gebhart/patrepeval huggingface dataset:
Time-Dependent Proteome Alterations under Osmotic Stress during Aerobic and Anaerobic Growth in Escherichia coli (2006)

Escherichia coli lives in the mammalian gastrointestinal tract anaerobically at high osmolarity as well as in the soil aerobically at varying osmolarities. Adaptation to these varying environmental conditions is crucial for growth and survival of E. coli. Two-dimensional protein gels were used to visualize global time-dependent changes (10 to 60 min) in the proteome of cells responding to osmotic stress (0.4 M NaCl or 0.7 M sorbitol) under aerobic or anaerobic conditions. The protein profiles revealed an induction of 12 proteins (Dps, HchA, HdhA, InfB, OsmC, OsmY, ProX, KatE, PspA, TalA, TktB, and TreF) under osmotic stress in an aerobic milieu. Eleven additional proteins (OtsB, YceI, YciE, YciF, YgaU, YjbJ, AcnA, MetL, PoxB, Ssb, and YhbO) were induced by osmotic stress imposed by NaCl. Most of the accumulated proteins were cross-protecting proteins (e.g., OsmY, OsmC, Dps, and KatE) which are regulated at the transcriptional level predominantly by RpoS and other regulators (e.g., integration host factor, OxyR, H-NS, LRP, and FIS). Comparative analysis of the proteome of E. coli grown under aerobic or anaerobic conditions under osmotic stress (NaCl) revealed an overlap of the up-regulated proteins of more than 50%. Ten proteins (PoxB, AcnA, TalA, TktB, KatE, PspA, Ssb, TreF, MetL, and YhbO) were detectable only under aerobic, high-osmolality conditions. Time-dependent alterations of the proteome were monitored, allowing classification of the up-regulated proteins into early, middle, and long-term phases of adaptation. Only a few proteins were found to be down-regulated upon osmotic stress.
Demonstration of a III-nitride edge-emitting laser diode utilizing a GaN tunnel junction contact (2016)

We demonstrate a III-nitride edge emitting laser diode (EELD) grown on a (2021) bulk GaN substrate with a GaN tunnel junction contact for hole injection. The tunnel junction was grown using a combination of metal-organic chemical-vapor deposition (MOCVD) and ammonia-based molecular-beam epitaxy (MBE) which allowed to be regrown over activated p-GaN. For a laser bar with dimensions of 1800 µm x 2.5 µm, without facet coatings, the threshold current was 284 mA (6.3 kA/cm<sup>2</sup>) and the single facet slope efficiency was 0.33 W/A (12% differential efficiency). A differential resistivity at high current density of 2.3 × 10<sup>-4</sup> Ω cm<sup>2</sup> was measured.
Utility of the sperm chromatin structure assay as a diagnostic and prognostic tool in the human fertility clinic (1999)

The sperm chromatin structure assay (SCSA) was used to measure over 500 human semen samples from two independent studies: Study I, 402 samples from 165 presumably fertile couples wishing to achieve pregnancy over 12 menstrual cycles; Study II, samples from 115 patients seeking fertility counselling. The SCSA measures susceptibility to DNA denaturation in situ in spermatozoa exposed to acid for 30 s, followed by acridine orange staining. SCSA data from the male partners of 73 couples (group 1) achieving pregnancy during months 1-3 of Study I were used as the standard of 'sperm chromatin compatible with high fertility' and were significantly different from those of 40 couples (group 3) achieving pregnancy in months 4-12 (P < 0.01) and those of male partners of 31 couples (group 4) not achieving pregnancy (P < 0.001). Group 2 contained couples who had a miscarriage. SCSA values for Study II were almost twice that of the Study I fertility standards. Within-couple repeatability tended to be less for group 3 than for groups 1, 2 or 4. Based on logistic regression, spermatozoa with denatured DNA (cells outside the main population, COMP alpha t) were the best predictor for whether a couple would not achieve pregnancy. Some 84% of males in group 1 had COMP alpha t < 15%, while no couples achieved pregnancy in group 1 with > or = 30% COMP alpha t, a threshold level considered not compatible with good fertility. Using selected cut-off values for chromatin integrity, the SCSA data predicted seven of 18 miscarriages (39%).
Inotersen Treatment for Patients with Hereditary Transthyretin Amyloidosis (2018)

Inotersen improved the course of neurologic disease and quality of life in patients with hereditary transthyretin amyloidosis. Thrombocytopenia and glomerulonephritis were managed with enhanced monitoring. (Funded by Ionis Pharmaceuticals; NEURO-TTR ClinicalTrials.gov number, NCT01737398 .).
Unique Lipoprotein Phenotype and Genotype Associated With Exceptional Longevity (2003)

Individuals with exceptional longevity and their offspring have significantly larger HDL and LDL particle sizes. This phenotype is associated with a lower prevalence of hypertension, cardiovascular disease, the metabolic syndrome, and increased homozygosity for the I405V variant in CETP. These findings suggest that lipoprotein particle sizes are heritable and promote a healthy aging phenotype.
GST pi gene is frequently coamplified with INT2 and HSTF1 proto-oncogenes in human breast cancers. (1991)

The glutathione S-transferase gene (GST pi) is located on the same chromosome band (11q13) as proto-oncogenes INT2 and HSTF1 which are frequently amplified in breast cancer. Using the Southern blot technique, we looked for the amplification of the GST pi gene in 17 fresh tumors from human mammary carcinoma. The tumors were preselected because either they had an amplification of the INT2 proto-oncogene detected by dot blot, or their karyotypes exhibited or did not exhibit homogeneously staining regions, a cytogenetic character indicating amplification. Coamplification of GST pi, HSTF1 and INT2 was observed in five tumors, and coamplification of GST pi and HSTF1 without amplification of INT2 in another tumor. We also observed coamplification of GST pi, INT2, HSTF1 in the mammary carcinoma cell line MDA/MB134, whereas GST pi alone was amplified in the mammary epithelial cell line HBL100. These results indicate that INT2, HSTF1 and GST pi belong to the same large amplicon. Since GST pi is involved in intracellular detoxication and since chemotherapeutic drugs are among its substrates, it will be of interest to study GST pi gene expression as well as the response to chemotherapy in patients presenting this amplicon.
Morpholino-Mediated Increase in Soluble Flt-1 Expression Results in Decreased Ocular and Tumor Neovascularization (2012)

Morpholino oligomers targeting the VEGFR1 mRNA exon/intron 13 junction promote production of soluble FLT-1 over membrane bound FLT-1, resulting in suppression of lesional volume in laser induced CNV and breast adenocarcinoma. Thus, morpholino manipulation of alternative splicing offers translational potential for therapy of angiogenic disorders.
Use of Proximity Ligation to Screen for Inhibitors of Interactions between Vascular Endothelial Growth Factor A and Its Receptors (2008)

The PLA may offer significant advantages over conventional methods for screening the interactions of ligands with their receptors. The assay may prove useful for parallel analyses of large numbers of samples in the screening of inhibitor libraries for promising agents. The technique provides dose-response curves, allowing IC(50) values to be calculated.
Identification and Characterization of a Peptide with Affinity to Head and Neck Cancer (2009)

Within the sequence of HBP-1 is a RGDLXXL motif, and most likely it is targeting the alpha(v)beta(6) receptor of the integrin family of cell adhesion receptors. HBP-1 represents a promising lead structure for the development of targeted therapies or diagnostic procedures in patients with HNSCC.
Maximum a posteriori estimation for multivariate Gaussian mixture observations of Markov chains (1994)

In this paper, a framework for maximum a posteriori (MAP) estimation of hidden Markov models (HMM) is presented. Three key issues of MAP estimation, namely, the choice of prior distribution family, the specification of the parameters of prior densities, and the evaluation of the MAP estimates, are addressed. Using HMM's with Gaussian mixture state observation densities as an example, it is assumed that the prior densities for the HMM parameters can be adequately represented as a product of Dirichlet and normal-Wishart densities. The classical maximum likelihood estimation algorithms, namely, the forward-backward algorithm and the segmental k-means algorithm, are expanded, and MAP estimation formulas are developed. Prior density estimation issues are discussed for two classes of applications/spl minus/parameter smoothing and model adaptation/spl minus/and some experimental results are given illustrating the practical interest of this approach. Because of its adaptive nature, Bayesian learning is shown to serve as a unified approach for a wide range of speech recognition applications.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Effect of Initial Combination Therapy With Sitagliptin, a Dipeptidyl Peptidase-4 Inhibitor, and Metformin on Glycemic Control in Patients With Type 2 Diabetes (2007)

The initial combination of sitagliptin and metformin provided substantial and additive glycemic improvement and was generally well tolerated in patients with type 2 diabetes.
Reconstruction of high-resolution 3D dose from matrix measurements: error detection capability of the COMPASS correction kernel method (2011)

The COMPASS system (IBA Dosimetry) is a quality assurance (QA) tool which reconstructs 3D doses inside a phantom or a patient CT. The dose is predicted according to the RT plan with a correction derived from 2D measurements of a matrix detector. This correction method is necessary since a direct reconstruction of the fluence with a high resolution is not possible because of the limited resolution of the matrix used, but it comes with a blurring of the dose which creates inaccuracies in the dose reconstruction. This paper describes the method and verifies its capability to detect errors in the positioning of a MLC with 10 mm leaf width in a phantom geometry. Dose reconstruction was performed for MLC position errors of various sizes at various locations for both rectangular and intensity-modulated radiotherapy (IMRT) fields and compared to a reference dose. It was found that the accuracy with which an error in MLC position is detected depends on the location of the error relative to the detectors in the matrix. The reconstructed dose in an individual rectangular field for leaf positioning errors up to 5 mm was correct within 5% in 50% of the locations. At the remaining locations, the reconstruction of leaf position errors larger than 3 mm can show inaccuracies, even though these errors were detectable in the dose reconstruction. Errors larger than 9 mm created inaccuracies up to 17% in a small area close to the penumbra. The QA capability of the system was tested through gamma evaluation. Our results indicate that the mean gamma provided by the system is slightly increased and that the number of points above gamma 1 ensures error detection for QA purposes. Overall, the correction kernel method used by the COMPASS system is adequate to perform QA of IMRT treatment plans with a regular MLC, despite local inaccuracies in the dose reconstruction.
TWEAK Induces Angiogenesis and Proliferation of Endothelial Cells (1999)

TWEAK is a recently described member of the Tumor Necrosis Factor (TNF) ligand family whose transcripts are present in a wide variety of human tissues (Chicheportiche, Y., Bourdon, P. R., Xu, H., Hsu Y. M., Scott, H., Hession, C., Garcia, I., and Browning, J. L. (1997) J. Biol. Chem. 272, 32401-32410). TWEAK is a weak inducer of apoptosis in transformed cells when administered with interferon-gamma or cycloheximide (Chicheportiche, Y., Bourdon, P. R., Xu, H., Hsu Y. M., Scott, H., Hession, C., Garcia, I., and Browning, J. L. (1997) J. Biol. Chem. 272, 32401-32410; Masters, S. A., Sheridan, J. P., Pitti, R. M., Brush, A. G., and Ashkenazi, A. (1998) Curr. Biol. 8, 525-528) and also promotes IL-8 secretion in cultured cells. We report here that picomolar concentrations of recombinant soluble TWEAK induce proliferation in a variety of normal human endothelial cells and in aortic smooth muscle cells and reduce culture requirements for serum and growth factors. Blocking antibodies to Vascular Endothelial Growth Factor (VEGF) do not significantly inhibit TWEAK-induced proliferation, indicating that TWEAK does not function indirectly through up-regulation of VEGF. Pellets containing TWEAK induce a strong angiogenic response when implanted in rat corneas, suggesting a role for TWEAK in vasculature formation in vivo.
Detection of activated Mr 21,000 protein, the product of ras oncogenes, using antibodies with specificity for amino acid 12. (1986)

Antisera raised to a set of chemically synthesized peptides spanning position 12 of ras Mr 21,000 protein (p21) (residues 5 to 17) were able to distinguish between different forms of p21 according to the amino acid at the twelfth codon. The peptide immunogens differed in one amino acid corresponding to position 12 of the protein; the substitutions were valine, serine, arginine, aspartate, alanine, or cysteine at this position. Normal p21 contains glycine at position 12; the other amino acid substitutions are those which would result from a single base change in codon 12 and may therefore be the activating mutations most likely to occur in human tumors. The peptide antisera were evaluated by the Western immunoblot procedure for reactivity with v-ki-ras p21 expressed in Escherichia coli containing the corresponding position 12 mutations. Five of the antisera reacted with p21, and of these, anti-serine, -valine, -arginine, and -aspartate peptide antibodies were specific for their cognate protein. Similar analysis using mammalian cells as sources of position 12 variant forms of p21 demonstrated the ability of these antisera to distinguish among their oncogenic forms of p21 differing by single amino acid substitutions.
Enzyme‐Carrying Polymeric Nanofibers Prepared via Electrospinning for Use as Unique Biocatalysts (2002)

Improvement of catalytic efficiency of immobilized enzymes via materials engineering was demonstrated through the preparation of bioactive nanofibers. Bioactive polystyrene (PS) nanofibers with a typical diameter of 120 nm were prepared and examined for catalytic efficiency for biotransformations. The nanofibers were produced by electrospinning functionalized PS, followed by the chemical attachment of a model enzyme, alpha-chymotrypsin. The observed enzyme loading as determined by active site titration was up to 1.4% (wt/wt), corresponding to over 27.4% monolayer coverage of the external surface of nanofibers. The apparent hydrolytic activity of the nanofibrous enzyme in aqueous solutions was over 65% of that of the native enzyme, indicating a high catalytic efficiency as compared to other forms of immobilized enzymes. Furthermore, nanofibrous alpha-chymotrypsin exhibited a much-improved nonaqueous activity that was over 3 orders of magnitude higher than that of its native counterpart suspended in organic solvents including hexane and isooctane. It appeared that the covalent binding also improved the enzyme's stability against structural denaturation, such that the half-life of the nanofibrous enzyme in methanol was 18-fold longer than that of the native enzyme.
Quantitative measurement of pathogen specific human memory T cell repertoire diversity using a CDR3β-specific microarray (2007)

This novel strategy appears to be robust and can be adapted to any situation where complex mixtures of highly similar sequences need to be quantitatively resolved.
Remix: making art and commerce thrive in the hybrid economy (2009)

Introduction Part One: Cultures (Cultures of Our Past Culture of Our Future RO, Extended RW, Revived Cultures Compared) Part Two: Economies (Two Economies: Commercial and Sharing Hybrid Economies Economy Lessons) Part Three: Enabling the Future (Reforming Law Reforming Us Conclusion)
Dip-Pen Nanolithography:  What Controls Ink Transport? (2002)

The influence of temperature and humidity on the growth rates of 1-octadecanethiol (ODT) and 16-mercaptohexadecanoic acid (MHA) monolayers deposited onto a gold substrate has been systematically studied in the context of dip-pen nanolithography (DPN) experiments. By analyzing a statistically meaningful data set, we conclude that for both inks the deposition rate increases with increasing temperature, and that this temperature dependence is strongly affected by relative humidity, chemical nature of the ink and substrate, and writing speed. We attribute these observations to the different solubilities of the ink molecules in water (both the water in the meniscus and on the cantilever walls). In addition, we report a set of experiments that demonstrate meniscus formation even at 0% relative humidity due to residual water that moves to the point of contact between tip and sample.
Presynaptic Control of Striatal Glutamatergic Neurotransmission by Adenosine A1–A2AReceptor Heteromers (2006)

The functional role of heteromers of G-protein-coupled receptors is a matter of debate. In the present study, we demonstrate that heteromerization of adenosine A1 receptors (A1Rs) and A2A receptors (A2ARs) allows adenosine to exert a fine-tuning modulation of glutamatergic neurotransmission. By means of coimmunoprecipitation, bioluminescence and time-resolved fluorescence resonance energy transfer techniques, we showed the existence of A1R-A2AR heteromers in the cell surface of cotransfected cells. Immunogold detection and coimmunoprecipitation experiments indicated that A1R and A2AR are colocalized in the same striatal glutamatergic nerve terminals. Radioligand-binding experiments in cotransfected cells and rat striatum showed that a main biochemical characteristic of the A1R-A2AR heteromer is the ability of A2AR activation to reduce the affinity of the A1R for agonists. This provides a switch mechanism by which low and high concentrations of adenosine inhibit and stimulate, respectively, glutamate release. Furthermore, it is also shown that A1R-A2AR heteromers constitute a unique target for caffeine and that chronic caffeine treatment leads to modifications in the function of the A1R-A2AR heteromer that could underlie the strong tolerance to the psychomotor effects of caffeine.
Arbitrary view position and direction rendering for large-scale scenes (2002)

This paper presents a new method for rendering views, especially those of large-scale scenes, such as broad city landscapes. The main contribution of our method is that we are able to easily render any view from an arbitrary point to an arbitrary direction on the ground in a virtual environment. Our method belongs to the family of work that employs plenoptic functions; however, unlike other works of this type, this particular method allows us to render a novel view from almost any point on the plane at which images are taken. Previous methods, on the other hand, have some restraints concerning their re-constructable area. Thus, when synthesizing a large-scale virtual environment such as a city, our method has a great advantage. One of the applications of our method is a driving simulator in the ITS domain. We can generate any view on any lane on the road from images taken by running along just one lane. Our method, using an omni-directional camera or a measuring device of a similar type, first captures panoramic images by running along a straight line, recording the capturing position of each image. When rendering, the method divides the stored panoramic images into vertical slits, selects some suitable ones based on our theory, and reassembles them for generating an image. The method can make a virtual city with walk-through capabilities. In that virtual city, people can move and look rather freely. In this paper, we describe the basic theory of a new plenoptic function, analyze the applicable areas of the theory and the characteristics of generated images, and demonstrate a complete working system using both indoor and outdoor scenes.
Redes sociais, experiência pública e política do dissenso. (2013)

Este trabalho discute as mobilizações que são constituídas a partir das redes sociais - no caso, as chamadas Marchas pela liberdade, ocorridas em 2011 no Brasil -, como pontos de vinculação entre sujeitos conduzidos no âmbito de uma experiência comunitária que extravasa as comunidades virtuais, além de expressarem um litígio que entrevê uma lógica dissensual na aparente consensualidade democrática. Sua materialização é consolidada a partir de um acontecimento que se liga a campos problemáticos recorrentes na pauta pública e que se finda com a expressão dos corpos em devir e em ação política, como pôde ser observado na análise das redes. Os eventos sugerem uma relação com a política caracterizada por formas de organização não abarcadas nos tradicionais mecanismos de instituição do debate público.
Asymmetric Catalysis of Epoxide Ring-Opening Reactions (2000)

The discovery of the metal salen-catalyzed asymmetric ring-opening (ARO) of epoxides is chronicled. A screening approach was adopted for the identification of catalysts for the addition of TMSN(3) to meso-epoxides, and the chiral (salen)CrN(3) complex was identified as optimal. Kinetic and structural studies served to elucidate the mechanism of catalysis, which involves cooperative activation of both epoxide and azide by two different metal centers. Covalently linked bimetallic complexes were constructed on the basis of this insight, and shown to catalyze the ARO with identical enantioselectivity but 1-2 orders of magnitude greater reactivity than the monomeric analogues. Extraordinarily high selectivity is observed in the kinetic resolution of terminal epoxides using the (salen)CrN(3)/TMSN(3) system. A search for a practical method for the kinetic resolution reaction led to the discovery of highly enantiomer-selective hydrolytic ring-opening using the corresponding (salen)Co(III) catalyst. This system displays extraordinary substrate generality, and allows practical access to enantiopure terminal epoxides on both laboratory and industrial scales.
The Novel Antioxidant Edaravone: From Bench to Bedside (2008)

Over the last decade, important advances have been made to support the fact that reactive oxygen species (ROS) are generated and play a harmful role during the acute and late stages of cerebral ischemia. Several drugs, such as radical scavengers and antioxidants, have been evaluated in preclinical and clinical studies. Edaravone (3-methyl-1-phenyl-2-pyrazolin-5-one; Radicut, Mitsubishi Tanabe Pharma Corporation) is a novel antioxidant that is currently used in Japan for the treatment of patients in the acute stage of cerebral infarction. Edaravone scavenges ROS and inhibits proinflammatory responses after brain ischemia in animals and humans. In particular, postischemic inflammation, leading to brain edema and infarction due to neuronal damage and endothelial cell death, can be ameliorated by edaravone. In addition to these antistroke effects, edaravone has also been shown to prevent oxidative damage to various extracerebral organs. Therefore, in addition to its usefulness in the treatment of stroke, edaravone is expected to play an integral role in the treatment of many oxidative stress-related diseases.