gebhart/patrepeval huggingface dataset:
A human prostatic stromal myofibroblast cell line WPMY-1: a model for stromalepithelial interactions in prostatic neoplasia (1999)

Here we report the characterization of an SV40 large-T antigen-immortalized stromal cell line, WPMY-1, derived from the same prostate as our previously described epithelial cell lines. The WPMY-1 cells were determined to be myofibroblasts on the basis of co-expression of smooth muscle alpha-actin and vimentin. They also show positive staining for androgen receptor, large-T antigen, and positive but heterogeneous staining for p53 and pRb. Their growth is stimulated by the synthetic androgen mibolerone to 145% of control (100%). Platelet-derived growth factor BB, epidermal growth factor and basic fibroblast growth factor, at 10 ng/ml, stimulated growth to 138, 143 and 146% of control, respectively. Transforming growth factor-beta, at 10 ng/ml, inhibited serum-induced growth to 65% of control in the presence of 1% serum, and bFGF-induced growth to 30% of control. A serum-free medium was developed for optimal growth of WPMY-1 cells. They show anchorage-independent growth in soft agar. Studies on paracrine interactions show that myofibroblast-conditioned medium causes a marked inhibition of growth in WPE1-10 cells, while conditioned medium from WPE1-10 prostatic epithelial cells caused only a small increase in the growth of WPMY-1 cells. WPMY-1 cells secrete very low levels of MMP-9 but high levels of MMP-2, markedly higher than the epithelial cells. These epithelial and myofibroblast cell lines, derived from the same prostate, provide novel and useful models for studies on paracrine stromal-epithelial interactions in carcinogenesis, tumor progression, prevention and treatment of prostate cancer and benign prostatic hyperplasia.
Mixed reality (2006)

Mixed reality systems seek to smoothly link the physical and data processing (digital) environments. Although mixed reality systems are becoming more prevalent, we still do not have a clear understanding of this interaction paradigm. Addressing this problem, this article introduces a new interaction model called Mixed Interaction model. It adopts a unified point of view on mixed reality systems by considering the interaction modalities and forms of multimodality that are involved for defining mixed environments. This article presents the model and its foundations. We then study its unifying and descriptive power by comparing it with existing classification schemes. We finally focus on the generative and evaluative power of the Mixed Interaction model by applying it to design and compare alternative interaction techniques in the context of RAZZLE, a mobile mixed reality game for which the goal of the mobile player is to collect digital jigsaw pieces localized in space.
A polycatenated DNA scaffold for the one-step assembly of hierarchical nanostructures (2008)

A unique DNA scaffold was prepared for the one-step self-assembly of hierarchical nanostructures onto which multiple proteins or nanoparticles are positioned on a single template with precise relative spatial orientation. The architecture is a topologically complex ladder-shaped polycatenane in which the "rungs" of the ladder are used to bring together the individual rings of the mechanically interlocked structure, and the "rails" are available for hierarchical assembly, whose effectiveness has been demonstrated with proteins, complementary DNA, and gold nanoparticles. The ability of this template to form from linear monomers and simultaneously bind two proteins was demonstrated by chemical force microscopy, transmission electron microscopy, and confocal fluorescence microscopy. Finally, fluorescence resonance energy transfer between adjacent fluorophores confirmed the programmed spatial arrangement between two different nanomaterials. DNA templates that bring together multiple nanostructures with precise spatial control have applications in catalysis, biosensing, and nanomaterials design.
Fuzzy Assessment of Sleep-disordered Breathing During Continuous Positive Airway Pressure Therapy (1998)

We propose a new method of quantifying sleep-disordered breathing (SDB) for the purpose of automating continuous positive airway pressure (CPAP) titration. Our algorithm, based on fuzzy logic, emulates the less-than-crisp kind of decision-making generally employed at the human level. Three input variables were first derived on a breath-by-breath basis from respiratory airflow measurements. These were: (1) the relative duration of inspiratory flow limitation in each breath; (2) the degree of hypopnea relative to the past 15 breaths; and (3) the intensity of snoring. Using these descriptors as inputs, our fuzzy inference algorithm produced a "severity index" (SI) quantifying the degree of SDB. Severity index was determined in CPAP titration procedures conducted on one normal snorer and 12 patients with moderate-to-severe obstructive sleep apnea. SI computed over the last 6 minutes of each CPAP level was compared against other more-conventional indices of SDB, such as total pulmonary resistance (RL), the number of apneas and hypopneas (NAH), and the number of arousals (NAr). In all but one of the subjects, the correlation coefficients for SI vs each of RL, NAH, and NAr were significantly different from zero, but not different from each other. The group correlation coefficients for SI vs RL, NAH, and NAr were 0.89, 0.86, and 0.87, respectively, demonstrating that SI accurately quantifies SDB. SI collapses multiple features of the airflow pattern into a single index and, therefore, may be useful as a "feedback" variable for the automatic control of CPAP therapy.
Generation of picosecond CuK/spl alpha/ X-ray pulses and application to time-resolved X-ray diffraction (1996)

Summary form only given. Generation of picosecond X-ray pulses has applications to time-resolved diffraction studies. For the generation of picosecond narrow linewidth hard X-ray pulses one can use the optical excitation of an X-ray diode. This technique allows for the generation of picosecond X-ray pulses with spatial and spectral characteristics similar to the X-ray radiation generated by conventional X-ray tubes. Here, we report the results on the generation of CuKa X-ray pulse shorter than 10 ps by driving an X-ray diode with 1.5 ps, 193 nm laser pulses at repetition rate of 300 Hz.
Phase and intensity characterization of femtosecond pulses from a chirped-pulse amplifier by frequency-resolved optical gating (1995)

Frequency-resolved optical gating (FROG) measurements were made to characterize pulses from a Ti:sapphire chirped-pulse amplified laser system. By characterizing both the pulse intensity and the phase, the FROG data provided the first direct observation to our knowledge of residual phase distortion in a chirped-pulse amplifier. The FROG technique was also used to measure the regenerative amplifier dispersion and to characterize an amplitude-shaped pulse. The data provide an experimental demonstration of the value of FROG for characterizing complex pulses, including tailored femtosecond pulses for quantum control.
Specific Amino Acid Dependency Regulates Invasiveness and Viability of Androgen-Independent Prostate Cancer Cells (2003)

Androgen-independent prostate cancer is resistant to therapy and is often metastatic. Here we studied the effect of deprivation of tyrosine and phenylalanine (Tyr/Phe), glutamine (Gln), or methionine (Met), in vitro on human DU145 and PC3 androgen-independent prostate cancer cells, and on nontumorigenic human infant foreskin fibroblasts and human prostate epithelial cells. Deprivation of the amino acids similarly inhibited growth of DU145 and PC3 cells, arresting the cell cycle at G0/G1. Met and Tyr/Phe deprivation induces apoptosis in DU145, but only Met deprivation induces apoptosis in PC3 cells. The growth of normal cells is inhibited, but no apoptosis is induced by amino acid deprivation. Tyr/Phe deprivation inhibits expression and phosphorylation of focal adhesion kinase (FAK) and extracellular-regulated kinase (ERK) in DU145 but not PC3 or normal cells. Met deprivation inhibits phosphorylation but not protein expression of FAK and ERK in PC3. Therefore, apoptosis of DU145 and PC3 cells by amino acid restriction is FAK and ERK dependent. Tyr/Phe and Met deprivation inhibits invasion of DU145 and PC3, but Gln deprivation only inhibits invasion of DU145 cells. This indicates that the inhibition of invasion is not dependent on induction of apoptosis. The inhibition of invasion by Tyr/Phe restriction in DU145 and Met restriction in PC3 is consistent with the inhibition on FAK/ERK signaling. The inhibition of Tyr/Phe restriction in PC3 and Gln restriction in DU145 is not associated with inhibition of FAK/ERK. This indicates that FAK/ERK-dependent and independent pathways are modulated by specific amino acid restriction. This study shows the potential for specific amino acid restriction to treat prostate cancer.
A Novel P-Channel Flash Electrically-Erasable Programmable Read-Only Memory (EEPROM) Cell with Oxide-Nitride-Oxide (ONO) as Split Gate Channel Dielectric (2001)

A novel p-channel flash electrically-erasable programmable read-only memory (EEPROM) cell, which is programmed/erased via channel Fowler-Nordheim (FN) tunneling, is described in this paper. Channel FN tunneling is a high efficiency and low-power-consumption approach to flash cell operation. High endurance up to 1 M cycles was demonstrated with small window closure. The new flash cell exhibits good reliability which is quite insensitive to disturb or over program. In order to simplify the process, the interpoly dielectric and select gate dielectrics are fabricated using the same oxide-nitride-oxide (ONO) stack during formation of this cell. Hence, this cell shows good potential for achieving simple processing, low power consumption and negligible disturbance during operation.
Quantitative phenotyping via deep barcode sequencing (2009)

Next-generation DNA sequencing technologies have revolutionized diverse genomics applications, including de novo genome sequencing, SNP detection, chromatin immunoprecipitation, and transcriptome analysis. Here we apply deep sequencing to genome-scale fitness profiling to evaluate yeast strain collections in parallel. This method, Barcode analysis by Sequencing, or "Bar-seq," outperforms the current benchmark barcode microarray assay in terms of both dynamic range and throughput. When applied to a complex chemogenomic assay, Bar-seq quantitatively identifies drug targets, with performance superior to the benchmark microarray assay. We also show that Bar-seq is well-suited for a multiplex format. We completely re-sequenced and re-annotated the yeast deletion collection using deep sequencing, found that approximately 20% of the barcodes and common priming sequences varied from expectation, and used this revised list of barcode sequences to improve data quality. Together, this new assay and analysis routine provide a deep-sequencing-based toolkit for identifying gene-environment interactions on a genome-wide scale.
IgE Transcripts in the Circulation of Allergic Children Reflect a Classical Antigen-Driven B Cell Response and Not a Superantigen-Like Activation (2010)

Allergic asthma is the most frequent chronic disorder in childhood. Although IgE is a central effector molecule in allergic diseases, the nature of the IgE response is still under debate. The objective of our study was to clarify whether the IgE repertoire in the circulation of allergic children represents a classical Ag-driven and oligoclonal B cell response, a superantigen-like activation of a subset of B cells, or a polyclonal B-1 cell expansion. Using a highly sensitive RT-PCR method, we amplified, cloned, and sequenced IgE H chain transcripts from 13 children with allergic asthma. We gained 1366 functional IgE sequences, which currently represent the most extensive collection of human IgE transcripts. Compared to IgM transcripts from the same children, the somatic mutation rate was significantly enhanced in IgE transcripts (21 per thousand versus 72 per thousand; p < 0.001), which renders a polyclonal B-1 response unlikely. Moreover, IgE sequences displayed significantly enhanced Ag selection and hence were indicative of a classical Ag-driven immune response with affinity maturation (p < 0.001). In contrast to several recent studies, the usage pattern of variable gene segment of the H Ig chain in IgE transcripts followed the germline complexity, arguing against a superantigen-like interaction. We conclude that IgE transcripts in the circulation of children with allergic asthma reflect a classical adaptive B-2 cell response. This study provides reference data for a better characterization of the IgE response under immunomodulating therapies, such as anti-IgE therapy or allergen-specific immunotherapy.
Effects of the Human Amniotic Membrane on Axonal Outgrowth of Dorsal Root Ganglia Neurons in Culture (2007)

This study shows that AM exhibits location-dependent neuritic growth-promoting effects that might influence the clinical outcome of (amniotic membrane transplantation) in neurotrophic conditions.
Reproducibility of coronary lumen, plaque, and vessel wall reconstruction and of endothelial shear stress measurements in vivo in humans (2003)

The purpose of this study was to assess the reproducibility of an in vivo methodology to reconstruct the lumen, plaque, and external elastic membrane (EEM) of coronary arteries and estimate endothelial shear stress (ESS). Ten coronary arteries without significant stenoses (five native and five stented arteries) were investigated. The 3D lumen and EEM boundaries of each coronary artery were determined by fusing end-diastolic intravascular ultrasound images with biplane coronary angiograms. Coronary flow was measured. Computational fluid dynamics was used to calculate local ESS. Complete data acquisition was then repeated. Analysis was performed on each data set in a blinded manner. The intertest correlation coefficients for all arteries for the two measurements of lumen radius, EEM radius, plaque thickness, and ESS were r = 0.96, 0.96, 0.94, 0.91, respectively (all P values < 0.0001). The 3D anatomy and ESS of human coronary arteries can be reproducibly estimated in vivo. This methodology provides a tool to examine the effect of ESS on atherogenesis, remodeling, and restenosis; the contribution of arterial remodeling and plaque growth to changes in the lumen; and the impact of new therapies.
Role of the Nrf2 signaling system in health and disease (2014)

A key component of cytoprotective gene regulation is the transcription factor nuclear factor erythroid 2-related factor 2 (Nrf2), also known as nuclear factor erythroid 2-like 2, from the gene NFE2L2. Under normal conditions, Nrf2 in the cell is targeted for proteasomal degradation by its inhibitor Kelch-like ECH-associated inhibitor 1 (Keap1). When stimulated by oxidative stress, electrophiles, or kinase activation, conformational changes in the Nrf2-Keap1 complex inhibit proteasomal degradation of Nrf2, facilitating an increase in the amount of Nrf2 that binds to antioxidant response element sequences in the promoter regions of a variety of antioxidant, detoxification, and metabolic control genes. Nrf2 activation is mostly associated with beneficial cytoprotective gene regulation, but it can also have deleterious effects. For example, gene mutations in some types of cancers can lead to constitutive activation of Nrf2 and give the tumor cells growth advantages and increased drug resistance. Because cases exist where Nrf2/Keap1/ARE signaling is either too low or too high, there is great interest in the development of both Nrf2 activators and Nrf2 inhibitors as the basis of new therapies.
Chiral separation methods for pharmaceutical and biotechnological products (2011)

Contributors. Preface. 1 Overview of Chiral Separations (Satinder Ahuja). 2 Regulatory & Development Considerations of Chiral Compounds (Robert L. Zeid). 3 Basic Considerations in Method Development for Chiral Compounds (Satinder Ahuja). 4 Separations of Chiral Compounds on Polysaccharide Columns (Clinton W. Amoss and Norbert M. Maier). 5 Chiral Separations by Various Techniques (Jian G. Ning). 6 Chiral Discrimination Study for Polysaccharide Based Chiral Stationary Phase (Yun K. Ye). 7 Comparison of Chiral Chromatographic Columns for Pharmaceuticals (Gregory K. Webster). 8 Chiral Separation Screens for Pharmaceutical Analysis and Purification in an Industrial Laboratory Environment (Robert DePianta, Kenneth Douville, Beverly Nickerson, and Ricardo E. Borjas). 9 The Separation of Enantiomers by Gas Chromatography on Chiral Stationary Phases (Volker Schurig). 10 Separations of Chiral Compounds by SFC (Ziqiang Wang). 11 Chiral Separations by Capillary Electrophoresis (Debby Mangelings and Yvan Vander Heyden). 12 High-Throughput Screening and Method-Development Strategies to Separate Chiral Drug Compounds in HPLC, SFC, and CE (Hasret Ates, Debby Mangelings and Yvan Vander Heyden). 13 Use of Enantioselective Synthesis and Preparative Chiral Chromatography to Access a Challenging Enantiopure Pharmaceutical Candidate from a Mixture of Four Stereoisomers (Christopher J. Welch, Derek H. Henderson, William R. Leonard, Mirlinda Biba, Mike Zacuto, Fred Fleitz, Amude Kassim, Cheng-yi Chen, and Peter Sajonz). 14 A Look into the Future: Chiral Analysis Using Chemical Sensor Technology (Gregory K. Webster and William J. Buttner). 15 Chirality of Biomolecules and Biotechnology Products (Satinder Ahuja). Index.
Enhancement of Glutathione <italic>S</italic>-Transferase Activity of the Mouse Forestomach by Inhibitors of Benzo[<italic>a</italic>]pyrene-Induced Neoplasia of the Forestomach<xref ref-type="fn" rid="fn2">2</xref><xref ref-type="fn" rid="fn3">3</xref> (1981)

The effects of glutathione S-transferases (GST) activity and acid-soluble sulfhydryl levels of a number of compounds previously investigated for their capacity to inhibit benzo[a]pyrene (BP)-induced neoplasia of the mouse forestomach were determined. Five of the compounds studied increased the GST activity of the forestomach 78-182%. The five compounds were: p-methoxyphenol, 2-tert-butyl-4-hydroxyanisole, coumarin, alpha-angelicalactone, and benzyl isothiocyanate. With the exception of benzyl isothiocyanate. With the exception of benzyl isothiocyanate, these compounds also increased acid-soluble sulfhydryl levels, but to a lesser magnitude. All five chemicals inhibited BP-induced neoplasia of the forestomach. These data indicate that enhancement of the GST activity by an amount of about 75% or greater is associated with a reduced carcinogenic response of the forestomach to BP. The data also suggest that such enhancement might be used as a method of identifying compounds likely to inhibit BP and other carcinogens detoxified in a similar manner. Inasmuch as inhibition of the action of carcinogens may involve mechanisms other than detoxification by GST, the failure to increase GST activity substantially does not rule out the possibility of a compound being an inhibitor.
Representing software usage models with stochastic automata networks (2002)

The benefits of usage models in the statistical testing of software have been recognized by the software engineering community and discrete state formalisms have been largely used to describe such usage models of software. The Markov Chains formalism (MC) is a natural choice to do so. However, in this paper we suggest the use of a more sophisticated discrete state formalism, the Stochastic Automata Networks (SAN). In many problems of the performance evaluation area, the SAN models present advantages over MC models. Therefore, it seems natural to us to verify similar advantages in the modeling of usage models.This paper presents a case study of building a software usage model using SAN formalism. A software tool called DOCSEDITOR is modeled using MC and SAN. The models are compared in terms of number of states, scalability, and readability. It is not the objective of this paper to present a full framework to develop and analyse usage models with SAN, but just to show some evident advantages of the use of SAN instead of MC. In order to do this, the conclusion points out the indexes than can be computed from both models and suggests the next steps on future work.
100GB/S two-iteration concatenated BCH decoder architecture for optical communications (2010)

This paper presents a two-iteration concatenated Bose-Chaudhuri-Hocquenghem (BCH) code and its high-speed low-complexity two-parallel decoder architecture for 100 Gb/s optical communications. The proposed architecture features a very high data processing rate as well as excellent error correction capability. A low-complexity syndrome computation architecture and a high-speed dual-processing pipelined simplified inversonless Berlekamp-Massey (Dual-pSiBM) key equation solver architecture were applied to the proposed concatenated BCH decoder with an aim of implementing a high-speed low-complexity decoder architecture. The proposed two-iteration concatenated BCH code structure with block interleaving methods allows the decoder to achieve 8.91dB of net coding gain performance at 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-15</sup> decoder output bit error rate to compensate for serious transmission quality degradation. Thus, it has potential applications in next generation forward error correction schemes for 100 Gb/s optical communications.
Abnormal findings on liver function tests (2000)

Evaluating abnormal liver test results requires careful attention to the corresponding clinical data obtained during history taking and physical examination. Generally, it is helpful to separate liver tests into three categories: tests that assess synthetic function, tests that assess hepatocellular necrosis (hepatocellular enzymes), and tests that assess cholestasis. The clinical setting together with the specific pattern of liver function abnormalities can narrow differential diagnosis and provide a cost-effective approach to assessing patients and identifying those who need liver biopsy.
Fatty acid synthase is up-regulated during hepatitis C virus infection and regulates hepatitis C virus entry and production (2008)

As far as we know, this is the first line of evidence that demonstrates that HCV infection directly induces FASN expression, and thus suggests a possible mechanism by which HCV infection alters the cellular lipid profile and causes diseases such as steatosis.
EHMTI-0178. CGRP monoclonal antibody LY2951742 for the prevention of migraine: a phase 2, randomized, double-blind, placebo-controlled study (2014)

Methods Eligible subjects with 4-14 migraine headache days (MHD) per month were randomized in a double-blind manner to LY2951742 or placebo, administered subcutaneously, every other week over a 12-week period. The primary endpoint was the mean change from baseline in number of MHD in the last 28 day period (month three); secondary end points included the mean change in headache days, migraine attacks, and the 50% responder rate at month 3.