gebhart/patrepeval huggingface dataset:
Association of theCYP1B1*3allele with survival in patients with prostate cancer receiving docetaxel (2008)

Using a single nucleotide polymorphism association study in 52 men with prostate cancer receiving docetaxel, we found that individuals carrying two copies of the CYP1B1*3 polymorphic variant had a poor prognosis after docetaxel-based therapies compared with individuals carrying at least one copy of the CYP1B1*1 allele (30.6 versus 12.8 months; P=0.0004). The association between CYP1B1*3 and response to therapy was not observed in similar subjects receiving non-taxane-based therapy (P=0.18). The systemic clearance of docetaxel was also unrelated to CYP1B1 genotype status (P=0.39), indicating that the association of CYP1B1*3 with clinical response is not due to docetaxel metabolism. To explain these results, we hypothesized that an indirect gene-drug interaction was interfering with the primary mechanism of action of docetaxel, tubulin polymerization. We therefore conducted tubulin polymerization experiments with taxanes in the presence or absence of certain CYP1B1 estrogen metabolites, which are known to bind to nucleophilic sites in proteins and DNA, that revealed the primary estrogen metabolite of CYP1B1, 4-hydroxyestradiol (4-OHE2), when oxidized to estradiol-3,4-quinone strongly inhibits tubulin polymerization. The 4-OHE2 is also formed more readily by the protein encoded by the CYP1B1*3 allele, validating further our data in patients. Furthermore, estradiol-3,4-quinone reacted in vitro with docetaxel to form the 4-OHE2-docetaxel adduct. This pilot study provides evidence that CYP1B1*3 may be an important marker for estimating docetaxel efficacy in patients with prostate cancer. This link is likely associated with CYP1B1*3 genotype-dependent estrogen metabolism.
A novel system for the improvement of colonic cleansing during colonoscopy (2012)

Suboptimal bowel cleansing prior to colonoscopy impairs the efficacy and safety of the procedure. A new system for intracolonic cleansing has been developed, which includes a disposable catheter device that is inserted through the working channel of a standard colonoscope and an irrigation unit with predefined pressure and flow rate. The aim of the current study was to assess the safety and efficacy of this novel system for the improvement of bowel cleansing during colonoscopy. A total of 42 patients with suboptimal bowel preparation were systematically allocated, in a 1:1 ratio, to either the study group (JetPrep system, n = 21) or the control group (syringe irrigation, n = 21). The cleansing efficacy was evaluated using a segmental scoring scale to rate the bowel preparation level before and after irrigation. One patient from the study group was excluded from the efficacy analysis due to treatment with both techniques. The JetPrep system was significantly superior to syringe irrigation (P = 0.0001). No adverse events were reported. This study suggests that the safety profile of the JetPrep system is comparable to standard irrigation and shows that the device significantly improves suboptimal bowel preparation.
Comparison of Analytical Techniques for Purity Evaluation of Single-Walled Carbon Nanotubes (2005)

We compare popular analytical techniques, including scanning and transmission electron microscopy (SEM and TEM), thermogravimetric analysis (TGA), and Raman and near-infrared (NIR) spectroscopy, for the evaluation of the purity of bulk quantities of single-walled carbon nanotubes (SWNTs). Despite their importance as imaging techniques, SEM and TEM are not capable of quantitatively evaluating the purity of typical inhomogeneous bulk SWNT samples because the image frame visualizes less than 1 pg of SWNT material; furthermore, there is no published algorithm to convert such images into numerical data. The TGA technique is capable of measuring the amount of metal catalyst in an SWNT sample, but does not provide an unambiguous separation between the content of SWNTs and carbonaceous impurities. We discuss the utilization of solution-phase near-infrared spectroscopy and solution-phase Raman spectroscopy to quantitatively compare arbitrary samples of bulk SWNT materials of different purities. The primary goal of this paper is to provide the chemical community with a realistic evaluation of current analytical tools for the purity evaluation of a bulk sample of SWNTs. The secondary goal is to draw attention to the growing crisis in the SWNT industry as a result of the lack of quality control and the misleading advertising by suppliers of this material.
Quantifying Electronic and Ionic Conductivity Contributions in Carbon/Polyelectrolyte Composite Thin Films (2014)

A method for independently obtaining electronic and ionic contributions to electrical conductivity in thin-film samples comprised of carbon black (CB) mixed with polymer electrolyte is reported. The method relies upon careful control of the nature of the contact between the sample and the current-carrying electrodes. Electronic conductivities are derived from currents obtained using electronically-conductive glassy carbon electrodes to contact the sample, whereas ionic conductivities are derived from currents obtained using ionically-conductive Nafion electrodes to contact the sample. Conditions under which the measured currents are free from interference from redox reactions at the electrodes and capacitive charging at electrode-electrolyte interfaces are discussed. Electrical conduction was studied in a series of composite carbon black/polymer samples under conditions of fixed temperature and variable relative humidity (RH). For samples containing 10–20 weight percent carbon black dispersed in Nafion, electronic conductivity was higher than ionic conductivity at all RH values tested (25–100% RH). Ionic conductivity increased with increasing RH in a manner consistent with expectation from prior studies on Nafion membranes, whereas electronic conductivity decreased with increasing RH due to water swelling and weakened electrical contacts among carbon particles in the network.
Stark spectroscopy of CdSe nanocrystallites: The significance of transition linewidths (1995)

We use Stark spectroscopy to examine the nature of the excited states of CdSe nanocrystallites. The Stark spectra we obtain are in the small coupling limit in which the changes induced by the electric field to the absorption spectrum are small compared to the transition linewidths. Within this limit, we theoretically examine the dependence of the line shape of Stark difference spectra on the linewidth of the transitions involved. For systems such as CdSe nanocrystallites, which have overlapping transitions coupled by the electric field, we find that the usual association of derivatives of absorption features with dipole moments and polarizabilities is problematic. We show that the Stark absorption spectrum of the CdSe nanocrystallites can be explained by polarizable and delocalized nonpolar excited states.
Studies on Aziridine-2-carboxylic Acid. I. Synthesis of the Optically Active l-Aziridine-2-carboxylic Acid and Its Derivatives (1978)

Abstract Lithium l-aziridine-2-carboxylate was synthesized from N-trityl-l-aziridine-carboxylic acid benzyl ester by the treatment with trifluoroacetic acid followed by the saponification with lithium hydroxide. Several N-acylaziridine-2-carboxylic acid esters were synthesized in good yield.
Book Review (1986)

Books reviewed in this article: BIOCHEMISTRY OF PLANT CELL WALLS. Edited by C. T. B rett &amp; J. R. H illman
Transcriptional regulation of Salmonella enterica virulence plasmid genes in cultured macrophages (1993)

The plasmid-carried spv genes promote virulence of salmonellae in mice by allowing bacterial growth in the reticuloendothelial tissue. When the bacteria are cultivated under normal laboratory conditions the spv genes appear dormant. This communication explores the transcriptional regulation of spv genes within murine macrophage-like J774-A.1 cells utilizing a new reporter system. Transcriptional fusions were constructed between promoter elements of the Salmonella enterica var. Typhimurium spv genes and the KS71A fimbrial gene cluster. The expression of KS71A fimbriae in fusion-carrying Escherichia coli strains was found to be under the control of the transcriptional activator gene spvR. In strains overproducing SpvR, KS71A fimbriae were assembled on the bacterial cell surface and could be detected by bacterial agglutination or immunofluorescence of intact bacteria; the reporter activity was quantified by estimating the percentage of fluorescent bacteria and by immunoblotting of cell lysates. The activity of the reporters, when transformed into the parent Typhimurium TML R66, was low and revealed less than 0.3% fimbriated cells under in vitro culture conditions. A 15-30-fold increase in fimbriation was observed when the bacteria were cultivated within J774-A.1 cells. No such increase occurred when the reporter fusions were transformed into TML R66 cured of the virulence plasmid. Insertional inactivation of the spvR gene of the virulence plasmid in Typhimurium TML R66 also abolished induction, whereas corresponding inactivation of spvA or spvB did not reduce induction. No increase in reporter activity was obtained in Typhimurium of line Q1, which is naturally avirulent for mice, although the strain was provided with virulence plasmid pEX102 of line TML R66. We conclude that the intracellular environment of J774-A.1 cells induces the spv genes and that this induction requires gene functions of both the bacterial chromosome and the virulence plasmid.
Tactile Imaging System for Localizing Lung Nodules during Video Assisted Thoracoscopic Surgery (2007)

Early detection and removal of small pulmonary nodules significantly improves long term survival rates for patients with lung cancer. To aid in the localization of these tumors during video assisted thoracoscopic surgery (VATS), a tactile imaging system (TIS) is presented. The system consists of a capacitive array sensor mounted on a minimally invasive surgical probe that is integrated with the thoracoscopic imaging. A vision-based algorithm localizes the probe in the live video and overlays a registered pseudo-color map of the measured pressure distribution on the streaming images. The surgeon can locate the hard nodules by scanning the tactile sensor head across the surface of the lung and observing the spatial variation in contact pressures caused by the elasticity differences in the underlying tissue. A validation experiment was conducted to compare the system to a current localization technique using a rigid rod. Results indicate that subjects could localize stiff lumps in lung phantoms more quickly and accurately using the TIS.
Designing systems that direct human action (2005)

In this paper we present a user-centered design process for Active Capture systems. These systems bring together techniques from human-human direction practice, multimedia signal processing, and human-computer interaction to form computational systems that automatically analyze and direct human action. The interdependence between the design of multimedia signal parsers and the user interaction script presents a unique challenge in the design process. We have developed an iterative user-centered design process for Active Capture systems that incorporates bodystorming, wizard-of-oz user studies, iterative parser design, and traditional user studies, based on our experience designing a portrait camera system that works with the user to record her name and take her picture. Based on our experiences, we lay out a set of recommendations for future tools to support such a design process.
Preferential inhibition of hepatocellular carcinoma by the flavonoid Baicalein through blocking MEK-ERK signaling (2012)

Baicalein is a purified flavonoid extracted from the roots of Scutellaria baicalensis or Scutellaria radix. Although previous studies have suggested that Baicalein possesses an in vitro anti-hepatocellular carcinoma activity, its in vivo effects and mechanisms of action are still not completely understood. In this study, Baicalein at concentrations of 40-120 µM exhibited significant cytotoxicity to three hepatocellular carcinoma (HCC) cell lines but marginal cytotoxicity to a normal liver cell line in vitro. Compared to a standard chemotherapy drug, 5-fluorouracil (5-FU), Baicalein had greater effect on HCC cells but less toxicity on normal liver cells. Treatment with Baicalein dramatically reduced mitochondrial transmembrane potential, and activated caspase-9 and caspase-3. Blockade of Baicalein-induced apoptosis with a pan-caspase inhibitor partially attenuated Baicalein-induced growth inhibition in HCC. Baicalein treatment significantly inhibited tumor growth of HCC xenografts in mice. Induction of apoptosis was demonstrated in Baicalein-treated xenograft tumors by the terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) assay. Furthermore, Baicalein treatment dramatically decreased the levels of phosphorylation of MEK1, ERK1/2 and Bad in vitro and in vivo. Overexpression of human MEK1 partially blocked Baicalein-induced growth inhibition. Consequently, these findings suggest that Baicalein preferentially inhibits HCC tumor growth through inhibition of MEK-ERK signaling and by inducing intrinsic apoptosis.
Immunoinformatics Comes of Age (2006)

With the burgeoning immunological data in the scientific literature, scientists must increasingly rely on Internet resources to inform and enhance their work. Here we provide a brief overview of the adaptive immune response and summaries of immunoinformatics resources, emphasizing those with Web interfaces. These resources include searchable databases of epitopes and immune-related molecules, and analysis tools for T cell and B cell epitope prediction, vaccine design, and protein structure comparisons. There is an agreeable synergy between the growing collections in immune-related databases and the growing sophistication of analysis software; the databases provide the foundation for developing predictive computational tools, which in turn enable more rapid identification of immune responses to populate the databases. Collectively, these resources contribute to improved understanding of immune responses and escape, and evolution of pathogens under immune pressure. The public health implications are vast, including designing vaccines, understanding autoimmune diseases, and defining the correlates of immune protection.
Differentiation of immortal cells inhibits telomerase activity. (1995)

Telomerase, a ribonucleic acid-protein complex, adds hexameric repeats of 5'-TTAGGG-3' to the ends of mammalian chromosomal DNA (telomeres) to compensate for the progressive loss that occurs with successive rounds of DNA replication. Although somatic cells do not express telomerase, germ cells and immortalized cells, including neoplastic cells, express this activity. To determine whether the phenotypic differentiation of immortalized cells is linked to the regulation of telomerase activity, terminal differentiation was induced in leukemic cell lines by diverse agents. A pronounced downregulation of telomerase activity was produced as a consequence of the differentiated status. The differentiation-inducing agents did not directly inhibit telomerase activity, suggesting that the inhibition of telomerase activity is in response to induction of differentiation. The loss of telomerase activity was not due to the production of an inhibitor, since extracts from differentiated cells did not cause inhibition of telomerase activity. By using additional cell lineages including epithelial and embryonal stem cells, down-regulation of telomerase activity was found to be a general response to the induction of differentiation. These findings provide the first direct link between telomerase activity and terminal differentiation and may provide a model to study regulation of telomerase activity.
Vitamin K-dependent synthesis and modification of precursor prothrombin in cultured H-35 hepatoma cells. (1976)

The ability of confluent monolayers of H-35 cells, originally obtained from a rat hepatoma, to synthesize prothrombin in response to vitamin K1 (phylloquinone) was studied. As demonstrated by radioimmunoassay, selective barium salt adsorption, and two coagulation assays which discriminate between precursor- and mature-prothrombin, these cells retained their ability to synthesize precursor prothrombin (preprothrombin) in the absence of exogenous phylloquinone (vitamin K). When phylloquinone was added to the medium (100 ng/ml), the existing intracellular concentration of preprothrombin was reduced to 50% within 1 hr after exposure to the vitamin and slowly declined thereafter to approximately 30% of control levels by 36 hr. Concomitant with the rapid loss of intracellular preprothrombin was the appearance of mature prothrombin in the medium. The appearance of prothrombin was biphasic: occurring during the initial 0-6 hr interval, and again at an increased rate during the next 18-24 hr interval. The amount of prothrombin appearing in the medium exceeded by severalfold the amount of precursor mobilized. These data demonstrate that monolayer cultures of H-35 hepatoma cells retain their ability to synthesize preprothrombin and other enzymes, responsible for post-translational modification of prothrombin and its subsequent secretion, under the influence of vitamin K.
LabVIEW program design for on-line data acquisition and predictive maintenance (2002)

The online design for data acquisition and predictive maintenance for a fan-motor system using the graphical programming language, LabVIEW is presented. The data set were created for different faults under varying rpm levels from the synthetically generated fault data and the normal base line data acquired from the fan-motor system. The data were processed and the extracted features were fed to a two layer backpropagation neural network. The design is to be implemented on an online basis.
An endemic problem in reverse-time migration (2014)

Summary This paper discusses an endemic problem existing in commonly used reverse-time migration (RTM) algorithms, and how to overcome the problem. The problem is illustrated by applying RTM to both synthetic and field datasets. False images appear in the migrated results when strong velocity gradients or complex reflection interfaces are present in the migration velocity model. We have found that the false image is formed by turned or reflected rays that have the same travel-time as the actual wave propagating times. To remove the false images from the migration results, we separate the upgoing and downgoing waves in both source and receiver wavefields, then apply the migration imaging condition to the separated waves. A computationally efficient method can be made to eliminate the false images in RTM.
Effect of the End Group of Regioregular Poly(3-hexylthiophene) Polymers on the Performance of Polymer/Fullerene Solar Cells (2007)

In this report, we have studied the influence of the nature of the end groups (bromine or hydrogen) of regioregular poly(3-hexylthiophene) (P3HT) polymers on the performance of polymer solar cells made with blend films of P3HT and 1-(3-methoxycarbonyl)-propyl-1-phenyl-(6,6)C61 (PCBM). Films and devices were studied before and after annealing at 140 °C for 2 h. The effects of the end-group type on the properties of pristine polymers and blend films were examined using optical absorption and emission spectroscopy, transient absorption spectroscopy, and measurements of photovoltaic device performance. It was observed that hydrogen end groups result in slightly higher absorption coefficients, higher photoluminescence intensities, faster and less dispersive charge recombination, and superior solar cell performance (notably a higher fill factor) compared to bromine end groups. The results are attributed to more-ordered polymer-chain packing in blend films made with hydrogen-capped P3HT, on account of the smaller size and weaker electrostatic interactions resulting from hydrogen compared to bromine. Some influence of the C−Br group on exciton quenching may also be present. The effect of the bromine end group on solar-cell performance became more pronounced with reducing incident-light intensity. Comparison of the polymer transport characteristics in organic field-effect transistor configuration indicated that the bromine end group enhances hole trapping.
Colony stimulating factor 1 receptor inhibition eliminates microglia and attenuates brain injury after intracerebral hemorrhage (2016)

Microglia are the first responders to intracerebral hemorrhage, but their precise role in intracerebral hemorrhage remains to be defined. Microglia are the only type of brain cells expressing the colony-stimulating factor 1 receptor, a key regulator for myeloid lineage cells. Here, we determined the effects of a colony-stimulating factor 1 receptor inhibitor (PLX3397) on microglia and the outcome in the context of experimental mouse intracerebral hemorrhage. We show that PLX3397 effectively depleted microglia, and the depletion of microglia was sustained after intracerebral hemorrhage. Importantly, colony-stimulating factor 1 receptor inhibition attenuated neurodeficits and brain edema in two experimental models of intracerebral hemorrhage induced by injection of collagenase or autologous blood. The benefit of colony-stimulating factor 1 receptor inhibition was associated with reduced leukocyte infiltration in the brain and improved blood-brain barrier integrity after intracerebral hemorrhage, and each observation was independent of lesion size or hematoma volume. These results demonstrate that suppression of colony-stimulating factor 1 receptor signaling ablates microglia and confers protection after intracerebral hemorrhage.
Laser Cooling below the One-Photon Recoil Energy by Velocity-Selective Coherent Population Trapping (1988)

We present a new laser-cooling scheme based on velocity-selective optical pumping of atoms into a nonabsorbing coherent superposition of states. This method has allowed us to achieve transverse cooling of metastable $^{4}\mathrm{He}$ atoms to a temperature of 2 \ensuremath{\mu}K, lower than both the usual Doppler cooling limit (23 \ensuremath{\mu}K) and the one-photon recoil energy (4 \ensuremath{\mu}K). The corresponding de Broglie wavelength (1.4 \ensuremath{\mu}m) is larger than the atomic-transition optical wavelength.
Multiple output selection-LAS algorithm in large MIMO systems (2010)

We present a low-complexity algorithm for detection in large MIMO systems based on the likelihood ascent search (LAS) algorithm. The key idea in our work is to generate multiple possible solutions or outputs from which we select the best one. We propose two possible approaches to achieve this goal and both are investigated. Computer simulations demonstrate that the proposed algorithm, Multiple Output Selection-LAS, which has the same complexity order as that of conventional LAS algorithms, is superior in bit error rate (BER) performance to LAS conventional algorithms. For example, with 20 antennas at both the transmitter and receiver, the proposed MOS-LAS algorithm needs about 4 dB less SNR to achieve a target BER of 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-4</sup> for 4-QAM.