gebhart/patrepeval huggingface dataset:
Detection of organic vapors by graphene films functionalized with metallic nanoparticles (2012)

Graphene synthesized by chemical vapor deposition has been used to study the sensing behavior of graphene for different organic vapors in ppm level. All the measurements were carried out at a room temperature with dry air as the background gas. Synthesis of graphene was carried out on a copper foil using methane gas as a precursor. The Raman spectroscopy was used to monitor the quality of graphene films transferred to SiO2/Si substrates, revealing the sensing channel to be mostly monolayer, bilayer, or tri-layer graphene. Graphene surface was functionalized with gold and platinum nanoparticles to enhance the gas sensing behavior. The adsorption/desorption behavior of organic vapors in dry air was analyzed based on the change in the conductivity with the different exposure times in different concentrations. Among the vapors tested, the sensitivity was in the order: acetic acid &gt; ethanol &gt; acetone from all surfaces (bare graphene, graphene decorated with gold and platinum nanoparticles). The devices were successfully tested for four key characteristics (response, recovery, repeatability, and reliability) of any practical gas sensors. The dynamic response behavior of the devices was also analyzed and fitted with the first order exponential function relating to the Langmuir approach. Based on the fit, the average response rate was obtained between 0.22% and 1.04% per ppm for different organic vapors with different surfaces. Average response rate of around 0.5% per ppm for organic vapors demonstrates a high sensitivity of the device at the room temperature under the ambient conditions.
Role of Ruthenium Oxidation States in Ligand-to-Ligand Charge Transfer Processes (2012)

We describe in this paper the properties of [Ru(II/III)(bpy)(2)ClL](+1/+2) and [Ru(II/III)(bpy)(2)L(2)](+2/+3). L = ditolyl-3-pyridylamine (dt3pya) is a redox active ligand related to triarylamines, which is very similar to 3-aminopyridine except for the reversible redox behavior. The monosubstituted complex shows a metal-to-ligand charge-transfer (MLCT) at 502 nm, and reversible waves in acetonitrile at E(0)(Ru(III/II)) = 1.07 V, E(0)(L(+/0)) = 1.46 V (NHE). The disubstituted complex shows an MLCT at 461 nm, a photorelease of dt3pya with quantum yield of 0.11 at 473 nm, and two reversible one-electron overlapped waves at 1.39 V associated with one of the ligands (1.37 V) and Ru(III/II) (1.41 V). Further oxidation of the second ligand at 1.80 V forms a 2,2'-bipiridine derivative, in an irreversible reaction similar to dimerization of triphenylamine to yield tetraphenylbenzidine. In the dioxidized state, the spectroelectrochemistry of the disubstituted complex shows a ligand-to-ligand charge transfer at 1425 nm, with a transition moment of 1.25 Å and an effective two-state coupling of 1200 cm(-1). No charge transfer between ligands was observed when Ru was in a 2+ oxidation state. We propose that a superexchange process would be involved in ligand-metal-ligand charge transfer, when ligands and metals are engaged in complementary π interactions, as in metal-ligand-metal complexes. Best orbital matching occurs when metallic donor fragments are combined with acceptor ligands and vice versa. In our case, Ru(III) bridge (an acceptor) and two dt3pya (donors, one of them being oxidized) made the complex a Robin-Day Class II system, while the Ru(II) bridge (a donor, reduced) was not able to couple two dt3pya (also donors, one oxidized).
Parecoxib Impairs Early Tendon Repair but Improves Later Remodeling (2004)

The results suggest that cyclooxygenase-2 inhibitors should be used with care in the early period after tendon injury.
Acute Compartment Syndrome: Update on Diagnosis and Treatment (1996)

Acute compartment syndrome can have disastrous consequences. Because unusual pain may be the only symptom of an impending problem, a high index of suspicion, accurate evaluation, and prophylactic treatment will allow the physician to intervene in a timely manner and prevent irreversible damage. Muscles tolerate 4 hours of ischemia well, but by 6 hours the result is uncertain; after 8 hours, the damage is irreversible. Ischemic injury begins when tissue pressure is 10 to 20 mm Hg below diastolic pressure. Therefore, fasciotomy generally should be done when tissue pressure rises past 20 mm Hg below diastolic pressure.
Abl Family Tyrosine Kinases Regulate Sialylated Ganglioside Receptors for Polyomavirus (2010)

Sialylated lipids serve as cellular receptors for polyomaviruses. Using pharmacological inhibitors and cell lines derived from knockout mice, we demonstrate that Abl family tyrosine kinases are required for replication of mouse polyomavirus and BK virus, a human polyomavirus associated with allograft failure following kidney transplantation. We show that decreasing Abl family kinase activity results in low levels of cell surface ganglioside receptors for mouse polyomavirus and that inhibition of sialidase activity promotes virion binding in the absence of Abl family kinase activity. These data provide evidence that Abl family kinases reduce ganglioside turnover in the plasma membrane by inhibiting host cell sialidase activity. Thus, Abl family kinases regulate the susceptibility of cells to polyomavirus infection by modulating gangliosides required for viral attachment.
The Methodology off Sememic Analysis with Special Application to the English Preposition (1964)

This paper summarizes stratificational theory, and applies its linguistic methods in a sememic analysis of English prepositions. The phenomenon of interlocking diversification is shown to be quite generally present among the prepositions. Also, the analysis of prepositions is shown to entail a partial sememic analysis of other words; it therefore provides a starting point for the sememic analysis, on stratificational principles, of the rest of the language.
Quantitative phosphoproteomic analysis reveals system-wide signaling pathways downstream of SDF-1/CXCR4 in breast cancer stem cells (2014)

Breast cancer is the leading cause of cancer-related mortality in women worldwide, with an estimated 1.7 million new cases and 522,000 deaths around the world in 2012 alone. Cancer stem cells (CSCs) are essential for tumor reoccurrence and metastasis which is the major source of cancer lethality. G protein-coupled receptor chemokine (C-X-C motif) receptor 4 (CXCR4) is critical for tumor metastasis. However, stromal cell-derived factor 1 (SDF-1)/CXCR4-mediated signaling pathways in breast CSCs are largely unknown. Using isotope reductive dimethylation and large-scale MS-based quantitative phosphoproteome analysis, we examined protein phosphorylation induced by SDF-1/CXCR4 signaling in breast CSCs. We quantified more than 11,000 phosphorylation sites in 2,500 phosphoproteins. Of these phosphosites, 87% were statistically unchanged in abundance in response to SDF-1/CXCR4 stimulation. In contrast, 545 phosphosites in 266 phosphoproteins were significantly increased, whereas 113 phosphosites in 74 phosphoproteins were significantly decreased. SDF-1/CXCR4 increases phosphorylation in 60 cell migration- and invasion-related proteins, of them 43 (>70%) phosphoproteins are unrecognized. In addition, SDF-1/CXCR4 upregulates the phosphorylation of 44 previously uncharacterized kinases, 8 phosphatases, and 1 endogenous phosphatase inhibitor. Using computational approaches, we performed system-based analyses examining SDF-1/CXCR4-mediated phosphoproteome, including construction of kinase-substrate network and feedback regulation loops downstream of SDF-1/CXCR4 signaling in breast CSCs. We identified a previously unidentified SDF-1/CXCR4-PKA-MAP2K2-ERK signaling pathway and demonstrated the feedback regulation on MEK, ERK1/2, δ-catenin, and PPP1Cα in SDF-1/CXCR4 signaling in breast CSCs. This study gives a system-wide view of phosphorylation events downstream of SDF-1/CXCR4 signaling in breast CSCs, providing a resource for the study of CSC-targeted cancer therapy.
Ground truth extraction from LiDAR data for image orthorectification (2008)

The availability of high accuracy GCPs (ground control points) and DEMs (digital elevation models) becomes the key issue for successful implementation of an image orthorectification project. It is a very difficult task for collecting a large number of high quality GCPs by using traditional methods to meet all the requirements for digital photogrammetric and orthorectification process. Airborne light detection and ranging (LiDAR) - also referred to as airborne laser scanning (ALS), provides an alternative for high-density and high-accuracy three-dimensional terrain point data acquisition. One of the appealing features in the LiDAR output is the direct availability of three dimensional coordinates of points and intensity data in object space. With LiDAR data, high- accuracy and high-resolution intensity image, hillshade DSM (digital surface model) image, and DEM can be generated. Due to high planimetric accuracy characteristics of LiDAR data, ground truth can be extracted from these LiDAR-derived products (e.g., hillshade image and intensity image). This study investigated the feasibility of using LiDAR-derived hillshade DSM image and intensity image to extract ground truth for aerial image orthorectification. Two sets of GCPs were extracted from hillshade image and intensity image separately, and then were used as the inputs for aerial triangulation processing. LiDAR- derived DEM was then employed for differential rectification to produce the final orthoimage. The assessment of the planimetric accuracy of orthorectified images by using different set of GCPs was conducted by comparing the coordinates of some checking points from orthoimages and correspondent GPS surveyed coordinates.
Fluorescence Polarization is a Useful Technology for Reagent Reduction in Assay Miniaturization (2000)

The use of fluorescence polarization (FP) has increased significantly in the development of sensitive and robust assays for high throughput screening of chemical compound libraries during the past few years. In this study, we show that FP is a useful assay miniaturization technology for reagent reduction during high throughput screening. We developed and optimized several FP assays for binding to estrogen receptor alpha and two protein kinases with an assay volume of 100 microl. Without any re-optimization, a consistent signal window was maintained in 384- or 1536-well format when the assay volume varied from 2.5-100 microl at constant concentrations of all assay components. In contrast, the signal window decreased with decreasing assay volume at constant reagent concentration in the protein kinase C scintillation proximity assay (SPA) and prompt fluorescence assay. In addition, the effect of evaporation on the signal window was minimal for the FP assays. Our study suggests that FP is superior to SPA and prompt fluorescence in terms of reagent reduction in the miniaturized assay format.
355. Towards Cystic Fibrosis and Airway Gene Therapy: Evaluation of EGFP Gene Expression in Murine Nasal Airways Mediated by Simian Immunodeficiency Virus Vectors Pseudotyped with Sendai Virus Glycoproteins F and HN (2005)

Cystic Fibrosis (CF) is the most common lethal autosomal recessive disease in the Caucasian, and the cystic fibrosis transmembrane conductance regulator (CFTR) gene was identified to its causative gene. Mutations in the CFTR lead to imbalanced ion and water movement across the airway epithelium, resulting in thickened mucus, chronic bacterial infection and inflammation. Such severe pathological changes in airway are responsible for the morbidity and mortality in CF patients. Then, the airway epithelial cells are the important targets for CF gene therapy. However, few vectors can transduce them because of the existence of thickened mucus layer on the apical surface of epithelial cells and/or lack of virus receptors on apical site of the epithelial cells. We have shown that recombinant Sendai virus (SeV), murine parainfluenza virus, can easily penetrate the mucus layer and efficiently transduce the airway epithelial cells from the apical side. In order to improve the lentivirus vector entry, we developed a novel pseudotyped lentivirus vector based on a simian immunodeficiency virus (SIV: SIVagm TYO1) with SeV envelop proteins, fusion protein (F) and hemagglutinin-neuraminidase (HN). Although the SIV vector could not be pseudotyped with the intact F and HN, it could be successfully pseudotyped after the modification of cytoplasmic regions of both F and HN. Thus prepared F/HN pseudotyped SIV vector carrying EGFP transgene was produced by transient transfection in 293T cells to the titers up to 108 transduction units (TU)/ml, and easily concentrated to more than 1010 TU/ml by ultra-centrifugation with the same procedures for VSV-G pseudotyped vectors. Although the VSV-G pseudotyped lentivirus vectors have been used for administration to airways with pre-conditioning treatment using detergents, such treatment should be omitted considering the future clinical trials to human. From this point of view, F/HN pseudotyped SIV vector was evaluated in vivo in the absence of pre-conditioning. In this study, we administrated 100 |[mu]|l vector (4|[times]|108 TU/head) into mouse nasal cavity with syringe driver and observed EGFP expression. Although no or minimum expression was detected by administration of the VSV-G pseudotyped SIV vector, clear, frequent and stable GFP expression was observed in the epithelial cells of nasal cavity in the case of F/HN pseudotyped SIV vector even one month after the transduction. Detailed quantitative results will be summarized in the very near future. Our novel pseudotyped SIV vector with SeV envelope proteins, F and HN, would be of great value as a tool for gene therapy of respiratory diseases such as CF.
Robotic handwriting: Multi-contact manipulation based on Reactional Internal Contact Hypothesis (2014)

When one uses a hand-held tool, the fingers often make the tool to be in contact with the palm in the form of multi-contact manipulation. Multi-contact manipulation is useful for object-environment interaction tasks because it can provide both powerful grasping of the object body and dexterous manipulation of the object end-effector. However, dealing with the internal link contact with the object is not trivial. In this paper, we propose Reactional Internal Contact Hypothesis that regards the internal contact force as a reaction force so that the desired finger force can be reduced. By taking a handwriting task as an example, optimal configuration search and grasping force computation problems are addressed based on this hypothesis and validated via dynamic simulation.
In vitro quantification of specific microRNA using molecular beacons (2011)

MicroRNAs (miRNAs), a class of non-coding RNAs, have become a major focus of molecular biology research because of their diverse genomic origin and ability to regulate an array of cellular processes. Although the biological functions of miRNA are yet to be fully understood, tissue levels of specific miRNAs have been shown to correlate with pathological development of disease. Here, we demonstrate that molecular beacons can readily distinguish mature- and pre-miRNAs, and reliably quantify miRNA expression. We found that molecular beacons with DNA, RNA and combined locked nucleic acid (LNA)-DNA backbones can all detect miRNAs of low (<1 nM) concentrations in vitro, with RNA beacons having the highest detection sensitivity. Furthermore, we found that molecular beacons have the potential to distinguish miRNAs that have slight variations in their nucleotide sequence. These results suggest that the molecular beacon-based approach to assess miRNA expression and distinguish mature and precursor miRNA species is quite robust, and has the promise for assessing miRNA levels in biological samples.
An introduction to grassland agriculture (1995)

Contributing Authors. Preface. The Metric System. PART I. CHARACTERISTICS OF FORAGE SPECIES. 1. Forages and Grasslands in a Changing World (Robert F. Barnes and C. Jerry Nelson) 2. Structure and Morphology of Grasses (Lowell E. Moser and C. Jerry Nelson) 3. Structure and Morphology of Legumes and Other Forbs (Robert B. Mitchell and C. Jerry Nelson) 4. Physiology of Forage Plants (Jennifer W. MacAdam and C. Jerry Nelson) 5. Environmental Aspects of Forage Management (Jeffrey J. Volenec and C. Jerry Nelson) 6. Grasses for Northern Areas (John A. Balasko and C. Jerry Nelson) 7. Grasses for Southern Areas (Darren D. Redfearn and C. Jerry Nelson) 8. Legumes for Northern Areas (Robert L. McGraw and C. Jerry Nelson) 9. Legumes for Southern Areas (Lynn E. Sollenberger and Michael Collins) 10. Forbs (Danny H. Smith and Michael Collins) Compendium of Common Forages, Following (Kenneth J. Moore) PART II. FORAGE MANAGEMENT. 11. Forage Establishment (Dennis R. Cosgrove and Michael Collins) 12. Forage Fertilization and Nutrient Management (David J. Barker and Michael Collins) 13. Integrated Pest Management in Forages (Gary W. Fick, William O. Lamp, and Michael Collins) 14. Naturalized Grassland Ecosystems and Their Management (Charles P. West and C. Jerry Nelson) 15. Forage Improvement and Seed Production (Darrell A. Miller and C. Jerry Nelson) PART III. FORAGE UTILIZATION. 16. Forage Quality (Michael Collins and John O. Fritz) 17. Forage Utilization (Charles T. Dougherty and Michael Collins) 18. Forage-Related Animal Disorders (Michael Collins and David B. Hannaway) 19. Preservation of Forage as Hay and Silage (Michael Collins and Vance N. Owens) 20. Grazing Management Systems (Vivien G. Allen and Michael Collins) Appendix: Common and Botanical Names of Forages. Glossary. Index
Models of Selective Stimulation with a Flat Interface Nerve Electrode for Standing Neuroprosthetic Systems (2006)

The long-term goal of our research is to restore standing function via selective activation of target fascicles in the femoral nerve by a flat interface nerve electrode (FINE). The optimal number and location of contacts within a FINE had not been determined previously. A realistic three-dimensional finite element model based on a cross section of human femoral nerve and FINE is presented. Simulated voltages are applied as an extracellular field to the MRG double-cable axon model. Initial simulations indicate that optimal contacts may exist for each fascicular group but an acceptable selectivity may require nerve reshaping.
Direct imaging of monovacancy-hydrogen complexes in a single graphitic layer (2014)

Understanding how foreign chemical species bond to atomic vacancies in graphene layers can advance our ability to tailor the electronic and magnetic properties of defective graphenic materials. Here, we use ultrahigh-vacuum scanning tunneling microscopy (UHV-STM) and density functional theory to identify the precise structure of hydrogenated single atomic vacancies in a topmost graphene layer of graphite and establish a connection between the details of hydrogen passivation and the electronic properties of a single atomic vacancy. Monovacancy-hydrogen complexes are prepared by sputtering of the graphite surface layer with low-energy ions and then exposing it briefly to an atomic hydrogen environment. High-resolution experimental UHV-STM imaging allows us to determine unambiguously the positions of single missing atoms in the defective graphene lattice and, in combination with the ab initio calculations, provides detailed information about the distribution of low-energy electronic states on the periphery of the monovacancy-hydrogen complexes. We found that a single atomic vacancy where each \ensuremath{\sigma} dangling bond is passivated with one hydrogen atom shows a well-defined signal from the nonbonding \ensuremath{\pi} state, which penetrates into the bulk with a $\sqrt{3}\ifmmode\times\else\texttimes\fi{}\sqrt{3}R{30}^{\ensuremath{\circ}}$ periodicity. However, a single atomic vacancy with full hydrogen termination of \ensuremath{\sigma} dangling bonds and additional hydrogen passivation of the extended \ensuremath{\pi} state at one of the vacancy's monohydrogenated carbon atoms is characterized by complete quenching of low-energy localized states. In addition, we discuss the migration of hydrogen atoms at the periphery of the monovacancy-hydrogen complexes, which dramatically change the vacancy's low-energy electronic properties, as observed in our low-bias, high-resolution STM imaging.
Diabetic Retinopathy dark lesion detection: Preprocessing phase (2011)

Diabetic Retinopathy is the common cause of vision loss and blindness in patients with diabetes. Diabetic Retinopathy indicative lesions include dark lesions such as Microaneurysms and Hemorrhages; and bright lesions like Exudates. Automatic detection of distinct lesions in digital color fundus photographs is a critical step in development of diabetic retinopathy automatic detection systems. Dark lesions are the early signs of the disease. In addition, preprocessing phase is affectively required in any automatic dark lesion detection system for contrast enhancement around the dark lesions. Therefore, in this paper several different methods of preprocessing digital color fundus photographs, as the first critical step of dark lesions detection, are summarized.
Prolonged exercise to fatigue in humans impairs skeletal muscle Na<sup>+</sup>-K<sup>+</sup>-ATPase activity, sarcoplasmic reticulum Ca<sup>2+</sup>release, and Ca<sup>2+</sup>uptake (2004)

Prolonged exhaustive submaximal exercise in humans induces marked metabolic changes, but little is known about effects on muscle Na+-K+-ATPase activity and sarcoplasmic reticulum Ca2+ regulation. We therefore investigated whether these processes were impaired during cycling exercise at 74.3 +/- 1.2% maximal O2 uptake (mean +/- SE) continued until fatigue in eight healthy subjects (maximal O2 uptake of 3.93 +/- 0.69 l/min). A vastus lateralis muscle biopsy was taken at rest, at 10 and 45 min of exercise, and at fatigue. Muscle was analyzed for in vitro Na+-K+-ATPase activity [maximal K+-stimulated 3-O-methylfluorescein phosphatase (3-O-MFPase) activity], Na+-K+-ATPase content ([3H]ouabain binding sites), sarcoplasmic reticulum Ca2+ release rate induced by 4 chloro-m-cresol, and Ca2+ uptake rate. Cycling time to fatigue was 72.18 +/- 6.46 min. Muscle 3-O-MFPase activity (nmol.min(-1).g protein(-1)) fell from rest by 6.6 +/- 2.1% at 10 min (P <0.05), by 10.7 +/- 2.3% at 45 min (P <0.01), and by 12.6 +/- 1.6% at fatigue (P <0.01), whereas 3[H]ouabain binding site content was unchanged. Ca2+ release (mmol.min(-1).g protein(-1)) declined from rest by 10.0 +/- 3.8% at 45 min (P <0.05) and by 17.9 +/- 4.1% at fatigue (P < 0.01), whereas Ca2+ uptake rate fell from rest by 23.8 +/- 12.2% at fatigue (P=0.05). However, the decline in muscle 3-O-MFPase activity, Ca2+ uptake, and Ca2+ release were variable and not significantly correlated with time to fatigue. Thus prolonged exhaustive exercise impaired each of the maximal in vitro Na+-K+-ATPase activity, Ca2+ release, and Ca2+ uptake rates. This suggests that acutely downregulated muscle Na+, K+, and Ca2+ transport processes may be important factors in fatigue during prolonged exercise in humans.