gebhart/patrepeval huggingface dataset:
Salmonella Flagellin-Dependent Proinflammatory Responses Are Localized to the Conserved Amino and Carboxyl Regions of the Protein (2001)

Flagellin, the monomeric subunit of flagella, is an inducer of proinflammatory mediators. Bacterial flagellin genes have conserved domains (D1 and D2) at the N terminus and C terminus and a middle hypervariable domain (D3). To identify which domains induced proinflammatory activity, r6-histidine (6HIS)-tagged fusion constructs were generated from the Salmonella dublin (SD) fliC flagellin gene. A full-length r6HIS SD flagellin (6HIS flag) induced IkappaBalpha loss poststimulation and NF-kappaB activation in Caco-2BBe cells and was as potent as native-purified SD flagellin. IFN-gamma-primed DLD-1 cells stimulated with 1 microg/ml of 6HIS flag induced high levels of NO (60 +/- 0.95 microM) comparable to the combination of IL-1beta and IFN-gamma (77 +/- 1.2) or purified native SD flag (66.3 +/- 0.98). Selected rSD flagellin proteins representing the D1, D2, or D3 domains alone or in combination were tested for proinflammatory properties. Fusion proteins representing the D3, amino, or carboxyl regions alone did not induce proinflammatory mediators. The results with a recombinant protein containing the amino D1 and D2 and carboxyl D1 and D2 separated by an Escherichia coli hinge (ND1-2/ECH/CD2) indicated that D1 and D2 were bioactive when coupled to an ECH element to allow protein folding. This chimera, but not the hinge alone, induced IkappaBalpha degradation, NF-kappaB activation, and NO and IL-8 production in two intestinal epithelial cell lines. ND1-2/ECH/CD2-1 also induced high levels of TNF-alpha (900 pg/ml) in human monocytes comparable to native SD flagellin (991.5 pg/ml) and 6HIS flag (987 pg/ml). The potent proinflammatory activity of flagellin, therefore, resides in the highly conserved N and C D1 and D2 regions.
Electrical Impedance Tomography of Cell Viability in Tissue With Application to Cryosurgery (2004)

Tissue damage that is associated with the loss of cell membrane integrity should alter the bulk electrical properties of the tissue. This study shows that electrical impedance tomography (EIT) should be able to detect and image necrotic tissue inside the body due to the permeabilization of the membrane to ions. Cryosurgery, a minimally invasive surgical procedure that uses freezing to destroy undesirable tissue, was used to investigate the hypothesis. Experimental results with liver tissue demonstrate that cell damage during freezing results in substantial changes in tissue electrical properties. Two-dimensional EIT simulations of liver cryosurgery, which employ the experimental data, demonstrate the feasibility of this application.
Automatic registration of F-18 labeled BMS-747158 stress and rest myocardial perfusion images using 6D cross-correlation optimization (2010)

1687 Objectives Optimization of a same day imaging protocol for F-18 labeled PET perfusion tracers is necessary to achieve improved accuracy and maintain clinical efficiency. We developed a 6D (X, Y, Z, transaxial angle (TA), sagittal angle (SA) and magnification (M)) for blending the rest the stress images using a cross-correlation (CC) algorithm. Methods The stress and rest images were centered on the center of mass of the myocardium. Following centering, +/-10 pixel shifts in X,Y,Z were used to identify the peak CC shift. We then calculated the CC peak to identify the TA and SA rotations (+/- 10 deg). To find the magnification CC peak, images were magnified, and renormalized to conserve the maximum pixel value. Image data were acquired on Biograph 64 scanners using a 30 minute listmode acquisition. The phantom was prepared to simulate patient concentrations at rest and adenosine stress with a 40% septal defect at stress, based on Phase I data. Thirty patients enrolled in the Phase II clinical trial of BMS747158 from two centers were used to validate the technique prospectively. Simulated images were visually inspected to identify misregistration artifacts. Results The algorithm produced accurate X,Y and angular shifts of the phantom. Magnification was less accurate, due to renormalization (see table). All 30 patients were registered without introducing an overlay artifact. Conclusions The automatic registration program utilized can be used to create simulated same day datasets from two day BMS747158 datasets. These virtual same day studies can be used to identify optimal imaging protocols more efficiently, giving investigators valuable insight into protocol trade-offs prior to the initiation of large scale randomized trials
Identification of etoposide glucuronide as a major metabolite of etoposide in the rat and rabbit. (1988)

Isolated livers from male Sprague-Dawley rats were perfused at 20 ml/min for 3 h at 37 degrees C with 100 ml of an oxygenated, recirculating solution of 20% rat blood in Krebs bicarbonate buffer containing 20 micrograms/ml [3H]etoposide. Ninety % of administered radioactivity was eliminated in bile over a 3-h collection period. The clearance of etoposide was 3.56 ml/min indicating that, in the rat, it is not highly extracted. Its clearance is, therefore, independent of hepatic blood flow. Etoposide was both excreted into the bile and metabolized by the liver. Perfusate and bile samples analyzed by reverse-phase high-performance liquid chromatography techniques were found to contain three peaks of radioactivity. Positive and negative ion fast atom bombardment mass spectrometry identified the first two peaks as etoposide glucuronides and the third peak as parent drug. Following the i.v. administration of etoposide to rabbits, etoposide glucuronide was also identified in rabbit urine. The recovery of etoposide both from rabbit urine and rat bile was increased by preincubation with glucuronidase. However, the glucuronides were relatively resistant to the action of glucuronidase and showed varying sensitivity to the type of glucuronidase and the reaction conditions used. These studies document the presence of etoposide glucuronide as an etoposide metabolite in two mammalian species and suggest that previous clinical studies using beta-glucuronidase to quantitate glucuronide formation may have underestimated this metabolite due to its relative resistance to some glucuronidase preparations.
Moving superhydrophobic surfaces toward real-world applications (2016)

Standardized wear and durability testing is needed to advance the best materials
Biomedical microwave inversion in conducting cylinders of arbitrary shapes (2009)

We introduce a non-linear inversion algorithm for use in microwave biomedical imaging when the object of interest is surrounded by an arbitrarily shaped conducting enclosure. The algorithm utilizes the Gauss-Newton inversion method and a combined additive and multiplicative regularizer. The conducting enclosure is taken into account via a FEM-based forward solver which is able to efficiently model arbitrarily shaped boundaries. Results for the 2D scalar case are given when the enclosure is a circle, triangle, and square, and include simple and complex biological scatterers, based on synthetic data. The results show that the algorithm is capable of reconstructing objects in all cylinder types.
The Huntington disease locus is most likely within 325 kilobases of the chromosome 4p telomere. (1989)

The genetic defect responsible for Huntington disease was originally localized near the tip of the short arm of chromosome 4 by genetic linkage to the locus D4S10. Several markers closer to Huntington disease have since been isolated, but these all appear to be proximal to the defect. A physical map that extends from the most distal of these loci, D4S90, to the telomere of chromosome 4 was constructed. This map identifies at least two CpG islands as markers for Huntington disease candidate genes and places the most likely location of the Huntington disease defect remarkably close (within 325 kilobases) to the telomere.
Enhanced absorption in elliptical silicon nanowire arrays for solar energy harvesting (2014)

A crystalline Si thin film solar cell with elliptical silicon nanowire (SiNW)-decorated surface is presented. The elliptical SiNW solar cell performs broadband light absorption in the low energy region while maintaining strong absorption in the high energy region. For the elliptical SiNW solar cells with 1-μm underlying Si substrate, J sc can be improved to 24.2 mA/cm 2 , which is 16% higher than that of the circular SiNW-decorated solar cells. After integration with an Ag reflector, the elliptical SiNW solar cells can achieve higher J sc of 26.3 mA/cm 2 , demonstrating a photocurrent enhancement of 12.6% as compared with circular SiNW control device.
Binding of human extracellular superoxide dismutase C to sulphated glycosaminoglycans (1988)

The secretory enzyme extracellular superoxide dismutase (EC-SOD) occurs in at least three forms, which differ with regard to heparin affinity: A lacks affinity, B has intermediate affinity, and C has relatively strong affinity. The affinity of EC-SOD C for various sulphated glycosaminoglycans (GAGs) was assessed (a) by determining the concentration of NaCl required to release the enzyme from GAG-substituted Sepharose 4B and (b) by determining the relative potencies of the GAGs to release EC-SOD C from heparan sulphate-Sepharose 4B. Both methods indicated the same order of affinity. Heparin bound EC-SOD C about 10 times as avidly as the studied heparan sulphate preparation, which in turn was 10 and 150 times as efficient as dermatan sulphate and chondroitin sulphate respectively. Chondroitin sulphate showed weak interaction with EC-SOD C at physiological ionic strength. Heparin subfractions with high or low affinity for antithrombin III were equally efficient. The binding of EC-SOD C to heparin-Sepharose was essentially independent of pH in the range 6.5-9; below pH 6.5 the affinity increased, and beyond pH 9.5 there was a precipitous fall in affinity. The inhibitory effect of NaCl on the binding of EC-SOD C to GAGs indicates that the interaction is of electrostatic nature. EC-SOD C carries a negative net charge at neutral pH, and it is suggested that the binding occurs between the negative charges of the GAG sulphate groups and a structure in the C-terminal end of the enzyme that has a cluster of positive charges. These results are compatible with the notion that heparan sulphate proteoglycans on cell surfaces or in the intercellular matrix may serve to bind EC-SOD C in tissues.
Stereoselective synthesis of α-L-Fucp-(1,2)- and -(1,3)-β-D-Galp(1)-4-methylumbelliferone using glycosyl donor substituted by propane-1,3-diyl phosphate as leaving group (2000)

The synthesis of the disaccharides α-L-Fucp-(1,2)- and α-L-Fucp-(1,3)-β-D-Galp(1)-4-methylumbelliferone as fucosidase substrates was accomplished by activation of the anomeric centre of 2,3,4-tri-O-acetyl- and 2,3,4,6-tetra-O-acetyl-α,β-L-fuco- and -D-galactopyranosyl propane-1,3-diyl phosphates with TMSOTf and with minimal protection of 4-methylumbelliferyl β-D-galactopyranoside.
Unusual Chromatin in Human Telomeres (1994)

We report that human telomeres have an unusual chromatin structure characterized by diffuse micrococcal nuclease patterns. The altered chromatin manifested itself only in human telomeres that are relatively short (2 to 7 kb). In contrast, human and mouse telomeres with telomeric repeat arrays of 14 to 150 kb displayed a more canonical chromatin structure with extensive arrays of tightly packed nucleosomes. All telomeric nucleosomes showed a shorter repeat size than bulk nucleosomes, and telomeric mononucleosomal particles were found to be hypersensitive to micrococcal nuclease. However, telomeric nucleosomes were similar to bulk nucleosomes in the rate at which they sedimented through sucrose gradients. We speculate that mammalian telomeres have a bipartite structure with unusual chromatin near the telomere terminus and a more canonical nucleosomal organization in the proximal part of the telomere.
Permeation of Aromatic Hydrocarbon Vapors through Silicalite−Zeolite Membranes (1996)

Vapor permeances of pure aromatics through silicalite zeolite membranes follow the relative order m-xylene > p-xylene > benzene ≈ toluene > ethylbenzene ≈ o-xylene near 380 K with permeance ratios as high as 20. This trend does not follow the size order of the kinetic diameters, and therefore the kinetic diameter is not the determining factor for the permeation. Activation energies for the aromatics varied from 13 to 57 kJ/mol. In binary and ternary mixtures, the faster permeating compounds were slowed to rates similar to slower permeating molecules, and thus no separation was obtained for any mixture. These findings are consistent with single file transport, where all molecules have equal chances of entering the pores, but they cannot pass each other in the narrow channels and the slowest species determines the permeation rates.
Anomalous Coiling of SiGe/Si and SiGe/Si/Cr Helical Nanobelts (2006)

The fabrication of nanohelices by the scrolling of strained bilayers is investigated. It is shown that structure design is dominated by edge effects rather than bulk crystal properties such as the Young's modulus when the dimensions of the structures are reduced below 400 nm. SiGe/Si/Cr, SiGe/Si, and Si/Cr helical nanobelts are used as test structures. Dimensions of the belt width are reduced from 1.30 microm to 300 nm, and parameters controlling helicity angle, chirality, diameter, and pitch of the nanohelices are investigated. An anomalous scrolling direction deviating from the preferred <100> scrolling direction has been found for small structures. Making use of the anomalous scrolling, it is possible to fabricate three-dimensional helices with helicity angles less than 45 degrees , which is advantageous for micro- and nanoelectromechanical systems.
A microchip for nucleic acid isolation and enrichment (2012)

This paper presents a microchip that effectively isolates and enriches target-binding single-stranded DNA (ssDNA) in a randomized DNA mixture using solid-phase extraction (SPE) and electrophoresis. The microchip consists of isolation and enrichment microchambers that are connected by a microchannel partially filled with agarose gel. Single-stranded DNA oligomers in the randomized mixture are captured via specific binding onto human immunoglobulin E (IgE) that is immobilized on microbeads in the isolation chamber. Following elution, the oligomers are separated from impurities via electrophoretic transport through the gel-filled microchannel to the enrichment chamber. Experimental results show that this approach can enhance the sensitivity of ssDNA detection methods in dilute and complex biological samples.
Energy-efficient communication in battery-constrained portable devices (2005)

Portable devices (such as personal digital assistants and laptops with wireless connectivity) are becoming ubiquitous. As their functionality and capabilities increase, their energy consumption requirements also increase. Yet, these devices have to operate on limited batteries. In order to maximize the battery lifetime, it is necessary to optimize the use of energy at various components of such a device. In this paper, we consider a single portable device operating on a limited battery that transmits information over an interference-limited wireless channel. We seek to optimize the power consumption on the communication radio in this device, by controlling both the operation mode and the transmission power. We model the general problem using dynamic programming, obtain the optimal solutions for insightful special cases and explore various design tradeoffs. Our work provides an analytical framework for stochastic modeling and optimization of energy spent for communications in battery-operated portable devices.
Giving advice about preferred actions to reinforcement learners via knowledge-based kernel regression (2005)

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Presence of the Plasma Membrane Proteolipid (Plasmolipin) in Myelin (1990)

Plasma membrane proteolipid (plasmolipin), which was originally isolated from kidney membranes, has also been shown to be present in brain. In this study, we examined the distribution of plasmolipin in brain regions, myelin, and oligodendroglial membranes. Immunoblot analysis of different brain regions revealed that plasmolipin levels were higher in regions rich in white matter. Plasmolipin was also detected in myelin, myelin subfractions, and oligodendroglial membranes. Immunocytochemical analysis of the cerebellum revealed that plasmolipin was localized in the myelinated tracts. Plasmolipin levels in myelin were enriched during five successive cycles of myelin purification, similar to the enrichment of myelin proteolipid apoprotein (PLP) and myelin basic protein (MBP). In contrast, levels of Na+,K(+)-ATPase and a 70-kDa protein were decreased. When myelin or white matter was extracted with chloroform/methanol, it contained, in addition to PLP, a significant amount of plasmolipin. Quantitative immunoblot analysis suggested that plasmolipin constitutes in the range of 2.2-4.8% of total myelin protein. Plasmolipin, purified from kidney membranes, was detected by silver stain on gels at 18 kDa and did not show immunological cross-reactivity with either PLP or MBP. Thus, it is concluded that plasmolipin is present in myelin, possibly as a component of the oligodendroglial plasma membrane, but is structurally and immunologically different from the previously characterized myelin proteolipids.
Anti-4-1BB monoclonal antibody enhances rejection of large tumor burden by promoting survival but not clonal expansion of tumor-specific CD8+ T cells. (2002)

Anti-4-1BB monoclonal antibody (mAb) has been shown to induce antitumor immunity by a CD4/CD8-dependent mechanism, but its direct effect on tumor-specific CD8+ T cells in tumor rejection is unclear. Here we used transgenic CD8+ T cells against the unmutated tumor rejection antigen P1A to analyze whether this mAb can promote CD8+ T-cell function against large tumors in the absence of CD4+ T-helper cells. RAG-2(-/-) mice were challenged with P1A-expressing plasmacytoma J558. Once tumor size reached a diameter of 0.85-1.75 cm, mice were treated with P1A-specific CD8+ CTL (P1CTL) in conjunction with anti-4-1BB mAb or control IgG. All of the mice showed a partial regression of tumor, but mice treated with anti-4-1BB mAb exhibited markedly enhanced tumor rejection, delayed tumor progression, and prolonged survival. Correspondingly, we observed a substantial increase in the number of P1CTL in anti-4-1BB mAb-treated mice. Surprisingly, anti-4-1BB mAb did not accelerate division of the tumor-specific CD8+ T cells, and the increase in tumor-specific T-cell number was due to reduced activation-induced cell death. These results indicate that anti-4-1BB mAb can promote CD8+ T cell-mediated protection against large tumors in the absence of CD4+ T-cell help by promoting P1CTL survival without increasing initial clonal expansion.
The estrogen receptor influences microtubule-associated protein tau (MAPT) expression and the selective estrogen receptor inhibitor fulvestrant downregulates MAPT and increases the sensitivity to taxane in breast cancer cells (2010)

Expression of MAPT protein isoforms of less than 70 kDa is correlated with a low sensitivity to taxanes in breast cancer cells. ER influences MAPT expression and fulvestrant increases the sensitivity to taxanes in MAPT- and ER-positive breast cancer cells.
Application of the Back Propagation Neural Network Algorithm with Monotonicity Constraints for Two‐Group Classification Problems* (1993)

ABSTRACT Neural network techniques are widely used in solving pattern recognition or classification problems. However, when statistical data are used in supervised training of a neural network employing the back‐propagation least mean square algorithm, the behavior of the classification boundary during training is often unpredictable. This research suggests the application of monotonicity constraints to the back propagation learning algorithm. When the training sample set is preprocessed by a linear classification function, neural network performance and efficiency can be improved in classification applications where the feature vector is related monotonically to the pattern vector. Since most classification problems in business possess monotonic properties, this technique is useful in those problems where any assumptions about the properties of the data are inappropriate.
Polarized Raman studies of crystalline and amorphous orientation in polyethylene (1978)

Abstract Polarized Raman intensities have been obtained from thin films of oriented low‐density polyethylene (PE) immersed in silicone oil to minimize surface scattering. Studies were made using the 1170 cm −1 crystalline band and the 1081 cm −1 amorphous band, and from these the orientation averages 〈cos 2 θ〉 and 〈cos 4 θ〉 were calculated. These were found to compare favorably with the values of 〈cos 2 θ〉 for the polymer chain in the crystalline and amorphous phases obtained from measurements of infrared dichroism. Both orientation averages could be theoretically fitted by using reasonable parameters.
Low density lipoprotein receptor-related protein and gp330 bind similar ligands, including plasminogen activator-inhibitor complexes and lactoferrin, an inhibitor of chylomicron remnant clearance. (1992)

The low density lipoprotein receptor-related protein/alpha 2-macroglobulin receptor (LRP) and gp330, two members of the low density lipoprotein receptor gene family, share a multitude of cysteine-rich repeats. LRP has been shown to act as an endocytosis-mediating receptor for several ligands, including protease-antiprotease complexes and plasma lipoproteins. The former include alpha 2-macroglobulin-protease complexes and plasminogen activator inhibitor-activator complexes. The latter include chylomicron remnant-like particles designated beta-very low density lipoproteins (beta-VLDL) complexed with apoprotein E or lipoprotein lipase. The binding specificity of gp330 is unknown. In the current studies we show that gp330 from rat kidney membranes binds several of these ligands on nitrocellulose blots. We also show that both LRP and gp330 bind an additional ligand, bovine lactoferrin, which is known to inhibit the hepatic clearance of chylomicron remnants. Lactoferrin blocked the LRP-dependent stimulation of cholesteryl ester synthesis in cultured human fibroblasts elicited by apoprotein E-beta-VLDL or lipoprotein lipase-beta-VLDL complexes. Cross-competition experiments in fibroblasts showed that the multiple ligands recognize at least three distinct, but partially overlapping sites on the LRP molecule. Binding of all ligands to LRP and gp330 was inhibited by the 39-kDa protein, which co-purifies with the two receptors, suggesting that the 39-kDa protein is a universal regulator of ligand binding to both receptors. The correlation of the inhibitory effects of lactoferrin in vivo and in vitro support the notion that LRP functions as a chylomicron remnant receptor in liver. LRP and gp330 share a multiplicity of binding sites, and both may function as endocytosis-mediating receptors for a large number of ligands in different organs.