gebhart/patrepeval huggingface dataset:
Simulation and design of planarizing materials for reverse-tone step and flash imprint lithography (2008)

Reverse-tone step and flash imprint lithography SFIL-R shows promise as a cost-efficient, high-resolution patterning technique; however, the generation of satisfactory patterns requires the successful application of a planarizing topcoat over topography through spincoating. Photopolymerizable nonvolatile fluids are ideal topcoat materials because they planarize better than volatile fluids during spincoating and can continue to level after spincoating. Fluid mechanics analyses indicate that complete planarization using capillary force is slow. Therefore, defining the acceptable or critical degree of planarization DOPcrit becomes necessary. Finite difference simulation of the spincoat and postspin leveling processes was used to determine the planarization time for various topographic and material property combinations. A new material, Si-14, was designed to have ideal planarization characteristics low viscosity-15.1 cP; low shrinkage-5.1% and satisfy SFIL-R processing requirements oxygen etch resistance-33 wt% silicon, photocurable and was used to validate our models through profilometry and interferometry experiments. During spincoating, minimizing the spin speed generates more planar films; however, this increases the spin time. To rectify this problem, a two-stage spincoating process-a first step with high spin speeds to achieve the target thickness quickly and a second step with low spin speeds to improve planarization-was proposed and experimentally demonstrated.
A Novel Cycloaddition Reaction of α-Diazo-γ-amido Ketones Catalyzed by Rhodium(II) Acetate. Scope and Mechanistic Details of the Process (1996)

α-Diazo ketones containing an amido group in the γ-position have been found to undergo a novel rhodium(II)-catalyzed cycloaddition reaction. Intramolecular cyclization of the keto carbenoid onto the oxygen atom of the amide group generates a carbonyl ylide dipole as a transient species. This highly stabilized dipole does not readily undergo 1,3-dipolar cycloaddition but rather transfers a proton to produce a cyclic ketene N,O-acetal. The ketene acetal is unstable to moisture and upon standing is readily hydrolyzed to a γ-keto δ-lactone and an amine. In the absence of any significant amount of water, the ketene N,O-acetal undergoes conjugate addition with the activated π-bond of the dipolarophile to give a zwitterion intermediate. The anionic portion of the zwitterion adds to the neighboring carbonyl group. This is followed by epoxide ring formation with charge dissipation leading to an amido-substituted spiro cyclopentyl epoxide. In certain cases a hydroxy lactone was also isolated and its formation can be attributed to the competitive hydrolysis of the zwitterionic intermediate. The Rh(II)-catalyzed reaction of the diazo ketoamide derived from N-benzylpiperidone with DMAD afforded two different types of cycloadducts. In addition to the spiro cyclopentyl epoxide, a product derived from trapping of the carbonyl ylide dipole was also obtained, thereby providing additional support for the proposed mechanism.
An analysis programming language applied to the double delay problem in aviation (2017)

Seamless integration and interoperation of simulations has been a goal of simulationists for many decades. The goal of this research is to advance the field of simulation interoperability and our approach is for this to happen at the analysis level. In this paper, we are introducing a novel language called Predictive Query Language (PQL) that uses a federation of models to provide future predictions. It builds upon current predictive analytics systems in that it creates the data that will populate the database, rather than mining existing data. As an example of how this language works, we use the double delay problem in aviation. This example has dual purpose of showing the utility of PQL while shedding light on an important problem in aviation.
Heterogeneous Sensory Innervation and Extensive Intrabulbar Connections of Olfactory Necklace Glomeruli (2009)

The mammalian nose employs several olfactory subsystems to recognize and transduce diverse chemosensory stimuli. These subsystems differ in their anatomical position within the nasal cavity, their targets in the olfactory forebrain, and the transduction mechanisms they employ. Here we report that they can also differ in the strategies they use for stimulus coding. Necklace glomeruli are the sole main olfactory bulb (MOB) targets of an olfactory sensory neuron (OSN) subpopulation distinguished by its expression of the receptor guanylyl cyclase GC-D and the phosphodiesterase PDE2, and by its chemosensitivity to the natriuretic peptides uroguanylin and guanylin and the gas CO(2). In stark contrast to the homogeneous sensory innervation of canonical MOB glomeruli from OSNs expressing the same odorant receptor (OR), we find that each necklace glomerulus of the mouse receives heterogeneous innervation from at least two distinct sensory neuron populations: one expressing GC-D and PDE2, the other expressing olfactory marker protein. In the main olfactory system it is thought that odor identity is encoded by a combinatorial strategy and represented in the MOB by a pattern of glomerular activation. This combinatorial coding scheme requires functionally homogeneous sensory inputs to individual glomeruli by OSNs expressing the same OR and displaying uniform stimulus selectivity; thus, activity in each glomerulus reflects the stimulation of a single OSN type. The heterogeneous sensory innervation of individual necklace glomeruli by multiple, functionally distinct, OSN subtypes precludes a similar combinatorial coding strategy in this olfactory subsystem.
A simplified method for stabilization of flail chest injuries in small animals (1995)

Two dogs and one cat with flail chest injuries were treated by a new technique of external thoracic wall stabilization using a single circumcostal suture for each affected rib and a splint device. Application of the splint device was quick and required minimal manipulation of the patient. Stabilization of the flail chest resulted in improved respiration in each animal. The splint device was left in place in two of the animals as the sole means of rib fixation. No evidence of infection or other adverse effects were noted with this technique.
Non‐invasive mass transfer measurements in complex biofilm‐coated structures (2008)

We demonstrate a novel application of (13)C pulsed field gradient (PFG) NMR to monitor mass transfer, due to both flow and diffusion, in a 3D complex porous support structure modified by biofilm growth. This enables timescales an order of magnitude larger than previously possible to be accessed with respect to displacement probability distribution (propagator) measurements. The evolution in the propagator shape with observation time to the Gaussian asymptote (constant dispersion coefficient) is consequently well resolved. We also simulated the measured displacement propagators with good agreement between experiment and prediction. The methodology has significant potential for the selective characterization of the transport of nutrients, metabolic products, pollutants and biocides in such complex biofilm-containing structures.
Tunable multipole resonances in plasmonic crystals made by four-beam holographic lithography (2016)

Plasmonic nanostructures confine light to sub-wavelength scales, resulting in drastically enhanced light-matter interactions. Recent interest has focused on controlled symmetry breaking to create higher-order multipole plasmonic modes that store electromagnetic energy more efficiently than dipole modes. Here we demonstrate that four-beam holographic lithography enables fabrication of large-area plasmonic crystals with near-field coupled plasmons as well as deliberately broken symmetry to sustain multipole modes and Fano-resonances. Compared with the spectrally broad dipole modes we demonstrate an order of magnitude improved Q-factors (Q = 21) when the quadrupole mode is activated. We further demonstrate continuous tuning of the Fano-resonances using the polarization state of the incident light beam. The demonstrated technique opens possibilities to extend the rich physics of multipole plasmonic modes to wafer-scale applications that demand low-cost and high-throughput.
Linked color imaging improves the visibility of colorectal polyps: a video study (2017)

LCI improved polyp visibility compared to WL for both expert and non-expert endoscopists. It is useful for improving polyp visibility in any location, any size, any morphology, any histology, and any preparation level.
Ligand-Promoted C-3 Selective C–H Olefination of Pyridines with Pd Catalysts (2011)

Pd-catalyzed C-3 selective olefination of pyridines is developed for the first time using 1,10-phenanthroline as the ligand. This finding provides a novel disconnection for the synthesis of pyridine-containing alkaloids and drug molecules as well as a new approach for developing Pd-catalyzed C-H functionalizations of pyridines.
High OX-40 expression in the tumor immune infiltrate is a favorable prognostic factor of overall survival in non-small cell lung cancer (2019)

High OX-40 IHC expression in the tumor immune infiltrate is associated with favorable prognosis and increased levels of immune-related genes including IFN-gamma in patients with surgically resected stage I-III NSCLC. Its prognostic utility is independent of PD-L1 and other common markers of immune activation. High OX-40 expression potentially identifies a unique subgroup of NSCLC that may benefit from co-stimulation with OX-40 agonist antibodies and potentially enhance the efficacy of existing immune checkpoint therapies.
Collection device for keeping microbiota viability (2018)

Trabajo presentado en el IX Workshop de la Sociedad Espanola de Probioticos y Prebioticos (SEPyP), celebrado en Zaragoza (Espana) el 15 y 16 de febrero de 2018
A 245 GHz ASK modulator and demodulator with 40 Gbits/sec data rate in 0.13 &#x03BC;m SiGe BiCMOS technology (2013)

This paper presents a 245 GHz ASK modulator and demodulator capable of 40 Gbit/s operation. The design is based on 0.13 μm SiGe BiCMOS technology. The chip includes a 245 GHz SPST switch, a wide-band driver amplifier, and an ASK demodulator. The ASK demodulator consists of a power detector followed by a wide-band high gain amplifier. The modulator consumes 31 mW and the demodulator consumes 100 mW.
TPSLVM: A Dimensionality Reduction Algorithm Based On Thin Plate Splines (2014)

Dimensionality reduction (DR) has been considered as one of the most significant tools for data analysis. One type of DR algorithms is based on latent variable models (LVM). LVM-based models can handle the preimage problem easily. In this paper we propose a new LVM-based DR model, named thin plate spline latent variable model (TPSLVM). Compared to the well-known Gaussian process latent variable model (GPLVM), our proposed TPSLVM is more powerful especially when the dimensionality of the latent space is low. Also, TPSLVM is robust to shift and rotation. This paper investigates two extensions of TPSLVM, i.e., the back-constrained TPSLVM (BC-TPSLVM) and TPSLVM with dynamics (TPSLVM-DM) as well as their combination BC-TPSLVM-DM. Experimental results show that TPSLVM and its extensions provide better data visualization and more efficient dimensionality reduction compared to PCA, GPLVM, ISOMAP, etc.
Role of calcium and calmodulin in flow-induced nitric oxide production in endothelial cells (1994)

These experiments demonstrate that exposure of cultured endothelial cells (EC) to well-defined laminar fluid flow results in an elevated rate of NO production. NO production was monitored by release of NOx (NO2- + NO3(2-) and by cellular guanosine 3',5'-cyclic monophosphate (cGMP) concentration. NO synthase (NOS) inhibitor blocked the flow-mediated stimulation of both NOx and cGMP, indicating that both measurements reflect NO production. Exposure to laminar flow increased NO release in a biphasic manner, with an initial rapid production consequent to the onset of flow followed by a less rapid, sustained production. A similar rapid increase in NO production resulted from an increase in flow above a preexisting level. The rapid initial production of NO was not dependent on shear stress within a physiological range (6-25 dyn/cm2) but may be dependent on the rate of change in shear stress. The sustained release of NO was dependent on physiological levels of shear stress. The calcium (Ca2+) or calmodulin (CaM) dependence of the initial and sustained production of NO was compared with bradykinin (BK)-mediated NO production. Both BK and the initial production were inhibited by Ca2+ and CaM antagonists. In contrast, the sustained shear stress-mediated NO production was not affected, despite the continued functional presence of the antagonists. Dexamethasone had no effect on either the initial or the sustained shear stress-mediated NO production. An inducible NOS does not, therefore, explain the apparent Ca2+/CaM independence of the sustained shear stress-mediated NO production.(ABSTRACT TRUNCATED AT 250 WORDS)
Chemoenzymatic Total Synthesis of ent-Oxycodone: Second-, Third-, and Fourth-Generation Strategies (2019)

Four distinct approaches to <i>ent</i>-oxycodone were designed and accomplished. All rely on the same starting material, the diene diol derived from phenethyl acetate by the whole-cell fermentation with <i>E. coli</i> JM109 (pDTG601A), a strain that overexpresses toluene dioxygenase. The key step in the first-generation approach involves the construction of the C-9/C-14 bond by a SmI<sub>2</sub>-mediated cyclization of a keto aldehyde. The second-generation design relies on the use of the Henry reaction to accomplish this task. In both of these syntheses, Parker's cyclization was employed to construct the D-ring. The third-generation synthesis provides an improvement over the second in that the nitrogen atom at C-9 is introduced by azidation of the C-9/C-10 olefin, followed by reduction and lactam formation between the C-9 amine and the Fukuyama-type lactone. Finally, the fourth generation takes advantage of the keto-nitrone reductive coupling to generate the C-9/C-14 linkage. The four generations of the total syntheses of <i>ent</i>-oxycodone were accomplished in 13, 18, 16, and 11 operations (19, 23, 24, and 18 steps), respectively. Experimental and spectral data are provided for all new compounds.
A Hybrid Markov Chain Monte Carlo Method for Generating Permeability Fields Conditioned to Multiwell Pressure Data and Prior Information (1998)

Summary It is necessary to construct and sample the a posteriori probability density functions (pdf's) for the rock property fields to properly evaluate the uncertainty in reservoir performance predictions. In this work, the a posteriori pdf is constructed based on prior means and variograms (covariance function) for log-permeability and multiwell pressure data. Within the context of sampling the probability density function, we argue that the notion of equally probable realizations is the wrong paradigm for reservoir characterization. If the simulation of Gaussian random fields with a known variogram is the objective, it is shown that the variogram should not be incorporated directly into the objective function if simulated annealing (SA) is applied either to sample the a posteriori pdf or to estimate a global minimum of the associated objective function. It is shown that the hybrid Markov chain Monte Carlo (MCMC) method provides a way to explore more fully the set of plausible log-permeability fields and does not suffer from the high rejection rates of more standard MCMC methods.
Temporal graph patterns by timed automata (2022)

Temporal graphs represent graph evolution over time, and have been receiving considerable research attention. Work on expressing temporal graph patterns or discovering temporal motifs typically assumes relatively simple temporal constraints, such as journeys or, more generally, existential constraints, possibly with finite delays. In this paper we propose to use timed automata to express temporal constraints, leading to a general and powerful notion of temporal basic graph pattern (BGP). The new difficulty is the evaluation of the temporal constraint on a large set of matchings. An important benefit of timed automata is that they support an iterative state assignment, which can be useful for early detection of matches and pruning of non-matches. We introduce algorithms to retrieve all instances of a temporal BGP match in a graph, and present results of an extensive experimental evaluation, demonstrating interesting performance trade-offs. We show that an on-demand algorithm that processes total matchings incrementally over time is preferable when dealing with cyclic patterns on sparse graphs. On acyclic patterns or dense graphs, and when connectivity of partial matchings can be guaranteed, the best performance is achieved by maintaining partial matchings over time and allowing automaton evaluation to be fully incremental.
TNF and granulocyte macrophage-colony stimulating factor interdependence mediates inflammation via CCL17 (2018)

TNF and granulocyte macrophage-colony stimulating factor (GM-CSF) have proinflammatory activity and both contribute, for example, to rheumatoid arthritis pathogenesis. We previously identified a new GM-CSF→JMJD3 demethylase→interferon regulatory factor 4 (IRF4)→CCL17 pathway that is active in monocytes/macrophages in vitro and important for inflammatory pain, as well as for arthritic pain and disease. Here we provide evidence for a nexus between TNF and this pathway, and for TNF and GM-CSF interdependency. We report that the initiation of zymosan-induced inflammatory pain and zymosan-induced arthritic pain and disease are TNF dependent. Once arthritic pain and disease are established, blockade of GM-CSF or CCL17, but not of TNF, is still able to ameliorate them. TNF is required for GM-CSF-driven inflammatory pain and for initiation of GM-CSF-driven arthritic pain and disease, but not once they are established. TNF-driven inflammatory pain and TNF-driven arthritic pain and disease are dependent on GM-CSF and mechanistically require the same downstream pathway involving GM-CSF→CCL17 formation via JMJD3-regulated IRF4 production, indicating that GM-CSF and CCL17 can mediate some of the proinflammatory and algesic actions of TNF. Given we found that TNF appears important only early in arthritic pain and disease progression, targeting a downstream mediator, such as CCL17, which appears to act throughout the course of disease, could be effective at ameliorating chronic inflammatory conditions where TNF is implicated.
Experimental validation of Highly Doped Erbium-Doped Fibre for the design of a+20 dBm, single pump and compact, WDM L-band EDFA (2006)

Highly doped EDFs with 13.4 to 34.7-dB/m absorption coefficients were inserted in a two-stage EDFA to enable a MSA-compliant packaging. Experimental validations led to the desigh of a low noise 20-dBm single-pumped WDM L-band EDFAt
High-Frequency Ultrasonographic Evaluation of Conjunctival Intraepithelial Neoplasia and Squamous Cell Carcinoma (2003)

High-frequency ultrasonography may be used to assess the extent of squamous conjunctival neoplasia. While the 50-MHz system offered better resolution, 20-MHz ultrasonography allowed for a wider and deeper field of view. High-frequency ultrasonography was useful in determining tumor thickness, shape, and internal reflectivity, and especially in revealing tumor extension into the sclera, eye, and orbit.
Anti-inflammatory Effects of South American Tanacetum vulgare (1998)

In recent years the role of phenolic compounds and sesquiterpene lactones, particularly parthenolide, in the anti-migraine and anti-inflammatory effects of Tanacetum parthenium (Asteraceae) has attracted much attention. However, the closely-related cosmopolitan species T. vulgare has remained outside the mainstream of research in this field. After treating the aerial parts of T. vulgare with dichloromethane and methanol, and applying conventional column and thin-layer chromatographic techniques, it was possible to isolate from the moderately lipophilic fractions the principles responsible for the anti-inflammatory activity of this plant against the mouse-ear oedema induced by 12-O-tetradecanoylphorbol 13-acetate. These were identified by ultraviolet and nuclear magnetic resonance spectroscopy as parthenolide (93% oedema inhibition at 0.5 mg/ear, ID50 (dose of drug inhibiting the oedema by 50%) = 0.18 micromol/ear) and the methoxyflavones jaceosidin (80% oedema inhibition at 0.5 mg/ear, ID50 = 0.50 micromol/ear), eupatorin, chrysoeriol and diosmetin. Because in molar terms the potency of parthenolide was nearly three times greater than that of the most active of the flavones and because it is obtained from the plant in considerably larger amounts, the flavonoids must only be partially responsible, and to a minor extent, for the observed in-vivo anti-inflammatory local effect.
Impact of perceptions of bus service performance on mode choice preference (2015)

As transit service performance should be considered from the transit passengers’ perspectives, it is essential to determine passengers’ perceptions of service performance and to understand the role of these perceptions in travel decisions. As the bus market share has steadily declined, the aim of this study is to explore the impact of perceptions of bus service performance on mode choice preference to increase bus ridership. To achieve this research objective, an intention survey is conducted to obtain bus passengers’ attitudes. Exploratory factor analysis and confirmatory factor analysis are used to measure passengers’ perceptions and to extract the main factors from the bus service attributes. Next, structural equation modeling is used to reveal how passengers’ perceptions vary by demographics and trip characteristics. Finally, multinomial logit modeling is used to explore the impact of perception factors on mode choice preference. The results of this study show that perceptions of the reliability and comfort of bus services have a more significant impact on passengers’ mode choice preference than perceptions of availability and safety do. The implications in terms of improving bus service reliability and comfort can increase bus ridership.