gebhart/patrepeval huggingface dataset:
AR Possesses an Intrinsic Hormone-Independent Transcriptional Activity (2002)

Recent research has highlighted the functional importance of chromatin structure in transcriptional regulation. We have used Xenopus oocytes as a model system to investigate the action of AR in the context of chromatin. By manipulating the levels of AR expression, we have observed both agonist-dependent and -independent activation by AR. Expression of AR at relatively low levels resulted in strong agonist-dependent activation, whereas high levels of AR also led to hormone-independent activation. By using gel mobility shift and deoxyribonuclease I footprinting assays, we demonstrate that AR expressed in Xenopus oocytes binds to a consensus androgen response element in vitro in a ligand-independent manner. Expression of the coactivators steroid receptor coactivator-1, receptor-associated coactivator-3, and p300 stimulated both agonist-dependent and -independent activation by AR. Furthermore, this hormone-independent activity of AR is also observed in mammalian cells. Antagonists such as casodex can inhibit hormone-independent activity of AR, and this inhibition appears to correlate with the enhanced association with corepressor silencing mediator of retinoid and thyroid hormone receptors. Altogether, our studies reveal that AR has a capacity to activate transcription in a ligand-independent manner.
Discovery of NKT cells and development of NKT cell-targeted anti-tumor immunotherapy (2015)

Natural Killer T (NKT) cells are unique lymphocytes characterized by their expression of a single invariant antigen receptor encoded by Vα14Jα18 in mice and Vα24Jα18 in humans, which recognizes glycolipid antigens in association with the monomorphic CD1d molecule. NKT cells mediate adjuvant activity to activate both CD8T cells to kill MHC-positive tumor cells and NK cells to eliminate MHC-negative tumor at the same time in patients, resulting in the complete eradication of tumors without relapse. Therefore, the NKT cell-targeted therapy can be applied to any type of tumor and also to anyone individual, regardless of HLA type.Phase IIa clinical trials on advanced lung cancers and head and neck tumors have been completed and showed significantly prolonged median survival times with only the primary treatment. Another potential treatment option for the future is to use induced pluripotent stem cell (iPS)-derived NKT cells, which induced adjuvant effects on anti-tumor responses, inhibiting in vivo tumor growth in a mouse model.
Imaging with concave large-aperture therapeutic ultrasound arrays using conventional synthetic-aperture beamforming (2008)

Several dual-mode ultrasound array (DMUA) systems are being investigated for potential use in image- guided surgery. In therapeutic mode, DMUAs generate pulsed or continuous-wave (CW) high-intensity focused ultrasound (HIFU) beams capable of generating localized therapeutic effects within the focal volume. In imaging mode, pulse-echo data can be collected from the DMUA elements to obtain B-mode images or other forms of feedback on the state of the target tissue before, during, and after the application of the therapeutic HIFU beam. Therapeutic and technological constraints give rise to special characteristics of therapeutic arrays. Specifically, DMUAs have concave apertures with low f-number values and are typically coarsely sampled using directive elements. These characteristics necessitate pre- and post-beamforming signal processing of echo data to improve the spatial and contrast resolution and maximize the image uniformity within the imaging field of view (IxFOV). We have recently developed and experimentally validated beamforming algorithms for concave large-aperture DMUAs with directive elements. Experimental validation was performed using a 1 MHz, 64-element, concave spherical aperture with 100 mm radius of curvature. The aperture was sampled in the lateral direction using elongated elements 1-lambda x 33.3-lambda with 1.333-lambda center-to-center spacing (lambda is the wavelength). This resulted in f-number values of 0.8 and 2 in the azimuth and elevation directions, respectively. In this paper, we present a new DMUA design approach based on different sampling of the shared concave aperture to improve image quality while maintaining therapeutic performance. A pulse-wave (PW) simulation model using a modified version of the Field II program is used in this study. The model is used in generating pulse-echo data for synthetic-aperture (SA) beamforming for forming images of a variety of targets, e.g., wire arrays and speckle-generating cyst phantoms. To provide validation for the simulation model and illustrate the improvements in image quality, we show SA images of similar targets using pulse-echo data acquired experimentally using our existing 64-element prototype. The PW simulation model is used to investigate the effect of transducer bandwidth as well as finer sampling of the concave DMUA aperture on the image quality. The results show that modest increases in the sampling density and transducer bandwidth result in significant improvement in spatial and contrast resolutions in addition to extending the DMUA IxFOV.
Delta algorithms (1998)

Delta algorithms compress data by encoding one file in terms of another. This type of compression is useful in a number of situations: strong multiple versions of data, displaying differences, merging changes, distributing updates, storing backups, transmitting video sequences, and others. This article studies the performance parameters of several delta algorithms, using a benchmark of over 1,300 pairs of files taken from two successive releases of GNU software. Results indicate that modern delta compression algorithms based on Ziv-Lempel techniques significantly outperform diff , a popular but older delta compressor, in terms of compression ratio. The modern compressors also correlate better with the actual difference between files without sacrificing performance.
Expression of envelope glycoprotein (E) of Japanese encephalitis virus by recombinant vaccinia virus. (1989)

Vaccinia virus recombinants inserted with cDNA clones of Japanese encephalitis (JE) virus envelope glycoprotein (E) gene were constructed. The E gene product was detected in the recombinant virus-infected BHK21 cells by immunofluorescence (IF) and Western blotting. The intensity of IF observed was higher by the recombinant of the TK promoter--P7.5 promoter--inserted cDNA construct than by the P7.5 promoter--TK promoter--inserted cDNA construct. The E gene product was hardly detected by the recombinant carrying the TK promoter only upstream to the inserted cDNA, although the glycoprotein E mRNA had been transcribed.
Characterization of a novel isozyme of cGMP-dependent protein kinase from bovine aorta (1989)

Two isozymic forms of cGMP-dependent protein kinase (designated types I alpha and I beta) were purified to homogeneity from bovine aorta smooth muscle. Type I alpha was apparently the same as the well characterized bovine lung cGMP-dependent protein kinase. Type I beta had a subunit Mr = 80,000 compared with Mr = 78,000 for type I alpha, and both forms were dimeric with similar calculated native Mr (170,000-178,000). Both enzymes contained two cGMP-binding sites per subunit, exhibited similar specificities for the peptide substrates tested, photoaffinity labeled with 8-N3[32P] cAMP, and catalyzed autophosphorylation. Silver-stained peptide maps of types I alpha and I beta were similar but not identical; however, autoradiographs of peptide maps of these enzymes prelabeled by either autophosphorylation or photoaffinity labeling showed clearly different patterns. The amino-terminal sequence of a breakdown product of type I beta could not be aligned confidently with any of the published sequence of bovine lung cGMP-dependent protein kinase. [3H]cGMP dissociation curves for types I alpha and I beta were both biphasic, but the dissociation rate of the slow component of type I beta was faster than the corresponding component of type I alpha. The concentration of cGMP required for half-maximal activation (K alpha) was slightly lower for type I alpha than for type I beta (0.29 and 0.44 microM, respectively), and the two enzymes had similar K alpha values for cAMP (16 and 18 microM, respectively). Types I alpha and I beta exhibited different K alpha values for several cGMP analogs. The abundance of type I beta in specific tissues suggested that it could have an important physiological role.
Reduced Body Weight, Adipose Tissue, and Leptin Levels Despite Increased Energy Intake in Female Mice Lacking Acylation-Stimulating Protein (2000)

Acylation-stimulating protein (ASP) is a potent lipogenic protein produced by adipocytes. In vitro studies have shown that ASP increases triglyceride synthesis and glucose transport in both murine and human adipocytes. Our initial study indicated that complement C3-deficient (−/−) mice (and, therefore, ASP deficient) demonstrated altered dietary postprandial triglyceride clearance. In the present study we examined the phenotype of female mice longitudinally on different diets. Female C3(−/−) mice on both low (10% of energy) and high (40% of energy) fat diets displayed an average reduction in total body weight of 10.1 ± 0.5% (P < 0.0003, by ANOVA) compared with the C3(+/+) littermates. Reductions in white adipose tissue mass accounted for most of this weight difference (59% reduction; P < 0.01 on low fat diet). Plasma leptin levels were significantly reduced in C3(−/−) mice on both high (P < 0.001) and low fat diets (P < 0.01). This reduction was significant even after adjusting for the reduced body weight and body fat (P < 0.001). Leptin reductions in the C3(−/−) were greater on the high fat diet and were associated with increased food intake (18 ± 2% increase; P< 0.001). Furthermore, there was a decrease in basal glucose levels and basal insulin levels [12.8% decrease in glucose at 14 weeks (HF; P < 0.05) and 41% decrease in insulin at 26 weeks (HF; P < 0.05)]. These in vivo experiments demonstrate that female mice lacking ASP have marked alterations of body weight, adiposity, plasma leptin, and plasma insulin levels. Decreased adiposity and leptin levels occurred in the ASP-deficient animals despite increased energy intake, suggesting that energy expenditure was elevated in these animals. Thus, ASP appears to have an important role in the regulation of energy balance in mice.
Combined Gas and Supercritical Fluid Chromatography for the High Resolution Separation of Volatile and Nonvolatile Compounds (1987)

Separation de melanges de composes organiques volatils et non volatils sur une seule colonne, en une seule etape continue
A single amino acid substitution (F363I) converts the regiochemistry of the spearmint (−)-limonene hydroxylase from a C6- to a C3-hydroxylase (2000)

The essential oils of peppermint and spearmint are distinguished by the position of oxygenation on the constituent p-menthane monoterpenes. Peppermint produces monoterpenes bearing an oxygen at C3, whereas spearmint produces monoterpenes bearing an oxygen at C6. Branching of the monoterpene biosynthetic pathways in these species is determined by two distinct cytochrome P450s that catalyze the regiospecific hydroxylation of (-)-4S-limonene at C3 or C6 exclusively. cDNAs encoding the limonene-3-hydroxylase from peppermint and the limonene-6-hydroxylase from spearmint have been isolated, shown to be 70% identical at the amino acid level, and functionally expressed. A combination of domain swapping and reciprocal site-directed mutagenesis between these two enzymes demonstrated that the exchange of a single residue (F363I) in the spearmint limonene-6-hydroxylase led to complete conversion to the regiospecificity and catalytic efficiency of the peppermint limonene-3-hydroxylase.
Global burden of COPD: systematic review and meta-analysis (2006)

The aim of this study was to quantify the global prevalence of chronic obstructive pulmonary disease (COPD) by means of a systematic review and random effects meta-analysis. PubMed was searched for population-based prevalence estimates published during the period 1990-2004. Articles were included if they: 1) provided total population or sex-specific estimates for COPD, chronic bronchitis and/or emphysema; and 2) gave method details sufficiently clearly to establish the sampling strategy, approach to diagnosis and diagnostic criteria. Of 67 accepted articles, 62 unique entries yielded 101 overall prevalence estimates from 28 different counties. The pooled prevalence of COPD was 7.6% from 37 studies, of chronic bronchitis alone (38 studies) was 6.4% and of emphysema alone (eight studies) was 1.8%. The pooled prevalence from 26 spirometric estimates was 8.9%. The most common spirometric definitions used were those of the Global Initiative for Chronic Obstructive Lung Disease (13 estimates). There was significant heterogeneity, which was incompletely explained by subgroup analysis (e.g. age and smoking status). The prevalence of physiologically defined chronic obstructive pulmonary disease in adults aged > or =40 yrs is approximately 9-10%. There are important regional gaps, and methodological differences hinder interpretation of the available data. The efforts of the Global Initiative for Chronic Obstructive Lung Disease and similar groups should help to standardise chronic obstructive pulmonary disease prevalence measurement.
A SMART scheduler for multimedia applications (2003)

Real-time applications such as multimedia audio and video are increasingly populating the workstation desktop. To support the execution of these applications in conjunction with traditional non-real-time applications, we have created SMART, a Scheduler for Multimedia And Real-Time applications. SMART supports applications with time constraints, and provides dynamic feedback to applications to allow them to adapt to the current load. In addition, the support for real-time applications is integrated with the support for conventional computations. This allows the user to prioritize across real-time and conventional computations, and dictate how the processor is to be shared among applications of the same priority. As the system load changes, SMART adjusts the allocation of resources dynamically and seamlessly. It can dynamically shed real-time computations and regulate the execution rates of real-time tasks when the system is overloaded, while providing better value in underloaded conditions than previously proposed schemes.We have implemented SMART in the Solaris UNIX operating system and measured its performance against other schedulers commonly used in research and practice in executing real-time, interactive, and batch applications. Our experimental results demonstrate SMART's superior performance over fair queueing and UNIX SVR4 schedulers in supporting multimedia applications.
An investigation into graph cut parameter optimisation for image-fusion applications (2012)

The graph cut technique has been employed successfully in a large number of computer graphics and computer vision related problems. The algorithm has yielded particularly impressive results in the field of image fusion, e.g., texture tiling, image stitching, and image and video editing. An analysis of the literature shows that authors use different variations of the algorithm, such as different cost functions and parameters. However, there are no detailed investigations on how these parameters influence results and what parameters are most suitable for what type of application. In this paper we analyse the use of graph cut algorithms in different image fusion applications. We list and classify relevant parameters, suggest new cost functions for seam optimisation, and analyse the effect of parameter choices on different application scenarios. Based on the results we develop guidelines assisting users to employ the graph cut technique effectively in different image fusion applications.
Secreted Antibody/Granzyme B Fusion Protein Stimulates Selective Killing of HER2-overexpressing Tumor Cells (2004)

Targeted cell killing is required for effective treatment of cancers. We previously described the generation of a chimeric immunocasp-3 protein and its potent selective antitumor activity (Jia, L. T., Zhang, L. H., Yu, C. J., Zhao, J., Xu, Y. M., Gui, J. H., Jin, M., Ji, Z. L., Wen, W. H., Wang, C. J., Chen, S. Y., and Yang, A. G. (2003) Cancer Res. 63, 3257-3262). Here we extend the repertoire of another chimeric pro-apoptotic protein immunoGrB, which comprises an anti-HER2 single-chain antibody, a Pseudomonas exotoxin A translocation domain and active granzyme B. Human lymphoma Jurkat cells transfected with the immunoGrB gene expression vector were able to produce and secrete the chimeric protein. The immunoGrB molecule selectively recognized and destroyed HER2-overexpressing tumor cells both in vitro and in nude mouse after intramuscular injection of the immunoGrB expression plasmid. Further in vivo study showed that intravenous administration of immunoGrB gene-modified lymphocytes led to suppression of HER2-overexpressing tumor growth and prolonged animal survival because of continuous secretion of immunoGrB molecules into blood and lymph fluid. These results demonstrate that the chimeric immunoGrB molecule, which is capable of antibody-directed targeting and granzyme B-mediated killing, has therapeutic potential against HER2 tumors, especially in cases in which caspase-dependent apoptosis is inhibited.
High Temperature Sensors Based on Metal–Insulator–Silicon Carbide Devices (1997)

High temperature gas sensors based on catalytic metal–insulator–silicon carbide (MISiC) devices are developed both as capacitors and Schottky diodes. A maximum operation temperature of 1000 °C is obtained for capacitors based on 4H-SiC, and all sensors work routinely for several weeks at 600 °C. Reducing gases like hydrocarbons and hydrogen lower the flat band voltage of the capacitor and the barrier height of the diode. The time constants for the gas response are in the order of milliseconds and because of this good performance the sensors are tested for combustion engine control. For temperatures around 600 °C total combustion occurs on the sensor surface and the signal is high for fuel in excess and low for air in excess. At temperatures around 400°C the response is more linear. The high temperature operation causes interdiffusion of the metal and insulator layers in these devices, and this interdiffusion has been studied. At sufficiently high temperatures the inversion capacitance shows different levels for hydrogen free and hydrogen containing ambients, which is suggested to be due to a reversible hydrogen annealing effect at the insulator–silicon carbide interface.
Eset partners with Oct4 to restrict extraembryonic trophoblast lineage potential in embryonic stem cells (2009)

The histone H3 Lys 9 (H3K9) methyltransferase Eset is an epigenetic regulator critical for the development of the inner cell mass (ICM). Although ICM-derived embryonic stem (ES) cells are normally unable to contribute to the trophectoderm (TE) in blastocysts, we find that depletion of Eset by shRNAs leads to differentiation with the formation of trophoblast-like cells and induction of trophoblast-associated gene expression. Using chromatin immmunoprecipitation (ChIP) and sequencing (ChIP-seq) analyses, we identified Eset target genes with Eset-dependent H3K9 trimethylation. We confirmed that genes that are preferentially expressed in the TE (Tcfap2a and Cdx2) are bound and repressed by Eset. Single-cell PCR analysis shows that the expression of Cdx2 and Tcfap2a is also induced in Eset-depleted morula cells. Importantly, Eset-depleted cells can incorporate into the TE of a blastocyst and, subsequently, placental tissues. Coimmunoprecipitation and ChIP assays further demonstrate that Eset interacts with Oct4, which in turn recruits Eset to silence these trophoblast-associated genes. Our results suggest that Eset restricts the extraembryonic trophoblast lineage potential of pluripotent cells and links an epigenetic regulator to key cell fate decision through a pluripotency factor.
Considerations in bringing a cancer biomarker to clinical application. (1992)

Specific challenges face our application of emerging biomarkers to early lung cancer detection. These challenges might be considered frontiers to be bridged between established biomedical disciplines, requiring expertise often beyond the range of individual investigators. Cross-disciplinary research already has led to new appreciation of the mechanisms which underlie the phenotypic expression of the transformed cell and places within our grasp the tools which might lead to successful early lung cancer detection. Prior to the successful application of newly described markers, further cross-disciplinary research must (a) refine the selection of biologically appropriate markers, (b) validate such markers against acknowledged disease end points, (c) establish quantitative criteria for marker presence/absence, and (d) confirm marker predictive value in prospective population trials.
Photocontrol of cell adhesion on amino-bearing surfaces by reversible conjugation of poly(ethylene glycol) via a photocleavable linker (2011)

Dynamic control of cell adhesion on substrates is a useful technology in tissue engineering and basic biology. This paper describes a method for the control of cell adhesion on amino-bearing surfaces by reversible conjugation of an anti-fouling polymer, poly(ethylene glycol) (PEG), via a newly developed photocleavable linker, 1-(5-methoxy-2-nitro-4-prop-2-ynyloxyphenyl)ethyl N-succinimidyl carbonate (1). This molecule has alkyne and succinimidyl carbonate at each end, which are connected by photocleavable 2-nitrobenzyl ester. Under this molecular design, the molecule crosslinked azides and amines, whose linkage cleaved upon application of near-UV light. By using aminosilanised glass and silicon as model substrates, we studied their reversible surface modification with PEG-azide (M(w) = 5000) based on contact angle measurements, ellipsometry, and AFM morphological observations. Protein adsorption and cell adhesion dramatically changed by PEGylation and the following irradiation, which can be used for cellular patterning. Also, the capability of the substrate to change cell adhesiveness by photoirradiation during cell cultivation was demonstrated by inducing cell migration. We believe this method will be useful for dynamic patterning of cells on protein-based scaffolds.
Inhibition of experimental corneal neovascularisation by bevacizumab (Avastin) (2006)

Topically administered bevacizumab (Avastin) at a concentration of 4 mg/ml limits corneal neovascularisation following chemical injury in the male Long Evans rat model.
Effect of Endothelin-A Receptor Blockade With Atrasentan on Tumor Progression in Men With Hormone-Refractory Prostate Cancer: A Randomized, Phase II, Placebo-Controlled Trial (2003)

Atrasentan is an oral, targeted therapy with favorable tolerability and the potential to delay progression of HRPCa.
I. TNF-induced liver injury (1998)

Tumor necrosis factor-alpha (TNF-alpha) functions as a two-edged sword in the liver. TNF-alpha is required for normal hepatocyte proliferation during liver regeneration. It functions both as a comitogen and to induce the transcription factor nuclear factor-kappaB, which has antiapoptotic effects. On the other hand, TNF-alpha is the mediator of hepatotoxicity in many animal models, including those involving the toxins concanavalin A and lipopolysaccharide. TNF-alpha has also been implicated as an important pathogenic mediator in patients with alcoholic liver disease and viral hepatitis.