gebhart/patrepeval huggingface dataset:
Abstract A02: Beta-catenin-independent activation of TCF1/LEF1 in human hematopoietic tumor cells through interaction with ATF2 transcription factors (2013)

Abstract The role of Wnt signaling in embryonic development and stem cell maintenance is well established and aberrations leading to the constitutive up-regulation of this pathway are frequent in several types of human cancers. Upon ligand-mediated activation, Wnt receptors promote the stabilization of beta-catenin, which translocates to the nucleus and binds to the T-cell factor/lymphoid enhancer factor (TCF/LEF) family of transcription factors to regulate the expression of Wnt target genes. When not bound to beta-catenin, the TCF/LEF proteins are believed to act as transcriptional repressors. Using a specific lentiviral reporter, we identified hematopoietic tumor cells displaying constitutive TCF/LEF transcriptional activation in the absence of beta-catenin stabilization. Suppression of TCF/LEF activity in these cells mediated by an inducible dominant-negative TCF4 (DN-TCF4) inhibited both cell growth and the expression of Wnt target genes. Further, expression of TCF1 and LEF1, but not TCF4, stimulated TCF/LEF reporter activity in certain human cell lines independently of beta-catenin. By a complementary approach in vivo, TCF1 mutants, which lacked the ability to bind to beta-catenin, induced Xenopus embryo axis duplication, a hallmark of Wnt activation, and the expression of the Wnt target gene Xnr3. Through generation of different TCF1-TCF4 fusion proteins, we identified three distinct TCF1 domains that participate in the beta-catenin-independent activity of this transcription factor. TCF1 and LEF1 physically interacted and functionally synergized with members of the activating transcription factor 2 (ATF2) family of transcription factors. Moreover, knockdown of ATF2 expression in lymphoma cells phenocopied the inhibitory effects of DN-TCF4 on the expression of target genes associated with the Wnt pathway and on cell growth. Together, our findings indicate that, through interaction with ATF2 factors, TCF1/LEF1 promote the growth of hematopoietic malignancies in the absence of beta-catenin stabilization, thus establishing a new mechanism for TCF1/LEF1 transcriptional activity distinct from that associated with canonical Wnt signaling. Citation Format: Luca Grumolato, Guizhong Liu, Tomomi Haremaki, Sathish Kumar Mungamuri, Phyllus Mong, Gal Akiri, Pablo Lopez-Bergami, Adriana Arita, Anouar Youssef, Marek Mlodzik, Ze'ev A. Ronai, Joshua Brody, Daniel C. Weinstein, Stuart A. Aaronson. Beta-catenin-independent activation of TCF1/LEF1 in human hematopoietic tumor cells through interaction with ATF2 transcription factors. [abstract]. In: Proceedings of the Third AACR International Conference on Frontiers in Basic Cancer Research; Sep 18-22, 2013; National Harbor, MD. Philadelphia (PA): AACR; Cancer Res 2013;73(19 Suppl):Abstract nr A02.
Direct Asymmetric Amination of α-Branched Cyclic Ketones Catalyzed by a Chiral Phosphoric Acid (2015)

Here we report the direct asymmetric amination of α-substituted cyclic ketones catalyzed by a chiral phosphoric acid, yielding products with a N-containing quaternary stereocenter in high yields and excellent enantioselectivities. Kinetic resolution of the starting ketone was also found to occur on some of the substrates under milder conditions, providing enantioenriched α-branched ketones, another important building block in organic synthesis. The utility of this methodology was demonstrated in the short synthesis of (S)-ketamine, the more active enantiomer of this versatile pharmaceutical.
EVM Calculation for Broadband Modulated Signals (2004)

Abstract: We present a normalization that facilitates calculation of error vector magnitude (EVM) from measurements. We derive the definition of EVM for a common industry standard from a more basic equation. We compare EVM for various modulation types for a given average symbol power under simple distortion conditions.
Data entry workers perceptions and satisfaction response to the "Stop and Stretch" software program (2006)

Cumulative Trauma Disorder (CTD) is a collection of chronic musculoskeletal disorders caused by frequent, sustained, and repetitive movements, most notably by computer usage at the workplace. A computer based break reminder program (Stop and Stretch) has been developed and installed to prevent CTDs caused by prolonged computer usage at the workplace. We investigated users' opinions to the Stop and Stretch program at their work place. 19 computer users were recruited as the subjects of the study. We conducted a survey after all the subjects used the Stop and Stretch program for one month. Among the nineteen subjects, 52.5% or 10 noticed a difference of symptoms after using the program; 63.3% or 12 thought the program had positive effect on their productivity; 100% or all 19 thought the program was easy to follow; 100% or all 19 thought it was helpful; 94.7% or18 were satisfied with the program; and the same value would recommend the program to others. When grouped into those who had prior experience with using stretch and exercise as part of their work routine15 subjects had no prior experience; and 14 participants within that group were satisfied or very satisfied with the program; 93.3% or 14 would recommend it to co-workers; and over half of those 15 thought the program is easy to use. The study provided insight to the response to using "stretch break software" and provided indicators of satisfaction with the Stop and Stretch program and that the program had sufficient usability and acceptance within a workplace setting which might be applied in other work settings similar to these.
Alleviating Garbage Collection Interference Through Spatial Separation in All Flash Arrays. (2019)

We present SWAN, a novel All Flash Array (AFA) management scheme. Recent flash SSDs provide high I/O bandwidth (e.g., 3-10GB/s) so the storage bandwidth can easily surpass the network bandwidth by aggregating a few SSDs. However, it is still challenging to unlock the full performance of SSDs. The main source of performance degradation is garbage collection (GC). We find that existing AFA designs are susceptible to GC at SSD-level and AFA software-level. In designing SWAN, we aim to alleviate the performance interference caused by GC at both levels. Unlike the commonly used temporal separation approach that performs GC at idle time, we take a spatial separation approach that partitions SSDs into the front-end SSDs dedicated to serve write requests and the back-end SSDs where GC is performed. Compared to temporal separation of GC and application I/O, which is hard to be controlled by AFA software, our approach guarantees that the storage bandwidth always matches the full network performance without being interfered by AFA-level GC. Our analytical model confirms this if the size of front-end SSDs and the back-end SSDs are properly configured. We provide extensive evaluations that show SWAN is effective for a variety of workloads.
Practical methods for sparsity based video anomaly detection (2013)

Video anomaly detection can be used in the transportation domain to identify unusual patterns such as traffic violations, accidents, unsafe driver behavior, street crime, and other suspicious activities. Recently, sparse reconstruction techniques have been used for image classification, and shown to provide excellent robustness to occlusion. This progress has also been leveraged for sparsity based video anomaly detection where test trajectories are expressed as sparse linear combinations of example trajectories from a given (normal or anomalous) class. While sparsity based anomaly detection techniques are promising, they pose practical challenges due to their increased computational burden and the need for generous manually labeled training (even if only for normal event trajectories). Our work focuses on overcoming these limitations. Our central contribution is a dictionary design and optimization technique that can effectively reduce the size of training dictionaries that enable sparsity based classification/anomaly detection without adversely influencing detection performance. We also suggest the use of state of the art automatic trajectory clustering techniques for initializing dictionaries which can alleviate the burden of manual labeling. Experimental results show that significant computational advantages can be obtained with the proposed techniques with little performance loss over using large and manually labeled dictionaries of example trajectories.
BUCKLING RESPONSE OF LAMINATES WITH SPATIALLY VARYING FIBER ORIENTATIONS (1993)

The buckling response of a symmetrically laminated composite panel with a spatially varying fiber orientation has been analyzed. Variation of the fiber orientation angle as a function of the position in the panel results in a composite laminate with stiffness properties that are functions of the panel coordinates. The laminates are therefore termed variable stiffness panels. The fiber orientation is assumed to vary only in one spatial direction, although the analysis can be extended to fiber orientations that vary in two spatial directions. The Ritz Method has been used to find the buckling loads and buckling modes for the variable stiffness panels for two different cases. In one of the cases the fiber orientation is assumed to change in the direction of the applied load. The other case is the one in which the fiber orientation varies in a direction perpendicular to the loading direction. Improvements in the buckling load of up to 80 percent over straight fiber configurations were found. Results for three different panel aspect ratios are presented.
Tyrosine phosphorylation of IgM- and IgD-associated molecules of a human B lymphoma cell line B104 (1992)

We investigated tyrosine phosphorylation and structural properties of the IgM-associated molecules in comparison with IgD-associated molecules in a recently established human surface IgM+, IgD+ B lymphoma cell line, B104, the growth of which was irreversibly inhibited by anti-IgM mAbs but not by anti-IgD mAbs. Tyrosine kinase activity and tyrosine phosphorylated proteins were detected in anti-IgM and anti-IgD immunoprecipitates from digitonin lysates of B104 cells with the use of an in vitro kinase assay followed by a re-immunoprecipitation experiment with anti-phosphotyrosine mAbs. Tyrosine phosphorylated proteins of 74, 58-44, 41, and 39 kDa were detected in anti-IgM immunoprecipitates, whereas tyrosine phosphorylated proteins of 74, 58-44, and 39 kDa, but not 41 kDa, were detected in anti-IgD immunoprecipitates. Crosslinking of surface IgM and surface IgD stimulated rapid tyrosine phosphorylation of different sets of proteins which included tyrosine-phosphorylated proteins of the same or similar molecular weights as those detected in the anti-IgM and anti-IgD immunoprecipitates respectively. After deglycosylation by N-glycosidase, both the IgM- and IgD-associated phosphoproteins (pp58-pp39) gave rise to the same three bands of 29, 27, and 26 kDa. Proteolytic peptide mapping of these three deglycosylated proteins showed that the primary structures of the IgM- and IgD-associated molecules are identical, suggesting that the IgM- and IgD-associated phosphoproteins (pp58-pp39) are the products of the same or closely related genes. One of the products, pp41, may be associated with IgM, but not with IgD, although the same gene product may be associated with IgD in a different glycosylation pattern.
Mass production of volume holographic optical elements (vHOEs) using Bayfol<sup>®</sup> HX photopolymer film in a roll-to-roll copy process (2017)

Volume Holographic Optical Elements (vHOEs) gained wide attention as optical combiners for the use in augmented and virtual reality (AR and VR, respectively) consumer electronics and automotive head-up display applications. The unique characteristics of these diffractive grating structures – being lightweight, thin and flat – make them perfectly suitable for use in integrated optical components like spectacle lenses and car windshields. While being transparent in Off-Bragg condition, they provide full color capability and adjustable diffraction efficiency. The instant developing photopolymer Bayfol® HX film provides an ideal technology platform to optimize the performance of vHOEs in a wide range of applications. Important for any commercialization are simple and robust mass production schemes. In this paper, we present an efficient and easy to control one-beam recording scheme to copy a so-called master vHOE in a step-and-repeat process. In this contact-copy scheme, Bayfol® HX film is laminated to a master stack before being exposed by a scanning laser line. Subsequently, the film is delaminated in a controlled fashion and bleached. We explain working principles of the one-beam copy concept and discuss the mechanical construction of the installed vHOE replication line. Moreover, we treat aspects like master design, effects of vibration and suppression of noise gratings. Furthermore, digital vHOEs are introduced as master holograms. They enable new ways of optical design and paths to large scale vHOEs.
Animal-free production of ccc-supercoiled plasmids for research and clinical applications (2004)

The topological structure of plasmid DNA can be characterized by capillary gel electrophoresis (CGE analysis)-an important tool for quality control and stability assessments in DNA storage or application. Hence, a large-scale manufacturing process was developed that allows the removal of undesired open circular (oc) or linear plasmid topologies, bacterial genomic DNA, RNA, proteins as well as lipopolysaccharides (endotoxins) and results in obtaining supercoiled (covalently closed circular, ccc) plasmid DNA in a pure form without using any animal-derived substances. Using CGE, the development and in-line monitoring for pharmaceutical plasmid production starting from fermentation control throughout the whole manufacturing process including the formulated and filled product can be performed the first time in a way conforming to good manufacturing practices (GMP). Plasmid stability data were obtained from analysis of shear effects influencing the plasmid quality in DNA drug delivery formulation and application (e.g. gene gun or jet injection). The physical stability of plasmid DNA is for the first time evaluated in DNA storage experiments on the level of different plasmid forms.
Evaluating the Performance of Deep Learning Techniques on Classification Using Tensor Flow Application (2018)

In Deep Learning, Artificial intelligence is the overall bigger domain, in which machines given the capability to learn new instances of data and then adapt to the basic domain of Machine Learning. Deep Learning is a subset of it, which goes into further accuracy that uses neural networking technology to go in and enable more complex situational data to come in and make more precise decisions. The objective of this research is to find out the details like Ratio of training data, Noise, Batch Size, Properties of features, learning rate, Type of Activation function, Level of Regularization, Rate of Regularization in constructing Neural Network on four different Classification Datasets after directly manipulating design providing in Tensor flow playground application. The Evaluation parameters consider in our experiments are Test loss and Training lose. The findings in our research is to specify that, how many hidden layers and number of neurons in each hidden layer are needed, for each type of classification problem. These findings help the researchers to fix the Maximum number of neurons and hidden layers needed in solving the four different types of classification problems by achieving test loss less than 0.005.
Correlation of Hyperandrogenism with Hyperinsulinism in Polycystic Ovarian Disease* (1980)

We evaluated basal plasma total immunoreactive insulin (insulin), androstenedione, and testosterone in 14 obese women: 8 with polycystic ovarian disease (PCOD) and 6 obese controls. All 3 hormones were significantly elevated (P less than 0.02 to P less than 0.001) in PCOD patients. A significant correlation among basal levels of plasma insulin, androstenedione, and testosterone was demonstrated. The PCOD group had significantly higher levels of glucose at 1, 2, and 3 h, with similar significant increases in plasma insulin levels at 0, 2, and 3 h. A significant correlation was found between plasma insulin response areas and plasma testosterone (P less than 0.001) in the control and PCOD patients. These studies demonstrate that hyperandrogenism correlates with hyperinsulinism.
Signal acquisition and processing in medical diagnostic ultrasound (1997)

As uses for ultrasound increase, so does the need for effective signal processing techniques. In this article we provide an overview of signal acquisition and processing in modern medical ultrasound imaging equipment and present some of the more important concepts in practice today. Images and data types typical of current ultrasound equipment are reviewed; fundamental acoustics and design parameters that affect signal quality and processing strategies are discussed; and current research directions are presented.
An activated aryl hydrocarbon receptor causes DNA damage and stress response in mouse liver (2006)

1065 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD), was classified as a group I carcinogen by the International Agency for Research on Cancer (IARC). It acts through an aryl hydrocarbon receptor (AhR) mediated mechanism, active in humans and exprimental animals. The activated AhR, a nuclear transcription factor, forms in the presence of TCDD an heterodimer with the aromatic hydrocarbon nuclear translocator (ARNT) protein and induces or suppresses the transcription of numerous genes, including cytochrome P450 1A1 (CYP1A1). It has been hypothesised that TCDD may be indirectly genotoxic via generation of reactive oxygen species (ROS). This may lead to DNA damage via direct interaction or via generation of reactive metabolites from endogenous compounds. We determined the amount of the oxidative damage marker 8-oxo-2′-deoxyguanosine (8-oxo-dG) using HPLC-MS/MS in mouse liver after treatment of the animals with TCDD. We also measured 8-oxo-dG in livers of a transgenic mouse model, which expresses a constitutively active AhR (CA-AhR). Transcription of the AhR gene battery in this mouse model is stimulated in the absence of any ligand. Microarrays, representing genes involved in stress and toxicity, were performed with hepatic RNA isolated from TCDD-treated, and from transgenic mice and compared to wild type and vehicle controls, respectively. 96 h after treatment of wild type mice with 1 μg/kg TCDD increased levels of 8-oxo-dG were observed in hepatic DNA. In the livers of CA-AhR mice basal 8-oxo-dG levels were even higher than in TCDD-treated wild type mice. Interestingly, the effect seems to be higher in male than in female mice. In contrast, the catalytic activity of hepatic CYP1A enzymes, measured as 7-ethoxyresorufin-O-deethylase (EROD), was much lower in CA-AhR than in TCDD-treated wild type mice. Apart from an explicit induction of CYP1A1, microarray data indicate, among others, differential expression of hepatic genes involved in apoptotic processes, e.g. Bcl-2 or Bax for both the TCDD-treated and the transgenic mice. In conclusion, a (permanent) activation of the AhR leads on the one hand to increased oxidative hepatic DNA damage. On the other hand apoptotic pathways seem to be modified, possibly in response to oxidative stress.
Estimation of ultrasound attenuation from broadband echo-signals using bandpass filtering (2008)

A problem with video signal analysis for estimating frequency-dependent ultrasonic attenuation is that relative echogenicity versus depth curves are distorted when broadband pulses are used. In this correspondence, we present results that demonstrate improved accuracy of attenuation estimates computed from B-mode or envelope data derived after narrowband (1 MHz BW) filtering at different frequencies around the center frequency of the broadband echo signal. Based on the premise that transducer center frequencies are selected in part on penetration or imaging depth requirements, simulation and experimental results for a typical ultrasound imaging system show that narrowband video signal analysis for frequencies lower than or at the center frequency of the broadband pulse provide unbiased attenuation estimation over this depth. Filtered signals above the center frequency of the pulse yield accurate results only at shallow depths.
Importance of T Cells, Gamma Interferon, and Tumor Necrosis Factor in Immune Control of the Rapid Grower<i>Mycobacterium abscessus</i>in C57BL/6 Mice (2007)

Mycobacterium abscessus is an emerging rapidly growing mycobacterium that causes tuberculous-like lesions in humans. We studied the immune control of this organism in C57BL/6 mice challenged intravenously with 10(7) CFU. Bacteria were eliminated from both the spleen and the liver within 90 days, and liver histology showed organized granulomatous lesions. A T- and B-cell requirement was investigated by challenging Rag2-/-, Cd3epsilon-/-, and muMT-/- mice. Rag2-/- and Cd3epsilon-/- mice were significantly impaired in the ability to clear M. abscessus from the liver and spleen, and muMT-/- mice were significantly impaired in the ability to clear M. abscessus from the liver, suggesting that infection control was primarily T cell dependent in the spleen and both T and B cell dependent in the liver. The liver granulomatous response was similar to that of wild-type controls in muMT-/- mice but completely absent in Cd3epsilon-/- and Rag2-/- mice. We studied the involvement of gamma interferon (IFN-gamma) and tumor necrosis factor (TNF) by challenging C57BL/6 mice deficient in the IFN-gamma receptor (Ifngr1-/-) and in TNF (Tnf-/-). Ifngr1-/- mice were significantly impaired in M. abscessus control both in the spleen and in the liver, and granulomas were profoundly altered. The effect was even more substantial in Tnf-/- mice; they failed to control M. abscessus infection in the liver and died within 20 to 25 days after infection with many hepatic inflammatory foci and major lesions of ischemic necrosis in the liver and kidney. These features were not observed with the closely related species M. chelonae. T-cell immunity, IFN-gamma, and TNF are central factors for the control of M. abscessus in C57BL/6 mice, as they are for the control of pathogenic slowly growing mycobacteria.
Gene Therapy: A Potential Approach for Cancer Pain (2011)

Chronic pain is experienced by as many as 90% of cancer patients at some point during the disease. This pain can be directly cancer related or arise from a sensory neuropathy related to chemotherapy. Major pharmacological agents used to treat cancer pain often lack anatomical specificity and can have off-target effects that create new sources of suffering. These concerns establish a need for improved cancer pain management. Gene therapy is emerging as an exciting prospect. This paper discusses the potential for viral vector-based treatment of cancer pain. It describes studies involving vector delivery of transgenes to laboratory pain models to modulate the nociceptive cascade. It also discusses clinical investigations aimed at regulating pain in cancer patients. Considering the prevalence of pain among cancer patients and the growing potential of gene therapy, these studies could set the stage for a new class of medicines that selectively disrupt nociceptive signaling with limited off-target effects.