gebhart/patrepeval huggingface dataset:
Abstract A55: Potent, dual cIAP1/XIAP antagonists induce apoptosis in a melanoma stem cell population. (2013)

Abstract The inhibitor of apoptosis proteins (IAP) are key regulators of anti-apoptotic and pro-survival signaling pathways. Overexpression of IAPs occurs in various cancers and has been associated with tumor progression and resistance to treatment. IAP antagonists activate the E3 ligase function of cIAP1 and stimulate rapid autoubiquitylation and proteosomal degradation of both cIAP1 and cIAP2. Elimination of these proteins leads to a switch in TNFα signalling from being pro-survival to being pro-apoptotic. However, a strong pro-apoptotic effect from cIAP loss cannot be achieved without sustained antagonism of XIAP-mediated caspase inhibition. Therefore, a best in class profile for IAP antagonists requires potent dual antagonism of cIAP1 and XIAP. Astex has used fragment based-drug discovery to develop a second generation of IAP antagonists, which are non-peptidomimetic and do not contain an alanine as a warhead. This series has the ability not only to efficiently degrade cIAP1 but also to potently antagonize XIAP, delivering a dual cIAP1/XIAP inhibitory profile which is not apparent in the first generation of IAP antagonists based on an alanine warhead. Here, we report the structural understanding of the unique molecular profile of the series together with the enhanced activity of these compounds in melanoma cancer stem cells (CSC). CSC populations are more resistant to apoptosis than the bulk cell population and they have been associated with resistance to cancer therapy, relapse and cancer progressions. Blockade of the apoptotic pathway by up-regulation of anti-apoptotic factors has been implicated in conferring resistance in CSC fractions and increased XIAP expression has also been reported in these cells. We have analysed the CD133+ population of three melanoma cell lines (SK-MEL-2, SK-MEL-5 and SK-MEL-28) and measured activation of caspase-3 (NucView™ cell staining) after treatment with IAP antagonists in presence of TNFα. Our potent dual cIAP1/XIAP antagonists (XIAP EC50 &amp;lt;= 5 nM in cells) have a significantly enhanced apoptosis-inducing capacity (p&amp;lt;0.05), on the CSC fraction in all three cell lines, compared to alanine-containing cIAP1 selective antagonists, with reduced XIAP potency (XIAP EC50 &amp;gt; 35 nM in cells). The enhanced XIAP potency of our compounds is overriding the resistance in CSC subpopulations, highlighting the importance of dual antagonism in promoting efficient induction of apoptosis. Citation Information: Mol Cancer Ther 2013;12(11 Suppl):A55. Citation Format: Gianni Chessari, Maria Ahn, Keisha Hearn, Christopher N. Johnson, Jon Lewis, Neil Thompson, George Ward, Pamela Williams. Potent, dual cIAP1/XIAP antagonists induce apoptosis in a melanoma stem cell population. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2013 Oct 19-23; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(11 Suppl):Abstract nr A55.
A Simple Method to Identify the Unprocessed Strychnos Seeds used in Herbal Medicinal Products (2008)

The seeds of Strychnos nux-vomica are popularly used in the treatment of arthritis. Being extremely toxic, the raw seeds are forbidden and must be processed before clinical use. The quality of crude and processed Strychnos seeds can be controlled by examining the toxic alkaloids using established HPLC methods. But this procedure does not work in the case where the seeds are powdered and mixed with other medicinal materials in proprietary production. In this quality control study on Strychnos seeds, the contents of two major toxic alkaloids (strychnine and brucine) and a major non-alkaloid constituent (loganic acid) in twenty-four samples of Strychnos seeds (nine processed and fifteen unprocessed) were compared using published HPLC-UV methods. The results showed that the better the seeds were processed, the less loganic acid was found. The alkaloids and non-alkaloid components simultaneously decreased in processed seeds. The content ratio between alkaloids and loganic acid was clearly different in well-processed and crude Strychnos seeds. Based on this interesting discovery, a simple chromatographic method was established which allows a simultaneous determination of loganic acid and the alkaloids strychnine and brucine. The relative peak area (RPA) of strychnine-to-loganic acid was revealed to be a reliable key quality control parameter in order to effectively identify the processed seeds. This new method has been successfully applied to detect the insufficiently processed Strychnos material in marketed herbal medicinal products.
Experiments with a low-cost system for computer graphics material model acquisition (2015)

We consider the design of an inexpensive system for acquiring material models for computer graphics rendering applications in animation, games and conceptual design. To be useful in these applications a system must be able to model a rich range of appearances in a computationally tractable form. The range of appearance of interest in computer graphics includes materials that have spatially varying properties, directionality, small-scale geometric structure, and subsurface scattering. To be computationally tractable, material models for graphics must be compact, editable, and efficient to numerically evaluate for ray tracing importance sampling. To construct appropriate models for a range of interesting materials, we take the approach of separating out directly and indirectly scattered light using high spatial frequency patterns introduced by Nayar et al. in 2006. To acquire the data at low cost, we use a set of Raspberry Pi computers and cameras clamped to miniature projectors. We explore techniques to separate out surface and subsurface indirect lighting. This separation would allow the fitting of simple, and so tractable, analytical models to features of the appearance model. The goal of the system is to provide models for physically accurate renderings that are visually equivalent to viewing the original physical materials.
Vibrational self-alignment of a rigid object exploiting friction (2010)

In this paper, one-dimensional self-alignment of a rigid object via stick-slip vibrations is studied. The object is situated on a table, which has a prescribed periodic motion. Friction is exploited as the mechanism to move the object in a desired direction and to stop and self-align the mass at a desired end position with the smallest possible positioning error. In the modeling and analysis of the system, theory of discontinuous dynamical systems is used. Analytic solutions can be derived for a model based on Coulomb friction and an intuitively chosen table acceleration profile, which allows for a classification of different possible types of motion. Local stability and convergence is proven for the solutions of the system, if a constant Coulomb friction coefficient is used. Next, near the desired end position, the Coulomb friction coefficient is increased (e.g. by changing the roughness of the table surface) in order to stop the object. In the transition region from low friction to high friction coefficient, it is shown that, under certain conditions, accumulation of the object to a unique end position occurs. This behavior can be studied analytically and a mapping is given for subsequent stick positions.
Role of the Low-Density Lipoprotein Receptor in Entry of Bovine Viral Diarrhea Virus (2006)

Among several proposed cellular receptors for bovine viral diarrhea virus (BVDV), the low-density lipoprotein (LDL) receptor is of special interest because it is also considered a receptor for the related hepatitis C virus. It has been reported that an anti-LDL receptor monoclonal antibody blocked the infection of bovine cells by BVDV and that the resistance of bovine CRIB cells (cells resistant to infection with BVDV) (E. F. Flores and R. O. Donis, Virology 208:565-575, 1995) to BVDV infection was due to a lack of the LDL receptor (V. Agnello et al., Proc. Natl. Acad. Sci. USA 96:12766-12771, 1999). In connection with our studies on BVDV entry, we reevaluated the putative role of the LDL receptor as a cellular receptor for BVDV. It was first clearly demonstrated that neither of two monoclonal antibodies against the LDL receptor inhibited BVDV infection of two bovine cell lines. Furthermore, the LDL receptor was detected on the surface of CRIB cells. The functionality of the LDL receptor on CRIB cells was demonstrated by the internalization of fluorescently labeled LDL. In conclusion, at present no experimental evidence supports an involvement of the LDL receptor in BVDV invasion.
Development and application of reduced‐order modeling procedures for subsurface flow simulation (2008)

Abstract The optimization of subsurface flow processes is important for many applications, including oil field operations and the geological storage of carbon dioxide. These optimizations are very demanding computationally due to the large number of flow simulations that must be performed and the typically large dimension of the simulation models. In this work, reduced‐order modeling (ROM) techniques are applied to reduce the simulation time of complex large‐scale subsurface flow models. The procedures all entail proper orthogonal decomposition (POD), in which a high‐fidelity training simulation is run, solution snapshots are stored, and an eigen‐decomposition (SVD) is performed on the resulting data matrix. Additional recently developed ROM techniques are also implemented, including a snapshot clustering procedure and a missing point estimation technique to eliminate rows from the POD basis matrix. The implementation of the ROM procedures into a general‐purpose research simulator is described. Extensive flow simulations involving water injection into a geologically complex 3D oil reservoir model containing 60 000 grid blocks are presented. The various ROM techniques are assessed in terms of their ability to reproduce high‐fidelity simulation results for different well schedules and also in terms of the computational speedups they provide. The numerical solutions demonstrate that the ROM procedures can accurately reproduce the reference simulations and can provide speedups of up to an order of magnitude when compared with a high‐fidelity model simulated using an optimized solver. Copyright © 2008 John Wiley &amp; Sons, Ltd.
QuOCS: The Quantum Optimal Control Suite (2022)

Quantum optimal control includes the family of pulse-shaping algorithms that aim to unlock the full potential of a variety of quantum technologies. Our Quantum Optimal Control Suite (QuOCS) unites experimental focus and model-based approaches in a unified framework. The easy usage and installation of QuOCS and the availability of various combinable optimization strategies is designed to improve the performance of many quantum technology platforms, such as color defects in diamond, superconducting qubits, atom- or ion-based quantum computers. It can also be applied to the study of more general phenomena in physics. In this paper, we describe the software and the main toolbox of gradient-free and gradient-based algorithms. We then show how the user can connect it to their experiment. In addition, we provide illustrative examples where our optimization suite solves typical quantum optimal control problems, in both open- and closed-loop settings. Integration into existing experimental control software is already provided for the experiment control software Qudi [J. M. Binder et al., SoftwareX, 6, 85-90, (2017)], and further extensions are investigated and highly encouraged. QuOCS is available from GitHub, under Apache License 2.0, and can be found on the PyPI repository.
Evaluation of motion performance on scanning‐backlight LCDs (2009)

The scanning‐backlight technique to improve the motion performance of LCDs is introduced. This technique, however, has some drawbacks such as double edges and color aberration, which may become visible in moving patterns. A method combining accurate measurements of temporal luminance transitions with the simulation of human‐eye tracking and spatiotemporal integration is used to model the motion‐induced profile of an edge moving on a scanning‐backlight LCD‐TV panel that exhibits the two drawbacks mentioned above. The model results are validated with a perception experiment including different refresh rates, and a high correspondence is found between the simulated apparent edge and the one that is perceived during actual motion. Apart from the motion‐induced edge blur, the perception of a moving line or square‐wave grating can also be predicted by the same method starting from the temporal impulse and frame‐sequential response curves, respectively. Motion‐induced image degradation is evaluated for both a scanning‐ and continuous‐backlight mode based on three different characteristics: edge blur, line spreading, and modulation depth of square‐wave grating. The results indicate that the scanning‐backlight mode results in better motion performance.
UC and EUC Weak Bit-Commitments Using Seal-Once Tamper-Evidence (2013)

Based on tamper-evident devices, i.e., a type of distinguishable, sealed envelopes, we put forward weak bit-commitment protocols which are UC-secure. These commitments are weak in that it is legitimate that a party could cheat. Unlike in several similar lines of work, in our case, the party is not obliged to cheat, but he has ability to cheat if and when needed. The empowered party is the sender, i.e., the protocols are also sender-strong.
1,3-Propanediammonium diperchlorate (1992)

C 3 H 12 N 2 2+ .2ClO 4 - cristallise dans P2 1 /c avec a=7.298, b=14.388, c=9.708A, β=96.79°, Z=4; affinement jusqu'a R=0.053. L'un des atomes N du cation est entoure de huit atomes O des perchlorate, l'autre atome N par sept atomes O dans la gamme des faibles liaisons hydrogene de 2.95 a 3.23A. Les groupes ammonium ont une conformation avec cinq des six atomes hydrogene employes dans sept liaisons hydrogene.
Influence of a Polyphenol-Enriched Protein Powder on Exercise-Induced Inflammation and Oxidative Stress in Athletes: A Randomized Trial Using a Metabolomics Approach (2013)

ClinicalTrials.gov, U.S. National Institutes of Health, identifier: NCT01775384.
Principal molecular axis and transition dipole moment orientations in liquid crystal systems: an assessment based on studies of guest anthraquinone dyes in a nematic host (2016)

An assessment of five different definitions of the principal molecular axis along which molecules align in a nematic liquid crystal system has been made by analysing fully atomistic molecular dynamics (MD) simulations of a set of anthraquinone dyes in the cyanobiphenyl-based nematic host mixture E7. Principal molecular axes of the dyes defined by minimum moment of inertia, minimum circumference, minimum area, maximum aspect ratio, and surface tensor models were tested, and the surface tensor model was found to give the best description. Analyses of MD simulations of E7 alone showed that the surface tensor model also gave a good description of the principal molecular axes of the host molecules, suggesting that this model may be applicable more generally. Calculated dichroic order parameters of the guest-host systems were obtained by combining the surface tensor analysis with fixed transition dipole moment (TDM) orientations from time-dependent density functional theory (TD-DFT) calculations on optimised structures of the dyes, and the trend between the dyes generally matched the trend in the experimental values. Additional analyses of the guest-host simulations identified the range of conformers explored by the flexible chromophores within the dyes, and TD-DFT calculations on corresponding model structures showed that this flexibility has a significant effect on the TDM orientations within the molecular frames. Calculated dichroic order parameters that included the effects of this flexibility gave a significantly improved match with the experimental values for the more flexible dyes. Overall, the surface tensor model has been shown to provide a rationale for the experimental alignment trends that is based on molecular shape, and molecular flexibility within the chromophores has been shown to be significant for the guest-host systems: the computational approaches reported here may be used as a general aid in the predictive design of dyes with appropriate molecular shapes and flexibilities for guest-host applications.
SU‐GG‐J‐41: Treatment Beam's‐Eye‐View Speed‐Modulated CBCT Imaging Used in a Triple Imaging Modality to Track Moving Tumors during Treatment Delivery (2010)

Purpose : To track the target trajectory during the treatment based on the pre‐treatment CBCT projection images when the gantry is selectively slowed down at the treatment angles, the synchronized 3D surface imaging and the EPID in movie mode. Methods and Materials : A gantry‐speed device slows down the CBCT gantry speed (2min/360degrees) by half for a 6 degrees arc centered on the MV treatment beam, allowing us acquire twice as many frames within the treatment arc (22frames/5.5fps). The treatment arc is chosen to accommodate a typical full breathing period (4s). A CBCT kV beam‐on trigger is used to acquire 3D surface images using the AlignRT cameras. Phantom experiments were performed using a programmable respiratory motion platform. During the treatment delivery, MV imaging was performed in movie mode (3fps) while the surface cameras tracked the chest‐wall component. A mutual information algorithm was employed to compare the kV an MV images. Results : CBCT reconstruction was performed using every other frame when in the slow treatment arc for correct reconstruction. The longer scanning times were translated in ∼10–15% additional CBCT dose when 4 beams were used. For simple trajectory, the kV and MV images were phase correlated ∼98% of the time for the high contrast tumor and ∼92% for the low contrast tumor. Phase knowledge provided by the surface cameras increased the later kV‐MV correlation to ∼97%. Patient‐like trajectories were tested where the most irregular trace (3mm baseline‐shift) showed a moderate kV‐MV correlation, enabling one to interrupt the treatment for a second on‐line baseline correction. Conclusion : The selective beams‐eye‐view slow‐arc CBCT technique in conjunction with surface cameras and MV imaging has been demonstrated to be an effective tool for tumor tracking due to its treatment time immediacy and minimal impact on treatment flow.
Physical Models from Physical Templates Using Biocompatible Liquid Crystal Elastomers as Morphologically Programmable Inks For 3D Printing (2023)

Front Cover: In article number 2200343, Robert J. Clements, Elda Hegmann and co-workers present a photo-crosslinkable smectic-A liquid crystal elastomer (LCE) designed for 3D printing. X-ray diffraction data indicate a steady orientation of the LC units within the 3D structure with the LCE layer normal oriented perpendicular to the printed strut surfaces. This LCE transfers its anisotropic properties to cells, inducing cell anisotropy relevant for numerous tissues.
Gap symmetry of the noncentrosymmetric superconductor W3Al2C (2021)

A detailed zero-field and transverse-field muon spin relaxation/rotation ($\ensuremath{\mu}\mathrm{SR}$) experiments have been carried out on the recently discovered noncentrosymmetric superconductor ${\mathrm{W}}_{3}{\mathrm{Al}}_{2}\mathrm{C}$ to speculate about its superconducting ground state. Bulk nature of superconductivity below 7.6 K is confirmed through magnetization and specific heat measurements. No change in the zero field $\ensuremath{\mu}\mathrm{SR}$ spectra collected above and below ${T}_{c}$ is visible, ruling out the possibility of spontaneous magnetic field below ${T}_{c}$. This confirms that time-reversal symmetry is preserved for ${\mathrm{W}}_{3}{\mathrm{Al}}_{2}\mathrm{C}$ upon entering in the superconducting ground state. Temperature-dependent superfluid density [${\ensuremath{\rho}}_{s}(T)$], which directly reflects the superconducting gap symmetry is obtained by the analysis of spectra obtained from the transverse-field $\ensuremath{\mu}\mathrm{SR}$ experiments. Despite a noncentrosymmetric structure, ${\mathrm{W}}_{3}{\mathrm{Al}}_{2}\mathrm{C}$ adopts a fully gapped spin-singlet superconducting ground state as confirmed through the analysis of ${\ensuremath{\rho}}_{s}(T)$ and ${C}_{e}(T)$. The zero-temperature value of gap is ${\mathrm{\ensuremath{\Delta}}}_{0}$ = 1.139(5) meV with gap-to-${T}_{c}$ ratio $2{\mathrm{\ensuremath{\Delta}}}_{0}/{k}_{B}{T}_{c}\ensuremath{\approx}3.48$, classifying this material as a weakly coupled superconductors. We have also revealed that the ratio ${T}_{c}/{\ensuremath{\lambda}}_{\mathrm{eff}}^{\ensuremath{-}2}$ is comparable to the class of unconventional superconductors, which points towards an unconventional pairing mechanism in ${\mathrm{W}}_{3}{\mathrm{Al}}_{2}\mathrm{C}$.
Model of 2,3-bisphosphoglycerate metabolism in the human erythrocyte based on detailed enzyme kinetic equations1: in vivo kinetic characterization of 2,3-bisphosphoglycerate synthase/phosphatase using 13C and 31P NMR (1999)

This is the first in a series of three papers [see also Mulquiney and Kuchel (1999) Biochem. J. 342, 579-594; Mulquiney and Kuchel (1999) Biochem. J. 342, 595-602] that present a detailed mathematical model of erythrocyte metabolism which explains the regulation and control of 2,3-bisphosphoglycerate (2,3-BPG) metabolism. 2,3-BPG is a modulator of haemoglobin oxygen affinity and hence plays an important role in blood oxygen transport and delivery. This paper presents an in vivo kinetic characterization of 2,3-BPG synthase/phosphatase (BPGS/P), the enzyme that catalyses both the synthesis and degradation of 2,3-BPG. Much previous work had indicated that the behaviour of this enzyme in vitro is markedly different from that in vivo. (13)C and (31)P NMR were used to monitor the time courses of selected metabolites when erythrocytes were incubated with or without [U-(13)C]glucose. Simulations of the experimental time courses were then made. By iteratively changing the parameters of the BPGS/P part of the model until a good match between the NMR-derived data and simulations were achieved, it was possible to characterize BPGS/P kinetically in vivo. This work revealed that: (1) the pH-dependence of the synthase activity results largely from a strong co-operative inhibition of the synthase activity by protons; (2) 3-phosphoglycerate and 2-phosphoglycerate are much weaker inhibitors of 2,3-BPG phosphatase in vivo than in vitro; (3) the K(m) of BPGS/P for 2,3-BPG is significantly higher than that measured in vitro; (4) the maximal activity of the phosphatase in vivo is approximately twice that in vitro, when P(i) is the sole activator (second substrate); and (5) 2-phosphoglycollate appears to play no role in the activation of the phosphatase in vivo. Using the newly determined kinetic parameters, the percentage of glycolytic carbon flux that passes through the 2, 3-BPG shunt in the normal in vivo steady state was estimated to be 19%.