gebhart/patrepeval huggingface dataset:
Non-ischaemic cardiomyopathy (2012)

Abstract From the glimpses provided in this chapter it will be clear that there have been huge advances in our understanding of the aetiological basis for the cardiomyopathies— particularly the molecular genetics—and of the pathophysiology of these disorders. However, it must be acknowledged that, thus far, these exciting data have not translated into specific therapies. Our recent paper demonstrating that the metabolic modulator perhexiline partially corrects cardiac energetic impairment in patients with hypertrophic cardiomyopathy, and that this translates into improved symptoms and exercise capacity, may be a forerunner of such therapeutic translation.
Morphology and elastic modulus of novel poly[oligo(ethylene glycol) diacrylate]‐montmorillonite nanocomposites (2005)

Abstract Novel thermosetting poly[oligo(ethylene glycol) diacrylate]‐sodium montmorillonite nanocomposites containing a range of clay volume fractions were prepared by an in situ polymerization method. X‐ray diffraction showed that the basal plane spacing of the clay was increased to approximately 1.7 nm regardless of clay volume fraction. Transmission electron microscopy confirmed the basal spacing and intercalated structure. The elastic moduli of the composites were measured using ultrasonic pulse‐echo equipment. The results show that the Young's modulus and shear modulus increase with nominal clay volume fraction up to 0.22, and are in good agreement with the well‐established Christensen method and derived Hashin–Shtrikman bounds for conventional composites provided that the true volume fraction of clay reinforcement filler is calculated. At low clay volume fractions, the composites were transparent. When the nominal clay volume fraction was further increased, cracks and porous surfaces appeared, as observed by scanning electron microscopy. These defects decreased the elastic modulus, indicating an upper limit for clay additions in this preparation route. © 2005 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 43: 1785–1793, 2005
NAD(P)H‐flavin oxidoreductase from the bioluminescent bacterium, Vibrio fischeri ATCC 7744, is a flavoprotein (1994)

The NAD(P)H-flavin oxidoreductase gene from the bioluminescent bacterium, Vibrio fischeri ATCC 7744, was expressed in Escherichia coli, and the enzyme purified using Cibacron Blue 3G-A affinity column chromatography from crude extracts in a single step. The purified enzyme had a typical flavoprotein absorption spectrum and flavin mononucleotide (FMN) was identified as a prosthetic group, non-covalently bound in a molar ratio of 1:1. The enzyme catalyzed the electron transfer from NADH via FMNH2 to various other electron acceptors. Reduced flavin produced by flavin reductase participated non-enzymatically in the following reactions: H2O2-forming NADH oxidase-like, oxygen-insensitive nitroreductase-like, diaphorase (quinone reductase)-like and bacterial luciferase reactions.
In-Depth Compositional and Structural Characterization of N-Glycans Derived from Human Urinary Exosomes (2019)

The study of exosomes has become increasingly popular due to their potentially important biological roles. Urine can be used as an effective source of exosomes for noninvasive investigations into the pathophysiological states of the urinary system, but first, detailed characterization of exosomal components in healthy individuals is essential. Here, we significantly extend the number of N-glycan compositions, including sulfated species, identified from urinary exosomes and determine the sialic acid linkages for many of those compositions. Capillary electrophoresis-mass spectrometry (CE-MS), matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS), and capillary liquid chromatography-tandem mass spectrometry (LC-MS/MS) were used to identify N-glycan and sulfated N-glycan compositions. Second, because the alteration of sialylation patterns has been previously implicated in various disease states, ion-exchange chromatography, microfluidic capillary electrophoresis (CE), and MALDI-MS were adopted to resolve positional isomers of sialic acids. Structures of the sialyl-linkage isomers were assigned indirectly through α2-3 sialidase treatment and sialic acid linkage-specific alkylamidation (SALSA). In total, we have identified 219 N-glycan structures that include 175 compositions, 64 sialic acid linkage isomers, 26 structural isomers, and 27 sulfated glycans.
A power combined W-band HBT oscillator (2002)

In this paper, the development of a power combined W-band heterojunction bipolar transistor (HBT) oscillator is reported. The oscillation frequency is 105.9 GHz, and the output power is +0.6 dBm with a phase noise of -88 dBc/Hz at 1 MHz offset. We believe this is the first report of a W-band fundamental mode power combined oscillator.
Evaluation of compact models for negative-tone development layers at 20/14nm nodes (2015)

With the introduction of negative tone develop (NTD) resists to production lithography nodes, multiple NTD resist modeling challenges have surpassed the accuracy limits of the existing modeling infrastructure developed for the positive polarity process. We report the evaluation of two NTD resist modeling algorithms. The new modeling terms represent, from the first principles, the NTD resist mechanisms of horizontal shrink and horizontal development bias. Horizontal shrink describes the impact of the physical process of out-gassing on remaining resist edge location. Horizontal development bias accounts for the differential in the peak and minimum development rate with exposure intensity observed in NTD formulations. We review specific patterning characteristics by feature type, modeling accuracy impact presented by these NTD mechanisms, and their description in our compact models (Compact Model 1, CM1). All the new terms complement the accuracy advantage observed with existing CM1 resist modeling infrastructure. The new terms were tested on various NTD layers. The results demonstrate consistent model accuracy improvement for both calibration and verification. Furthermore, typical NTD model fitting challenges, such as large SRAF-induced wafer CD jump, can be overcome by the new NTD terms. Finally, we propose a joint-tuning approach for the calibration of compact models for the NTD resist.
Target gene activation by 1,25-dihydroxyvitamin D3 in osteosarcoma cells is independent of calcium influx. (1994)

Analogs of the seco-steroid hormone, 1,25-dihydroxyvitamin D3 [1,25-(OH)-2D3] can preferentially stimulate genomic or nongenomic signaling pathways in osteoblasts. In this study, we used 1,25-(OH)2D3 analogs and voltage-sensitive Ca2+ channel (VSCC) ligands, including dihydropyridines (Bay K 8644 and nitrendipine), in an osteosarcoma cell model to examine the relationship between 1,25-(OH)2D3-stimulated Ca2+ influx and genomic and nongenomic pathways leading to osteoblast activation. Northern blotting experiments demonstrated that an analog of 1,25-(OH)2D3, 1,24-dihydroxy-22-ene-24-cyclopropyl D3, increased messenger RNA (mRNA) levels of both osteopontin (OPN) and osteocalcin (OCN) without triggering Ca2+ influx through VSCCs. Nitrendipine (an inhibitor of L-type VSCCs) did not block the mRNA increase induced by either analog 1,24-dihydroxy-22-ene-24-cyclopropyl D3 or 1,25-(OH)2D3. 1-Deoxy analogs of 1,25-(OH)2D3, 25-hydroxy-16-ene-23-yne-D3, or 25-hydroxy-23-yne-D3, which stimulate Ca2+ influx, did not produce mRNA accumulation for OPN and OCN, consistent with their poor binding to nuclear receptors. Likewise, Bay K 8644, an agonist of VSCCs that produces Ca2+ influx, did not increase mRNA levels for OPN or OCN. Experiments using a construct derived from the sequence of the genomic OPN promoter region and a luciferase reporter confirmed the analog specificity in stimulating transcription. Together these results indicate that 1,25-(OH)2D3-mediated up-regulation of genes encoding OPN and OCN is independent of Ca2+ influx and suggest that the stimulation of Ca2+ influx by 1,25-(OH)2D3 is not required for target gene activation.
Audio-Visual Emotion Recognition Using Gaussian Mixture Models for Face and Voice (2008)

Emotion expression associated with human communication is known to be a multimodal process. In this work, we investigate the way that emotional information is conveyed by facial and vocal modalities, and how these modalities can be effectively combined to achieve improved emotion recognition accuracy. In particular, the behaviors of different facial regions are studied in detail. We analyze an emotion database recorded from ten speakers (five female, five male), which contains speech and facial marker data. Each individual modality is modeled by Gaussian mixture models (GMMs). Multiple modalities are combined using two different methods: a Bayesian classifier weighting scheme and support vector machines that use post classification accuracies as features. Individual modality recognition performances indicate that anger and sadness have comparable accuracies for facial and vocal modalities, while happiness seems to be more accurately transmitted by facial expressions than voice. The neutral state has the lowest performance, possibly due to the vague definition of neutrality. Cheek regions achieve better emotion recognition accuracy compared to other facial regions. Moreover, classifier combination leads to significantly higher performance, which confirms that training detailed single modality classifiers and combining them at a later stage is an effective approach.
Investigation on improvement in channel estimation accuracy using data signal muting in downlink coordinated multiple-point transmission and reception in LTE-Advanced (2011)

Accurate channel estimation for multiple cells is essential in downlink coordinated multi-point (CoMP) transmission/reception. Therefore, this paper investigates a technique to improve the channel estimation for downlink CoMP in Long-Term Evolution (LTE)-Advanced. Particularly, the performance of data signal muting, i.e., muting data signals that collide with the channel state information reference signal (CSI-RS) of the neighboring cell, is evaluated considering various CoMP schemes and intra-eNodeB and inter-eNodeB CoMP scenarios. In a multi-cell link level simulation, coordinated scheduling and coordinated beamforming (CS/CB) CoMP is employed. The simulation results show that data signal muting is effective in improving the channel estimation accuracy and consequently the throughput performance, especially for sets of user equipment at the cell boundary. Furthermore, the tradeoff relation between accurate channel estimation by muting larger numbers of data signals and a high peak data rate, i.e., low overhead, is also investigated. It is shown that when the number of coordinated cells is set to three, the improvement in performance is almost saturated when the data signals that collide with the CSI-RSs of the other two coordinated cells are muted in a synchronized network.
Fibrin Gels Containing GDNF Microspheres Increase Axonal Regeneration After Delayed Peripheral Nerve Repair (2012)

These findings demonstrate that early measures of nerve regeneration after delayed nerve repair is improved by GDNF microspheres implanted at the coaptation site.
Enhanced Nonlinear Absorption in Low-Finesse Metal-Dielectric Fabry-Perot Resonators (2009)

We report on the nonlinear optical properties of metal-dielectric Fabry-Perot resonators with broad spectral bandwidths in the visible, peak transmittance larger than 70 %, and a nonlinear absorption up to 20× larger than bulk ZnO.
Effects of extending conjugation length on the two-photon absorption spectra of fluorene molecules (2004)

By systematically altering the structural properties of various fluorene-based molecules, we determine how these changes affect their two-photon absorbing capabilities. Here we emphasize the effects of conjugation extension, however other structural motifs were also investigated.
Boltzmann machines for time-series (2017)

We review Boltzmann machines extended for time-series. These models often have recurrent structure, and back propagration through time (BPTT) is used to learn their parameters. The per-step computational complexity of BPTT in online learning, however, grows linearly with respect to the length of preceding time-series (i.e., learning rule is not local in time), which limits the applicability of BPTT in online learning. We then review dynamic Boltzmann machines (DyBMs), whose learning rule is local in time. DyBM's learning rule relates to spike-timing dependent plasticity (STDP), which has been postulated and experimentally confirmed for biological neural networks.
Geometrical tuning art for entirely subwavelength grating waveguide based integrated photonics circuits (2016)

Subwavelength grating (SWG) waveguide is an intriguing alternative to conventional optical waveguides due to the extra degree of freedom it offers in tuning a few important waveguide properties, such as dispersion and refractive index. Devices based on SWG waveguides have demonstrated impressive performances compared to conventional waveguides. However, the high loss of SWG waveguide bends jeopardizes their applications in integrated photonic circuits. In this work, we propose a geometrical tuning art, which realizes a pre-distorted refractive index profile in SWG waveguide bends. The pre-distorted refractive index profile can effectively reduce the mode mismatch and radiation loss simultaneously, thus significantly reduce the bend loss. This geometry tuning art has been numerically optimized and experimentally demonstrated in present study. Through such tuning, the average insertion loss of a 5 μm SWG waveguide bend is reduced drastically from 5.43 dB to 1.10 dB per 90° bend for quasi-TE polarization. In the future, the proposed scheme will be utilized to enhance performance of a wide range of SWG waveguide based photonics devices.
Integration And Process Challenges Of Self Assembly Applied To Die-To-Wafer Hybrid Bonding (2023)

We report the integration and process challenges of self assembly in die-to-wafer hybrid bonding. The bonding quality, step height and Cu integrity are discussed in the context of technology implementation in high volume manufacturing. In-depth characterizations of surfaces and bonding structures are performed and used to propose process improvements.
Structure-function relationship in antimony corrole photosensitizers: Time-resolved electron paramagnetic resonance and optical study (2007)

Three photosensitizers based on tris-(pentafluorophenyl)antimony corroles that differ in oxidation state and axial ligands, namely, (pyridine) Sb (III)-, (oxo) Sb (V)- and (difluoro) Sb (V) complexes, were studied by time-resolved electron paramagnetic resonance spectroscopy and laser flash photolysis. The magnetic and orientational parameters of the corroles oriented in a nematic liquid crystal as well as their triplet lifetimes in liquid toluene were determined and interpreted in terms of their structure and geometry. The negative zero-field splitting parameter D assigned to all studied corroles is explained by the asymmetric π-electron withdrawal effect caused by perfluorinated peripheral aryl groups, which force the triplet electron spins to align in head-to-tail configuration. The effect of the axial ligands on the photoexcited triplet state properties of the corroles is correlated with their different efficiency to perform photoassisted aerobic oxygenation of some organic molecules. This is explained by the dependence of the main parameters of the photoexcited complexes on the interaction between the central ion and corrole π-system. This interaction is strongly influenced by axial ligands coordination, affecting the macrocycle symmetry, planarity, and rigidity.
Patterns of Recurrence in Patients with Melanoma and Histologically Negative But RT-PCR-Positive Sentinel Lymph Nodes (2003)

Because the pattern of recurrence of patients with only RT-PCR evidence of melanoma in SLNs was identical to that in patients who had histologically evident melanoma in the SLN and underwent subsequent completion lymphadenectomy, we conclude that completion lymphadenectomy might be ineffective in decreasing the recurrence rate of patients with only RT-PCR evidence of melanoma in SLNs.
Cysteinyl leukotriene receptor 1 modulates autophagic activity in retinal pigment epithelial cells (2020)

The retinal pigment epithelium (RPE), which is among the tissues in the body that are exposed to the highest levels of phagocytosis and oxidative stress, is dependent on autophagy function. Impaired autophagy and continuous cellular stress are associated with various disorders, such as dry age-related macular degeneration (AMD), a disease for which effective therapies are lacking. Cysteinyl leukotriene receptor (CysLTR) 1 is a potential modulator of autophagy; thus, the aim of this study was to investigate the role of CysLTR1 in autophagy regulation in the RPE cell line ARPE-19. The polarized ARPE-19 monolayer exhibited expression of CysLTR1, which was colocalized with β-tubulin III. In ARPE-19 cells, autophagic activity was rhythmically regulated and was increased upon CysLTR1 inhibition by Zafirlukast (ZK) treatment. H<sub>2</sub>O<sub>2</sub> affected the proautophagic regulatory effect of ZK treatment depending on whether it was applied simultaneously with or prior to ZK treatment. Furthermore, mRNA levels of genes related to the leukotriene system, autophagy and the unfolded protein response were positively correlated. As CysLTR1 is involved in autophagy regulation under basal and oxidative stress conditions, a dysfunctional leukotriene system could negatively affect RPE functions. Therefore, CysLTR1 is a potential target for new treatment approaches for neurodegenerative disorders, such as AMD.
Thermal, Fluid, and Mass Transport Modeling of a Gas-Jet Reagent Delivery System for Laser Chemical Vapor Deposition (LCVD) (2001)

A gas-jet reagent delivery system for laser chemical vapor deposition (LCVD) is modeled with respect to heat transfer, fluid flow, and mass transport. A commercial package was used to model the geometry and flow field surrounding an LCVD reaction zone. The deposition temperature was analyzed for various materials and flow conditions. The forced flow environment was compared against buoyancy-driven flow, which is more typical of a statically filled chamber. A finite difference code was also developed to analyze the effect of the gas-jet on the concentration gradients above the deposition zone.
Fully automatic segmentation of short and long axis cine cardiac MR (2009)

The authors would like to thank the editor, BioMed Central, for the open access to the publication
FOCUS — Development of a Global Communication and Modeling Platform for Applied and Computational Medicinal Chemists (2015)

Communication of data and ideas within a medicinal chemistry project on a global as well as local level is a crucial aspect in the drug design cycle. Over a time frame of eight years, we built and optimized FOCUS, a platform to produce, visualize, and share information on various aspects of a drug discovery project such as cheminformatics, data analysis, structural information, and design. FOCUS is tightly integrated with internal services that involve-among others-data retrieval systems and in-silico models and provides easy access to automated modeling procedures such as pharmacophore searches, R-group analysis, and similarity searches. In addition, an interactive 3D editor was developed to assist users in the generation and docking of close analogues of a known lead. In this paper, we will specifically concentrate on issues we faced during development, deployment, and maintenance of the software and how we continually adapted the software in order to improve usability. We will provide usage examples to highlight the functionality as well as limitations of FOCUS at the various stages of the development process. We aim to make the discussion as independent of the software platform as possible, so that our experiences can be of more general value to the drug discovery community.
Year One Summary of X-energy Pebble Fuel Development at ORNL (2017)

The Advanced Reactor Concepts X-energy (ARC-Xe) Pebble Fuel Development project at Oak Ridge National Laboratory (ORNL) has successfully completed its first year, having made excellent progress in accomplishing programmatic objectives. The primary focus of research at ORNL in support of X-energy has been the training of X-energy fuel fabrication engineers and the establishment of US pebble fuel production capabilities able to supply the Xe-100 pebble-bed reactor. These efforts have been strongly supported by particle fuel fabrication and characterization expertise present at ORNL from the Advanced Gas Reactor (AGR) Fuel Development and Qualification Program.
Miniemulsionspolymerisation und Struktur von Polymer‐ und Hybridnanopartikeln (2009)

Abstract Maximaler Erfolg dank Miniemulsion : Der Miniemulsionsprozess ermöglicht die Bildung komplexer Polymernanopartikel und die Verkapselung unterschiedlichster Materialien in einer Polyschale (siehe Beispiele). Eine Funktionalisierung der Nanopartikel gelingt einfach. Polymerisationen zur Erzeugung von Polymernanopartikeln gelingen in umweltfreundlichen Lösungsmitteln wie H 2 O. magnified image Der Miniemulsionsprozess ermöglicht die Bildung von komplexen polymeren Nanopartikeln und die Verkapselung eines festen oder flüssigen, eines anorganischen oder organischen, eines hydrophoben oder hydrophilen Materials in einer Polyschale. Dabei lassen sich verschiedenste Materialien von organischen und anorganischen Pigmenten, Magnetit oder anderen festen Nanopartikeln bis hin zu hydrophilen oder hydrophoben Flüssigkeiten wie Duftstoffen, Medikamenten oder Photoinitiatoren verkapseln. Eine Funktionalisierung der Nanopartikel kann einfach erzielt werden. Ein Vorteil gegenüber Polymerisationsprozessen in organischen Lösungsmitteln ist die Tatsache, dass Polymerisationen zum Erhalt polymerer Nanopartikel in umweltfreundlichen Lösungsmitteln, meistens Wasser, durchgeführt werden können.
Progressive Increase In Polyamine Levels In 9l Cells in vitro During the Cell Cycle: Comparison Between Cells Isolated By Centrifugal Elutriation and Cells Grown In Synchrony (1984)

Centrifugal elutriation was used to separate 9L rat brain tumour cells into fractions enriched in the G1, S, or G2/M phases of the cell cycle. Cells enriched in early G1 phase were recultured, grown in synchrony, and harvested periodically for analysis of their DNA distribution and polyamine content. Mathematical analysis of the DNA distributions indicated that excellent synchrony was obtained with low dispersion throughout the cell cycle. Polyamine accumulation began at the time of seeding, and intracellular levels of putrescine, spermidine, and spermine increased continuously during the cell cycle. In cells in the G2/M phase of the cell cycle, putrescine and spermidine levels were twice as high as in cells in the G1 phase. DNA distribution and polyamine levels were also analysed in cells taken directly from the various elutriation fractions enriched in G1, S, or G2/M. Because we did not obtain pure S or G2/M populations by elutriation or by harvesting synchronized cells, a mathematical procedure--which assumed that the measured polyamine levels for any population were linearly related to the fraction of cells in the G1, S, and G2/M phases times the polyamine levels in these phases and that polyamine levels did not vary within these phases--was used to estimate 'true' phase-specific polyamine levels (levels to be expected if perfect synchrony were achieved). Estimated 'true' phase-specific polyamine levels calculated from the data obtained from cells either sorted by elutriation or obtained from synchronously growing cultures were very similar.