycoproteins stimulate the membrane association of the matrix protein (1996)

We have analyzed the mechanism by which the matrix (M1) protein associates with cellular membranes during influenza A virus assembly. Interaction of the M1 protein with the viral hemagglutinin (HA) or neuraminidase (NA) glycoprotein was extensively analyzed by using wild-type and transfectant influenza viruses as well as recombinant vaccinia viruses expressing the M1 protein, HA, or NA. Membrane binding of the M1 protein was significantly stimulated at the late stage of virus infection. Using recombinant vaccinia viruses, we found that a relatively small fraction (20 to 40%) of the cytoplasmic M1 protein associated with cellular membranes in the absence of other viral proteins, while coexpression of the HA and the NA stimulated membrane binding of the M1 protein. The stimulatory effect of the NA (>90%) was significant and higher than that of the HA (>60%). Introduction of mutations into the cytoplasmic tail of the NA interfered with its stimulatory effect. Meanwhile, the HA may complement the defective NA and facilitate virus assembly in cells infected with the NA/TAIL(-) transfectant. In conclusion, the highly conserved cytoplasmic tails of the HA and NA play an important role in virus assembly.
Predictive Control With Constraints (2001)

1. Introduction to Predictive Control. 2. A Standard Formulation of Predictive Control. 3. Solving Predictive Control Problems. 4. Step Response and Transfer Function Formulations. 5. Tuning. 6. Stability. 7. Robust Predictive Control. 8. Perspectives. 9. Case Studies. 10. The Model Predictive Control Toolbox. References Appendices A. Some Commercial MPC Products B. MATLAB Program basicmpc C. The MPC Toolbox D. Solutions to Problems
Neutralization of the Positive Charges of Surfactant Protein C (1995)

Pulmonary surfactant protein C (SP-C) is a small, extremely hydrophobic peptide with a highly conservative primary structure. The protein is characterized by two adjacent palmitoylated cysteine residues, two positively charged residues (one arginine residue and one lysine residue) in the N-terminal region, and a long hydrophobic stretch. SP-C enhances the adsorption of phospholipids into an air-water interface. To determine the importance of the positively charged residues, we carried out experiments with natural porcine SP-C and modified porcine SP-C (SP-Cm) in which the positive charges had been blocked by phenylglyoxal. Circular dichroism experiments showed that SP-Cm had an increased content of alpha-helix. Natural SP-C, but not SP-Cm, catalyzed insertion of phospholipids into a monolayer at the airwater interface. This reduced insertion was due to a strong reduction of binding of phospholipid vesicles to the monolayer. The insertion catalyzed by the natural porcine SP-C was decreased by an increased pH of the subphase. In contrast to natural SP-C, SP-Cm induced lipid mixing between phospholipid vesicles. The extent of lipid mixing was a function of the SP-C content. We conclude that the positively charged residues of SP-C are important for the binding of phospholipid vesicles to the monolayer, a process that precedes the insertion of phospholipids into the monolayer.
Antigen Retrieval Immunohistochemistry (2011)

As a review for the 20th anniversary of publishing the antigen retrieval (AR) technique in this journal, the authors intend briefly to summarize developments in AR-immunohistochemistry (IHC)-based research and diagnostics, with particular emphasis on current challenges and future research directions. Over the past 20 years, the efforts of many different investigators have coalesced in extending the AR approach to all areas of anatomic pathology diagnosis and research and further have led to AR-based protein extraction techniques and tissue-based proteomics. As a result, formalin-fixed paraffin-embedded (FFPE) archival tissue collections are now seen as a literal treasure of materials for clinical and translational research to an extent unimaginable just two decades ago. Further research in AR-IHC is likely to focus on tissue proteomics, developing a more efficient protocol for protein extraction from FFPE tissue based on the AR principle, and combining the proteomics approach with AR-IHC to establish a practical, sophisticated platform for identifying and using biomarkers in personalized medicine.
Essential features of the assembly origin of tobacco mosaic virus RNA as studied by directed mutagenesis (1986)

The assembly origin of tobacco mosaic virus RNA contains three stable hairpin loops. Coat protein disks bind first to loop 1 (the 3' most) during virus assembly, but the whole region is coated in a concerted fashion even in conditions of limiting protein. It is shown by in vitro packaging assays using mutant assembly origin transcripts that rapid and specific assembly initiation occurs in the absence of loops 2 and 3, but is abolished on removal of loop 1. Deletion or alteration of the unpaired AAGAAGUCG sequence at the apex of loop 1 also abolishes rapid packaging; this sequence is therefore instrumental in disk binding. Alteration of this sequence to (A)9 leads to packaging at a very low rate (half time 12 hours) which is apparently non-sequence specific. Substitution of (CCG)3 evokes packaging with a half time of 3 hours, as compared to 15 seconds for the wild type assembly origin. These results suggest that the three-base G periodicity within this sequence element is an important feature in assembly nucleation.
Initiation of hematopoiesis and vasculogenesis in murine yolk sac explants (1995)

The blood islands of the visceral yolk sac (VYS) are the initial sites of hematopoiesis in mammals. We have developed a yolk sac explant culture system to study the process of blood cell and endothelial cell development from extraembryonic mesoderm cells. No benzidine-positive cells or beta H1-globin mRNA expression was detected at the primitive streak or neural plate stage of development (E7.5). However, when isolated E7.5 dissected tissues were cultured for 36 to 72 hours in serum-free medium, hundreds of hemoglobin-producing cells and embryonic globin gene expression were identified in both intact yolk sac and VYS mesoderm explants. Explanted E7.5 extraembryonic mesoderm tissues thus recapitulate in vivo primitive erythropoiesis and do not require the presence of a vascular network or the VYS endoderm. Yolk sac blood islands also contain endothelial cells that arise by vasculogenesis and express flk-1. We detected flk-1 mRNA as early as the primitive streak stage of mouse embryogenesis. Culture of embryo proper and intact VYS explants, which contain both mesoderm and endoderm cells, produced capillary networks and expressed flk-1. In contrast, vascular networks were not seen when VYS mesoderm was cultured alone, although flk-1 expression was similar to that of intact VYS explants. The addition of vascular endothelial growth factor to VYS mesoderm explants did not induce vascular network formation. These results suggest that the VYS endoderm or its extracellular matrix is necessary for the coalescence of developing endothelial cells into capillary networks.
Finite element modeling of electrode-skin contact impedance in electrical impedance tomography (1993)

In electrical impedance tomography (EIT), we inject currents through and measure voltages from an array of surface electrodes. The measured voltages are sensitive to electrode-skin contact impedance because the contact impedance and the current density through this contact impedance are both high. We used large electrodes to provide a more uniform current distribution and reduce the contact impedance. A large electrode differs from a point electrode in that it has shunting and edge effects which cannot be modeled by a single resistor. We used the finite element method (FEM) to study the electric field distributions underneath an electrode, and developed three models: a FEM model, a simplified FEM model and a weighted load model. We showed that the FEM models considered both shunting and edge effects and matched closely the experimental measurements. FEM models for electrodes can be used to improve the performance of an electrical impedance tomography reconstruction algorithm.
Multiroute Synthesis of Porous Anionic Frameworks and Size-Tunable Extraframework Organic Cation-Controlled Gas Sorption Properties (2009)

Under diverse and dramatically different chemical environments, including organic solvents, an ionic liquid, and a deep eutectic solvent, a series of porous anionic framework materials that contain size-tunable, ion-exchangeable extraframework organic cations have been prepared. Even though a large fraction of the pore space is occupied with charge-balancing cations, some of these materials exhibit a very high gas uptake capacity (e.g., 70.6 cm(3)/g for CO(2) at 1 atm and 273 K), suggesting that the charged anionic framework and extraframework cations may help to enhance the gas adsorption.