gebhart/patrepeval huggingface dataset:
The role of chemical‐induced stress responses in immunosuppression: A review of quantitative associations and cause‐effect relationships between chemical‐induced stress responses and immunosuppression (1993)

Although there is an increasing awareness that drugs and chemicals can modulate the immune system by indirect mechanisms, few compounds have been thoroughly evaluated in this regard. Several environmentally relevant chemicals induce stresslike responses, as indicated by elevated glucocorticoid levels. Comparable glucocorticoid levels induced by physical or psychological stressors are consistently associated with suppression of one or more immunological parameters. Thus, it seems likely that stress-related neuroendocrine mechanisms are important in immunosuppression by some environmental chemicals. Distinguishing direct and indirect (stress-related) mechanisms of immunosuppression is generally possible, and this could be done as a routine part of immunotoxicity assessment. Although it is clear that glucocorticoids can contribute to such immunosuppression, it is also clear that several other neuroendocrine mediators associated with stress responses can be immunomodulatory. Thus, correlation between glucocorticoid levels and immunosuppression does not conclusively demonstrate a cause-effect relationship. Demonstrating such relationships has been difficult, but it has been done in a few cases of drug-induced thymic hypoplasia by monitoring several parameters known to be affected by glucocorticoids and by measuring the ability of a glucocorticoid antagonist (RU 486) or adrenalectomy to block changes in these parameters. A similar strategy might be useful for evaluation of the role of glucocorticoids in drug- or chemical-induced suppression of a variety of immune functions, but the effects of RU 486 on neuroendocrine feedback circuits and the possibility of consequent immunological changes must be considered when the data are interpreted. This approach could also be applied to evaluation of the roles in chemical-induced immunosuppression of other neuroendocrine mediators for which antagonists or agents that block the synthesis or release of the mediator are available. However, it is likely that a comprehensive (and perhaps predictive) understanding of the relationship between chemically induced stress responses and immunosuppression will require more detailed and quantitative elucidation of the mechanisms and regulation of neuroendocrine-immune interactions.
Batch and semicontinuous emulsion copolymerization of vinyl acetat–butyl acrylate. I. Bulk, surface, and colloidal properties of copolymer latexes (1983)

Abstract Vinyl acetate (VAc)–butyl acrylate (BuA) comonomer mixtures with various composition were polymerized by batch and semicontinuous emulsion polymerization processes. PVAc and PBuA homopolymer latexes as well as the (VAc‐BuA) copolymer latexes were characterized with respect to particle size, molecular weight, acid end groups on particle surfaces, and colloidal stability against electrolytes. The surface and colloidal properties of these latexes were also compared before and after aging and acid hydrolysis. The average particle size of batch latexes was independent of copolymer composition, whereas for semicontinuous latexes it decreased with increasing BuA content and was always lower than that of the corresponding batch latex. The molecular weight distribution (MWD) for batch latexes was narrower and much less dependent on composition than that of the semicontinuous latexes; bimodal MWD was found in most semicontinuous latexes with a substantial amount of low MW fraction. The total weak and strong acid end groups on particle surfaces for semicontinuous latexes is higher, and more dependent on composition, than the batch latexes. Acid‐induced hydrolysis results in a drastic change in the type and concentration of the surface groups of the semicontinuous latex particles. Colloidal stability against electrolytes showed that both electrostatic (due to surface acid groups) and steric [due to surface poly(vinyl alcohol)] mechanisms are contributing. However, for semicontinuous latexes, increasing PVAc content above 50 mol % resulted in a proportional increase and ultimately dominant role of steric stabilization. The results were interpreted in terms of differences in reactivity ratios and water solubilities of the two monomers and their effects on the locus of initiation and growth in the two polymerization processes, as well as the monomer sequence within the polymer chain and degree of homogeniety of the copolymer composition within the particle.
Self-aligned quadruple patterning-compliant placement (2015)

Self-Aligned Quadruple Patterning (SAQP) will be one of the leading candidates for sub-14nm node and beyond. However, compared with triple patterning, making a feasible standard cell placement has following problems. (1) When coloring conflicts occur between two adjoining cells, they may not be solved easily since SAQP layout has stronger coloring constraints. (2) SAQP layout cannot use stitch to solve coloring conflict. In this paper, we present a framework of SAQP-aware standard cell placement considering the above problems. When standard cell is placed, the proposed method tries to solve coloring conflicts between two cells by exchanging two of three colors. If some conflicts remain between adjoining cells, dummy space will be inserted to keep coloring constraints of SAQP. We show some examples to confirm effectiveness of the proposed framework. To our best knowledge, this is the first framework of SAQP-aware standard cell placement.
Abstract 2926: Structure-based design of quadruplex-binding small molecule compounds: The essential role of water molecules (2022)

Abstract The compounds CM03 and SOP1812 are tri- and tetra-substituted naphthalene diimide derivatives with high affinity for several human DNA quadruplexes. They have been designed by computer modelling based on co-crystal structures of 1st-generation substituted naphthalene diimides with human intramolecular telomeric quadruplexes. CM03 and SOP1812 have single-digit 1-20 nM anti-proliferative activity in a panel of human pancreatic ductal adenocarcinoma (PDAC) cell lines (Marchetti et al., J. Med. Chem, 2018, 61, 2500-2517: Ahmed et al., ACS Med Chem Lett, 2020, 11, 1634-1644) and significant anti-tumor activity in the MIA-PACA2 xenograft model for PDAC as well as in the more demanding KPC model. SOP1812 is bio-available at therapeutic doses and is well tolerated at these levels in animal models. It is currently being evaluated as a candidate for clinical development by Qualigen Therapeutics Inc. The role of water in protein-drug binding is well documented and known to be important for accurate estimates of drug binding energies and for docking/virtual screening studies. To date this factor has not been seriously considered in studies of ligand-quadruplex interactions even though virtual screening has emerged as an important tool for finding new chemotypes and optimizing compound libraries in silico. A high-resolution crystal structure of a naphthalene diimide quadruplex complex (PDB id 3UYH: Micco et al., J. Med. Chem., 2013, 56, 2959-2974) has now been analyzed in detail. Patterns of water molecules have been found in each of the four quadruplex grooves, associated with the cationic side chains. Only a nitrogen atom on each N-methyl-piperazine cationic end groups is in direct hydrogen bonded contact with a phosphate group. The morpholino groups each have a small and well-defined cluster of water molecules mediating between cationic nitrogen atom and phosphate group. The rest of each groove is filled by a second cluster of waters, suggesting that larger substituents can be accommodated. Data from a library of naphthalene diimide derivatives is being examined to validate the role of these waters, especially with respect to their relative mobilities and ease of displacement. Citation Format: Stephen Neidle. Structure-based design of quadruplex-binding small molecule compounds: The essential role of water molecules [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2926.
Flavin-Dependent Monooxygenases NotI and NotI′ Mediate Spiro-Oxindole Formation in Biosynthesis of the Notoamides (2019)

The fungal indole alkaloids are a unique class of complex molecules that have a characteristic bicyclo[2.2.2]diazaoctane ring and frequently contain a spiro-oxindole moiety. While various strains produce these compounds, an intriguing case involves the formation of individual antipodes by two unique species of fungi in the generation of the potent anticancer agents (+)- and (-)-notoamide A. NotI and NotI′ have been characterized as flavin-dependent monooxygenases that catalyze epoxidation and semi-Pinacol rearrangement to form the spiro-oxindole center within these molecules. This work elucidates a key step in the biosynthesis of the notoamides and provides an evolutionary hypothesis regarding a common ancestor for production of enantiopure notoamides.
Optical Amplifiers for Cost and Energy Efficient Spatial Division Multiplexing (2013)

Cost and energy efficient optical amplifiers are key components for long haul transmission systems featuring increased capacity by spatial division multiplexing. Optimized module design and modular upgrade capabilities enable reduced cost and energy per bit.
Dependence of oxygen quenching of intercalated methylene blue triplet lifetime on DNA base‐pair composition (1986)

Abstract We utilize the dynamic quenching of the triplet state of methylene blue by molecular oxygen to observe changes in the rate at which oxygen can penetrate the helix as a function of base‐pair composition. The results indicate that the interior of the oligonucleotide dA‐dT is more accessible than dG‐dC to small molecules such as dioxygen.
Cu–SiO2Hybrid Bonding (2014)

Three-dimensional technology will enable a future generation of microelectronic devices with vertical interconnection being one of the challenging issues. One of the possible techniques to address this issue appears to be the formation of interconnections via bonding of Cu pads. In this chapter, direct bonding of patterned Cu–SiO2 surfaces at room temperature with atmospheric pressure and ambient air is described. High bonding quality with precise alignment between the Cu interconnects is achieved for both wafer-to-wafer (W2W) and die-to-wafer (D2W) bonding approaches. Electrical characterizations and reliability of Cu–Cu contacts are presented for multiple contact areas and postbonding annealing temperatures, showing the high quality of the technique.
E-021 Quantitative Evaluation of Metal Artifact Reduction for Coiled Aneurysms in Cone-Beam CT (2016)

<h3>Purpose</h3> During minimally invasive embolization of brain aneurysms the aneurysm sac is filled with metal coils. The post-coiling cone-beam CT image quality is impaired by artifacts originating from the radiopaque metal mass. The artifact streaks run through the brain parenchyma, which hampers their inspection for hemorrhages and other events. Metal artifact reduction improves the image quality of cone-beam CT affected by streak artifacts. While several metal artifact reduction schemes have been described in the literature, there is little objective quantitative evaluation on clinical data. In this article we use pre- and post-coiling cone-beam CT data, and apply a metric (peak signal-to-noise ratio) to quantify the improvement in image quality. <h3>Materials and methods</h3> For 22 retrospective aneurysm coiling cases, cone-beam CT acquisitions prior and post embolization were available. The former dataset was used as gold standard reference to evaluate the latter without and with metal artifact reduction. To this purpose the pre- and post-coiling datasets were co-registered, and the brain cavity and coiling mass were segmented. The metric was then applied to the non-coiled brain parenchyma. <h3>Results</h3> The mean squared error improved for 20 out of 22 patients after metal artifact reduction was applied. The average mean squared error was reduced by 264 HU. The peak signal-to-noise ratio was improved by 6.8 dB. The average additional computation time for the metal artifact reduction algorithm amounted 20 seconds. <h3>Conclusion</h3> Metal artifact reduction has been found to objectively improve the image quality quantified by the peak signal-to-noise ratio for most patients. It is therefore considered a useful tool for interventional use when the image contains metal parts. <h3>Disclosures</h3> <b>D. Ruijters:</b> 5; C; Philips Healthcare. <b>P. van de Haar:</b> 5; C; Philips Healthcare. <b>G. Kaila:</b> None. <b>T. Grünhagen:</b> 5; C; Philips Healthcare. <b>J. Moret:</b> None. <b>L. Spelle:</b> None.
Distortion and prospective motion corrected zoomed functional imaging of the human brain at 9.4 Tesla (2017)

Purpose/Introduction: Sub-millimeter single-shot echo-planar imaging at ultra-high field is challenging due to stronger distortions evoked by increased B0-inhomogeneities as well as increased blurring and a reduction of the echo-time yielding the maximum BOLD contrast caused by faster T2 * relaxation. Therefore, a shorter echo-train length (ETL) is required, either by utilizing partial Fourier acquisition or parallel imaging techniques. A further reduction of the ETL can be achieved with the reduced field of view (rFOV) method [1]. But even highly accelerated images can suffer from distortions which can be accurately measured and corrected by the point-spread-function (psf) mapping technique [2, 3]. Another issue of high resolution fMRI, is the increased vulnerability to subject motion. Here, we combined rFOV imaging with psf distortion correction and prospective motion correction for high-resolution functional imaging at 9.4 Tesla. Subjects and Methods: Measurements were performed on a whole body scanner (Siemens Healthcare, Germany) using a 16-Tx/31-Rx array [4]. An outer volume suppression pulse was implemented in an EPI sequence [1]. The slice positions of the psf-mapping and functional measurements were updated using data from a camera (Metria Innovation Inc., USA) which tracked a moire´ phase marker fixed to the subject’s bite bar [6]. Parameters: TR = 2000 ms, TE = 25 ms, FA = 80, GRAPPA = 3 (FLEET ACS-scan, [7]), 6/8 partial Fourier, FoV = 150 9 75 mm2, 17 slices, 0.65 mm isotropic, ETL = 36 ms. Paradigm: 20 periods, 10 s flickering circular checkerboard (8 Hz, 7 visual field) + 26.5 s isolimuninant background. Images were reconstructed using in-house developed Matlab routines. From the fMRI data, residual motion was estimated before distortion correction. Results: Although the short ETL used here resulted in already quite small distortions (Fig. 1: a,b), a clear improvement of anatomical matching can be seen when the distortion correction is applied (Fig. 1: c). According to the camera data, the subject presented here moved less than 0.24 mm/0.57. However, the retrospective estimate was even smaller (max. 0.21 mm/0.09). Discussion/Conclusion: We demonstrated anatomically matching sub-millimeter fMRI with reduced interpolation blurring due to avoiding retrospective motion correction. In addition, the echo-train length was shortened in order to limit T2 * -blurring. However, the increased SAR caused by the additional outer volume suppression required a reduction of the number of slices. To reduce SAR, implementation of static B1 +-shimming or even 2D-selective excitation may help [7]. Nevertheless, the presented approach can probably help to investigate the actual resolution of single-shot EPI at high field and can possibly be also used for measuring differences in functional layers.
Living Transition Metal‐Catalyzed Alkene Polymerization: Polyolefin Synthesis and New Polymer Architectures (2009)

This chapter contains sections titled: Introduction Living α-Olefin Polymerization Living Propylene Polymerization Living Polymerization of Ethylene Living Nonconjugated Diene Polymerization Living Homo- and Copolymerizations of Cyclic Olefins Random Copolymers Block Copolymers Outlook and Summary References
High-Frequency Acoustic Propagation and Adaptive Signal Processing: An Integrated Research Program (2001)

Abstract : The long term goals are two-fold. The first is to develop an improved understanding of how acoustic signals propagate through the ocean and how this propagation effects the characteristics of received acoustic signals. The second goal is to use this improved understanding to improve the ability to quantify the performance of adaptive signal processing algorithms in realistic ocean environments and to develop more capable signal processing algorithms. The objective of this work is to combine the analysis of high-frequency acoustic propagation with the development and analysis of adaptive signal processing algorithms. The application of current interest is underwater acoustic communications so the research is conducted within that context. The specific objectives are to 1. Develop statistical characterizations of the underwater acoustic channel which are useful for the development and analysis of adaptive signal processing algorithms. 2. Determine the predictability of the deterministic and statistical characteristics of the underwater acoustic channel. 3. Develop techniques to quantify the performance of least squares adaptive algorithms in the presense of realistic acoustic channel fluctuations. 4. Develop new adaptive algorithms which exploit characteristics of the underwater acoustic environment to improve performance.
Investigation into the optimum beam shape and fluence for selective ablation of dental calculus at λ = 400 nm (2010)

Supplying laser light to a tooth using an optical fiber with coaxial water-cooling is determined to be the most appropriate method when selectively removing calculus with a frequency-doubled Ti:sapphire laser. Fluences over 2 J/cm(2) are required to remove calculus efficiently since photo-bleaching stalls calculus removal below that value.
Degradation of ZnGa2O4:Cr3+ luminescent nanoparticles in lysosomal-like medium (2019)

The ultimate goal of in vivo imaging is to provide safe tools to probe the inside of a body in order to obtain pathological information, monitor activities, and examine disease progression or regression. In this context zinc gallate doped with chromium III (ZGO) nanoparticles with persistent luminescence properties have been previously developed, and their biodistribution as well as in vitro toxicity were evaluated. However, to date, nothing is known about their potential transformations in biological media, which may hinder their biomedical applications. In order to know if these nanoparticles could degrade, the present work consists of studying their fate over time depending on both their coating and the aqueous media in which they are dispersed. ZGO nanoparticles have been dispersed in three different aqueous solutions for up to 90 days and characterized by numerous techniques. Among the evaluated dispersion media, Artificial Lysosomal Fluid (ALF) mimicking the intracellular lysosome environment elicited significant degradation of ZGO nanoparticles. The chelating agents present in ALF have proved to play a major role in the degradation of the ZGO, by stabilizing the nanoparticles and increasing the contact. An important time decrease of the luminescence properties has also been observed, which correlated with the release of ions from ZGO nanoparticles as well as their decreasing size. This information is valuable since it indicates, for the first time, the long-term degradation of persistent luminescent nanoprobes in an in vivo like model medium. Therefore, possible elimination of the imaging probes after in vivo preclinical applications could be foreseen.
In situ process diagnostics and intelligent materials processing : symposium held December 2-5, 1997, Boston, Massachusetts, U.S.A. (1998)

This book, first published in 1998, focuses on the rapidly developing field of sensor technology for process monitoring and control during fabrication of advanced materials and structures. Research in sensor driven, closed-loop control of the fabrication process (i.e., process-state monitoring), as well as product-state (e.g., wafer-state) monitoring are discussed. Featured are process techniques that include chemical vapor deposition (CVD), metalorganic chemical vapor deposition (MOCVD), plasma-enhanced chemical vapor deposition (PECVD), molecular beam epitaxy (MBE), rapid thermal processing (RTP), reactive-ion and plasma etching, electron beam evaporation, pulsed laser deposition (PLD), and sputtering. Materials of interest include electronic and optical thin films such as semiconductors, epitaxial oxides, metals and dielectrics, as well as particles and nanostructured materials. Sensing techniques for monitoring variables such as temperature, composition, optical properties, film thickness and particle-size distribution are highlighted. Topics include: sensor technologies and semiconductor diagnostics; sensor technologies and thin-film diagnostics; in situ diagnostics of oxide film growth and processes and intelligent processing of electronic ceramics.
Fast parallel soft Vlterbl decoder mapping on a reconfigurable DSP platform (2004)

The Viterbi algorithm is used to decode convolutional codes (CC). Viterbi decoding is a computation/communication intensive algorithm. Recently, with the emerging of WLAN standards delivering high rates, performance requirements of Viterbi decoders have increased dramatically. So far, such decoders have only been implemented using fixed ASIC with the datapath designed specially for the Viterbi algorithm, sacrificing flexibility. In this paper, we introduce a reconfigurable DSP platform targeting wireless communication algorithms in general with specific accelerators for the Viterbi algorithm.
Microwave Nonlinearities in Ge/Si Avalanche Photodiodes having a Gain-Bandwidth Product of 300 GHz (2009)

The nonlinearity of a 300 GHz gain bandwidth Separate Absorption Charge Multiplication (SACM) Ge/Si avalanche photodiode was examined experimentally for varying multiplication factors. The maximum second order dynamic range was 84.8 dB∙Hz1/2. The largest third order dynamic range was 101.5 dB∙Hz2/3.
Cross-Polarization Reduction of Linear-to-Circular Polarizing Reflective Surfaces (2019)

This letter proposes an efficient design process to reduce the cross polarization of linear-to-circular reflection polarizers illuminated by practical feeds. In particular, we propose a two-step process, where first a geometrical optimization of the unit cell is applied along one plane of the reflector, followed by a progressive rotation of the unit cell in the orthogonal plane. An offset flat polarizer comprised of dipole unit cells fed by a standard gain horn has been used to illustrate the process. Significant improvements in cross-polarization discrimination are demonstrated by simulation. Two breadboards have been manufactured, and their response is compared in order to demonstrate the validity of the design process. Good agreement with measurements is observed corroborating the proposed technique.