gebhart/patrepeval huggingface dataset:
The Role of Uptake and Efflux Transporters in the Disposition of Glucuronide and Sulfate Conjugates (2022)

Glucuronidation and sulfation are the most typical phase II metabolic reactions of drugs. The resulting glucuronide and sulfate conjugates are generally considered inactive and safe. They may, however, be the most prominent drug-related material in the circulation and excreta of humans. The glucuronide and sulfate metabolites of drugs typically have limited cell membrane permeability and subsequently, their distribution and excretion from the human body requires transport proteins. Uptake transporters, such as organic anion transporters (OATs and OATPs), mediate the uptake of conjugates into the liver and kidney, while efflux transporters, such as multidrug resistance proteins (MRPs) and breast cancer resistance protein (BCRP), mediate expulsion of conjugates into bile, urine and the intestinal lumen. Understanding the active transport of conjugated drug metabolites is important for predicting the fate of a drug in the body and its safety and efficacy. The aim of this review is to compile the understanding of transporter-mediated disposition of phase II conjugates. We review the literature on hepatic, intestinal and renal uptake transporters participating in the transport of glucuronide and sulfate metabolites of drugs, other xenobiotics and endobiotics. In addition, we provide an update on the involvement of efflux transporters in the disposition of glucuronide and sulfate metabolites. Finally, we discuss the interplay between uptake and efflux transport in the intestine, liver and kidneys as well as the role of transporters in glucuronide and sulfate conjugate toxicity, drug interactions, pharmacogenetics and species differences.
Transvection and long‐distance gene regulation (1990)

Numerous genes contain regulatory elements located many tens of kilobases away from the promoter they control. Specific mechanisms must be required to ensure that such distant elements can find and interact with their proper targets but not with extraneous genes. This review explores the connections between transvection phenomena, the activation of domains of homeotic gene expression, position effect variegation and silencers. These various examples of long-distance effects suggest that, in all cases, related forms of chromatin packaging may be involved.
Food safety considerations for innovative nutrition solutions (2015)

Failure to secure safe and affordable food to the growing global population leads far too often to disastrous consequences. Among specialists and other individuals, food scientists have a key responsibility to improve and use science-based tools to address risk and advise food handlers and manufacturers with best-practice recommendations. With collaboration from production agriculture, food processors, state and federal agencies, and consumers, it is critical to implement science-based strategies that address food safety and that have been evaluated for effectiveness in controlling and/or eliminating hazards. It is an open question whether future food safety concerns will shift in priority given the imperatives to supply sufficient food. This report brings together leading food safety experts to address these issues with a focus on three areas: economic, social, and policy aspects of food safety; production and postharvest technology for safe food; and innovative public communication for food safety and nutrition.
A preliminary study on the effect of motion correction on HARDI reconstruction (2014)

Post-acquisition motion correction is widely performed in diffusion-weighted imaging (DWI) to guarantee voxel-wise correspondence between DWIs. Whereas this is primarily motivated to save as many scans as possible if corrupted by motion, users do not fully understand the consequences of different types of interpolation schemes on the final analysis. Nonetheless, interpolation might increase the partial volume effect while not preserving the volume of the diffusion profile, whereas excluding poor DWIs may affect the ability to resolve crossing fibers especially with small separation angles. In this paper, we investigate the effect of interpolating diffusion measurements as well as the elimination of bad directions on the reconstructed fiber orientation diffusion functions and on the estimated fiber orientations. We demonstrate such an effect on synthetic and real HARDI datasets. Our experiments demonstrate that the effect of interpolation is more significant with small fibers separation angles where the exclusion of motion-corrupted directions decreases the ability to resolve such crossing fibers.
Microstructure and electronic properties of InGaN alloys (2003)

Abstract The In x Ga 1− x N system has electronic band gaps extending from under 1eV to 3.4 eV, and as such they are used as the active layer in commercially available visible‐light emitting devices. There are many interesting features that make these nitride semiconductor alloys especially useful for efficient light emitters. It has been conjectured that the combination of piezoelectric fields and local composition inhomogeneities may be responsible for the observed high emission efficiencies, in spite of their characteristic high dislocation densities. But it is very difficult to grow In x Ga 1− x N layers with high indium composition. This paper presents an overview of the properties of In x Ga 1− x N epilayers based on a systematic study of thick layers and of quantum well structures. We find that the microstructure of thick films varies significantly with indium composition. For x &lt; 0.08, the composition is uniform and unperturbed by dislocations. For 0.10 &lt; x &lt; 0.20, secondary phases nucleate at threading dislocations. For x &gt; 0.20, spontaneous phase separation occurs resulting in a polycrystalline, inhomogeneous layer. A correlation between optical properties and microstructure is presented. It is observed that the misfit strain is affected by threading dislocations. Mechanisms of misfit strain relaxation are presented for In x Ga 1− x N layers grown on standard GaN on sapphire and on epitaxial‐lateral‐overgrowth GaN layers. In addition, we have studied the properties of quantum well structures using several novel techniques. The electrostatic fields across the wells have been profiled using electron holography in the TEM. The effect of well thickness on the strength of the fields is reported. The effects of localization by compositional fluctuations and of internal field screening have been studied using time‐resolved cathodoluminescence spectroscopy. In spite of significant progress that has been made in the last ten years, much work remains ahead in order to master the science and technology of these alloys. (© 2003 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
Patient with Lobular Carcinoma of the Breast and Activating AKT1 E17K Variant (2021)

This demonstrates that applying available Precision Medicine tools like MTB and real world data sets from patient populations with similar clinical and genomic profiles may provide more options for treatment.
Seismic signal enhancement based on the low‐rank methods (2020)

ABSTRACT Based on the fact that the Hankel matrix constructed by noise‐free seismic data is low‐rank, low‐rank approximation (or rank‐reduction) methods have been widely used for removing noise from seismic data. Due to the linear‐event assumption of the traditional low‐rank approximation method, it is difficult to define a rank that optimally separates the data subspace into signal and noise subspaces. For preserving the most useful signal energy, a relatively large rank threshold is often chosen, which inevitably leaves residual noise. To reduce the energy of residual noise, we propose an optimally damped rank‐reduction method. The optimal damping is applied via two steps. In the first step, a set of optimal damping weights is derived. In the second step, we derive an optimal singular value damping operator. We review several traditional low‐rank methods and compare their performance with the new one. We also compare these low‐rank methods with two sparsity‐promoting transform methods. Examples demonstrate that the proposed optimally damped rank‐reduction method could get significantly cleaner denoised images compared with the state‐of‐the‐art methods.
Piezoelectric Properties of Bismuth Layered-Structure Ferroelectric Bi2WO6 Mono-Domain Crystals (2007)

Bismuth tungstate, Bi <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> WO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">6</sub> (BWO), mono-domain crystals grown by a slow cooling technique were characterized. Observation of the etch-pit patterns of all the crystal substrate surfaces confirmed that the grown crystals consisted of a mono-domain fabric. The electromechanical coupling factor, k <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">31</sub> , and mechanical quality factor, Q <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">m</sub> , of the crystals were 24% and over 4000 at room temperature, respectively. The resonance response revealed that the BWO crystals maintained the piezoelectricity up to 400degC.
Production of large O-containing neutral hydrocarbon species by aCH4-O2microwave discharge (1994)

The product of O-containing species in ${\mathrm{CH}}_{4}$-${\mathrm{O}}_{2}$ plasmas has been studied as a function of the oxygen partial pressure in a microwave flow tube with 2.465 GHz, 6 W, and 2.2 torr total pressure. Mass spectrometry, coupled with ${\mathrm{Li}}^{+}$-ion attachment techniques, was used for the identification of the products. Studies have clearly shown the presence of various O-containing stable polymer molecules, ${\mathrm{C}}_{\mathit{n}}$${\mathrm{H}}_{2\mathit{n}+2}$O, ${\mathrm{C}}_{\mathit{n}}$${\mathrm{H}}_{2\mathit{n}}$O, and ${\mathrm{C}}_{\mathit{n}}$${\mathrm{H}}_{2\mathit{n}}$${\mathrm{O}}_{2}$ (n goes up to 9). The relative concentration profiles of these products have been determined as a function of ${\mathrm{O}}_{2}$ composition in the feed gas. An assumption was presented that alcohols, aldehydes, and possibly O-containing radical species form in the ${\mathrm{CH}}_{4}$-${\mathrm{O}}_{2}$ plasma. A reaction scheme is speculated which may account for these observed profiles.
Helicobacter gastroduodenitis: a serious infectious diseaseAntibiotic treatment may prevent deaths in the decades ahead (1997)

Learning from asthma deathsNeed to relate deaths to prevalence, severity, and treatment in different populations
Adiabatic pseudospectral methods for multidimensional vibrational potentials (1993)

We describe a new algorithm for computing eigenvalues, spectral intensities, and selected eigenvectors of multidimensional vibrational potential surfaces. The method involves a synthesis of pseudospectral and sequential adiabatic reduction methods and merges the storage and computational advantages of the former with the improved basis set generated by the latter. The recursive residue generation method, which utilizes a Lanczos-based diagonalization procedure, is employed to calculate the observables. As a test case, we apply the method to computation of the infrared and stimulated emission pumping spectra for the HCN molecule and demonstrate a very large (one to three orders of magnitude) reduction in computational effort (for comparable accuracy) as compared to discrete variable representation (DVR)/adiabatic reduction or standard collocation approaches. We expect that this advantage will be increased considerably for larger (e.g., tetra-atomic) systems and will permit accurate basis set calculations on such systems to be carried out in a straightforward fashion.
Small‐Molecule‐Mediated Cleavage of RNA in Living Cells (2012)

RNA im Visier: Bei einem Ansatz zur gezielten Spaltung von Ziel-RNA mithilfe niedermolekularer Substanzen in lebenden Zellen (siehe Schema) bewirkt ein difunktionelles kleines Molekül (blau), das eine spezifische Wiederholungssequenz von drei Nucleotiden erkennt und auf Lichteinwirkung hin spaltet, den Abbau langer Wiederholungs-RNA-Sequenzen vom Myotone-Dystrophy-1(DM1)-Typ. As a service to our authors and readers, this journal provides supporting information supplied by the authors. Such materials are peer reviewed and may be re-organized for online delivery, but are not copy-edited or typeset. Technical support issues arising from supporting information (other than missing files) should be addressed to the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Pulse Delay Measurements in Cascaded Quantum-Well Gain and Absorber Media (2010)

A tunable delay of ultrashort laser pulses in semiconductor waveguide structures are demonstrated in cascaded amplifying and absorbing semiconductor waveguides and compared with a single sectioned waveguide. The single sectioned waveguide shows a low transmission at the maximum delay. This is effectively avoided with the cascaded waveguide configuration, where it is demonstrated viable achieving a net pulse delay while maintaining a transmission of unity. For both types of devices, a pulse advancement is observed, at large pulse energies, that existing models are unable to account for.
Molecular features that predict the response to antimetabolite chemotherapies (2017)

This study demonstrates through unbiased analyses that the activities of metabolic pathways likely contribute to therapeutic response.
Beta-Actin Is Involved in Modulating Erythropoiesis during Development by Fine-Tuning Gata2 Expression Levels (2013)

The functions of actin family members during development are poorly understood. To investigate the role of beta-actin in mammalian development, a beta-actin knockout mouse model was used. Homozygous beta-actin knockout mice are lethal at embryonic day (E)10.5. At E10.25 beta-actin knockout embryos are growth retarded and display a pale yolk sac and embryo proper that is suggestive of altered erythropoiesis. Here we report that lack of beta-actin resulted in a block of primitive and definitive hematopoietic development. Reduced levels of Gata2, were associated to this phenotype. Consistently, ChIP analysis revealed multiple binding sites for beta-actin in the Gata2 promoter. Gata2 mRNA levels were almost completely rescued by expression of an erythroid lineage restricted ROSA26-promotor based GATA2 transgene. As a result, erythroid differentiation was restored and the knockout embryos showed significant improvement in yolk sac and embryo vascularization. These results provide new molecular insights for a novel function of beta-actin in erythropoiesis by modulating the expression levels of Gata2 in vivo.
Enhancing physical activity on the dance floor through a mobile phone application (2014)

Research indicates that there is a potential for persuasive technologies to be used as a means for increasing physical activity. In this exploratory work, we developed a mobile web application to gather movement data to explore the potential of a health tool in the context of a dance floor to promote physical activity. We wanted to explore if the mobile application in combination with the context and mechanisms seen in other health applications could drive physical activity. In total, 208 participants generated 20,279 data points through the mobile application on the dance floor. The result from this work points out that the concept should be further investigated in more studies.
Analysis of a decision directed beamformer (1995)

Studies a technique for using decision direction to extract digital signals from antenna array data. The algorithm alternates between 1) estimating and demodulating the received signals and 2) using the resulting bit decisions to regenerate the signal waveforms and recompute the beamformer weights. An analysis of the (asymptotic) symbol error rate performance of the algorithm for the case of M-ary PSK signals is included, along with several representative simulation examples.
On the crumpling of polycrystalline graphene by molecular dynamics simulation (2015)

Crumpled graphene has been emerging as a valuable component for a variety of devices such as supercapacitors or hydrophobic surface coatings due to its geometric change from a 2D to a 3D structure accompanied by changes in its material behavior. As polycrystalline graphene is easier to produce than pristine graphene, certain applications of crumpled graphene may be better suited to polycrystalline graphene. However, the crumpling process of polycrystalline graphene and its relevant mechanical properties remain poorly understood. Here we employ molecular dynamics simulation to model the behavior of polycrystalline graphene under geometric confinement and elucidate the effect of grain size, with a focus on the mechanical stabilizing mechanisms and properties of the crumpled structures in comparison to pristine graphene. Simulation results show that crumpled polycrystalline graphene exhibits a slight negative correlation between average grain size and measured hardness, bulk modulus, and crumpled size. As the size of the grains decreases, the crumpled structures formed are harder and smaller, with sharp edges caused by the grain boundaries. These findings provide evidence towards the feasibility of using polycrystalline graphene in place of pristine graphene in applications involving crumpled carbon structures.
CYTOTOXIC ASSESSMENT OF L-ASCORBIC ACID/MONTMORILLONITE UPON HUMAN DERMAL FIBROBLASTS IN VITRO: MTT ACTIVITY ASSAY (2008)

This first-attempt study tended to inspect the cytotoxic effects of montmorillonite (MMT) or 0.01 N phosphoric acid treated MMT supplemented with L-ascorbic acid (LAA) upon human dermal fibroblasts for possible applications. Light micrographs of human dermal fibroblast cell cultures revealed that more dense black spots in larger sizes were observed when higher levels of MMT were supplemented into the fibroblast culture, indicating that more dermal fibroblasts were covered by MMT particles. Compared with the supplementation of LAA alone, this study selected mitochondrial dehydrogenase activity (MTT) assay as an indicator bioreaction to show possible cytotoxic (or allergic) responses upon human dermal fibroblasts in vitro when LAA/acid-treated MMT composites were added. Statistical analysis showed that LAA augmented with either MMT or 0.01 N phosphoric-acid-treated MMT provoked insignificant cytotoxic responses to human dermal fibroblasts. Thus, an augmentation of MMT or 0.01 N phosphoric-acid-treated MMT to LAA should be biologically feasible for possible skin applications according to this human dermal fibroblasts model.
Exploiting low power circuit topologies for soft error mitigation (2016)

Alpha particle experimental results for arithmetic circuits implemented using transmission gate logic are shown to have 35% lower soft error rate as well as 30% lower power consumption compared to standard CMOS circuits. Analytical models confirm the experimental trends and help optimize and predict the power-SER trade-off.
METHOTREXATE, IN VIVO OF MERCAPTOPURINE ALONE OR IN COMBINATION WITH DE NOVO PURINE SYNTHESIS INHIBITION AND ANTILEUKEMIC EFFECTS (2013)

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Continuous speech recognition under non-stationary musical environments based on speech state transition model (2002)

We propose a non-stationary noise reduction method based on the speech state transition model. Our proposed method estimates the speech signal under non-stationary noisy environments such as musical background by applying the speech state transition model to Kalman filtering estimation. The speech state transition model represents the state transition of the speech component in non-stationary noisy speech and is modeled by using Taylor expansion. In this model, the state transition of the noise component is estimated by using linear predictive estimation. In order to evaluate the proposed method, we carried out large vocabulary continuous speech recognition experiments under 3 types of music and compared the results with the conventional parallel model combination (PMC) method in word accuracy rate. As a result, the proposed method obtained a word accuracy rate that was superior to PMC.
H2C(X)–X···X–(X = Cl, Br) Halogen Bonding of Dihalomethanes (2017)

The dihalomethane–halide H2C(X)–X···X– (X = Cl, Br) halogen bonding was detected in a series of the cis-[PdX(CNCy){C(NHCy)═NHC6H2Me2NH2}]X•CH2X2 (X = Cl, Br) associates by single-crystal XRD followed by DFT calculations. Although ESP calculations demonstrated that the σ-hole of dichloromethane is the smallest among all halomethane solvents (the maximum electrostatic potential is only 2.6 kcal/mol), the theoretical DFT calculations followed by Bader’s QTAIM analysis (M06/DZP-DKH level of theory) confirmed the H2C(X)–X···X– halogen bond in both the solid-state and gas-phase optimized geometries. The estimated bonding energy in H2C(X)–X···X– is in the 1.9–2.8 kcal/mol range.
New drug‐resistant cassettes for gene disruption and epitope tagging in Schizosaccharomyces pombe (2005)

We describe new heterologous modules for PCR-based gene targeting in the fission yeast Schizosaccharomyces pombe. Two bacterial genes, hph and nat, which display dominant drug-resistance phenotypes, are used as new selectable markers in these modules. Both genes have been used successfully in the budding yeast Saccharomyces cerevisiae, in which hph confers resistance to hygromycin B, while nat confers nourseothricin resistance (Goldstein and McCusker, 1999). Vector modules for gene disruption and C-terminal tagging with 3HA, 13Myc and GFP(S65T) are constructed using previously constructed pFA6a-MX6-derived plasmids (Bähler et al., 1998; Wach et al., 1997). In combination with the existing systems that are based upon the G418-resistance gene (kan), triple gene deletions or tags could be constructed. In addition a vector for one-step integration of a monomeric RFP (mRFP) to the C-terminus of proteins of interest is developed. Finally, oligonucleotides that allow a simple marker switch from kan to hph or nat, and vice versa, are described. The new constructs developed here should facilitate post-genomic molecular analysis of protein functions in fission yeast.