gebhart/patrepeval huggingface dataset:
Circulating tumour cells: their utility in cancer management and predicting outcomes (2010)

Recent advances in technology now permit robust and reproducible detection of circulating tumour cells (CTCs) from a simple blood test. Standardization in methodology has been instrumental in facilitating multicentre trials with the purpose of evaluating the clinical utility of CTCs. We review the current body of evidence supporting the prognostic value of CTC enumeration in breast, prostate and colorectal cancer, using standardized approaches, and studies evaluating the correlation of CTC number with radiological outcome. The exploitation of CTCs in cancer management, however, is now extending beyond prognostication. As technologies emerge to characterize CTCs at the molecular level, biological information can be obtained in real time, with the promise of serving as a 'surrogate tumour biopsy'. Current studies illuminate the potential of CTCs as pharmacodynamic and predictive biomarkers and potentially their use in revealing drug resistance in real time. Approaches for CTC characterization are summarized and the potential of CTCs in cancer patient management exemplified via the detection of epidermal growth factor receptor mutations from CTCs in patients with non-small cell lung cancer. The opportunity to learn more about the biology of metastasis through CTC analysis is now being realized with the horizon of CTC-guided development of novel anticancer therapies.
Self-Assembly Limits in Structural Proteins (2004)

A mechanics-based model is presented which predicts a “neutral annulus” for quasi-crystalline self-assembling nanostructure such as collagen fibrils, wherein transcript length, torsional and axial stiffness along with primary and quaternary protein structure limit the size to which these structures may aggregate. In the present treatment, a neutral annulus is predicted at 0.625 of the fibril radius, wherein portions of the fibril interior to the neutral annulus are in compression, balanced by portions exterior to the neutral annulus which are in tension.
One-Pot Friedländer Quinoline Synthesis: Scope and Limitations (2010)

A highly effective one-pot Friedländer quinoline synthesis from o-nitroarylcarbaldehydes and ketones or aldehydes was developed and the scope and limitations of the method were examined. The o-nitroarylcarbaldehydes were reduced to o-aminoarylcarbaldehydes with iron in the presence of a catalytic amount of aqueous hydrochloric acid; the amino compounds were then condensed in situ with ketones or aldehydes to form mono- or disubstituted quinolines, respectively, in good-to-excellent yields (58-100%).
New insights into the control of neurotrophic growth factor receptor signaling: Implications for nervous system development and repair (2012)

Neurotrophic growth factors control neuronal development by activating specific receptor tyrosine kinase positive signaling pathways, such as Ras-MAPK and PI3K-Akt cascades. Once activated, neurotrophic factor receptors also trigger a cascade of molecular events, named negative receptor signaling, that restricts the intensity of the positive signals and modulates cellular behavior. Thus, to avoid signaling errors that ultimately could lead to aberrant neuronal physiology and disease, negative signaling mechanisms have evolved to ensure that suitable thresholds of neuronal stimulation are achieved and maintained during right periods of time. Recent findings have revealed that neurotrophic factor receptor signaling is tightly modulated through the coordinated action of many different protein regulators that limit or potentiate signal propagation in spatially and temporally controlled manners, acting at specific points after receptor engagement. In this review, we discuss progress in this field, highlighting the importance of these modulators in axonal growth, guidance, neural connectivity, and nervous system regeneration.
Effect of Natural Chelating Agents on the Intestinal Absorption of Radiostrontium in Rats (1994)

Effect of Natural Chelating Agents on the Intestinal Absorption of Radiostrontium in Rats Get access Y. Nishimura, Y. Nishimura Search for other works by this author on: Oxford Academic PubMed Google Scholar I. Kakuta, I. Kakuta Search for other works by this author on: Oxford Academic PubMed Google Scholar H. Takeda, H. Takeda Search for other works by this author on: Oxford Academic PubMed Google Scholar J. Inaba, J. Inaba Search for other works by this author on: Oxford Academic PubMed Google Scholar K. Imai, K. Imai Search for other works by this author on: Oxford Academic PubMed Google Scholar K. Watari, K. Watari Search for other works by this author on: Oxford Academic PubMed Google Scholar N. Matsusaka N. Matsusaka Search for other works by this author on: Oxford Academic PubMed Google Scholar Radiation Protection Dosimetry, Volume 53, Issue 1-4, 1 May 1994, Pages 331–334, https://doi.org/10.1093/rpd/53.1-4.331 Published: 01 May 1994
Modulation of the fibrinolytic response of cultured human vascular endothelium by extracellularly generated oxygen radicals. (1992)

Clinical and experimental data indicate that activated oxygen species interfere with vascular endothelial cell function. Here, the impact of extracellular oxidant injury on the fibrinolytic response of cultured human umbilical vein endothelial (HUVE) cells was investigated at the protein and mRNA levels. Xanthine (50 microM) and xanthine oxidase (100 milliunits), which produces the superoxide anion radical (O2-) and hydrogen peroxide (H2O2), was used to sublethally injure HUVE cells. Following a 15-min exposure, washed cells were incubated for up to 24 h in serum-free culture medium. Tissue-type plasminogen activator (t-PA) antigen, plasminogen activator inhibitor-1 (PAI-1) antigen, and PAI-1 activity were determined in 1.25 ml of conditioned medium and t-PA and PAI-1 mRNA in the cell extracts of 2 x 10(6) HUVE cells. Control cells secreted 3.9 +/- 1.3 ng/ml (mean +/- S.D., n = 12) within 24 h. Treatment with xanthine/xanthine oxidase for 15 min induced a 2.8 +/- 0.4-fold increase (n = 12, p less than 0.05) of t-PA antigen secretion after 24 h. The t-PA antigen was recovered predominantly in complex with PAI-1. The oxidant injury caused a 3.0 +/- 0.8-fold increase (n = 9, p less than 0.05) in t-PA mRNA within 2 h. Total protein synthesis was unaltered by xanthine/xanthine oxidase. The oxidant scavengers superoxide dismutase and catalase, in combination, abolished the effect of xanthine/xanthine oxidase on t-PA secretion and t-PA mRNA synthesis. Xanthine/xanthine oxidase treatment of HUVE cells did not affect the PAI-1 secretion in conditioned medium nor the PAI-1 mRNA levels in cell extracts. Thus extracellular oxidant injury induces t-PA but not PAI-1 synthesis in HUVE cells.
Hybrid D-PCM, A Combination of PCM and DPCM (1978)

After a short review of the basic principles of PCM and DPCM coding it is shown that combining the two methods in one coding system results in a combination of some favorable properties. The hybrid D-PCM system combines the bit-rate reduction of DPCM with a low error sensitivity. In another approach the hybrid D-PCM system is also derived from a usual DPCM system with a leaking integrator. Two different applications of the hybrid D-PCM system illustrate the possibilities and the performance of the hybrid D-PCM system.
Development of Key Technologies for White Lighting Based on Light-Emitting Diodes (LEDs) (2004)

This program was organized to focus on materials development issues critical to the acceleration of solid-state lighting, and was split into three major thrust areas: (1) study of dislocation density reduction for GaN grown on sapphire using 'cantilever epitaxy', and the impact of dislocation density on the performance of state-of-the-art high-power LEDs; (2) the evaluation of in situ techniques for monitoring gas phase chemistry and the properties of GaN-based layers during metal-organic vapor phase epitaxy (MOCVD), and (3) feasibility for using semiconductor nanoparticles ('quantum dots') for the down-conversion of blue or ultraviolet light to generate white light. The program included a partnership between Lumileds Lighting (epitaxy and device fabrication for high power LEDs) and Sandia National Laboratories (cantilever epitaxy, gas phase chemistry, and quantum dot synthesis). Key findings included: (1) cantilever epitaxy can provide dislocation density reduction comparable to that of more complicated approaches, but all in one epitaxial growth step; however, further improvements are required to realize significant gains in LED performance at high drive currents, (2) in situ tools can provide detailed knowledge about gas phase chemistry, and can be used to monitor and control epitaxial layer composition and temperature to provide improved yields (e.g., a fivefold increase in color targeting is demonstrated for 540nm LEDs), and (3) quantum efficiency for quantum dots is improved and maintained up to 70% in epoxy thin films, but further work is necessary to increase densification (absorption) and robustness before practical application to LEDs.
Purification and Properties of Epithelial Growth Inhibitor (EGI) from Human Platelets: Its Separation from Type β Transforming Growth Factor (TGF-β)1 (1986)

We previously reported that sera from various kinds of animals contain a protein(s) capable of inhibiting the growth of the non-malignant epithelial cell line derived from Buffalo rat liver (BRL). In the present study, a similar epithelial cell-specific growth inhibitor (EGI) was purified to homogeneity from an acid-ethanol extract of human platelets. During purification, EGI was separated from the major component of type beta transforming growth factor (TGF-beta), which can stimulate the colony formation of the non-malignant fibroblastic cell line derived from rat kidney (NRK) in soft agar in the presence of epidermal growth factor (EGF). The purified EGI had an Mr of 27,000, and was composed of two subunits identical in Mr. It significantly inhibited the growth in monolayer cultures of three non-malignant epithelial cell lines, BRL, MDCK (from Madin-Darby canine kidney) and BSC-1 (from African green monkey kidney), at doses lower than 40 pg/ml in medium containing 10% fetal calf serum. Its inhibitory activity was stable against heating at 90 degrees C for 3 min, but not against treatment with 50 mM dithiothreitol. In addition, TGF-beta was also partially purified from the same extract. The purified TGF-beta did not show any inhibitory activity toward the growth of BRL, MDCK, BSC-1, or NRK.
Mutagenesis by reversible promoter insertion to study the activation of NF-κB (2005)

Genetic dissection of signaling pathways in mammalian cells involves screening or selecting phenotypic mutants obtained by a variety of techniques. Limitations in current methods include inadequate genome coverage and difficulty in validating the link between mutation and phenotype. We describe an improved method for insertional mutagenesis with retroviral vectors and show that the ability to induce mutations increases greatly if a randomly inserted promoter directs transcription into the host DNA. The mutant phenotype is due to the expression of a hybrid transcript derived from the vector and the insertion site. Because other alleles of the affected gene remain intact, the phenotype is dominant, but is reversible by inactivating the promoter, for example, by site-specific recombination. Importantly, in mutant clones with multiple inserts, limited excision yields progeny with different patterns of inserts remaining. Characterizing these progeny allows the mutant phenotype to be associated with a specific target gene. Relative simplicity and robust target validation make the method suitable for a broad range of applications. We have used this technique to search for proteins that regulate NF-kappaB-dependent signaling in human cells. Two validated targets are the relA gene, which codes for the NF-kappaB p65 subunit, and the NF-kappaB regulator act1. Overexpression of the corresponding proteins, caused by insertion of a promoter into the first intron of each gene, leads to NF-kappaB-dependent secretion of factors that activate NF-kappaB through cell-surface receptors, establishing an autocrine loop.
Probabilistic relational reasoning for differential privacy (2012)

Differential privacy is a notion of confidentiality that protects the privacy of individuals while allowing useful computations on their private data. Deriving differential privacy guarantees for real programs is a difficult and error-prone task that calls for principled approaches and tool support. Approaches based on linear types and static analysis have recently emerged; however, an increasing number of programs achieve privacy using techniques that cannot be analyzed by these approaches. Examples include programs that aim for weaker, approximate differential privacy guarantees, programs that use the Exponential mechanism, and randomized programs that achieve differential privacy without using any standard mechanism. Providing support for reasoning about the privacy of such programs has been an open problem. We report on CertiPriv, a machine-checked framework for reasoning about differential privacy built on top of the Coq proof assistant. The central component of CertiPriv is a quantitative extension of a probabilistic relational Hoare logic that enables one to derive differential privacy guarantees for programs from first principles. We demonstrate the expressiveness of CertiPriv using a number of examples whose formal analysis is out of the reach of previous techniques. In particular, we provide the first machine-checked proofs of correctness of the Laplacian and Exponential mechanisms and of the privacy of randomized and streaming algorithms from the recent literature.
Permissive linker insertion sites in the outer membrane protein of 987P fimbriae of Escherichia coli (1994)

The FasD protein is essential for the biogenesis of 987P fimbriae of Escherichia coli. In this study, subcellular fractionation was used to demonstrate that FasD is an outer membrane protein. In addition, the accessibility of FasD to proteases established the presence of surface-exposed FasD domains on both sides of the outer membrane. The fasD gene was sequenced, and the deduced amino acid sequence was shown to share homologous domains with a family of outer membrane proteins from various fimbrial systems. Similar to porins, fimbrial outer membrane proteins are relatively polar, lack typical hydrophobic membrane-spanning domains, and posses secondary structures predicted to be rich in turns and amphipathic beta-sheets. On the basis of the experimental data and structural predictions, FasD is postulated to consist essentially of surface-exposed turns and loops and membrane-spanning interacting amphipathic beta-strands. In an attempt to test this prediction, the fasD gene was submitted to random in-frame linker insertion mutagenesis. Preliminary experiments demonstrated that it was possible to produce fasD mutants, whose products remain functional for fimbrial export and assembly. Subsequently, 11 fasD alleles, containing linker inserts encoding beta-turn-inducing residues, were shown to express functional proteins. The insertion sites were designated permissive sites. The inserts used are expected to be least detrimental to the function of FasD when they are inserted into surface-exposed domains not directly involved in fimbrial export. In contrast, FasD is not expected to accommodate such residues in its amphipathic beta-strands without being destabilized in the membrane and losing function. All permissive sites were sequenced and shown to be located in or one residue away from predicted turns. In contrast, 5 of 10 sequenced nonpermissive sites were mapped to predicted amphipathic beta-strands. These results are consistent with the structural predictions for FasD.
A handheld mirror simulation (2003)

We present the design and construction of a handheld mirror simulation device. The perception of the world reflected through a mirror depends on the viewer's position with respect to the mirror and the 3-D geometry of the world. In order to simulate a real mirror on a computer screen, images of the observed world, consistent with the viewer's position, must be synthesized and displayed in real- time. Our system is build around a LCD screen manipulated by the user, a single camera fixed on the screen, and a tracking device. The continuous input video stream and tracker data is used to synthesize, in real-time, a continuous video stream displayed on the LCD screen. The synthesized video stream is a close approximation of what the user would see on the screen surface if it were a real mirror. Our system provides a generic interface for applications involving rich, first-person interaction, such as the virtual daguerreotype.
Integración de un curso MOOC y de un PLN-PLE en un curso presencial sobre fundamentos de la programación (2017)

En este trabajo se describen las experiencias educativas en un curso sobre Fundamentos de Programación en computadoras para alumnos de Ciencias Sociales y Humanidades que integra clases presenciales con elementos de la educación virtual como la participación en un curso masivo y abierto en línea (MOOC) y la elaboración de entornos y redes personales de aprendizaje (PLE-PLN). Esta hibridación de componentes presenciales y virtuales requiere de una integración y sincronización adecuada. En este sentido se ha tomado al curso MOOC como un “ayudante” en la impartición de la parte práctica del curso presencial y en el salón de clases se revisa la parte teórica y se llevan a cabo ejercicios y comentarios que tratan de integrar a las dos modalidades educativas. Esta integración se ve reforzada por el PLN-PLE que cada uno de los estudiantes va desarrollando conforme al avance en clase y en el curso masivo. Los PLNs-PLEs en su conjunto se pueden considerar como ciber-espacios de intercambio de información y construcción del conocimiento. La coordinación central de las actividades de ambas modalidades educativas se realiza por medio de un entorno virtual de enseñanza aprendizaje (EVEA) implementado en Moodle. El diseño instruccional que se ha seguido en clases está sustentado por la metodología del aprendizaje basado en proyectos que le permite al profesor y a los alumnos tener una visión y un objetivo bien planteados desde el principio del ciclo escolar. El marco pedagógico que soporta a los elementos presenciales y virtuales se da dentro de un contexto de aprendizaje conectivista que pretende alcanzar diferentes niveles de interacción e involucramiento cognitivo entre los participantes
Surface Matching of Dielectric Lenses (1955)

Two methods of cancelling the surface reflections of dielectric lenses are described in this paper. The first utilizes a simulated quarter-wave matching layer, and the second a reactive wall embedded within the dielectric. The reactive wall may take a variety of physical forms, such as arrays of thin conducting disks which have a capacitive reactance, or arrays of thin wires which have an inductive reactance. Surface matching is obtained when the disks are placed approximately ⅜ wavelength inside the lens, or the wires ⅛ wavelength. Curves are presented that show how the reflections at the air and dielectric boundary are reduced for various angles of incidence and polarization when quarter-wave layer and reactive-wall matching are employed. The reactance of the array of disks for waves incident at various angles and polarizations is computed by means of Bethe's small aperture theory, and Babinet's principle. Measurements in wave guide of the reactance of an array of circular disks for various angles of incidence and for both E- and H-plane polarization show close agreement with the theory.
Physical Chemistry of Non-aqueous Solutions of Cellulose and Its Derivatives (2000)

Phase Equilibria and Liquid Crystalline Order in Solutions of Cellulose and Its Derivatives. Influence of the Solvent on the Equilibrium and Kinetic Rigidity of the Molecular Chain of Cellulose and Its Derivatives in Solution. Thermochemistry of Dissolution of Cellulose in Non-aqueous Solvents. Solvation of Cellulose and Its Derivatives in Non-aqueous Solutions. Mathematical Models of Cellulose and Its Derivatives in Solution. Rheological Behaviour of Lyotropic LC Systems Based on Cellulose and Its Derivatives. Index.
Developmental Process and Synchronized Bursts in Cultured Neuronal Networks (2014)

Cultured neuronal networks are very useful for studying fundamental mechanisms associated with nervous system development and functioning. We have investigated network development and synchronized burst activity of neuronal cells cultured on multi-electrode arrays (MEAs). Using immunofluorescence staining, we measured excitatory and inhibitory synapse densities during 1-month development of cultured rat cortical networks. We also cultured the neurons on MEAs at different densities to investigate minimum network size required for synchronized bursts. In addition, we performed neuronal cell patterning on MEAs to control the network construction. In this review, our recent findings published in some papers are presented.
Recombinant IA-2 Expressed in<i>E. coli</i>can be used for the Routine Detection of Autoantibodies in Type-I Diabetes (1998)

We have investigated the possibility of measuring autoantibodies to IA-2 (IA-2A) using recombinant protein expressed in E. coli in a new radioassay. The intracellular part of IA-2 (IA-2ic) was expressed in E. coli as a biotinylated fusion protein and affinity-purified on a streptavidin column. The average yield of IA-2ic was about 1 mg purified protein from one litre of culture medium with E. coli. We could demonstrate the immunological activity of this material by blocking the autoantibody reactivity to in vitro synthesised IA-2ic. The IA-2ic fusion protein was then radiolabelled with 125I, purified by HPLC, and used in an immunoprecipitation assay for the detection of IA-2A. Sera from 46 of 68 (67%) patients with Type-I diabetes were positive by this radioassay, in contrst to only 2 of 50 (4%) patients with autoimmune thyroid disease and 1 of 114 (1 %) controls. There was a correlation between this radioassay and the previously established radioligand assay using synthesized 35S-methionine-labelled IA-2ic in vitro (r = 0.79, p < 0.001). We conclude that E. coli-derived IA-2 has the correct immunogenic conformation, and can be used for the detection of IA-2A with a similar sensitivity and specificity as the validated radioligand assay. This new assay can facilitate the measurement of IA-2A in routine laboratories where the radioligand assay is inconvenient or not available.
Identification of the Ca2+/Calmodulin-dependent Protein Kinase II Regulatory Phosphorylation Site in the α-Amino-3-hydroxyl-5-methyl4-isoxazole-propionate-type Glutamate Receptor (1997)

Ca2+/CaM-dependent protein kinase II (CaM-KII) can phosphorylate and potentiate responses of alpha-amino3-hydroxyl-5-methyl-4-isoxazole-propionate-type glutamate receptors in a number of systems, and recent studies implicate this mechanism in long term potentiation, a cellular model of learning and memory. In this study we have identified this CaM-KII regulatory site using deletion and site-specific mutants of glutamate receptor 1 (GluR1). Only mutations affecting Ser831 altered the 32P peptide maps of GluR1 from HEK-293 cells co-expressing an activated CaM-KII. Likewise, when CaM-KII was infused into cells expressing GluR1, the Ser831 to Ala mutant failed to show potentiation of the GluR1 current. The Ser831 site is specific to GluR1, and CaM-KII did not phosphorylate or potentiate current in cells expressing GluR2, emphasizing the importance of the GluR1 subunit in this regulatory mechanism. Because Ser831 has previously been identified as a protein kinase C phosphorylation site (Roche, K. W., O'Brien, R. J., Mammen, A. L., Bernhardt, J., and Huganir, R. L. (1996) Neuron 16, 1179-1188), this raises the possibility of synergistic interactions between CaM-KII and protein kinase C in regulating synaptic plasticity.