gebhart/patrepeval huggingface dataset:
Recurrent epimutation of<i>SDHC</i>in gastrointestinal stromal tumors (2014)

Succinate dehydrogenase (SDH) is a conserved effector of cellular metabolism and energy production, and loss of SDH function is a driver mechanism in several cancers. SDH-deficient gastrointestinal stromal tumors (dSDH GISTs) collectively manifest similar phenotypes, including hypermethylated epigenomic signatures, tendency to occur in pediatric patients, and lack of KIT/PDGFRA mutations. dSDH GISTs often harbor deleterious mutations in SDH subunit genes (SDHA, SDHB, SDHC, and SDHD, termed SDHx), but some are SDHx wild type (WT). To further elucidate mechanisms of SDH deactivation in SDHx-WT GIST, we performed targeted exome sequencing on 59 dSDH GISTs to identify 43 SDHx-mutant and 16 SDHx-WT cases. Genome-wide DNA methylation and expression profiling exposed SDHC promoter-specific CpG island hypermethylation and gene silencing in SDHx-WT dSDH GISTs [15 of 16 cases (94%)]. Six of 15 SDHC-epimutant GISTs occurred in the setting of the multitumor syndrome Carney triad. We observed neither SDHB promoter hypermethylation nor large deletions on chromosome 1q in any SDHx-WT cases. Deep genome sequencing of a 130-kbp (kilo-base pair) window around SDHC revealed no recognizable sequence anomalies in SDHC-epimutant tumors. More than 2000 benign and tumor reference tissues, including stem cells and malignancies with a hypermethylator epigenotype, exhibit solely a non-epimutant SDHC promoter. Mosaic constitutional SDHC promoter hypermethylation in blood and saliva from patients with SDHC-epimutant GIST implicates a postzygotic mechanism in the establishment and maintenance of SDHC epimutation. The discovery of SDHC epimutation provides a unifying explanation for the pathogenesis of dSDH GIST, whereby loss of SDH function stems from either SDHx mutation or SDHC epimutation.
Immune response to progressor variants derived from transfection of an ultraviolet radiation-induced C3H mouse regressor tumor cell line with activated Harvey-ras oncogene. (1990)

Skin cancers induced in mice by UV radiation often exhibit a regressor phenotype. In order to determine how tumors escape the immune defenses of the normal immunocompetent host, we sought to isolate progressor variants from a UV radiation-induced C3H mouse regressor fibrosarcoma cell line, UV-2240, by transfection with an activated Ha-ras oncogene. A cotransfection protocol using pSV2-neo DNA, which confers resistance to the antibiotic G418, was used to select transfected cells. Injection of Ha-ras-transfected UV-2240 cells s.c. into immunocompetent C3H mice produced tumors in four of 36 animals. In contrast, UV-2240 cells transfected with pSV2-neo DNA alone or mock transfected with CaPO4 did not produce tumors in normal C3H mice. DNAs from cell lines established from Ha-ras-induced tumors contained unique Ha-ras sequences in addition to those sequences endogenous to UV-2240 cells. However, the Ha-ras-induced progressor variants did not overexpress the Mr 21,000 protein. The Ha-ra-induced progressor variants produced experimental lung metastasis in both normal C3H and nude mice, although they induced more lung nodules in nude mice than in normal C3H mice. In addition, all four Ha-ras-induced progressor variants produced significantly more experimental lung metastases in nude mice than did the parent UV-2240 cell line. However, both the parental UV-2240 cell line and the Ha-ras-induced progressor variants expressed similar levels of H-2Kk and H-2Dk antigens and were immunologically cross-reactive, as determined by in vitro cytotoxic T-lymphocyte and in vivo immunization-challenge assays. These results indicate that the progressor phenotype of the Ha-ras-induced tumor variants is not due to loss of tumor-specific transplantation or Class I major histocompatibility complex antigens. This implies that some tumor cells can escape the immune defenses of the normal immunocompetent host by mechanisms other than loss of tumor-specific transplantation and Class I major histocompatibility antigens.
Three Dimensional Imaging of LIGA-Made Microcomponents (2004)

Nickel and nickel-alloy microparts sized on the order of 5–1000 microns have been imaged in three dimensions using a new microscopic technique, Digital Volumetric Imaging (DVI). The gears were fabricated using Sandia National Laboratories’ LIGA technology (lithography, molding, and electroplating). The images were taken on a microscope built by Resolution Sciences Corporation by slicing the gear into one-micron thin slices, photographing each slice, and then reconstructing the image with software. The images were matched to the original CAD (computer aided design) model, allowing LIGA designers, for the first time, to see visually how much deviation from the design is induced by the manufacturing process. Calibration was done by imaging brass ball bearings and matching them to the CAD model of a sphere. A major advantage of DVI over scanning techniques is that internal defects can be imaged to very high resolution. In order to perform the metrology operations on the microcomponents, high-speed and high-precision algorithms are developed for coordinate metrology. The algorithms are based on a least-squares approach to data registration the {X,Y,Z} point clouds generated from the component surface onto a target geometry defined in a CAD model. Both primitive geometric element analyses as well as an overall comparison of the part geometry are discussed. Initial results of the micromeasurements are presented in the paper.
Antithrombotic Potential of Polymer-Coated Stents Eluting Platelet Glycoprotein IIb/IIIa Receptor Antibody (1996)

Platelet GP IIb/IIIa antibody eluting from polymer-coated stents reduces platelet deposition, improves blood flow, virtually abolishes cyclic flow variation, and improves patency rates after stent implantation in a rabbit iliac artery model. Its potential for reducing stent-related thrombosis in humans warrants further evaluation.
Effect of Ultraviolet Radiation on Cataract Formation (1988)

To investigate the relation of ultraviolet radiation and cataract formation, we undertook an epidemiologic survey of 838 watermen (mean age, 53 years) who worked on Chesapeake Bay. The annual ocular exposure was calculated from the age of 16 for each waterman by combining a detailed occupational history with laboratory and field measurements of sun exposure. Cataracts were graded by ophthalmologic examination for both type and severity. Some degree of cortical cataract was found in 111 of the watermen (13 percent), and some degree of nuclear cataract in 229 (27 percent). Logistic regression analysis showed that high cumulative levels of ultraviolet B exposure significantly increased the risk of cortical cataract (regression coefficient, 0.70; P = 0.04). A doubling of cumulative exposure increased the risk of cortical cataract by a factor of 1.60 (95 percent confidence interval, 1.01 to 2.64). Those whose annual average exposure was in the upper quartile had a risk increased by 3.30 (confidence interval, 0.90 to 9.97) as compared with those in the lowest quartile. Analysis using a serially additive expected-dose model showed that watermen with cortical lens opacities had a 21 percent higher average annual exposure to ultraviolet B (t-test, 2.23; P = 0.03). No association was found between nuclear cataracts and ultraviolet B exposure or between cataracts and ultraviolet A exposure. We conclude that there is an association between exposure to ultraviolet B radiation and cataract formation, which supports the need for ocular protection from ultraviolet B.
The continuous distributed monitoring model (2013)

In the model of continuous distributed monitoring, a number of observers each see a stream of observations. Their goal is to work together to compute a function of the union of their observations. This can be as simple as counting the total number of observations, or more complex non-linear functions such as tracking the entropy of the induced distribution. Assuming that it is too costly to simply centralize all the observations, it becomes quite challenging to design solutions which provide a good approximation to the current answer, while bounding the communication cost of the observers, and their other resources such as their space usage. This survey introduces this model, and describe a selection results in this setting, from the simple counting problem to a variety of other functions that have been studied.
La argumentación jurídica: un discurso de poder (2003)

Verdad, poder y Derecho son términos inescindibles, presentes en todo proceso de argumentación. Cuando el juez razona, denota el manejo de un preciso discurso que no es ajeno, ni mucho menos, a una determinada forma de saber, entendida ésta en términos de poder. He ahí una de las claras funciones de la Filosofía del Derecho: servir de intermediaria entre los saberes y prácticas jurídicas, de un lado,- de otro, el resto de las prácticas y los saberes sociales, lo que sólo se logra con un proceso interdisciplinario y no exclusivamente jurídico. La práctica del Derecho consiste, de manera fundamental, en argumentar, y en el presente escrito se pretende mostrar, no la razón de ser del Derecho, sino la forma como se asumen las razones jurídicas que sirven de justificación a una determinada decisión. Todo ello, claro está, dentro del contexto de un particular discurso: el discurso jurídico, entendido éste en términos de poder y no de verdad.
Collaborative calibration and sensor placement for mobile sensor networks (2012)

Mobile sensing systems carried by individuals or machines make it possible to measure position- and time-dependent environmental conditions, such as air quality and radiation. The low-cost, miniature sensors commonly used in these systems are prone to measurement drift, requiring occasional re-calibration to provide accurate data. Requiring end users to periodically do manual calibration work would make many mobile sensing systems impractical. We therefore argue for the use of collaborative, automatic calibration among nearby mobile sensors, and provide solutions to the drift estimation and placement problems posed by such a system.
Selection of Tumor-binding Ligands in Cancer Patients with Phage Display Libraries (2006)

Phage display has been used extensively in vitro and in animal models to generate ligands and to identify cancer-relevant targets. We report here the use of phage-display libraries in cancer patients to identify tumor-targeting ligands. Eight patients with stage IV cancer, including breast, melanoma, and pancreas, had phage-displayed random peptide or scFv library (1.6 x 10(8)-1 x 10(11) transducing units/kg) administered i.v.; tumors were excised after 30 minutes; and tumor-homing phage were recovered. In three patients, repeat panning was possible using phage recovered and amplified from that same patient's tumor. No serious side effects, including allergic reactions, were observed with up to three infusions. Patients developed antiphage antibodies that reached a submaximal level within the 10-day protocol window for serial phage administration. Tumor phage were recoverable from all the patients. Using a filter-based ELISA, several clones from a subset of the patients were identified that bound to a tumor from the same patient in which clones were recovered. The clone-binding to tumor was confirmed by immunostaining, bioassay, and real-time PCR-based methods. Binding studies with noncancer and cancer cell lines of the same histology showed specificity of the tumor-binding clones. Analysis of insert sequences of tumor-homing peptide clones showed several motifs, indicating nonrandom accumulation of clones in human tumors. This is the first reported series of cancer patients to receive phage library for serial panning of tumor targeting ligands. The lack of toxicity and the ability to recover clones with favorable characteristics are a first step for further research with this technology in cancer patients.
Sustained Nitric Oxide-Releasing Nanoparticles Induce Cell Death in Candida albicans Yeast and Hyphal Cells, Preventing Biofilm Formation <i>In Vitro</i> and in a Rodent Central Venous Catheter Model (2016)

Candida albicansis a leading nosocomial pathogen. Today, candidal biofilms are a significant cause of catheter infections, and such infections are becoming increasingly responsible for the failure of medical-implanted devices.C. albicansforms biofilms in which fungal cells are encased in an autoproduced extracellular polysaccharide matrix. Consequently, the enclosed fungi are protected from antimicrobial agents and host cells, providing a unique niche conducive to robust microbial growth and a harbor for recurring infections. Here we demonstrate that a recently developed platform comprised of nanoparticles that release therapeutic levels of nitric oxide (NO-np) inhibits candidal biofilm formation, destroys the extracellular polysaccharide matrices of mature fungal biofilms, and hinders biofilm development on surface biomaterials such as the lumen of catheters. We found NO-np to decrease both the metabolic activity of biofilms and the cell viability ofC. albicansin vitroandin vivo Furthermore, flow cytometric analysis found NO-np to induce apoptosis in biofilm yeast cellsin vitro Moreover, NO-np behave synergistically when used in combination with established antifungal drug therapies. Here we propose NO-np as a novel treatment modality, especially in combination with standard antifungals, for the prevention and/or remediation of fungal biofilms on central venous catheters and other medical devices.
SELECTIVITY IN SOLVENT EXTRACTION OF METAL IONS BY ORGANIC CATION EXCHANGERS SYNERGIZED BY MACROCYCLES: FACTORS RELATING TO MACROCYCLE SIZE AND STRUCTURE (1986)

ABSTRACT Crown ethers and related macrocycles strongly synergize the extraction (phase transfer) of certain metal Ions from aqueous nitrate solutions to toluene solutions of organophilic sulfonic, phosphoric, and carboxylic acids. For alkali metals, the degree of synergism is related to the size correspondence between the macrocycle cavity and the metal ion if macrocycles of similar type and substitution are considered. Alkaline earth metals are similarly strongly synergized but the size-correspondence relationship is less pronounced. Other factors seem to affect selectivity of these elements. Terr.-butylbenzo-substituted crown ethers of the same size are much less effective synergists for the alkaline earths than cyclohexano- or rerr.-butylcyclohexano-substituted compounds. However, with synergism in alkali metal extraction, the reverse is generally true; that is, ferf-butylbenzo-substituted crown ethers are better synergists than cyclohexano-substituted crown ethers. Effects involving the electron-withdrawing influence of the aromatic substituents and the flexibility of the ring may explain this selectivity reversal. The extraction of the divalent first-row transition metals, iron, cobalt, and nickel, is not synergized by any of the macrocycles. However, manganese and zinc with half and completely filled d-shells are synergized suggesting a possible correlation of synergistic coordination effects with ligand field stabilization in the first-row transition elements. Studies to determine the stoichiometry of the organic-phase complexes indicate a single crown ether associated with each molecule of the metal salt of the organic-phase acid. In some cases neutral organic acid molecules may also be associated with the complex.
Structural views of the ligand-binding cores of a metabotropic glutamate receptor complexed with an antagonist and both glutamate and Gd <sup>3+</sup> (2002)

Crystal structures of the extracellular ligand-binding region of the metabotropic glutamate receptor, complexed with an antagonist, (S)-(alpha)-methyl-4-carboxyphenylglycine, and with both glutamate and Gd3+ ion, have been determined by x-ray crystallographic analyses. The structure of the complex with the antagonist is similar to that of the unliganded resting dimer. The antagonist wedges the protomer to maintain an inactive open form. The glutamate/Gd3+ complex is an exact 2-fold symmetric dimer, where each bi-lobed protomer adopts the closed conformation. The surface of the C-terminal domain contains an acidic patch, whose negative charges are alleviated by the metal cation to stabilize the active dimeric structure. The structural comparison between the active and resting dimers suggests that glutamate binding tends to induce domain closing and a small shift of a helix in the dimer interface. Furthermore, an interprotomer contact including the acidic patch inhibited dimer formation by the two open protomers in the active state. These findings provide a structural basis to describe the link between ligand binding and the dimer interface.
Colonoscopy, Tumors, and Inflammatory Bowel Disease - New Diagnostic Methods (2006)

Accurate detection of premalignant lesions and early cancers in the colon is essential for curative endoscopic or surgical therapy, since the prognosis for the affected patients is closely related to the size and stage of the neoplastic lesion. Total colonoscopy is the accepted gold standard for screening and surveillance of colorectal cancer. This review summarizes recently published diagnostic developments and key findings in the areas of colonoscopy, colonic tumors, and inflammatory bowel diseases. Relevant findings have been reported for chromo-endoscopy in the diagnosis of colitis-associated neoplasia, as well as flat and depressed adenomas. Real-time Doppler capabilities have now been added to endoscopic optical coherence tomography; the results of large-scale testing of narrow-band imaging endoscopy in the colon are being awaited; and fluorescence imaging has recently been added to the facilities available in video endoscopy. Most importantly, endomicroscopy now for the first time allows single-cell subsurface imaging during ongoing colonoscopy procedures, opening the way to in-vivo molecular and functional imaging.
Molecular cloning with a pMEA300-derived shuttle vector and characterization of the Amycolatopsis methanolica prephenate dehydratase gene (1995)

An efficient restriction barrier for methylated DNA in the actinomycete Amycolatopsis methanolica could be avoided by using a nonmethylating Escherichia coli strain for DNA isolations. The A. methanolica prephenate dehydratase gene was cloned from a gene bank in a pMEA300-derived shuttle vector in E. coli and characterized.
Detection of pX proteins in human T-cell leukemia virus (HTLV)-infected cells by using antibody against peptide deduced from sequences of X-IV DNA of HTLV-I and Xc DNA of HTLV-II proviruses. (1984)

A 41-kilodalton protein was detected in four human T-cell leukemia virus type I (HTLV-I)-infected cell lines, a 68-kilodalton glycoprotein in MT-2 cells, and a 38-kilodalton protein in an HTLV-II-infected cell line by using antibody against a synthetic dodecapeptide, a portion of the polypeptide deduced from the nucleotide sequence of the X regions of HTLVs.
Bubble nucleation during devolatilization of polymer melts (1999)

Abstract Devolatilization of different types of polymer melts was studied experimentally and theoretically. The experimental work was carried out in a “falling‐strand”‐type apparatus built especially for this study. Polymer samples after devolatilization were examined by scanning electron microscopy. The micrographs obtained showed that strong nucleation of bubble nuclei occurs first in the vicinity of existing primary microbubbles. These bubble nuclei (secondary nuclei) form blisters (microbubbles) growing under appropriate conditions. The growth is controlled by momentum transfer and diffusion. The microbubbles then coalesce leading to formation of large voids and foaming of the polymer strands. The key parameter, the critical bubble radius triggering the process of growth, was assessed from the micrographs. The time dependence of the concentration of the residual styrene (dissolved gas) in polystyrene melt was determined by gas chromatography. A theoretical model of stress‐enhanced secondary nucleation in polymer melts during their devolatilization was developed. It shows that nucleation proceeds due to the growth of initially existing gas bubbles, when a sample is exposed to vacuum. In the vicinity of the bubbles homogeneous nucleation proceeds at an accelerated rate, because it is strongly enhanced by mechanical degradation of polymer macromolecules. The rate of devolatilization was calculated and compared with the experimental data. Theoretical results agreed with the experimental data rather good, although no adjustable parameters characteristic of some of the existing nucleation models were involved.
Inversion-based hardware gaussian random number generator: A case study of function evaluation via hierarchical segmentation (2006)

We present the design and implementation of a Gaussian random number generator (GRNG) via hierarchical segmentation. Gaussian samples are generated using the inversion method, which involves the evaluation of the inverse Gaussian cumulative distribution function (IGCDF). The IGCDF is highly nonlinear and is evaluated via piecewise polynomial approximations (splines) with a hierarchical segmentation scheme that involves uniform splines and splines with size varying by powers of two. This segmentation approach adapts the spline sizes according to the non-linearity of the function, allowing efficient evaluation of the IGCDF. Bit-widths of the fixed-point polynomial coefficients and arithmetic operators are optimized in an analytical manner to guarantee a precision accurate to one unit in the last place. Our architecture generates 16-bit Gaussian samples accurate to 8.2cr (standard deviations). A pipelined implementation on a Xilinx Virtex-4 XC4LX100-12 FPGA yields 371 MHz and occupies 543 slices, 2 block RAMs, and 2 DSP slices, generating one sample every clock cycle
A system and method for enhanced psychophysiological detection of deception (2003)

Through the pairing of perception (from our sensory systems - visual, auditory, and kinesthetic or VAK) with our representation systems (PS), deception reveals itself by multiple unconscious analog and digital language cues. Thus, indications that a person is being truthful, lying, or actively being deceptive can be recorded and analyzed using devices such as an electroencephalogram (EEG) or magnetoencephalogram (MEG). Consequently, the manner in which we demonstrate these microdynamic cues will dictate the significance that a particular element (either externally or internally driven) will have on our behavior or response, as an individual processes information that can be recorded and analyzed using such devices as an (EEG) or (MEG). In practice, a major difficulty with the reliability and validity of any lie detection technique is the extreme subjectivity of interpretation. Thus, to improve reliability, it is necessary to reduce the degree of subjectivity in the process through integration of methods or techniques. By base-lining how an individual processes information for lies and truths, and correlating these signatures with other micro-dynamics cues, a more accurate description of the deception can be established. Thus, merging techniques such as Human Dynamics' organizational neuro-somatopsychoform human cognitive subjective experience model, which establishes how an individual is processing information, and the Diogenes Company's Digital Voice Stress Analyzer technology for measurement of micro-dynamics of the autonomic microtremor, results in a system that is more reliable and accurate during the interrogation process generating a signature that can be observed and measured. These signatures/patterns provide the feedback required for determining incongruence in an individual's verbal and non-verbal cues, reflecting how an individual internally processes information that can be recorded and analyzed using the aforementioned devices.