gebhart/patrepeval huggingface dataset:
Combining MDE and UML to Reverse Engineer Web-Based Legacy Systems (2008)

The research in this paper focuses on an approach to reverse engineering Web-based legacy systems with the integration of model-driven engineering and UML. Three types of link-based models of Web-based legacy systems are presented. Web-based legacy systems are parsed to find judgement conditions of model, and UML diagrams are described based on the modelling rules.
Native oxide top- and bottom-confined narrow stripe <i>p</i>-<i>n</i> Al<i>y</i>Ga1−<i>y</i>As-GaAs-In<i>x</i>Ga1−<i>x</i>As quantum well heterostructure laser (1993)

A new form of AlyGa1−yAs-GaAs-InxGa1−xAs quantum well heterostructure (QWH) laser that is confined above and below the active region by an insulating low refractive index native oxide is demonstrated. The laser diodes are defined from a mesa edge by the selective lateral oxidation and anisotropic oxidation of high Al composition AlyGa1−yAs layers (y=0.85, 0.87) located above and below the QW and waveguide active region. This structure provides excellent current and optical confinement, resulting in continuous wave threshold currents of ∼8 mA and maximum output powers (uncoated laser) of 35 mW/ facet for a∼2.5 μm aperture.
Three-dimensional optical tomography of the premature infant brain (2002)

For the first time, three-dimensional images of the newborn infant brain have been generated using measurements of transmitted light. A 32-channel time-resolved imaging system was employed, and data were acquired using custom-made helmets which couple source fibres and detector bundles to the infant head. Images have been reconstructed using measurements of mean flight time relative to those acquired on a homogeneous reference phantom, and using a head-shaped 3D finite-element-based forward model with an external boundary constrained to match the measured positions of the sources and detectors. Results are presented for a premature infant with a cerebral haemorrhage predominantly located within the left ventricle. Images representing the distribution of absorption at 780 nm and 815 nm reveal an asymmetry consistent with the haemorrhage, and corresponding maps of blood volume and fractional oxygen saturation are generally within expected physiological values.
Reactive oxygen species-induced apoptosis and necrosis in bovine corneal endothelial cells. (1999)

The cytotoxic effects of photo-irradiated riboflavin and rose bengal are shown to be mediated by two distinct but parallel pathways, one leading to apoptosis and the other to necrosis. Possible involvement of NF-kappaB in cell death is suggested. These findings provide potential leads for future investigation into the molecular mechanisms of loss of corneal endothelial cells related to aging, oxidative stress, and possibly other similar causes.
Polarization dependence of response functions in 3×3 Sagnac optical fiber current sensors (1994)

We show theoretically that the response functions of a lossless Sagnac optical fiber current sensor based on a 3/spl times/3 coupler fundamentally depend on the polarization state of light entering the coupler even for systems with no linear birefringence. For a lossless, zero-birefringence system the desired response functions, sinusoids separated by 120/spl deg/ phase shifts, are obtained only for circularly polarized input light. The response functions for linearly polarized and depolarized inputs are sinusoids separated by 180/spl deg/ and yield zero-slope small-signal responses; in addition, two outputs are degenerate, so the responses are similar to those observed in 2/spl times/2 systems. Thus, 3/spl times/3 Sagnac systems offer no advantage over 2/spl times/2 systems for linearly polarized input light. The predicted polarization dependence of 3/spl times/3 Sagnac response functions is experimentally confirmed. This result establishes the need for increased system complexity in 3/spl times/3 Sagnac current sensors since polarization control optics are required to provide the proper input polarization.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Interleukins in glioblastoma pathophysiology: implications for therapy (2012)

Despite considerable amount of research, the poor prognosis of patients diagnosed with glioblastoma multiforme (GBM) critically needs new drug development to improve clinical outcomes. The development of an inflammatory microenvironment has long been considered important in the initiation and progression of glioblastoma; however, the success of developing therapeutic approaches to target inflammation for GBM therapy has yet been limited. Here, we summarize the accumulating evidence supporting a role for inflammation in the pathogenesis of glioblastoma, discuss anti-inflammatory targets that could be relevant for GBM treatment and provide a perspective on the challenges faced in the development of drugs that target GBM inflammation. In particular, we will review the function of IL-1β, IL-6 and IL-8 as well as the potential of kinase inhibitors targeting key players in inflammatory cell signalling cascades such as JAK, JNK and p38 MAPK.
Protein L. A novel bacterial cell wall protein with affinity for Ig L chains. (1988)

A novel Ig-binding protein has been isolated from the surface of bacteria belonging to the anaerobic species Peptococcus magnus. To solubilize the protein, peptococci were treated with different proteolytic enzymes (papain, pepsin, and trypsin) or with mutanolysin, a bacteriolytic agent known to digest the cell walls of streptococci. Papain, trypsin, and mutanolysin all solubilized peptides showing affinity for radiolabeled human IgG in Western blot analysis. Compared with papain and trypsin, mutanolysin liberated a more homogeneous material, which also had a higher m.w. This mutanolysin-solubilized protein (Mr 95 kDa) was obtained highly purified by a single isolation step on IgG-Sepharose, and the molecule was found to exhibit unique Ig-binding properties. Thus, in dot blots and in Western blots, human IgG, F(ab')2 and Fab fragments of IgG, and human kappa and lambda L chains all showed affinity for the protein. Moreover, the molecule also bound human IgM and IgA, whereas no binding was recorded for IgG-Fc fragments or IgG H chains. Finally, the protein bound to human polyclonal Ig L chains immobilized on polyacrylamide beads. These different data demonstrate that the isolated peptococcal protein binds Ig through L chain interaction. The name protein L is therefore suggested for this novel Ig-binding bacterial cell wall protein.
P‐glycoprotein expression and schedule dependence of adriamycin cytotoxicity in human colon carcinoma cell lines (1991)

Four human colon cancer cell lines (SW620, LS 180, DLD-I, and HCT-15) and Adriamycin-resistant sub-lines with varying degrees of P-glycoprotein expression were studied to evaluate the reversibility of Adriamycin resistance in human colon cancer. Two groups of cell lines were studied. In the first, including a series of Adriamycin-resistant SW620 and DLD-I sub-lines, and in parental HCT-15 cells, P-glycoprotein has a major role in Adriamycin resistance, as evidenced by a correlation between Adriamycin resistance, expression of the multidrug-resistance gene mdr-I and its product, P-glycoprotein (Pgp), decreased drug accumulation and reversibility by verapamil. In these cell lines, increasing doses of verapamil are required to fully reverse increasing levels of resistance. In the second group, including parental SW620, DLD-I and LS 180 cells and Adriamycin-selected LS 180 sub-lines, P-glycoprotein does not have a major role in Adriamycin resistance. There was correlation between the schedule dependence of Adriamycin cytotoxicity and the role of P-glycoprotein in modulating resistance. In the cell lines in which P-glycoprotein was a major determinant of Adriamycin resistance, the drug exposure (defined as the product of the concentration and the time of treatment) needed to achieve a given percent cell kill was reduced as much as 9-fold when cells were treated for 7 days as compared with 3 hr. By comparison, in cell lines in which P-glycoprotein played a lesser role, the drug exposure necessary to achieve a given percent kill increased under conditions of continuous treatment. In some human colon carcinoma cell lines Pgp appears to play a significant role in resistance to Adriamycin, and this can be overcome by the use of competitive inhibitors of Pgp. The increased sensitivity with continuous treatment observed in cell lines with P-glycoprotein-mediated resistance suggests that administration of drugs by continuous infusion may be valuable in reversing clinical drug resistance mediated predominantly by P-glycoprotein.
Copper(II) Nanosensor Based on a Gold Cysteamine Self-Assembled Monolayer Functionalized with Salicylaldehyde (2006)

Fabrication and electrochemical characterization of a novel nanosensor for determination of Cu2+ in subnanomolar concentrations is described. The sensor is based on gold cysteamine self-assembled monolayer functionalized with salicylaldehyde by means of Schiff's base formation. Cyclic voltammetry, Electrochemical impedance spectroscopy (EIS), and electrochemical quartz crystal microbalance were used to probe the fabrication and characterization of the modified electrode. The sensor was used for quantitative determination of Cu2+ by the EIS in the presence of parabenzoquinone in comparison with stripping Osteryoung square wave voltammetry (OSWV). The attractive ability of the sensor to efficiently preconcentrate trace amounts of Cu2+ allowed a simple and reproducible method for copper determination. A wide range linear calibration curve was observed, 5.0 x 10(-11)-5.0 x 10(-6) and 5.0 x 10(-10)-5.0 x 10(-6) M Cu2+, by using the EIS and OSWV, respectively. Moreover, the sensor presented excellent stability with lower than 10% change in the response, as tested for more than three months daily experiments, and a high repeatability with relative standard deviations of 6.1 and 4.6% obtained for a series of eight successive measurements in 5.0 x 10(-7) M Cu2+ solution, by the EIS and OSWV, respectively.
Organic–inorganic heterojunction light emitting diodes based on poly(p-phenylene vinylene)/cadmium sulfide thin films (1997)

We report on a solution processed novel electroluminescent heterostructure device consisting of an inorganic semiconductor, CdS, and a polymer emitter, poly(p-phenylene vinylene) (PPV). This configuration provides the advantage of excellent charge transporting properties of an inorganic semiconductor and the high luminescence quantum efficiency of an organic emitter. The electroluminescence spectrum obtained from this hetrostructure device is similar to the emission spectrum of pure PPV. Even with aluminum electrode, we have achieved stable electroluminescence at very low threshold voltage (3 V) and overall quantum efficiency of about 1% in these devices. The device emitted bright electroluminescence radiation (150 cd/m2) at a driving voltage of 10 V under the forward bias condition.
Efficient, Dynamic Coordination of Request Batches in C-SON Systems (2013)

Self-Organizing Mobile Networks contain a potentially large number of SON function instances that need to be coordinated in order to achieve system-level operational goals. Many SON functions (and thus their coordination) will be realized in a centralized way (C-SON) due to the required integration with a (centralized) legacy OAM system. In such systems, many configuration requests ("batches") are treated in regular time intervals For SON functions, this may lead to undesired effects (monopolization by high priority functions and frequent rollbacks of configuration actions). This paper proposes a novel coordination approach combining an output buffer of pending configuration requests with dynamic priorities for different SON function types. A simulated network scenario exhibiting a specific optimization problem (closure of a coverage hole) is used to evaluate the proposed method. The method is able to avoid the undesired effects and approximate legacy workflows in network optimization while still keeping the autonomous characteristic of SON functions.
Microporous Magnesium Aluminophosphate STA‐1: Synthesis with a Rationally Designed Template and Structure Elucidation by Microcrystal Diffraction (1997)

The design of inorganic solids and state-of-the-art microcrystallography at Europe's newest synchrotron facility go hand-in-hand in the synthesis and structure elucidation of STA-1, a low-density member (projection shown on the right) of the family of large-pore aluminophosphates.
Contrast-enhanced abdominal MR angiography: optimization of imaging delay time by automating the detection of contrast material arrival in the aorta. (1997)

Automatic triggering results in improved arterial-tovenous contrast. It increases arterial enhancement or enables MR angiograms to be obtained with less contrast material. The authors now routinely use this technique for aortorenal imaging with a gadolinium-based contrast material dose of 20 mmol (40 mL) in patients who weigh more than 50 kg and 10 mmol (20 mL) in patients who weigh less than 50 kg.
Phosphorylation of Tau Protein Associated as a Protective Mechanism in the Presence of Toxic, C-Terminally Truncated Tau in Alzheimer's Disease (2013)

Phosphorylation of Tau Protein Associated as a Protective Mechanism in the Presence of Toxic, C-Terminally Truncated Tau in Alzheimer's Disease
Coded aperture systems as non-conventional lensless imagers for the visible and infrared (2007)

Coded aperture imaging (CAI) has been used extensively at gamma- and X-ray wavelengths, where conventional refractive and reflective techniques are impractical. CAI works by coding optical wavefronts from a scene using a patterned aperture, detecting the resulting intensity distribution, then using inverse digital signal processing to reconstruct an image. This paper will consider application of CAI to the visible and IR bands. Doing so has a number of potential advantages over existing imaging approaches at these longer wavelengths, including low mass, low volume, zero aberrations and distortions and graceful failure modes. Adaptive coded aperture (ACAI), facilitated by the use of a reconfigurable mask in a CAI configuration, adds further merits, an example being the ability to implement agile imaging modes with no macroscopic moving parts. However, diffraction effects must be considered and photon flux reductions can have adverse consequences on the image quality achievable. An analysis of these benefits and limitations is described, along with a description of a novel micro optical electro mechanical (MOEMS) microshutter technology for use in thermal band infrared ACAI systems. Preliminary experimental results are also presented.
ARX-LF-based source-filter methods for voice modification and transformation (2009)

Two ARX-LF-based source/filters models for speech signals are presented. A robust glottal inversion technique is used to deconvolve the signal into an excitation component and a filter component. The excitation component is further decomposed into an LF part and a residual part. The first model, referred to as the LF-vocoder, is a high quality vocoder that replaces the residual part with modulated noise. The second model uses a sinusoidal harmonic representation of the residual signal. The latter does not degrade the signal during analysis/synthesis and provides higher quality for small modification factors, while the former has the advantage of being a compact, fully parametric representation that is suitable for low-bit-rate speech coding as well as parametric speech synthesis applications.
On Strong Pseudoprimes to Several Bases (1993)

With y/k denoting the smallest strong pseudoprime to all of the first k primes taken as bases we determine the exact values for y/, %, i//y, y/% and give upper bounds for y/$ , y^o, V\ \ We discuss the methods and underlying facts for obtaining these results. PrIMALITY TESTS BY MEANS OF STRONG PSEUDOPRIMES
원저 : 소아메밀알레르기의 진단 및 임상적 특성에 관한 연구 (1998)

목적 : 메밀은 우리나라에서 흔하게 발견되는 중요한 식품항원이며 그 증상이 단순한 두드러기에서부터 심한 경우에는 아나필락시?脊沮?다양하다. 식품알레르기의 진단은 문진, 알레르기피부시험 및 경구유발시험 등이 있는데 가장 정확한 검사는 경구유발시험이다. 그런데 경구유발시험을 일반 외래에서 일률적으로 실시하기에는 여러 어려움이 따른다. 이에 저자들은 손쉽게 시행할 수 있는 병력청취와 알레르기피부시험의 진단적 가치를 평가하고 메밀알레르기의 임상양상과 특성을 알아보기 위해서 본 연구를 실시하였다.
대상 및 방법 : 연세대학교 의과대학 세브란스병원 소아알레르기크리닉에 내원하여 피부시험을 실시하여 메밀항원에 양성 반응을 보였거나 메밀을 먹은 후 알레르기 증상을 보인 과거력이 있었던 환아들 중 경구유발시험이 가능했던 55명을 대상으로 하여 임상양상 및 특성을 분석하였다. 경구유발시험은 소량부터(가루를 입주위에 바르는 방법) 시작해서 증상이 안나타나면 점차 양을 늘려서 먹이는 방법으로 시행하였다.
결과 
1) 경구유발시험을 실시했던 총 55례중 양성 반응을 보여서 메밀알레르기로 진단할 수 있었던 경 우는 40례로 72.7%였다.
2) 이중 남아 32명(80%), 여아 8명(20%)으로 남아가 여아에 비하여 4배가 많았고, 호발연령은 5세이하가 25명(62.5%)으로 가장 많았다.
3) 피부시험과 과거력 모두에서 양성이었던 환아중 경구유발시험과 일치했던 환아는 31례(86.1%)로 매우 높은 예측도를 보였다.
4) 메밀을 섭취한 후 기관지천식이나 아나필락시?瘠?같은 위중한 증상을 보였던 경우가 약 60%나 되었다.
5) 증상을 유발시켰던 메밀의 양은 1-100gm 사이가 27례(67.5%)로 가장 많았고 11례(27.5%)에서는 소량으로 냄새를 맡거나 맛을 보는 것만으로도 증상이 유발되었다.
결론 :식품알레르기의 진단은 원인으로 생각되는 음식을 금식시킨후 증상이없을 때 유발시험을 실시하는 것이 가장 좋은 방법이다. 그러나 메밀은 심한 경우에는 아나필락시?脊沮?도 유발할 정도로 항원성이 강한 식품이며 알레르기피부시험과 과거력이 모두 양성인 경우 에는 그 예민도가 매우 높음으로 모든 환자들에게 일괄적으로 유발시험을 실시하기 전에 우 선 철저한 제한식을 권고하여 심한 알fp르기 증상을 예방하는 것이 좋을 것으로 사료된다.
The alpha 5 beta 1 integrin fibronectin receptor, but not the alpha 5 cytoplasmic domain, functions in an early and essential step in fibronectin matrix assembly. (1993)

The alpha 5 beta 1 integrin mediates cell adhesion and migration on fibronectin, a glycoprotein critical for normal vertebrate embryonic development. Indirect evidence reported to date suggests that this receptor also functions in the deposition of fibronectin matrices. We used a molecular genetic approach to critically evaluate this role of alpha 5 beta 1 integrins. Mutant Chinese hamster ovary (CHO) cells deficient in alpha 5 integrin expression could not assemble a fibronectin matrix. Reconstituting alpha 5 beta 1 integrin expression by transfecting them with a full-length cDNA encoding the human alpha 5 chain completely restored fibronectin matrix assembly. CHO cells expressing an alpha 5 chain lacking the cytoplasmic domain also assembled a fibronectin matrix. Removing the cytoplasmic domain of alpha 5 appears to increase its activity in fibronectin matrix assembly. In addition to alpha 5 beta 1 integrin binding to fibronectin's RGD-containing domain, cells must bind with high affinity to fibronectin's amino-terminal 29-kDa matrix assembly domain to form a fibronectin matrix. Studies with the alpha 5-deficient CHO cells show that the expression of alpha 5 beta 1 integrin is also necessary for cells to bind fragments containing this distinct site in fibronectin and that a fibronectin matrix increases binding of the 29-kDa fragment. Thus, alpha 5 beta 1 integrins not only mediate cell adhesion to fibronectin, but also play an essential role in the assembly of a fibronectin matrix. This role includes direct binding to fibronectin and modulating a distinct binding event involving the interaction of fibronectin's amino-terminal matrix assembly domain with the cell surface.
Role of Rho and Rho kinase in the activation of volume‐regulated anion channels in bovine endothelial cells (1999)

1. We have studied the modulation of volume-regulated anion channels (VRACs) by the small GTPase Rho and by one of its targets, Rho kinase, in calf pulmonary artery endothelial (CPAE) cells. 2. RT-PCR and immunoblot analysis showed that both RhoA and Rho kinase are expressed in CPAE cells. 3. ICl,swell, the chloride current through VRACs, was activated by challenging CPAE cells with a 25 % hypotonic extracellular solution (HTS) or by intracellular perfusion with a pipette solution containing 100 microM GTPgammaS. 4. Pretreatment of CPAE cells with the Clostridium C2IN-C3 fusion toxin, which inactivates Rho by ADP ribosylation, significantly impaired the activation of ICl,swell in response to the HTS. The current density at +100 mV was 49 +/- 13 pA pF-1 (n = 17) in pretreated cells compared with 172 +/- 17 pA pF-1 (n = 21) in control cells. 5. The volume-independent activation of ICl,swell by intracellular perfusion with GTPgammaS was also impaired in C2IN-C3-pretreated cells (31 +/- 7 pA pF-1, n = 11) compared with non-treated cells (132 +/- 21 pA pF-1, n = 15). 6. Activation of ICl,swell was pertussis toxin (PTX) insensitive. 7. Y-27632, a blocker of Rho kinase, inhibited ICl,swell and delayed its activation. 8. Inhibition of Rho and of Rho kinase by the above-described treatments did not affect the extent of cell swelling in response to HTS. 9. These experiments provide strong evidence that the Rho-Rho kinase pathway is involved in the VRAC activation cascade.
An optimized, fully automated system for fast and accurate identification of chromosomal rearrangements by multiplex-FISH (M-FISH) (1998)

Multiplex-FISH (M-FISH) is a recently developed technique by which each of the two dozen human chromosomes-the 22 autosomes and the X and Y sex chromosomes-can be stained or "painted" with uniquely distinctive colors. Using a combinatorial labeling technique and a specially designed filter set, each DNA probe can be identified by its unique spectral signature. Here we present several significant optimizations of the M-FISH technology. First, a new strategy for labeling the probes is described which allows for easy and fast production of the complex M-FISH probe mix. Second, a newly developed, completely motorized microscope equipped with an eight-position filter wheel and a new generation of filter sets is presented that allows fully automatic imaging of a complete metaphase spread within seconds. Third, to determine the characteristic spectral signatures for all different combinations of fluorochromes, we developed a novel multichannel image analysis method. The spectral analysis is solely guided by the image information itself and does not require any user interaction. A complete analysis of a metaphase spread can be accomplished in less than 3 min. Sophisticated built-in quality controls were developed, and the value of visual inspection of M-FISH images as a simple means of controlling the computer-generated chromosome classification are illustrated. In addition, we discuss advantages of adding new fluorochromes to the traditionally used five fluorochromes.
Comprehensive structure characterization of lipid a extracted from<i>Yersinia pestis</i>for determination of its phosphorylation configuration (2010)

We report on comprehensive structure characterization of lipid A extracted from Yersinia pestis (Yp) for determination of its phosphorylation configuration that was achieved by combining the methods of molecular biology with high-resolution tandem mass spectrometry. The phosphorylation pattern of diphosphorylated lipid A extracted from Yp has recently been found to be a heterogeneous mixture of C-1 and C-4' bisphosphate, C-1 pyrophosphate, and C-4' pyrophosphate (Proc. Natl. Acad. Sci. 2008, 105, 12742). To reduce the inherent phosphate heterogeneity of diphosphorylated lipid A extracted from Yp, we incorporated specific C-1 and C-4' position phosphatases into wild type KIM6+ Yp grown at 37 degrees C. Comprehensive high-resolution tandem mass spectrometric analyses of lipid A extracted from Yp modified with either the C-1 or C-4' phosphatase allowed for unambiguous structure assignment of monophosphorylated and diphosphorylated lipid A and distinction of isomeric bisphosphate and pyrophosphate forms. The prevalent aminoarabinose modification was determined to be exclusively attached to the lipid A disaccharide via a phospho-diester linkage at either or both the C-1 and C-4' positions.