gebhart/patrepeval huggingface dataset:
Inhibition of cancer cell urokinase plasminogen activator by its specific inhibitor PAI-2 and subsequent effects on extracellular matrix degradation. (1990)

Isotopically labeled [( 3H]serine, [3H]proline, and [35S]sulfate) subendothelial cell basement membranes were used to determine the role of urokinase plasminogen activator (uPA) and its specific inhibitor plasminogen activator inhibitor 2 (PAI-2) in colon cancer cell extracellular matrix degradation. Recombinant PAI-2 irreversibly inhibited low and high molecular weight purified human uPA in addition to both colon cancer cell-associated and secreted uPA, particularly if pro-uPA had been preactivated. Two selected lines (COLO394 and LIM1215) preferentially degraded differently labeled matrices in a time- and plasminogen-dependent manner. This process was inhibitable by PAI-2 in the medium at levels which suggested that some degree of "shielding" of cell surface uPA from inhibitor occurred. The ability of PAI-2 to regulate the invasive phenotype of cells which express cell surface or receptor-bound uPA is discussed.
XX true hermaphroditism in southern African blacks: an enigma of primary sexual differentiation. (1988)

A high incidence of 46,XX true hermaphroditism exists among southern African blacks. The gonadal distribution and clinical presentation of 38 patients are described. The aim of our study on 11 families with histologically proven XX true hermaphroditism was to determine whether a common genetic or environmental etiology could be identified. Pedigree analysis excluded the presence of a simple inheritance pattern, and no constant environmental factors could be implicated. Hybridization studies with Y chromosome--specific probes (pDP132, pDP61, pDP105, pDP31, pDP97, and pY431-HinfA) excluded the presence of a large portion of Yp in these patients. It is possible that smaller portions of the Y chromosome or one or more X-linked or autosomal mutations, either interacting and/or with incomplete penetrance, are present.
Similarity of Neuronal Cell Injury and Death in AIDS Dementia and Focal Cerebral Ischemia: Potential Treatment with NMDA Open‐Channel Blockers and Nitric Oxide‐Related Species (1996)

Using in vitro models, our laboratory in collaboration with those of Pierluigi Nicotera (University of Konstanz, Germany) and Stan Orrenius (Karolinska Institute) has recently shown that fulminant insults to the nervous system from excitotoxins or free radicals result in neuronal cell death from necrosis, while more subtle insults result in delayed apoptosis. Over the past dozen or so years, mounting evidence has suggested that excitotoxins, such as glutamate, result in neuronal cell death after stroke. More recent evidence has suggested that in addition to necrotic cell death in the ischemic core, a number of neurons may also undergo apoptosis. Thus, the hypothesis that intense injury leads to necrosis while mild insult (perhaps in the penumbra) leads to apoptosis may hold in focal cerebral ischemia. Another neurological malady with mounting evidence for a pathogenesis that is mediated at least in part by excitotoxins is HIV-1-associated cognitive/motor complex (originally termed the AIDS Dementia Complex and, for convenience, designated here AIDS dementia). AIDS dementia appears to be associated with several neuropathological abnormalities, including giant cell formation by microglia, astrogliosis, and neuronal injury or loss. Recently, neuronal and other cell injury in AIDS brains has been shown to result in apoptotic-like cell death. How can HIV-1 result in neuronal damage if neurons themselves are only rarely, if ever, infected by the virus? Experiments from several different laboratories, including our group in collaboration with that of Howard Gendelman (University of Nebraska Medical Center), have lent support to the existence of HIV- and immune-related toxins in a variety of in vitro and in vivo paradigms. In one recently defined pathway to neuronal injury, HIV-infected macrophages/ microglia as well as macrophages activated by HIV-1 envelope protein gp120 appear to secrete excitants/ neurotoxins. These substances may include arachidonic acid, platelet-activating factor, free radicals (NO. and O2.-), glutamate, quinolinate, cysteine, cytokines (TNF-alpha, IL1-beta, IL-6), amines, and as yet unidentified factors emanating from stimulated macrophages and possibly reactive astrocytes. A final common pathway for neuronal susceptibility appears to be operative, similar to that observed in stroke and several neurodegenerative diseases. This mechanism involves excessive activation of N-methyl-D-aspartate (NMDA) receptor-operated channels, with resultant excessive influx of Ca2+ and the generation of free radicals, leading to neuronal damage. With the very recent development of clinically-tolerated NMDA antagonists, as discussed here, there is hope for future pharmacological intervention.
Reactive ion etching of silicon using bromine containing plasmas (1990)

The characteristics of Si and SiO2 etching in HBr reactive ion etching plasmas have been studied by measuring etch rates, optical emission, scanning electron microscopy (SEM) cross-sectional analysis, and x-ray photoelectron spectroscopy (XPS). Etch rate measurements indicate that SiO2 is etched very slowly compared with Si, so that the Si/SiO2 etch selectivity may be as high as 400. Optical emission spectroscopy has been used to examine the gas phase species in the plasma, and emission from excited atomic bromine has been identified. The composition and thickness of reaction layers on silicon surfaces resulting from exposure to HBr plasmas has been obtained by XPS. It is found that the reaction layer on silicon due to HBr reactive ion etching is typically very thin, of the order of 1 monolayer thick. XPS has also been used to investigate the reaction layers on the sidewalls of etched trenches, and a thin oxidized layer has been detected for oxide-masked Si trench etching.
Valve Morphogenesis in the Diatom Genus Pleurosigma W. Smith(Bacillariophyceae): Nature's Alternative Sandwich (2005)

The loculate ("chambered") valve structure of centric diatoms like Triceratium favus Ehrenberg has been mentioned time and again in the nanostructure literature. Here we draw attention to the fundamentally different alternative sandwich model nature developed in the genus Pleurosigma, where it is nonloculate. This has so far been overlooked in nanostructural studies. We suggest some mechanical aspects that would offer interesting avenues for experimental testing. The first description of the natural fabrication process ("morphogenesis") is presented. This begins with the development of the raphe sternum, which then acts as a rigid backbone. The inner layer of the sandwich-structured valve develops next, with relatively large +/- round single internal foramina not yet closed by a sieve membrane, in offset arrangement. This serves as a substrate for rows of stubby hollow pillars, also in offset arrangement. Then the outer layer of the sandwich develops and two different patterns ("coarse-mesh" and "stellate bridges") have been observed. At first, the external areolar foramina are relatively large and +/- oval, gradually filling up until the tiny slits characteristic of the genus remain. In Pleurosigma species with double internal areolar foramina, small bridges grow from the opposite margins of the single foramina until they fuse. The sieve-membranes then close the internal areolar foramina. The finished valve is a lightweight structure expected to offer excellent strength with parsimonious expenditure of the raw material-silica.
EBV peptide epitope sensitization restores human cytotoxic T cell recognition of Burkitt’s lymphoma cells. Evidence for a critical role for ICAM-2 (1993)

The pathogenesis of EBV+ Burkitt's lymphoma (BL) suggests evasion of the CTL response against EBV. Two important features of this tumor have been previously suggested to explain this immune evasion, (a) absence/low expression of cellular adhesion molecules and (b) restricted expression of EBV latent Ag. To determine the relative importance of these features in relation to evasion of EBV-specific CTL, a group of BL cell lines with variable expression of the aforementioned phenotypic characteristics were assayed for specific CTL lysis after exogenous addition of EBV peptide epitopes. In spite of down-regulated expression of the adhesion molecules LFA-1, LFA-3, and/or ICAM-1, peptide-sensitized BL cells were recognized and lysed by EBV-specific CTL. Moreover, there was no significant difference between the CTL lysis of the BL cells and that of adhesion molecule-positive control cells over a wide range of peptide epitope concentrations. Blocking experiments with mAb to individual adhesion molecules suggested that virus-specific CTL recognition of lymphoblastoid cell lines was dependent on an intact LFA-3/CD2 pathway. In contrast, the CTL recognition of peptide-sensitized BL cells was critically dependent on the LFA-1/ICAM pathway, with an insignificant contribution by CD2/LFA-3. The consistently high expression of ICAM-2 on all BL cell lines suggests that the accessory function in CTL recognition of these cells is mediated by the LFA-1/ICAM-2 pathway. Thus, down-regulation of LFA-1, LFA-3, and/or ICAM-1 expression on BL cells does not provide an absolute barrier to tumor cell recognition by virus-specific CTL. The ability of virus-specific CTL to recognize peptide epitope-sensitized BL cells as efficiently as normal cells has demonstrated the importance of latent Ag expression in the CTL control of EBV+ tumors.
Design of Liquid Crystalline Block Molecules with Nonconventional Mesophase Morphologies:  Calamitic Bolaamphiphiles with Lateral Alkyl Chains (2001)

Novel bolaamphiphiles, consisting of a biphenyl rigid core, polar 2,3-dihydroxypropoxy groups at each terminal end, and an additional long alkyl chain in a lateral position have been synthesized. The structures of these ternary block molecules were systematically changed by variation of the length and position of the alkyl chain, by introduction of additional spacer units between one of the 2,3-dihydroxypropyl groups and the rigid core, and by replacement of one of the 2,3-dihydroxypropoxy groups by a single hydroxy group. The influence of these structural variations on the liquid crystalline properties of these new materials was investigated by polarized-light microscopy, differential scanning calorimetry, and X-ray diffraction. These investigation have shown that, by elongation of the lateral chain, a transition from a smectic monolayer structure (SmA1) via a strongly distorted layer structure (SmA+), a centered rectangular columnar phase (Colr/c2mm) and a noncentered rectangular columnar phase (Colr/p2gg) to a hexagonal columnar phase (Colh/p6mm) takes place. Elongation of the bolaamphiphilic core leads to the loss of the columnar phases, which are replaced by smectic phases, whereas reduction of its length favors the hexagonal columnar phase. This phase sequence is explained as a result of the microsegregation of the lateral alkyl chains from the rigid aromatic cores. The segregated alkyl chains are organized in columns that interrupt the smectic layers. The hydrogen bonding keep the bolaamphiphilic cores fixed end to end, so that they form networks of cylinders around the lipophilic columns. The space required by the alkyl chains with respect to the length of the bolaamphiphilic cores is restricted and largely determines the geometry of the cylinders, which leads to the observed phase sequence. The obtained mesophase morphologies, built up by three distinct sets of subspaces, are related to morphologies of some ternary block copolymers. Furthermore, the investigated compounds represent a novel class of materials, capable of forming supramolecular columnar mesophases.
All-plastic miniature fluorescence microscope for point-of-care readout of bead-based bioassays (2015)

A number of new platforms have been developed for multiplexed bioassays that rely on imaging targeted fluorescent beads labeled with different fluorescent dyes. We developed a compact, low-cost three-dimensional printed fluorescence microscope that can be used as a detector for mutiplexed, bead-based assays to support point-of-care applications. Images obtained with the microscope were analyzed to differentiate multiple analytes in a single sample with a comparable limit of detection to commercially available macroscopic assay platforms.
Characterization of Non-peptide Antagonist and Peptide Agonist Binding Sites of the NK1 Receptor with Fluorescent Ligands (1997)

Ligand recognition of the NK1 receptor (substance P receptor) by peptide agonist and non-peptide antagonist has been investigated and compared by the use of fluorescent ligands and spectrofluorometric methods. Analogues of substance P (SP) labeled with the environment-sensitive fluorescent group 5-dimethylaminonaphthalene-1-sulfonyl (dansyl) at either position 3, 8, or 11 or with fluorescein at the Nalpha position were synthesized and characterized. Peptides modified at the alpha-amino group or at positions 3 or 11 conserved a relatively good affinity for NK1 and agonistic properties. Modification at position 8 resulted in an 18, 000-fold decrease in affinity. A fluorescent dansyl analogue of the non-peptide antagonist CP96,345 was prepared and characterized. The quantum yield of fluorescence for dansyl-CP96,345 was much higher than for any of the dansyl-labeled peptides indicating that the micro-environment of the binding site is more hydrophobic for the non-peptide antagonist than for the peptide agonists. Comparison of collisional quenching of fluorescence by the water-soluble hydroxy-Tempo compound showed that dansyl-CP96,345 is buried and virtually inaccessible to aqueous quenchers, whereas dansyl- or fluoresceinyl-labeled peptides were exposed to the solvent. Anisotropy of all fluorescent ligands increased upon binding to NK1 indicating a restricted motional freedom. However, this increase in anisotropy was more pronounced for the dansyl attached to the non-peptide antagonist CP96,345 than for the fluorescent probes attached to different positions of SP. In conclusion, our data indicate that the environment surrounding non-peptide antagonist and peptide agonists are vastly different when bound to the NK1 receptor. These results support recent observations by mutagenesis and cross-linking work suggesting that peptide agonists have their major interaction points in the N-terminal extension and the loops forming the extracellular face of the NK1 receptor. Our data also suggest that neither the C terminus nor the N terminus of SP appears to penetrate deeply below the extracellular surface in the transmembrane domain of the receptor.
A simple and unambiguous definition of threshold voltage and its implications in deep-submicron MOS device modeling (1999)

A new definition of MOSFET threshold voltage is proposed, namely, the "critical-current at linear-threshold" method, which has a unique solution and is very simple to measure. This definition gives consistent values of threshold voltage for different regions of operation at long channel, and contains the information on short-channel effects at short channel, which is very useful for deep-submicron MOS device characterization and modeling. The proposed method effectively removes ambiguity of de facto industry standard of the constant-current method for MOS threshold voltage.
Degradable Poly(amino alcohol esters) As Potential DNA Vectors with Low Cytotoxicity (2003)

The synthesis of a new degradable polymer system, poly(amino alcohol esters) and the resulting polymers' potential for use in gene transfection vectors are reported. The polymerization proceeded in a one step reaction from commercially available bis(secondary amines) monomers (N,N'-dimethyl-1,3-propanediamine and N,N'-dimethyl-1,6-hexanediamine, respectively) through nucleophilic addition to the diglycidyl ester of dicarboxylic acid (diglycidyl adipate). Poly(amino alcohol ester) 1 and 2 were synthesized with a yield of 89% and 91% with Mn = 24,800 and Mn = 36,400, respectively. Poly(amino alcohol ester) 1 degraded hydrolytically in phosphate buffer at pH 7.4 with a half-life of approximately 5 days. Both polymers readily self-assembled with plasmid DNA into nanometer-sized DNA/polymer complexes less than 180 nm diameter and are significantly less cytotoxic than the commonly used DNA delivery polymer, poly(ethylene imine) (PEI).
Laminins and human disease (2000)

The laminin protein family has diverse tissue expression patterns and is involved in the pathology of a number of organs, including skin, muscle, and nerve. In the skin, laminins 5 and 6 contribute to dermal-epidermal cohesion, and mutations in the constituent chains result in the blistering phenotype observed in patients with junctional epidermolysis bullosa (JEB). Allelic heterogeneity is observed in patients with JEB: mutations that results in premature stop codons produce a more severe phenotype than do missense mutations. Gene therapy approaches are currently being studied in the treatment of this disease. A blistering phenotype is also observed in patients with acquired cicatricial pemphigoid (CP). Autoantibodies targeted against laminins 5 and 6 destabilize epithelial adhesion and are pathogenic. In muscle cells, laminin alpha 2 is a component of the bridge that links the actin cytoskeleton to the extracellular matrix. In patients with laminin alpha 2 mutations, the bridge is disrupted and mature muscle cells apoptose. Congenital muscular dystrophy (CMD) results. The role of laminin in diseases of the nervous system is less well defined, but the extracellular protein has been shown to serve an important role in peripheral nerve regeneration. The adhesive molecule influences neurite outgrowth, neural differentiation, and synapse formation. The broad spatial distribution of laminin gene products suggests that laminin may be involved in a number of diseases for which pathogenic mechanisms are still being unraveled.
Electrospinning of nanofibers (2005)

Abstract Nanotechnology is the study and development of materials at nano levels. It is one of the rapidly growing scientific disciplines due to its enormous potential in creating novel materials that have advanced applications. This technology has tremendously impacted many different science and engineering disciplines, such as electronics, materials science, and polymer engineering. Nanofibers, due to their high surface area and porosity, find applications as filter medium, adsorption layers in protective clothing, etc. Electrospinning has been found to be a viable technique to produce nanofibers. An in‐depth review of research activities on the development of nanofibers, fundamental understanding of the electrospinning process, and properties of nanostructured fibrous materials and their applications is provided in this article. A detailed account on the type of fibers that have been electrospun and their characteristics is also elaborated. It is hoped that the overview article will serve as a good reference tool for nanoscience researchers in fibers, textiles, and polymer fields. Furthermore, this article will help with the planning of future research activities and better understanding of nanofiber characteristics and their applications. © 2005 Wiley Periodicals, Inc. J Appl Polym Sci 96: 557–569, 2005
Evidence against the Rescue of Defective ΔF508-CFTR Cellular Processing by Curcumin in Cell Culture and Mouse Models (2004)

Curcumin, the yellow colored component of the spice turmeric, has been reported to rescue defective DeltaF508-cystic fibrosis transmembrane conductance regulator (CFTR) cellular processing in homozygous mutant mice, restoring nasal potential differences and improving survival (Egan, M. E., Pearson, M., Weiner, S. A., Rajendran, V., Rubin, D., Glockner-Pagel, J., Canny, S., Du, K., Lukacs, G. L., and Caplan, M. J. (2004) Science 304, 600-602). Because of the implied potential use of curcumin or similar compounds in the therapy of cystic fibrosis caused by the DeltaF508 mutation, we tried to reproduce and extend the pre-clinical data of Egan et al. Fluorometric measurements of iodide influx in Fischer rat thyroid cells expressing DeltaF508-CFTR showed no effect of curcumin (1-40 microm) when added for up to 24 h prior to assay in cells grown at 37 degrees C. Controls, including 27 degrees C rescue and 4 mm phenylbutyrate at 37 degrees C, were strongly positive. Also, curcumin did not increase short circuit current in primary cultures of a human airway epithelium homozygous for DeltaF508-CFTR with a 27 degrees C rescue-positive control. Nasal potential differences in mice were measured in response to topical perfusion with serial solutions containing amiloride, low Cl-, and forskolin. Robust low Cl- and forskolin-induced hyperpolarization of 22 +/- 3 mV was found in wild type mice, with 2.1 +/- 0.4 mV hyperpolarization in DeltaF508 homozygous mutant mice. No significant increase in Cl-/forskolin hyperpolarization was seen in any of the 22 DeltaF508 mice studied using different curcumin preparations and administration regimens, including that used by Egan et al. Assay of serum curcumin by ethyl acetate extraction followed by liquid chromatography/mass spectrometry indicated a maximum serum concentration of 60 nm, well below that of 5-15 microm, where cellular effects by sarcoplasmic/endoplasmic reticulum calcium pump inhibition are proposed to occur. Our results do not support further evaluation of curcumin for cystic fibrosis therapy.
Increasing the thermostability of d-xylose isomerase by introduction of a proline into the turn of a random coil (1999)

Thermostability can be increased by introducing prolines at suitable sites in target proteins. Two single (G138P, G247D) mutants and one double (G138P/G247D) mutant of xylose isomerase from Streptomyces diastaticus No.7, strain M1033 have been constructed by site-directed mutagenesis. With respect to the wild-type enzyme, G138P showed about a 100% increase in thermostability, and G247D showed an increased catalytic activity. Significantly, the double mutant, G138P/G247D displayed even higher activity than G247D and better heat stability than G138P. Its half life was about 2.5-fold greater than the wild-type enzyme, using xylose as a substrate. Molecular modelling suggested that the introduction of a proline residue in the turn of a random coil may cause the surrounding conformation to be tightened by reducing the backbone flexibility. The change in thermostability can, therefore, be explained based on changes in the molecular rigidity. Furthermore, the improvements in the properties of the double mutant indicated that the advantages of two single mutants can be combined effectively.