gebhart/patrepeval huggingface dataset:
Heterogeneity of DNA Methylation Status Analyzed by Bisulfite-PCR-SSCP and Correlation with Clinico-Pathological Characteristics in Colorectal Cancer (2001)

Aberrant DNA methylation has been identified as an important mechanism for inactivation of tumor suppressor genes and mismatch repair genes during carcinogenesis. We used bisulfite treatment and the PCR-single strand conformation polymorphism (SSCP) (BiPS) technique to analyze methylation status of the promoter regions of the hMLH1, p16, and HIC1 genes in several cancer cell lines and colorectal cancer tissues. The methylation of the hMLH1, p16 and HIC1 genes was observed in 2, 8, and 13 of 13 cancer cell lines, respectively. The SSCP for p16 and HIC1 in each of the methylation-positive cell lines were similar, indicating relative homogeneity of methylation status and complete methylation in the cell lines. Methylation was observed in 8, 5, and 21 of 25 colorectal cancer tissues for the hMLH1, p16, and HIC1 genes, respectively. The methylated bands revealed by BiPS analysis of the hMLH1 gene were homogeneous, whereas those of the p16 and HIC1 genes were different in each case. The methylation of the promoter region of the HIC1 gene in colorectal cancer was observed most frequently and could serve as a sensitive marker for colorectal cancer. Methylation status of the hMLH1 and p16 gene promoters was correlated with microsatellite instability status, tumor location, and differentiation but not with K-ras mutation or allelic loss of p53.
High-Intensity Exercise Training Protects the Brain Against Autoimmune Neuroinflammation: Regulation of Microglial Redox and Pro-inflammatory Functions (2021)

<b>Background</b>: Exercise training induces beneficial effects on neurodegenerative diseases, and specifically on multiple sclerosis (MS) and it's model experimental autoimmune encephalomyelitis (EAE). However, it is unclear whether exercise training exerts direct protective effects on the central nervous system (CNS), nor are the mechanisms of neuroprotection fully understood. In this study, we investigated the direct neuroprotective effects of high-intensity continuous training (HICT) against the development of autoimmune neuroinflammation and the role of resident microglia. <b>Methods</b>: We used the transfer EAE model to examine the direct effects of training on the CNS. Healthy mice performed HICT by treadmill running, followed by injection of encephalitogenic proteolipid (PLP)-reactive T-cells to induce EAE. EAE severity was assessed clinically and pathologically. Brain microglia from sedentary (SED) and HICT healthy mice, as well as 5-days post EAE induction (before the onset of disease), were analyzed <i>ex vivo</i> for reactive oxygen species (ROS) and nitric oxide (NO) formation, mRNA expression of M1/M2 markers and neurotrophic factors, and secretion of cytokines and chemokines. <b>Results</b>: Transfer of encephalitogenic T-cells into HICT mice resulted in milder EAE, compared to sedentary mice, as indicated by reduced clinical severity, attenuated T-cell, and neurotoxic macrophage/microglial infiltration, and reduced loss of myelin and axons. In healthy mice, HICT reduced the number of resident microglia without affecting their profile. Isolated microglia from HICT mice after transfer of encephalitogenic T-cells exhibited reduced ROS formation and released less IL-6 and monocyte chemoattractant protein (MCP) in response to PLP-stimulation. <b>Conclusions</b>: These findings point to the critical role of training intensity in neuroprotection. HICT protects the CNS against autoimmune neuroinflammation by reducing microglial-derived ROS formation, neurotoxicity, and pro-inflammatory responses involved in the propagation of autoimmune neuroinflammation.
Interference enhanced Raman scattering of hydrogenated amorphous silicon revisited (2001)

We report interference enhanced Raman scattering (IERS) of very thin and highly absorbing (α>105 cm−1) device-quality hydrogenated amorphous silicon (a-Si : H) films. The IERS technique, in general, can give a gain of 10– 103, depending on the optical constants of the material. The potential of this method is demonstrated experimentally using device-quality a-Si : H films at a wavelength of 514 nm. IERS is shown to produce an intensity gain (G) of 50 in the scattered intensity of a thin (19 nm) a-Si : H film as compared with the poor signal obtained for a thick specimen (1 µm) using conventional Raman scattering in backscattering configuration. The TA- and TO-like signatures of the enhanced spectra stand out clearly, thus being suitable for the structural characterization of this material. It is also shown that the intensity enhancement effect decreases when the incident radiation wavelength is changed to 604 nm, thus deviating from the required interference condition. IERS can have important applications in the study of many materials, such as metals, metallic alloys, semiconductors and surface adsorbates. Copyright © 2001 John Wiley & Sons, Ltd.
Spoof surface plasmons propagating along a periodically corrugated coaxial waveguide (2010)

Using the rigorous mode-matching technique, we have investigated a periodically corrugated perfectly conducting coaxial waveguide for the possibility of propagation of localized spoof surface plasmons. To verify our results, the computed band diagram of the structure has been compared with the one obtained using the body-of-revolution finite-difference time-domain method. The obtained spoof surface plasmon modes have been shown to be highly localized and slowly propagating. Variations of the obtained modal frequencies and mode profiles as a function of the depth and width of the grooves have also been investigated.
Superconducting spin valves based on epitaxial Fe/V superlattices (2008)

In superconducting spin valves of the type S/F1/N/F2 or F1/S/F2 with a superconducting layer S, two ferromagnetic layers F1 and F2, and a normal metallic layer N, the superconducting transition temperature ${T}_{\text{S}}$ depends on the relative magnetization direction of the ferromagnetic layers F1 and F2. The difference of the transition temperature $\ensuremath{\Delta}{T}_{\text{S}}={T}_{s}^{\text{AP}}\ensuremath{-}{T}_{s}^{\text{P}}$ with the magnetization direction of F1 and F2 either antiparallel or parallel is called the superconducting spin valve effect. We have prepared both types of spin valves by growing Fe/V thin-film heterostructures with epitaxial quality on MgO(001) substrates. In the S/F1/N/F2-type spin valves the ferromagnetic layers were the first two Fe layers of a [Fe/V] superlattice coupled antiferromagnetically via the interlayer exchange interaction. Here we observed a superconducting spin valve shift of up to $\ensuremath{\Delta}{T}_{\text{S}}\ensuremath{\approx}200\text{ }\text{mK}$ when aligning the sublattice magnetization in an external magnetic field. In the F1/S/F2-type spin valves the ferromagnetic layer F1 was either a [Fe/V] or a $[{\text{Fe}}_{x}{\text{V}}_{1\ensuremath{-}x}/\text{V}]$ superlattice, the F2 layer was a Fe-, a Co-, or a ${\text{Fe}}_{x}{\text{V}}_{1\ensuremath{-}x}$ film. Using weakly ferromagnetic ${\text{Fe}}_{x}{\text{V}}_{1\ensuremath{-}x}$ alloy layers as F1 and F2 we find a spin valve effect of up to $\ensuremath{\Delta}{T}_{\text{S}}\ensuremath{\approx}20\text{ }\text{mK}$, which is more than a factor of 2 larger than reported in the literature before for spin valves with comparable transition temperatures. Our results indicate that a high interface transparency and a large superconducting correlation length are prerequisites for the observation of a sizable superconducting spin valve effect.
Identification of a Novel Actin-Binding Domain within the Rho Guanine Nucleotide Exchange Factor TEM4 (2020)

Spatio-temporal activation of Rho GTPases is essential for their function in a variety of biological processes and is achieved in part by regulating the localization of their activators, the Rho guanine nucleotide exchange factors (RhoGEFs). In this study, we provide the first characterization of the full-length protein encoded by RhoGEF TEM4 and delineate its domain structure, catalytic activity, and subcellular localization. First, we determined that TEM4 can stimulate guanine nucleotide exchange on RhoA and the related RhoB and RhoC isoforms. Second, we determined that TEM4, like other Dbl RhoGEFs, contains a functional pleckstrin homology (PH) domain immediately C-terminal to the catalytic Dbl homology (DH) domain. Third, using immunofluorescence analysis, we showed that TEM4 localizes to the actin cytoskeleton through sequences in the N-terminus of TEM4 independently of the DH/PH domains. Using site-directed mutagenesis and deletion analysis, we identified a minimal region between residues 81 and 135 that binds directly to F-actin and has an ∼90-fold higher affinity for ATP-loaded F-actin. Finally, we demonstrated that a single point mutation (R130D) within full-length TEM4 abolishes actin binding and localization of TEM4 to the actin cytoskeleton, as well as dampens the in vivo activity of TEM4 towards RhoC. Taken together, our data demonstrate that TEM4 contains a novel actin binding domain and binding to actin is essential for TEM4 subcellular localization and activity. The unique subcellular localization of TEM4 suggests a spatially-restricted activity and expands the diversity of mechanisms by which RhoGEF function can be regulated.
Assemblies of Polyacrylonitrile-Derived Photoactive Polymers as Blue and Green Light Photo-Cocatalysts for Cu-Catalyzed ATRP in Water and Organic Solvents (2021)

Photoluminescent nanosized quasi-spherical polymeric assemblies prepared by the hydrothermal reaction of polyacrylonitrile (PAN), <i>ht</i>-PLP<sub>PAN</sub>, were demonstrated to have the ability to photo-induce atom transfer radical polymerization (ATRP) catalyzed by low, parts per million concentrations of Cu<sup>II</sup> complex with tris(2-pyridylmethyl)amine (TPMA). Such photo induced ATRP reactions of acrylate and methacrylate monomers were performed in water or organic solvents, using <i>ht</i>-PLP<sub>PAN</sub> as the photo-cocatalyst under blue or green light irradiation. Mechanistic studies indicate that <i>ht</i>-PLP<sub>PAN</sub> helps to sustain the polymerization by facilitating the activation of alkyl bromide species by two modes: 1) green or blue light-driven photoreduction of the Cu<sup>II</sup> catalyst to the activating Cu<sup>I</sup> form, and 2) direct activation of dormant alkyl bromide species which occurs only under blue light. The photoreduction of the Cu<sup>II</sup> complex by <i>ht</i>-PLP<sub>PAN</sub> was confirmed by linear sweep voltammetry performed under illumination. Analysis of the polymerization kinetics in aqueous media indicated even though Cu<sup>I</sup> complexes comprised only 1-1.4% of all Cu species at equilibrium, they exhibited high activation rate constant and activated the alkyl bromide initiators five to six orders of magnitude faster than <i>ht</i>-PLP<sub>PAN</sub>.
A Novel 2nd Generation Liquid Biofuel Production Concept Using Biomass Char (2010)

Second generation liquid biofuels from lignocellulosic feedstocks are part of a suite of solutions to peak oil and a safe climate economy. Biofuels have technological advantages over electrification for applications with minimal refuelling or recharging options such as air travel, shipping, agriculture and low or intermittent frequency trucking and rail. Existing thermal processing routes to liquid biofuels include Fischer-Tropsch liquids from gasification, refined liquids from hydrothermal processing and upgraded oils from flash pyrolysis. These are high quality fuels, but are expensive to produce and have limited safety advantages over existing petroleum fuels. A novel fuel production concept is proposed combining slow pyrolysis chars and superfine commutation technologies being developed for coal based liquid fuels. Char is micronized to a <10μm fraction and suspended in diesel or water to create a reduced cost, quality and energy density liquid biofuel. Process yields and efficiencies were derived from a review of the slow pyrolysis, char, coal commutation and combustion literature and used to develop theoretical estimates of process performance. Char structure and composition were also reviewed in the context of commutation and management of ash and alkalis in the fuel. The study concluded that char based fuels had potential applications where cost was critical but quality was not, such as diesel engines for agriculture, trucks, trains, shipping and backup electricity supply. Char water fuels are environmentally benign and increase safety by being non-flammable. Second generation biofuels from biomass char therefore warrant further investigation as solutions to peak oil and a safe climate economy.
Alterations in collagen production in mixed mononuclear leukocyte-fibroblast cultures. (1983)

The cell-cell interactions between fibroblasts and mononuclear leukocytes (MNL) which promote alterations in collagen accumulation were examined using a system of co-culture of human fibroblasts and peripheral blood MNL. The stimulation of collagen production was optimal after 48 h of co-culture and the increase in collagen correlated directly with the number of MNL added. The enhancement of collagen production was seen in both autologous and allogeneic co-cultures. Stimulation of non-collagenous protein was also noted. Co-culture supernatants contained soluble substances that were capable of stimulating collagen production, although they stimulated collagen production to a lesser degree than direct co-culture. Fractionation of these supernatants on Sephadex G-200 revealed a predominant area of stimulatory activity at 160,000 mol wt. Lesser areas of activity were noted at molecular weights of 80,000 and 25,000. Determination of the types of collagen produced by fibroblasts during co-culture with MNL showed that the ratio of type I:III collagen was decreased. These alterations in both the quantitative and qualitative accumulation of collagen mimic the changes often seen in wound healing and early inflammation suggesting that cellular interactions between fibroblasts and MNL may be important in the modulation of collagen production in normal and pathologic states.
Metastatic disease from spinal chordoma: a 10-year experience (2006)

Spinal chordoma metastasized to other locations in 19% of the patients in this series. In patients with local disease recurrence, metastatic lesions are more likely to develop. Metastatic lesions were shown to be aggressive in some cases. Surgery and chemotherapy can play a role in controlling metastatic disease.
Annealing behavior of hydrogen-implanted magnetic garnet (1985)

Ferromagnetic resonance spectra and x-ray rocking curves were used to measure magnetic and strain profiles of Gd, Tm, Ga substituted yttrium iron garnet films implanted with H2+ at 120 keV and at doses in the range (3–80)×1015 ions/cm2. The maximum strain occurred at a depth of 3600 Å, reaching a value of 2.9% at 40×1015 ions/cm2. At the highest dose, the garnet was amorphous in that region which had highest strain at lower dose. The strain has two components, one due to damage and one due to the presence of the hydrogen atoms. The second component disappears for annealing temperatures above 400 °C, at which temperature the hydrogen has been reported to be largely desorbed. The reduction of the first component with annealing follows the same pattern as other implant elements. The magnetic anisotropy exhibits a large anomalous nonlinear increase with dose. The excess over other implantation elements disappears for annealing temperatures above 400 °C. There is no significant change in gyromagnetic ratio with dose or annealing temperatures up to 600 °C.
A HYALURONAN PREPARATION (500–730 KDA) IN THE TREATMENT OF OSTEOARTHRITIS: A REVIEW OF CLINICAL TRIALS WITH HYALGAN® (2002)

SUMMARY The purpose of this paper is to review the intra‐articular treatment of osteoarthritis (OA) of the knee with the hyaiuronan preparation 500–730 kDa (Hyalgan®). Reviewing the results of 24 clinical trials, it can be concluded that 3–5 weekly injections of Hyalgan significantly improve the pain and functional status of patients with OA. Although the onset of improvement is delayed by 3–4 weeks, the effect can last at least six months and up to one year after treatment cessation. The benefits of Hyalgan compared with intra‐articular corticosteroids are also addressed. The potential for Hyalgan to have a structure‐modifying action by retarding stuctural progression in OA of the knee is considered. However, further studies of Hyalgan in OA in other joints, and in damaged joints in rheumatoid arthritis, are needed.
Efficient Deep-Blue Organic Light-Emitting Diodes Using Double-Emitting Layer (2012)

Efficient deep-blue organic light-emitting diodes were demonstrated using 1,4-tetranaphthalene doped in double-emitting layers (D-EMLs) consisting of 2-methyl-9,10-di(2-naphthyl)anthracene and 4'-(dinaphthalen-2-yl)-1,1'-binaphthyl as blue hosts. The device with D-EML exhibits good confinement of holes and electrons, as well as a broad recombination zone. The optimized device showed a peak current efficiency of 3.67 cd/A, a peak external quantum efficiency of 3.97%, and Commission Internationale de L'Eclairage coordinates of (0.16, 0.10).
Ka-Band LNA Module with 1.9dB NF for Communications Satellite Payload (2006)

A LNA module, integrated microwave assembly was developed for Ka-band communications satellite payload in the frequency range of 29.6 /spl sim/ 30.0 GHz. The noise figure of the module has been recorded as low as 1.9dB at ambient temperature. The module has been tested over temperature range of -15 /spl sim/ +71/spl deg/C and shows 33.3dB of gain within 0.7dBp-o variation as it has the function of gain compensation. The mass of the module is 94grams that provides the flexibility in payload assembly. Two low noise amplifier MMIC chips were used in the module and those chips had been fabricated using 0.15 /spl mu/m GaAs pHEMT process. This paper describes the design, fabrication and performance of the LNA module. This will include the MMIC design, the mechanical design of module, and the design of waveguide-to-microstrip transition.
Clinicopathologic profile and treatment outcomes of non-sensitizing <i>EGFR</i> and <i>HER2 (ERBB2)</i> activating mutations in NSCLC: Results from a single-center retrospective study. (2019)

9090 Background: The clinicopathologic characteristics and optimal treatment strategies for non-sensitizing EGFR ( ns- EGFR) and HER2 activating mutations in NSCLC remain unclear. Methods: Single-center retrospective study of patients seen at University of Colorado from 2008 – 2018 with stage IV NSCLC was performed. Clinicopathologic features and treatment outcomes of patients with ns-EGFR (Exon 18, Exon 20, L861Q) and HER2 mutations were collected. Best response to TKI was determined (RECIST v1.1). PFS was calculated using Kaplan-Meier method. Results: Among 359 patients, we identified 49 ns-EGFR (36 Exon 20, 10 Exon 18, 3 L861Q) and 28 HER2 mutations (27 Exon 20, 1 gene amplification) detected via NGS (65/77), real-time PCR (9/77), FISH (1/77) and undocumented (2/77). PDL1 &gt; 50% was seen in 44% ns- EGFR and 57% HER2. Adenocarcinoma was the most common histology (97%). Most patients were female (62%), never smokers (63%), and presented with metastatic disease (stage: I 5%, II 4%, III 6%, IV 85%). HER2+ NSCLC demonstrated a tropism for lung metastases (64%) that was significant when compared to EGFR Exon 19, EGFR L858R, ALK, ROS1, and KRAS cohorts (p &lt; 0.001). No differences were found when other metastatic sites were compared. Among evaluable patients, response rates to TKI therapy is shown. Aggregate median PFS on TKI for ns-EGFR and HER2+ NSCLC was 6 months compared to EGFR Exon 19 (15 months; p &lt; 0.01; HR 0.4; CI 0.24 – 0.67) and EGFR L858R (22 months; p &lt; 0.01; HR 0.27 and 0.8; CI 0.14 – 0.54). Aggregate median OS for ns-EGFR and HER2+ NSCLC was 28 months with no differences when compared to EGFR Exon 19 and L858R subgroups. Conclusions: HER2+ NSCLC appears to have a predisposition for lung metastases. Higher DCR was observed with newer generation TKIs, but novel targeted therapeutic approaches are needed as overall outcomes remain poor. [Table: see text]
Optimization, evaluation and calibration of a cross-strip DOI detector (2018)

This study depicts the evaluation of a SiPM detector with depth of interaction (DOI) capability via a dual-sided readout that is suitable for high-resolution positron emission tomography and magnetic resonance (PET/MR) imaging. Two different 12 × 12 pixelated LSO scintillator arrays with a crystal pitch of 1.60 mm are examined. One array is 20 mm-long with a crystal separation by the specular reflector Vikuiti enhanced specular reflector (ESR), and the other one is 18 mm-long and separated by the diffuse reflector Lumirror E60 (E60). An improvement in energy resolution from 22.6% to 15.5% for the scintillator array with the E60 reflector is achieved by taking a nonlinear light collection correction into account. The results are FWHM energy resolutions of 14.0% and 15.5%, average FWHM DOI resolutions of 2.96 mm and 1.83 mm, and FWHM coincidence resolving times of 1.09 ns and 1.48 ns for the scintillator array with the ESR and that with the E60 reflector, respectively. The measured DOI signal ratios need to be assigned to an interaction depth inside the scintillator crystal. A linear and a nonlinear method, using the intrinsic scintillator radiation from lutetium, are implemented for an easy to apply calibration and are compared to the conventional method, which exploits a setup with an externally collimated radiation beam. The deviation between the DOI functions of the linear or nonlinear method and the conventional method is determined. The resulting average of differences in DOI positions is 0.67 mm and 0.45 mm for the nonlinear calibration method for the scintillator array with the ESR and with the E60 reflector, respectively; Whereas the linear calibration method results in 0.51 mm and 0.32 mm for the scintillator array with the ESR and the E60 reflector, respectively; and is, due to its simplicity, also applicable in assembled detector systems.
FOORC: A FUZZY ONTOLOGY-BASED REPRESENTATION FOR OBESITY RELATED CANCER KNOWLEDGE (2016)

Obesity has a tight relationship with increased risks of different cancer types, such as Colorectal, Ovarian, Female Breast, Gallbladder, Adenocarcinoma, Kidney (Renal-Cell), Liver, and Pancreatic. It can also lead to some other diseases like diabetes and heart diseases. This paperproposes a fuzzy ontology that is based on OWL 2to represent the Obesity Related Cancer (ORC) domain knowledge. The diseases taxonomy isconstructed using the standard Disease Ontology. The presented FuzzyOntology includes more concepts than in crisp one and copes with the domain linguistic variables. It allows the users to query the Fuzzy Dl reasoner for element and get them back the fuzzy ontology for that element. It is expected to be good practice for ontologists and knowledge engineers in medical field aiding them to solve the overlapping concepts, linguistic variables, and reasoning problems by building their fuzzy ontologies. Building FOORC as an open ontology is a first attempt to organize information related to the obesity and cancer diseases in a formalized, structured manner that both physicians and intelligent systems can exploit it in knowledge sharing, reusability, and reasoning.