gebhart/patrepeval huggingface dataset:
The urokinase receptor (uPAR) and the uPAR-associated protein (uPARAP/ Endo180): membrane proteins engaged in matrix turnover during tissue remodeling (2004)

The breakdown of the barriers formed by extracellular matrix proteins is a pre-requisite for all processes of tissue remodeling. Matrix degradation reactions take part in specific physiological events in the healthy organism but also represent a crucial step in cancer invasion. These degradation processes involve a highly organized interplay between proteases and their cellular binding sites as well as specific substrates and internalization receptors. This review article is focused on two components, the urokinase plasminogen activator receptor (uPAR) and the uPAR-associated protein (uPARAP, also designated Endo180), that are considered crucially engaged in matrix degradation. uPAR and uPARAP have highly diverse functions, but on certain cell types they interact with each other in a process that is still incompletely understood. uPAR is a glycosyl-phosphatidylinositol-anchored glycoprotein on the surface of various cell types that serves to bind the urokinase plasminogen activator and localize the activation reactions in the proteolytic cascade system of plasminogen activation. uPARAP is an integral membrane protein with a pronounced role in the internalization of collagen for intracellular degradation. Both receptors have additional functions that are currently being unraveled. The present discussion of uPAR and uPARAP is centered on their protein structure and molecular and cellular function.
Hepatocyte nuclear factor 3 alpha belongs to a gene family in mammals that is homologous to the Drosophila homeotic gene fork head. (1991)

By analysis of cDNA clones that cross-hybridized with a portion of the cDNA encoding the recently described rat protein hepatocyte nuclear factor 3 alpha (HNF-3 alpha, previously called HNF-3A), we now describe two additional members, HNF-3 beta and HNF-3 gamma, of this gene family. A 110-amino-acid region in the DNA-binding domain of this family is not only very highly conserved in rodents (HNF-3 alpha, -3 beta, and -3 gamma are identical in 93 of 110 amino acids in this region) but also in Drosophila where the homeotic gene fork head has 88 of the 93 residues that are identical in the three rat genes. The HNF-3 family in rodents is expressed in cells that derive from the lining of the primitive gut; some of the embryonic Drosophila cells in which fork head is expressed also give rise to gut and salivary glands. Thus, it appears that this gene family, the DNA-binding portion of which is unlike that of any previously recognized DNA-binding proteins, may contribute to differentiation of cells in internal organs in both vertebrates and invertebrates.
Applications of color mixing models to electronic printing (1994)

The purpose of this study is to obtain some quantitative measures for the applicability of several color mixing models to a halftone printer. The printer, a Canon Color Laser Copier 500 (CLC-500), is treated as a black box and the measures are the difference between the calculated and measured spectra and Δ<i>E<sub>ab</sub></i>. Well-known color mixing theories of the Neugebauer equations, Yule-Nielsen model (YN), Clapper-Yule multiple internal reflections (CY), Beer-Bouguerlaw (BB), and Kubelka-Munk theories (KM) are applied to CLC-500 to see how well they can fit the experimental data. Results indicate that the spectral 8-color Neugebauer model has marginal success in fitting the experimental data and the relaxed 3-color version does not fit the data weli. Both YN and CY approaches can fit the data within printer variability. The fittings are rather poor for BB and KM. By using the halftone correction factor, good agreements are obtained for the BB and single-constant KM.
Insulin stimulates glyceraldehyde-3-phosphate dehydrogenase gene expression through cis-acting DNA sequences. (1988)

Glyceraldehyde-3-phosphate dehydrogenase [GAPDH; D-glyceraldehyde-3-phosphate:NAD+ oxidoreductase (phosphorylating), EC 1.2.1.12] mRNA levels are induced by physiologic concentrations of insulin in cultured 3T3-F442A adipocyte and H35 hepatoma cell lines. To examine the mechanism by which insulin regulates GAPDH mRNA levels in these two insulin-sensitive tissues, we have isolated a functional human GAPDH gene. When stably transfected and expressed in 3T3-F442A preadipocytes and H35 hepatoma cells, the intact human GAPDH gene is induced 10-fold by insulin in 3T3-F442A adipocytes and 3-fold by insulin in H35 hepatoma lines, which is similar to the induction obtained with the endogenous gene. A human GAPDH-chloramphenicol acetyltransferase construct, containing sequences -487 to +20 of the human gene fused to the chloramphenicol acetyltransferase gene, is regulated by insulin in stably transfected 3T3 adipocytes and stably or transiently transfected H35 hepatoma cell lines, whereas the Rous sarcoma virus-chloramphenicol acetyltransferase fusion protein is not. Thus, the inductive effect of insulin on human GAPDH gene expression is mediated through cis-acting sequences located between -487 and +20 of the human GAPDH gene.
Distributed PMD measurement with a polarization-OTDR in optical fibers (1999)

This paper presents a new method for the measurement of distributed polarization mode dispersion (PMD) in optical fibers. This method uses a polarization optical time-domain reflectometer (P-OTDR), and is based on a measurement of the degree of polarization of the backscattered light as a function of distance in the fiber. Both the average and the statistics of the degree of polarization are used to estimate the two relevant parameters for measuring PMD, namely, the beat length and the coupling length. At present, our P-OTDR gives qualitative results only. However, it enables to distinguish between high and low PMD sections in a long fiber link. This should already have practical applications, in particular for the characterization of installed fibers.
Evaluation of urovysion and cytology for bladder cancer detection (2013)

BACKGROUND Urine cytology has been used for screening of bladder cancer but has been limited by its low sensitivity. UroVysion is a multiprobe fluorescence in situ hybridization (FISH) assay that detects common chromosome abnormalities in bladder cancers. For this study, the authors evaluated the effectiveness of multiprobe FISH and urine cytology in detecting urothelial cell carcinoma (UCC) in the same urine sample. METHODS In total, 1835 cases with the following criteria were selected: valid results from both the multiprobe FISH assay and urine cytology in the same urine sample, histologic and/or cystoscopic follow‐up within 4 months of the original tests, or at least 3 years of clinical follow‐up information. The results of FISH and cytology were correlated with clinical outcomes derived from a combination of histologic, cystoscopic, and clinical follow‐up information. RESULTS Of 1835 cases, 1045 cases were from patients undergoing surveillance of recurrent UCC, and 790 were for hematuria. The overall sensitivity, specificity, positive predictive value, and negative predictive value in detecting UCC were 61.9%, 89.7%, 53.9%, and 92.4%, respectively, for FISH and 29.1%, 96.9%, 64.4%, and 87.5%, respectively, for cytology. The performance of both FISH and cytology generally was better in the surveillance population and in samples with high‐grade UCC. In 95 of 296 cases with atypical cytology that were proven to have UCC, 61 cases, mostly high‐grade UCC, were positive using the multiprobe FISH assay. CONCLUSIONS The UroVysion multiprobe FISH assay was more sensitive than urine cytology in detecting UCC, but it produced more false‐positive results. The current data suggest that the use of FISH as a reflex test after an equivocal cytologic diagnosis may play an effective role in detecting UCC. Cancer (Cancer Cytopathol) 2013;121:591–597. © 2013 American Cancer Society.
Pharmacokinetics of pterostilbene inSprague‐Dawley rats: The impacts of aqueous solubility, fasting, dose escalation, and dosing route on bioavailability (2013)

Aqueous solubility was identified as a barrier to its oral bioavailability while solubilizing PTS with HP-β-CD substantially increased its bioavailability; dose manipulation was a practical strategy to enhance its bioavailability and systemic exposure; and its delivery through oral mucosa was feasible. As PTS possessed superior pharmacokinetics, it is a favorable candidate for further development.
Role of endothelium and hypercholesterolemia in intimal thickening and lipid accumulation. (1979)

In experiments reported here we tested the hypothesis that persistent absence of endothelium favors intimal thickening, lipid accumulation, and atherosclerosis. Rabbit aortas were de-endothelialized with a balloon catheter at Day 0. Initially, all rabbits were fed a diet low in lipid. Some rabbits (Group I) were continued on a diet low in lipid for 8 to 20 weeks after de-endothelialization. Beginning 4 to 9 weeks after de-endothelialization, other rabbits were fed semisynthetic lipid-rich diets (Group II) or cholesterol-supplemented diets (Groups III) for 4 to 20 weeks. Lipid accumulation in all groups was significantly greater in the re-endothelialized intima than in adjacent intima lacking an endothelial lining. In aortas of Groups I, II, and III the degree of intimal thickening was significantly greater in re-endothelialized areas than in adjacent areas lacking endothelium. Intimal thickness was enhanced in re-endothelialized areas of hypercholesterolemic rabbits of Group III compared with normocholesterolemic rabbits of Group I but not in areas lacking endothelium. Thus, results of these experiments do not support the hypothesis that the absence of endothelium particularly favors intimal thickening and intimal lipid accumulation. Results indicate that intima covered by regenerated endothelium is significantly thicker and more likely to accumulate lipid.
Nucleotide sequence and deletion analysis of the xylanase gene (xynZ) of Clostridium thermocellum (1988)

The nucleotide sequence of the xynZ gene, encoding the extracellular xylanase Z of Clostridium thermocellum, was determined. The putative xynZ gene was 2,511 base pairs long and encoded a polypeptide of 837 amino acids. A region of 60 amino acids containing a duplicated segment of 24 amino acids was found between residues 429 and 488 of xylanase Z. This region was strongly similar to the conserved domain found at the carboxy-terminal ends of C. thermocellum endoglucanases A, B, and D. Deletions removing up to 508 codons from the 5' end of the gene did not affect the activity of the encoded polypeptide, showing that the active site was located in the C-terminal half of the protein and that the conserved region was not involved in catalysis. Expression of xylanase activity in Escherichia coli was increased up to 220-fold by fusing fragments containing the 3' end of the gene with the start of lacZ present in pUC19. An internal translational initiation site which was efficiently recognized in E. coli was tentatively identified 470 codons downstream from the actual start codon.
Robotic system for no‐scar gastrointestinal surgery (2008)

Further studies should determine whether this novel device can overcome some of the instrumentation-related challenges that have heretofore limited the development of natural orifice transluminal endoscopic surgery.
Characterization and radiobiologic parameters of medulloblastoma in vitro (1977)

Cultured cells from human medulloblastomas were demonstrated to have distinctive features and a “glial” potential from the morphological and ultrastructural parameters. The in vitro radiobiological survival curve parameters of cultured human medulloblastoma and non-malignant skin fibroblasts obtained under the same conditions of exponential growth were similar. In vitro conditions may underestimate the shoulder region of the survival curve. Since the shoulder region is the most important in clinical fractionated radiotherapy, multiple dose experiments might be useful in examining this portion of the survival curve more closely.
A Novel Bovine Virus Efficiently Transduces Inner Ear Neuroepithelial Cells (2005)

Disruption of the cellular composition or arrangement of the sensory epithelia due to hair cell or supporting cell damage leads to hearing loss and vestibular dysfunctions. These peripheral hearing disorders make good targets for gene therapy; however, development requires efficient gene transfer methods for the inner ear. Here we characterized the cellular tropism of a novel adeno-associated bovine virus vector (BAAV) in cultured rat inner ear epithelia. To help identify transduced cells, we used beta-actin-GFP as a reporter gene. We found that BAAV efficiently transduced auditory and vestibular hair cells as well as all types of supporting cells with no apparent pathological effects. The number of transduced hair cells significantly increased in both a dose- and a time-dependent manner. Transduction was independent of the cells' maturation state and was observed in both P2 and P10 cultures. Interestingly, even after several days of incubation with BAAV, hair cells demonstrated varying progression of beta-actin-GFP incorporation into the stereocilia. This suggests that the onset of viral transduction can occur throughout the course of the experiment. Of the other tested AAVs, AAV2 and AAV5 transduced only a small percentage of inner and vestibular hair cells, respectively, whereas no transduction was detected with AAV4.
Comparative anatomy of the aldo–keto reductase superfamily (1997)

The aldo-keto reductases metabolize a wide range of substrates and are potential drug targets. This protein superfamily includes aldose reductases, aldehyde reductases, hydroxysteroid dehydrogenases and dihydrodiol dehydrogenases. By combining multiple sequence alignments with known three-dimensional structures and the results of site-directed mutagenesis studies, we have developed a structure/function analysis of this superfamily. Our studies suggest that the (alpha/beta)8-barrel fold provides a common scaffold for an NAD(P)(H)-dependent catalytic activity, with substrate specificity determined by variation of loops on the C-terminal side of the barrel. All the aldo-keto reductases are dependent on nicotinamide cofactors for catalysis and retain a similar cofactor binding site, even among proteins with less than 30% amino acid sequence identity. Likewise, the aldo-keto reductase active site is highly conserved. However, our alignments indicate that variation ofa single residue in the active site may alter the reaction mechanism from carbonyl oxidoreduction to carbon-carbon double-bond reduction, as in the 3-oxo-5beta-steroid 4-dehydrogenases (Delta4-3-ketosteroid 5beta-reductases) of the superfamily. Comparison of the proposed substrate binding pocket suggests residues 54 and 118, near the active site, as possible discriminators between sugar and steroid substrates. In addition, sequence alignment and subsequent homology modelling of mouse liver 17beta-hydroxysteroid dehydrogenase and rat ovary 20alpha-hydroxysteroid dehydrogenase indicate that three loops on the C-terminal side of the barrel play potential roles in determining the positional and stereo-specificity of the hydroxysteroid dehydrogenases. Finally, we propose that the aldo-keto reductase superfamily may represent an example of divergent evolution from an ancestral multifunctional oxidoreductase and an example of convergent evolution to the same active-site constellation as the short-chain dehydrogenase/reductase superfamily.
Hormonal Cycle Modulates Arousal Circuitry in Women Using Functional Magnetic Resonance Imaging (2005)

Sex-specific behaviors are in part based on hormonal regulation of brain physiology. This functional magnetic resonance imaging (fMRI) study demonstrated significant differences in activation of hypothalamic-pituitary-adrenal (HPA) circuitry in adult women with attenuation during ovulation and increased activation during early follicular phase. Twelve normal premenopausal women were scanned twice during the early follicular menstrual cycle phase compared with late follicular/midcycle, using negative valence/high arousal versus neutral visual stimuli, validated by concomitant electrodermal activity (EDA). Significantly greater magnitude of blood oxygenation level-dependent signal changes were found during early follicular compared with midcycle timing in central amygdala, paraventricular and ventromedial hypothalamic nuclei, hippocampus, orbitofrontal cortex (OFC), anterior cingulate gyrus (aCING), and peripeduncular nucleus of the brainstem, a network of regions implicated in the stress response. Arousal (EDA) correlated positively with brain activity in amygdala, OFC, and aCING during midcycle but not in early follicular, suggesting less cortical control of amygdala during early follicular, when arousal was increased. This is the first evidence suggesting that estrogen may likely attenuate arousal in women via cortical-subcortical control within HPA circuitry. Findings have important implications for normal sex-specific physiological functioning and may contribute to understanding higher rates of mood and anxiety disorders in women and differential sensitivity to trauma than men.
Proteomics-based Compositional Analysis of Complex Cellulase–Hemicellulase Mixtures (2011)

Efficient deconstruction of cellulosic biomass to fermentable sugars for fuel and chemical production is accomplished by a complex mixture of cellulases, hemicellulases, and accessory enzymes (e.g., >50 extracellular proteins). Cellulolytic enzyme mixtures, produced industrially mostly using fungi like Trichoderma reesei, are poorly characterized in terms of their protein composition and its correlation to hydrolytic activity on cellulosic biomass. The secretomes of commercial glycosyl hydrolase-producing microbes was explored using a proteomics approach with high-throughput quantification using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Here, we show that proteomics-based spectral counting approach is a reasonably accurate and rapid analytical technique that can be used to determine protein composition of complex glycosyl hydrolase mixtures that also correlates with the specific activity of individual enzymes present within the mixture. For example, a strong linear correlation was seen between Avicelase activity and total cellobiohydrolase content. Reliable, quantitative and cheaper analytical methods that provide insight into the cellulosic biomass degrading fungal and bacterial secretomes would lead to further improvements toward commercialization of plant biomass-derived fuels and chemicals.
Quasi-Phase-Matched Faraday Rotation in Semiconductor Waveguides With a Magnetooptic Cladding for Monolithically Integrated Optical Isolators (2013)

Strategies are developed for obtaining nonreciprocal polarization mode conversion, also known as Faraday rotation, in waveguides in a format consistent with silicon-on-insulator or III-V semiconductor photonic integrated circuits. Fabrication techniques are developed using liftoff lithography and sputtering to obtain garnet segments as upper claddings, which have an evanescent wave interaction with the guided light. A mode solver approach is used to determine the modal Stokes parameters for such structures, and design considerations indicate that quasi-phase-matched Faraday rotation for optical isolator applications could be obtained with devices on the millimeter length scale.
Apolipoprotein M - a new biomarker in sepsis (2012)

Sepsis is one of the leading causes of mortality in non-cardiac intensive care units, and the need for markers of progression and severity are high. Also, treatment of sepsis is highly debated and potential new targets of treatment are of great interest. In the previous issue of Critical Care Kumaraswamy and colleagues have investigated whether plasma apolipoprotein M (apoM) is affected during different grades of sepsis, septic shock and systemic inflammatory response syndrome. Interestingly, plasma apoM was significantly decreased in all groups of patients with a relationship to severity of disease. This identifies apoM as a potential new biomarker in sepsis. It also underscores the possibility that altered high-density lipoprotein in sepsis patients can affect the course of disease. Thus, since apoM is the carrier of Sphingosine-1-P (S1P), a molecule with great influence on vascular barrier function, the study presented raises the interest and relevance for further studies of apoM and S1P in relation to sepsis and inflammation.
Fabrication and characterization of solid-state nanopore arrays for high-throughput DNA sequencing (2012)

We report the fabrication and characterization of uniformly sized nanopore arrays, integrated into an optical detection system for high-throughput DNA sequencing applications. Nanopore arrays were fabricated using focused ion beam milling, followed by TiO(2) coating using atomic layer deposition. The TiO(2) layer decreases the initial pore diameter down to the sub-10 nm range, compatible with the requirements for nanopore-based sequencing using optical readout. We find that the TiO(2) layers produce a lower photoluminescence background as compared with the more widely used Al(2)O(3) coatings. The functionality of the nanopore array was demonstrated by the simultaneous optical detection of DNA-quantum dot conjugates, which were electro-kinetically driven through the nanopores. Our optical scheme employs total internal reflection fluorescence microscopy to illuminate a wide area of the TiO(2)-coated membrane. A highly parallel system for observing DNA capture events in a uniformly sized 6 × 6 nanopore array was experimentally realized.
Revised effective ionic radii and systematic studies of interatomic distances in halides and chalcogenides (1976)

The effective ionic radii of Shannon & Prewitt [Acta Cryst. (1969), B25, 925-945] are revised to include more unusual oxidation states and coordinations. Revisions are based on new structural data, empirical bond strength-bond length relationships, and plots of (1) radii vs volume, (2) radii vs coordination number, and (3) radii vs oxidation state. Factors which affect radii additivity are polyhedral distortion, partial occupancy of cation sites, covalence, and metallic character. Mean Nb5+-O and Mo6+-O octahedral distances are linearly dependent on distortion. A decrease in cation occupancy increases mean Li+-O, Na+-O, and Ag+-O distances in a predictable manner. Covalence strongly shortens Fe2+-X, Co2+-X, Ni2+-X, Mn2+-X, Cu+-X, Ag+-X, and M-H- bonds as the electronegativity of X or M decreases. Smaller effects are seen for Zn2+-X, Cd2+-X, In2+-X, pb2+-X, and TI+-X. Bonds with delocalized electrons and therefore metallic character, e.g. Sm-S, V-S, and Re-O, are significantly shorter than similar bonds with localized electrons.
A New Algorithm to Locate Power-Quality Event Source With Improved Realization of Distributed Monitoring Scheme (2006)

This paper presents a systematic algorithm to locate the power-quality (PQ) event source in the distributed monitoring system. Firstly, this paper proposes an improved realization of a distributed monitoring scheme for PQ diagnosis. The algorithm utilizes the topology of power system and the direction of PQ events. As a result, the coverage matrix and the direction matrix are constructed. The algorithm determines the candidate areas for an event source by manipulating these two matrices. For more accurate results, it calculates the distance from the PQ monitor to the location of the PQ event source. It is explained with an illustrative example and is applied to IEEE test feeder in order to validate the accuracy. The proposed algorithm can replace the expert's analysis on the PQ event source with an automated computer program.