gebhart/patrepeval huggingface dataset:
Multistage bilateral noise filtering and edge detection for color image enhancement (2005)

Removing noise while preserving and enhancing edges is one of the most fundamental operations of image/video processing. When taking pictures with digital cameras, it is frequently found that the color images are corrupted by miscellaneous noise and, hence, noise filtering is necessary. The difficulty is that usually the filtering will reduce the sharpness of the image. On the other hand, optical lens imperfections are usually equivalent to spatial low pass filters and tend to result in blurred images. It is customary to apply edge enhancement algorithm on the image in order to improve the sharpness, but this process usually increase the noise level as a by-product. In this paper, we present a new integrated approach to address these issues. The proposed approach combines color edge detection, bilateral noise filter, and edge enhancement based on suitable color spaces. The experimental results show that the proposed approach can effectively reduce the noise while preserving and enhancing edges.
Regulation of mitosis via mitotic kinases: new opportunities for cancer management (2007)

Mitosis, a critical and highly orchestrated event in the cell cycle, decides how cells divide and transmit genetic information from one cell generation to the next. Errors in the choreography of these events may lead to uncontrolled proliferation, aneuploidy, and genetic instability culminating in cancer development. Considering the central role of phosphorylation in mitotic checkpoints, spindle function, and chromosome segregation, it is not surprising that several mitotic kinases have been implicated in tumorigenesis. These kinases play pivotal roles throughout cellular division. From DNA damage and spindle assembly checkpoints before entering mitosis, to kinetochore and centrosome maturation and separation, to regulating the timing of entrance and exit of mitosis, mitotic kinases are essential for cellular integrity. Therefore, targeting the mitotic kinases that control the fidelity of chromosome transmission seems to be a promising avenue in the management of cancer. This review provides an insight into the mechanism of mitotic signaling, especially the role of critical mitotic kinases. We have also discussed the possibilities of the use of mitotic kinases in crafting novel strategies in cancer management.
Oral and pulmonary delivery of FSH–Fc fusion proteins via neonatal Fc receptor-mediated transcytosis (2005)

We have shown that FSH-Fc fusion proteins have increased stability in blood and improved bioactivity in vivo, and that heterodimer FSH-Fc is more active in rats and monkeys than single chain FSH-Fc. These data suggest that Fc fusion proteins offer the potential for oral and pulmonary delivery of FSH.
Free-radical chemistry of cigarette smoke and its toxicological implications. (1985)

Cigarette smoke contains two very different populations of free radicals, one in the tar and one in the gas phase. The tar phase contains several relatively stable free radicals; we have identified the principal radical as a quinone/hydroquinone (Q/QH2) complex held in the tarry matrix. We suggest that this Q/QH2 polymer is an active redox system that is capable of reducing molecular oxygen to produce superoxide, eventually leading to hydrogen peroxide and hydroxyl radicals. In addition, we have shown that the principal radical in tar reacts with DNA in vitro, possibly by covalent binding. The gas phase of cigarette smoke contains small oxygen- and carbon-centered radicals that are much more reactive than are the tar-phase radicals. These gas-phase radicals do not arise in the flame, but rather are produced in a steady state by the oxidation of NO to NO2, which then reacts with reactive species in smoke such as isoprene. We suggest that these radicals and the metastable products derived from these radical reactions may be responsible for the inactivation of alpha 1-proteinase inhibitor by fresh smoke. Cigarette smoke oxidizes thiols to disulfides; we suggest the active oxidants are NO and NO2. The effects of smoke on lipid peroxidation are complex, and this is discussed. We also discuss the toxicological implications for the radicals in smoke in terms of a number of radical-mediated disease processes, including emphysema and cancer.
Treatment of fragile X-associated tremor ataxia syndrome (FXTAS) and related neurological problems (2008)

Fragile X-associated tremor/ataxia syndrome (FXTAS) is a progressive neurological disorder that affects older adult carriers, predominantly males, of premutation alleles (55 to 200 CGG repeats) of the fragile X (FMR1) gene. Principal features of FXTAS are intention tremor, ataxia, parkinsonism, cognitive decline, and peripheral neuropathy; ancillary features include, autonomic dysfunction, and psychiatric symptoms of anxiety, depression, and disinhibition. Although controlled trials have not been carried out in individuals with FXTAS, there is a significant amount of anecdotal information regarding various treatment modalities. Moreover, there exists a great deal of evidence regarding the efficacy of various medications for treatment of other disorders (eg, Alzheimer disease) that have substantial phenotypic overlap with FXTAS. The current review summarizes what is currently known regarding the symptomatic treatment, or potential for treatment, of FXTAS.
Reflective THz and MR imaging of burn wounds: a potential clinical validation of THz contrast mechanisms (2012)

Terahertz (THz) imaging is an expanding area of research in the field of medical imaging due to its high sensitivity to changes in tissue water content. Previously reported in vivo rat studies demonstrate that spatially resolved hydration mapping with THz illumination can be used to rapidly and accurately detect fluid shifts following induction of burns and provide highly resolved spatial and temporal characterization of edematous tissue. THz imagery of partial and full thickness burn wounds acquired by our group correlate well with burn severity and suggest that hydration gradients are responsible for the observed contrast. This research aims to confirm the dominant contrast mechanism of THz burn imaging using a clinically accepted diagnostic method that relies on tissue water content for contrast generation to support the translation of this technology to clinical application. The hydration contrast sensing capabilities of magnetic resonance imaging (MRI), specifically T2 relaxation times and proton density values N(H), are well established and provide measures of mobile water content, lending MRI as a suitable method to validate hydration states of skin burns. This paper presents correlational studies performed with MR imaging of ex vivo porcine skin that confirm tissue hydration as the principal sensing mechanism in THz burn imaging. Insights from this preliminary research will be used to lay the groundwork for future, parallel MRI and THz imaging of in vivo rat models to further substantiate the clinical efficacy of reflective THz imaging in burn wound care.
Core-Directed Protein Design. I. An Experimental Method for Selecting Stable Proteins from Combinatorial Libraries (1999)

The design of proteins represents a significant challenge to modern-day structural biology. A major obstacle here is the specification of well-packed hydrophobic cores to drive the folding and stabilization of the target. Computational approaches have been used to alleviate this by testing alternate sequences prior to the production and characterization of a few proteins. Here we present the experimental counterpart of this approach. We selected stable variants from a library of ubiquitin hydrophobic-core mutants as follows. Hexahistidine-tagged proteins were displayed on the surface of phage. These protein-phage were immobilized onto Ni-coated surfaces. The bound fusion-phage were treated with protease to remove unstable or poorly folded proteins. Stable phage fusions were eluted and infected into Escherichia coli, which allowed amplification for further selection, sequencing, or protein expression. Two Ni-derivatized supports were tested: Ni-NTA chips for surface plasmon resonance (SPR) and Ni-NTA agarose beads. SPR had an advantage in that the selection process could be monitored directly. This allowed individual clones and experimental conditions to be tested rapidly prior to preparative panning of the library, which was carried out using Ni-NTA agarose beads. We demonstrate the method by selecting stable core mutants of ubiquitin, the characterization of which is described in the following paper [Finucane, M. D., and Woolfson, D. N. (1999) Biochemistry 38, XXXXX-XXXXX]. As our method selects only on the basis of structure and stability, it will be of use in improving the stabilities and structural specificities of proteins of de novo design, and in establishing rules that link sequence and structure.
The nitric oxide pathway in pre-eclampsia: pathophysiological implications (1998)

Pre-eclampsia, one of the most significant health problems in human pregnancy, complicates approximately 6-8% of all gestations and is the leading cause of fetal growth retardation, infant morbidity and mortality, premature birth and maternal death. Recent research implicates free radicals in the pathophysiology of pre-eclampsia. This review covers the biochemistry of nitric oxide (NO) and possible interactions with other free radicals. Studies in the rat show that pregnancy is associated with enhanced production and responsiveness to NO in both reproductive tissues and blood vessels. Rats infused with NG-nitro-L-arginine methyl ester (L-NAME, a NO synthase inhibitor) have been used as an animal model of pre-eclampsia, and the effects of steroid hormones on blood pressure in this model have been tested. Results suggest that pre-eclampsia may be a state of NO deficiency. However, in humans there seem to be contradictions regarding the involvement of NO in maternal adaptation to pregnancy. It is suggested that NO may be one of several systems that act in concert to maintain a symbiotic relationship between mother and fetus. However, the input of each system may be genetically determined.
Fibroblast Growth Factor-2 Antagonist Activity and Angiostatic Capacity of Sulfated Escherichia coli K5 Polysaccharide Derivatives (2001)

The angiogenic basic fibroblast growth factor (FGF2) interacts with tyrosine kinase receptors (FGFRs) and heparan sulfate proteoglycans (HSPGs) in endothelial cells. Here, we report the FGF2 antagonist and antiangiogenic activity of novel sulfated derivatives of the Escherichia coli K5 polysaccharide. K5 polysaccharide was chemically sulfated in N- and/or O-position after N-deacetylation. O-Sulfated and N,O-sulfated K5 derivatives with a low degree and a high degree of sulfation compete with heparin for binding to 125I-FGF2 with different potency. Accordingly, they abrogate the formation of the HSPG.FGF2.FGFR ternary complex, as evidenced by their capacity to prevent FGF2-mediated cell-cell attachment of FGFR1-overexpressing HSPG-deficient Chinese hamster ovary (CHO) cells to wild-type CHO cells. They also inhibited 125I-FGF2 binding to FGFR1-overexpressing HSPG-bearing CHO cells and adult bovine aortic endothelial cells. K5 derivatives also inhibited FGF2-mediated cell proliferation in endothelial GM 7373 cells and in human umbilical vein endothelial (HUVE) cells. In all these assays, the N-sulfated K5 derivative and unmodified K5 were poorly effective. Also, highly O-sulfated and N,O-sulfated K5 derivatives prevented the sprouting of FGF2-transfected endothelial FGF2-T-MAE cells in fibrin gel and spontaneous angiogenesis in vitro on Matrigel of FGF2-T-MAE and HUVE cells. Finally, the highly N,O-sulfated K5 derivative exerted a potent antiangiogenic activity on the chick embryo chorioallantoic membrane. These data demonstrate the possibility of generating FGF2 antagonists endowed with antiangiogenic activity by specific chemical sulfation of bacterial K5 polysaccharide. In particular, the highly N,O-sulfated K5 derivative may provide the basis for the design of novel angiostatic compounds.
Aprotinin binding to amyloid fibrils (2000)

Different low molecular mass ligands have been used to identify amyloid deposits. Among these markers, the dyes Thioflavin T and Congo Red interact specifically with the beta-sheet structure arranged in a cross-beta conformation, which is characteristic of amyloid. However, the molecular details of this interaction remain unknown. When labelled with technetium-99m, the proteinase inhibitor aprotinin has been shown to represent a very important radiopharmaceutical agent for in vivo imaging of extra-abdominal deposition of amyloid in amyloidosis of the immunoglobulin type. However, no information is available as to whether aprotinin binds other types of amyloid fibrils and on the nature and characteristics of the interaction. The present work shows aprotinin binding to insulin, transthyretin, beta-amyloid peptide and immunoglobulin synthetic amyloid fibrils by a specific dot-blot ligand-binding assay. Aprotinin did not bind amorphous precipitates and/or the soluble fibril precursors. A Ka of 2.9 microM-1 for the binding of aprotinin to insulin amyloid fibrils was determined by Scatchard analysis. In competition experiments, analogues such as an aprotinin variant, a spermadhesin and the soybean trypsin inhibitor were tested and results suggest that both aprotinin and the spermadhesin interact with amyloid fibrils through pairing of beta-sheets of the ligands with exposed structures of the same type at the surface of amyloid deposits. An electrostatic component may also be involved in the binding of aprotinin to amyloid fibrils because important differences in binding constants are observed when substitutions V15L17E52 are introduced in aprotinin; on the other hand beta-sheet containing acidic proteins, such as the soybean trypsin inhibitor, are unable to bind amyloid fibrils.
A Reduction of Imitation Learning and Structured Prediction to No-Regret\n Online Learning (2010)

Sequential prediction problems such as imitation learning, where future\nobservations depend on previous predictions (actions), violate the common\ni.i.d. assumptions made in statistical learning. This leads to poor performance\nin theory and often in practice. Some recent approaches provide stronger\nguarantees in this setting, but remain somewhat unsatisfactory as they train\neither non-stationary or stochastic policies and require a large number of\niterations. In this paper, we propose a new iterative algorithm, which trains a\nstationary deterministic policy, that can be seen as a no regret algorithm in\nan online learning setting. We show that any such no regret algorithm, combined\nwith additional reduction assumptions, must find a policy with good performance\nunder the distribution of observations it induces in such sequential settings.\nWe demonstrate that this new approach outperforms previous approaches on two\nchallenging imitation learning problems and a benchmark sequence labeling\nproblem.\n
Extracellular Superoxide Dismutase Inhibits Inflammation by Preventing Oxidative Fragmentation of Hyaluronan (2007)

Extracellular superoxide dismutase (EC-SOD) is expressed at high levels in lungs. EC-SOD has a polycationic matrix-binding domain that binds to polyanionic constituents in the matrix. Previous studies indicate that EC-SOD protects the lung in both bleomycin- and asbestos-induced models of pulmonary fibrosis. Although the mechanism of EC-SOD protection is not fully understood, these studies indicate that EC-SOD plays an important role in regulating inflammatory responses to pulmonary injury. Hyaluronan is a polyanionic high molecular mass polysaccharide found in the extracellular matrix that is sensitive to oxidant-mediated fragmentation. Recent studies found that elevated levels of low molecular mass hyaluronan are associated with inflammatory conditions. We hypothesize that EC-SOD may inhibit pulmonary inflammation in part by preventing superoxide-mediated fragmentation of hyaluronan to low molecular mass fragments. We found that EC-SOD directly binds to hyaluronan and significantly inhibits oxidant-induced degradation of this glycosaminoglycan. In vitro human polymorphic neutrophil chemotaxis studies indicate that oxidative fragmentation of hyaluronan results in polymorphic neutrophil chemotaxis and that EC-SOD can completely prevent this response. Intratracheal injection of crocidolite asbestos in mice leads to pulmonary inflammation and injury that is enhanced in EC-SOD knock-out mice. Notably, hyaluronan levels are increased in the bronchoalveolar lavage fluid after asbestos-induced pulmonary injury, and this response is markedly enhanced in EC-SOD knock-out mice. These data indicate that inhibition of oxidative hyaluronan fragmentation probably represents one mechanism by which EC-SOD inhibits inflammation in response to lung injury.
Fibrinogen Stimulates Macrophage Chemokine Secretion Through Toll-Like Receptor 4 (2001)

Extravascular fibrin deposition is an early and persistent hallmark of inflammatory responses. Fibrin is generated from plasma-derived fibrinogen, which escapes the vasculature in response to endothelial cell retraction at sites of inflammation. Our ongoing efforts to define the physiologic functions of extravasated fibrin(ogen) have led to the discovery, reported here, that fibrinogen stimulates macrophage chemokine secretion. Differential mRNA expression analysis and RNase protection assays revealed that macrophage inflammatory protein-1alpha (MIP-1alpha), MIP-1beta, MIP-2, and monocyte chemoattractant protein-1 are fibrinogen inducible in the RAW264.7 mouse macrophage-like cell line, and ELISA confirmed that both RAW264.7 cells and primary murine thioglycolate-elicited peritoneal macrophages up-regulate the secretion of monocyte chemoattractant protein-1 >100-fold upon exposure to fibrinogen. Human U937 and THP-1 precursor-1 (THP-1) monocytic cell lines also secreted chemokines in response to fibrinogen, upon activation with IFN-gamma and differentiation with vitamin D(3), respectively. LPS contamination could not account for our observations, as fibrinogen-induced chemokine secretion was sensitive to heat denaturation and was unaffected by the pharmacologic LPS antagonist polymyxin B. Nevertheless, fibrinogen- and LPS-induced chemokine secretion both apparently required expression of functional Toll-like receptor 4, as each was diminished in macrophages derived from C3H/HeJ mice. Thus, innate responses to fibrinogen and bacterial endotoxin may converge at the evolutionarily conserved Toll-like recognition molecules. Our data suggest that extravascular fibrin(ogen) induces macrophage chemokine expression, thereby promoting immune surveillance at sites of inflammation.
Advanced Permeability and Anisotropy Measurements while Testing and Sampling in Real-Time Using a Dual Probe Formation Tester (2000)

Abstract Three new pressure-transient testing methods are employed to determine horizontal and vertical permeability using a dual probe formation tester. Real-time interpretation during acquisition of pressure data, is the focus of all three new pressure-testing techniques. In the first, a new spherical flow model with anisotropy, storage, and skin is developed from first principles for dual probe analysis. Historically, pressure transient solutions are presented as Laplace transforms and approximated in the time domain using numerical techniques. Typically, early, intermediate and late time periods are identified using derivative plots; but very often, the selection of appropriate data results in confusion. Here, the Laplace transform is inverted to yield a single, exact, closed form, analytical, time domain solution valid for all times, making real-time parameter matching possible with high accuracy. The second technique uses an oscillatory displacement source at the piston face, and the phase delay of the pressure pulse between the probes is used to determine permeability and anisotropic index. This technique is particularly useful when the second monitoring probe signal is weak (as in high permeability zones) or where there is large spacing between the probes. Pulse timing can usually be detected more accurately than its magnitude, thus extending the range of permeability and anisotropic measurements. This methodology, which is based on a derived relationship between wave phase and permeability, was developed by mathematical analogy with resistivity determination methods used in induction logging. In the above method, it is often possible to encounter "phase wrapping" for excessively tight formations, leaving an indeterminate permeability. To circumvent this problem, in the third method, a short, abrupt "pulse" having a well-defined "center frequency" is produced at the piston face, and its travel time is measured until arrival at the receiver probes. The harmonic, closed form expression is then used to translate this travel time to permeability. This new method is analogous to sonic wave models; although, of course, "waveforms" are often smeared due to the diffusive nature of the problem. Simulation results using a detailed finite element, dual probe model are compared against the above analytical methods to assess the effects of near wellbore parameters such as mudcake effectiveness, probe, and packer size. Field-test results are shown to demonstrate the successful implementation of these new testing methods. The three methods described above provide a practical level of redundancy in permeability prediction. Also, monitoring permeability and anisotropy changes while sampling are shown to be beneficial in identifying fluid type changes.
Extension of deep-ultraviolet lithography for patterning logic gates using alternating phase shifting masks (1999)

We present the combination of alternating phase-shifting masks and rule-based optical proximity correction (OPC) for the patterning of 0.13 μm polysilicon gate lines. Using the optimal process condition, a process window with 1.2 μm of depth of focus (DOF) and 15% exposure latitude is obtained for 0.13 μm isolated lines in resist. In addition, with the application of rule-based OPC, the common DOF for 0.13 μm lines of various line-to-space ratios can be improved from 0 to 0.6 μm.
Artificial finger skin having ridges and distributed tactile sensors used for grasp force control (2002)

An artificial elastic finger skin for robot fingers was developed for controlling the grasp force when the weight and friction coefficient of the grasped object are unknown. The elastic finger skin has ridges at the surface to divide the stick/slip area. It also has a pair of tactile sensors embedded per one ridge similar to human fingertips. The surface of the whole finger is curved so that the reaction force can be distributed. A finite element (FE) model of the elastic finger skin was developed to perform a dynamic contact analysis using the FE method in order to design the elastic finger skin. The elastic finger skin was then constructed. It was confirmed by calculation and experiment that the incipient slippage of the ridge that occurs near the edge of contact area can be detected. This result is useful for controlling the grasping force when the weight and friction coefficient between the elastic finger skin and grasping object are unknown.
Context-Aware Computing Applications (1994)

This paper describes systems that examine and react to an individual's changing context. Such systems can promote and mediate people's interactions with devices, computers, and other people, and they can help navigate unfamiliar places. We believe that a limited amount of information covering a person's proximate environment is most important for this form of computing since the interesting part of the world around us is what we can see, hear, and touch. In this paper we define context-aware computing, and describe four catagories of context-aware applications: proximate selection, automatic contextual reconfiguration, contextual information and commands, and contex-triggered actions. Instances of these application types have been prototyped on the PARCTAB, a wireless, palm-sized computer.