gebhart/patrepeval huggingface dataset:
Effect of Multilayer versus Monolayer Dodecanethiol on Selectivity and Pattern Integrity in Area-Selective Atomic Layer Deposition (2020)

Monolayer and multilayer dodecanethiols (DDT) can be assembled onto a copper surface from the vapor phase depending on the initial oxidation state of the copper. The ability of the copper-bound dodecanethiolates to block atomic layer deposition (ALD) and the resulting behavior at the interfaces of Cu/SiO<sub>2</sub> patterns during area-selective ALD (AS-ALD) are compared between mono- and multilayers. We show that multilayer DDT is ∼7 times more effective at blocking ZnO ALD from diethylzinc and water than is monolayer DDT. Conversely, monolayer DDT exhibits better performance than does multilayer DDT in blocking of Al<sub>2</sub>O<sub>3</sub> ALD from trimethylaluminum and water. Investigation into interfacial effects at the interface between Cu and SiO<sub>2</sub> on Cu/SiO<sub>2</sub> patterns reveals both a gap at the SiO<sub>2</sub> edges and a pitch size-dependent nucleation delay of ZnO ALD on SiO<sub>2</sub> regions of multilayer DDT-coated patterns. In contrast, no impact on ZnO ALD is observed on the SiO<sub>2</sub> regions of monolayer DDT-coated patterns. We also show that these interfacial effects depend on the ALD chemistry. Whereas an Al<sub>2</sub>O<sub>3</sub> film grows on the TaN diffusion barrier of a DDT-treated Cu/SiO<sub>2</sub> pattern, the ZnO film does not. These results indicate that the structure of the DDT layer and the ALD precursor chemistry both play an important role in achieving AS-ALD.
Noninvasive label-free monitoring of cosmetics and pharmaceuticals in human skin using nonlinear optical microscopy (Conference Presentation) (2017)

Over the past decade, nonlinear optical microscopy has seen a dramatic rise in its use in research settings due to its noninvasiveness, enhanced penetration depth, intrinsic optical sectioning, and the ability to probe chemical compounds with molecular specificity without exogenous contrast agents. Nonlinear optical techniques including two-photon excitation fluorescence (2PEF), fluorescence lifetime imaging microscopy (FLIM), second harmonic generation (SHG), coherent anti-Stokes and stimulated Raman scattering (CARS and SRS, respectively), as well as transient and sum frequency absorption (TA and SFA, respectively), have been widely used to explore the physiology and microanatomy of skin. Recently, these modalities have shed light on dermal processes that could not have otherwise been observed, including the spatiotemporal monitoring of cosmetics and pharmaceuticals. However, a challenge quickly arises when studying such chemicals in a dermatological context: many exogenous compounds have optical signatures that can interfere with the signals that would otherwise be acquired from intact skin. For example, oily solvents exhibit strong signals when probing CH2 vibrations with CARS/SRS; chemical sun filters appear bright in 2PEF microscopy; and darkly colored compounds readily absorb light across a broad spectrum, producing strong TA/SFA signals. Thus, this discussion will first focus on the molecular contrast in skin that can be probed using the aforementioned nonlinear optical techniques. This will be followed by an overview of strategies that take advantage of the exogenous compounds’ optical signatures to probe spatiotemporal dynamics while preserving endogenous information from skin.
Highly Nonlinear and Photorefractive Glasses (1992)

The realization of all-optical devices, whether for high speed or for micro-opto-electronic applications, requires materials which possess large nonlinear optical coefficients. The compositional versatility of glass combined with the relative ease of manufacture and fabrication, make the study of its nonlinear properties for these applications important. A brief review of three areas of research activity will be discussed.
WHO Is Recommending against the Use of COVID-19 Convalescent Plasma in Immunocompromised Patients? (2023)

Since December 2019, SARS-CoV-2 is ravaging the globe, currently accounting for over 660 million infected people and more than 6 [...].
Multi-Sensor Fusion Tracking Using Visual Information and WI-Fl Location Estimation (2007)

In a widely distributed camera network environment, object tracking is a important function for a surveillance application. This paper describes an object tracking scheme using sensor fusion approach which is composed of visual information from cameras and location information based on Wi-Fi location estimation system. Estimated location information is calculated by a set of received signal strength values of beacon packets from Wi-Fi access points (APs) around the targets. Different from the conventional approaches which use another kind of sensors (e.g., global positioning system (GPS), pressure sensors on the floors, laser-range scanners, etc.), our approach can cover wider areas both indoor and outdoor with lower cost. Particle filter is applied to combine those two different kinds of sensory input to achieve tracking the target in a stable performance. Wi-Fi observation model is involved in a conventional visual particle filtering scheme to evaluate importance weights of each particle. In this paper, we present experimental results applied to outdoor surveillance camera environment.
Air-Coupled Ultrasonic Spiral Phased Array for High-Precision Beamforming and Imaging (2022)

Sparse spiral phased arrays are advantageous for many emerging air-coupled ultrasonic applications, since grating lobes are prevented without being constrained to the half-wavelength element spacing requirement of well-known dense arrays. As a result, the limitation on the maximum transducer diameter is omitted and the aperture can be enlarged for improving the beamforming precision without requiring the number of transducers to be increased. We demonstrate that in-air imaging, in particular, benefits from these features, enabling large-volume, unambiguous and high-resolution image formation. Therefore, we created an air-coupled ultrasonic phased array based on the Fermat spiral, capable of transmit, receive and pulse-echo operation, as well as 3D imaging. The array consists of 64 piezoelectric 40-kHz transducers (Murata MA40S4S), spanning an aperture of 200mm. First, we provide an application-independent numerical and experimental characterization of the conventional beamforming performance of all operation modes for varying focal directions and distances. Second, we examine the resulting imaging capabilities using the single line transmission technique. Apart from the high maximum sound pressure level of 152 dB, we validate that unambiguous high-accuracy 3D imaging is possible in a wide field of view (&#x00B1;80&#x00B0;), long range (20cm to 5m+) and with a high angular resolution of up to 2.3&#x00B0;. Additionally, we demonstrate that object shapes and patterns of multiple reflectors are recognizable in the images generated using a simple threshold for separation. In total, the imaging capabilities achieved are promising to open up further possibilities, e.g. robust object classification in harsh environments based on ultrasonic images.
Capped mesoporous silica nanoparticles as stimuli-responsive controlled release systems for intracellular drug/gene delivery (2010)

With a better understanding of the unique features of capped MSN and its behaviors in biological environment, these multifunctional materials will find a wide variety of applications in the field of drug/gene delivery.
High temperature deuterium enrichment using TiC coated vanadium membranes (2019)

The current technology for hydrogen isotope separation requires enormous capital investment and energy consumption. Palladium-based membranes exhibit hydrogen isotope selectivity and provide a continuous method of isotope enrichment but have high material costs. Here, the authors investigate the potential of titanium carbide thin films coated on vanadium as a low-cost alternative, which enabled operation at high temperatures. Protium and deuterium exhibited nominally identical solubility in TiC coated vanadium over a range of 500–700 °C. Permeation tests from 600 to 700 °C revealed that protium permeated faster than deuterium, with the separation factor decreasing from 1.34 to 1.15 with increasing temperature. XPS depth-profiling showed a distinct interface between the TiC layer and the V foil in as-fabricated membranes. However, post-test analysis revealed significant V diffusion through TiC and segregation to the surface. Surface limitations resulting from this degradation accounted for changes in flux and may explain why the separation factor was lower than the value of 1.42 expected from high temperature interstitial diffusion of protium/deuterium in vanadium.
Structural Defects in Periodic and Quasicrystalline Binary Nanocrystal Superlattices (2011)

Binary nanocrystal superlattices (BNSLs) emerge as an important class of man-made materials where components and functionalities can be added, tuned, or combined in a predictable manner. These amazingly complex structures spontaneously self-assemble from colloidal solutions containing binary mixtures of functional (semiconducting, magnetic, plasmonic, etc.) nanocrystals. Further developments of the BNSL-based materials require a deep understanding and control over BNSL formation and structural perfection. Like any solid, BNSL can contain different kinds of structural defects. It is well-known that defects can have a tremendous effect on the material’s behavior. Defect engineering is used to modify and improve many of the mechanical, electrical, magnetic, and optical properties of conventional solids. In this work, we provide the first systematic analysis of structural defects in various BNSL structures. We used BNSLs as a platform for studying structural defects in both periodic (crystalline) and aperiodic (quasicrystalline) lattices, as well as for direct imaging of the interfaces between crystalline and quasicrystalline domains. Such direct observation of local imperfections in complex multicomponent lattices provides a unique insight into the fundamental aspects of crystal formation.
Treatment of PET nonwoven with a water vapor or carbon dioxide plasma (2000)

Gas plasma treatment of poly(ethylene terephthalate) nonwoven (NW–PET) was used to increase the hydrophilicity of single- and multilayer NW–PET. NW–PET was treated with a pulsatile CO2 or with a pulsatile H2O glow discharge. X-ray photoelectron spectroscopy (XPS) showed significantly more oxygen with CO2 glow-discharge-treated NW–PET than with H2O glow-discharge-treated-NW–PET surfaces. Moreover, the introduction rate of oxygen at a single layer of NW–PET was higher for a CO2 than for a H2O glow-discharge treatment. Titration data revealed significantly higher surface concentrations of carboxylic groups for CO2 glow-discharge NW–PET than for H2O glow-discharge-treated NW–PET. Mass spectrometry analysis revealed that the entire internal surface of a single layer of NW–PET was modified. XPS and contact measurements confirmed the modification of the internal surface of multilayers of NW–PET. H2O and CO2 glow-discharge-treated substrates consisting of six layers of NW–PET had a nonuniform surface concentration of carboxylic acid groups as determined with titration experiments. The outside layers of the substrate contained a higher surface concentration of carboxylic acid groups than did the inside layers. XPS analysis and titration data showed that the rinsing of H2O and CO2 glow-discharge-treated NW–PET with water changed the surface composition considerably. Part of the carboxylic acid group-containing species were washed off. © 2000 John Wiley & Sons, Inc. J Appl Polym Sci 75: 480–494, 2000
Effects of O‐methylated (−)‐epigallocatechin gallate (EGCG) on LPS‐induced osteoclastogenesis, bone resorption, and alveolar bone loss in mice (2017)

(-)-Epigallocatechin-3-<i>O</i>-gallate (EGCG), present in green tea, exhibits antioxidant and antiallergy effects. EGCG3″Me, a 3-<i>O</i>-methylated derivative of EGCG, has been reported to show similar biological functions; the inhibitory activity of EGCG3″Me in a mouse allergy model was more potent than that of EGCG, probably due to the efficiency of absorption from the intestine. However, the functional potency of these EGCGs is controversial in each disease model. We previously observed that EGCG suppressed inflammatory bone resorption and prevented alveolar bone loss in a mouse model of periodontosis. In this study, we examined the role of EGCG3″Me in bone resorption using a mouse model of periodontitis. Lipopolysaccharide (LPS)-induced osteoclast formation was suppressed by adding EGCG3″Me to cocultures of osteoblasts and bone marrow cells, and LPS-induced bone resorption was also inhibited by EGCG3″Me in calvarial organ cultures. EGCG3″Me acted on osteoblasts and suppressed prostaglandin E (PGE) production, which is critical for inflammatory bone resorption, by inhibiting the expression of COX-2 and mPGES-1, key enzymes for PGE synthesis. In osteoclast precursor macrophages, EGCG3″Me suppressed RANKL-dependent differentiation into mature osteoclasts. In a mouse model of periodontitis, LPS-induced bone resorption was suppressed by EGCG3″Me in organ culture of mouse alveolar bone, and the alveolar bone loss was further attenuated by the treatment of EGCG3″Me in the lower gingiva <i>in vivo</i>. EGCG3″Me may be a potential natural compound for the protection of inflammatory bone loss in periodontitis.
The Development of Phosphine‐Free "Tethered" Ruthenium(II) Catalysts for the Asymmetric Reduction of Ketones and Imines (2016)

In this account, we describe the design, synthesis and applications of tethered versions of the Ru(II)/N-tosyl-1,2-diphenylethylene-1,2-diamine (TsDPEN) class of catalyst that are commonly used for asymmetric transfer hydrogenation and asymmetric hydrogenation of ketones and imines. The review covers key aspects of the reaction mechanisms and examples of applications, including industrial applications to pharmaceutically important target molecules. In addition, closely related catalysts based on Rh(III) and Ir(III) are also described.
DiffPD: Differentiable Projective Dynamics with Contact. (2021)

We present a novel, fast differentiable simulator for soft-body learning and control applications. Existing differentiable soft-body simulators can be classified into two categories based on their time integration methods. Simulators using explicit time-stepping scheme require tiny time steps to avoid numerical instabilities in gradient computation, and simulators using implicit time integration typically compute gradients by employing the adjoint method to solve the expensive linearized dynamics. Inspired by Projective Dynamics (PD), we present DiffPD, an efficient differentiable soft-body simulator with implicit time integration. The key idea in DiffPD is to speed up backpropagation by exploiting the prefactorized Cholesky decomposition in PD to achieve a super-linear convergence rate. To handle contacts, DiffPD solves contact forces by analyzing a linear complementarity problem (LCP) and its gradients. With the assumption that contacts occur on a small number of nodes, we develop an efficient method for gradient computation by exploring the low-rank structure in the linearized dynamics. We evaluate the performance of DiffPD and observe a speedup of 4-19 times compared to the standard Newton's method in various applications including system identification, inverse design problems, trajectory optimization, and closed-loop control.
Indium tin oxide-coated glass modified with reduced graphene oxide sheets and gold nanoparticles as disposable working electrodes for dopamine sensing in meat samples (2012)

Sensitive, rapid, and accurate detection of dopamine (DA) at low cost is needed for clinical diagnostic and therapeutic purposes as well as to prevent illegal use of DA in animal feed. We employed a simple approach to synthesize reduced graphene oxide sheets (rGOS) and gold nanoparticles (AuNPs) at room temperature on indium tin oxide-coated glass (ITO) slides as disposable working electrodes for sensing DA. Graphene oxide (GO) was directly reduced on ITO to remove oxygenated species via a rapid and green process without using chemical reducing reagents. AuNPs were electrochemically deposited in situ on rGOS-ITO with fairly uniform density and size. The sensitivity of the AuNPs-rGOS-ITO sensor for DA detection is 62.7 μA mM(-1) cm(-2) with good selectivity against common electrochemically interfering species such as ascorbic acid (AA) and uric acid (UA), and the detection limit measured by differential pulse voltammetry (DPV), at a signal-noise ratio of 3, was 6.0 × 10(-8) M. The electrochemical catalysis of DA was proven to be a surface process with an electron transfer coefficient (α) of 0.478 and a rate constant (k(s)) of 1.456 s(-1). It correlates well with the conventional UV-vis spectrophotometric approach (R = 0.9973) but with more than thrice the dynamic range (up to 4.5 mM). The sensor also exhibited good stability and capability to detect DA in beef samples, and thus is a promising candidate for simple and inexpensive sub-nanomolar detection of DA, especially in the presence of UV-absorbing compounds.
Pharmacokinetic-pharmacodynamic correlation from mouse to human with pazopanib, a multikinase angiogenesis inhibitor with potent antitumor and antiangiogenic activity (2007)

With the development of targeted therapeutics, especially for small-molecule inhibitors, it is important to understand whether the observed in vivo efficacy correlates with the modulation of desired/intended target in vivo. We have developed a small-molecule inhibitor of all three vascular endothelial growth factor (VEGF) receptors (VEGFR), platelet-derived growth factor receptor, and c-Kit tyrosine kinases, pazopanib (GW786034), which selectively inhibits VEGF-induced endothelial cell proliferation. It has good oral exposure and inhibits angiogenesis and tumor growth in mice. Because bolus administration of the compound results in large differences in C(max) and C(trough), we investigated the effect of continuous infusion of a VEGFR inhibitor on tumor growth and angiogenesis. GW771806, which has similar enzyme and cellular profiles to GW786034, was used for these studies due to higher solubility requirements for infusion studies. Comparing the pharmacokinetics by two different routes of administration (bolus p.o. dosing and continuous infusion), we showed that the antitumor and antiangiogenic activity of VEGFR inhibitors is dependent on steady-state concentration of the compound above a threshold. The steady-state concentration required for these effects is consistent with the concentration required for the inhibition of VEGF-induced VEGFR2 phosphorylation in mouse lungs. Furthermore, the steady-state concentration of pazopanib determined from preclinical activity showed a strong correlation with the pharmacodynamic effects and antitumor activity in the phase I clinical trial.
The Prostanoid EP2Receptor Agonist Butaprost Increases Uveoscleral Outflow in the Cynomolgus Monkey (2006)

The prostanoid EP2 receptor agonist butaprost appears to lower IOP by increasing uveoscleral outflow, according to both physiological and morphologic findings. Although the prostanoid EP2 receptor is structurally and functionally distinct from the FP receptor, the effects of EP2 and FP receptor stimulation on aqueous humor outflow are similar.
Cover Feature: Directed Evolution of a Cp*RhIII‐Linked Biohybrid Catalyst Based on a Screening Platform with Affinity Purification (ChemBioChem 4/2021) (2021)

A promising way to enable abiotic C(sp2)−H bond functionalization in a protein matrix is by directed evolution of a biohybrid catalyst harboring a transition metal catalyst. The catalytic activity of Cp*RhIII-linked nitrobindin (NB) was improved through iterative cycles of directed evolution including conjugation of a Cp*RhIII cofactor as represented by an old-style lottery wheel in the cover feature artwork. A best evolved “prize-winning” Cp*Rh-linked NB variant has 4.9-fold enhanced activity for cycloaddition reactions of acetophenone oximes with alkynes. More information can be found in the full paper by A. Onoda, T. Hayashi, et al.
Comparison of long read methods for sequencing and assembly of a plant genome (2020)

Abstract Sequencing technologies have advanced to the point where it is possible to generate high accuracy, haplotype resolved, chromosome scale assemblies. Several long read sequencing technologies are available on the market and a growing number of algorithms have been developed over the last years to assemble the reads generated by those technologies. When starting a new genome project, it is therefore challenging to select the most cost-effective sequencing technology as well as the most appropriate software for assembly and polishing. For this reason, it is important to benchmark different approaches applied to the same sample. Here, we report a comparison of three long read sequencing technologies applied to the de novo assembly of a plant genome, Macadamia jansenii . We have generated sequencing data using Pacific Biosciences (Sequel I), Oxford Nanopore Technologies (PromethION) and BGI (single-tube Long Fragment Read) technologies for the same sample. Several assemblers were benchmarked in the assembly of PacBio and Nanopore reads. Results obtained from combining long read technologies or short read and long read technologies are also presented. The assemblies were compared for contiguity, accuracy and completeness as well as sequencing costs and DNA material requirements. Overall, the three long read technologies produced highly contiguous and complete genome assemblies of Macadamia jansenii . At the time of sequencing, the cost associated with each method was significantly different but continuous improvements in technologies have resulted in greater accuracy, increased throughput and reduced costs. We propose updating this comparison regularly with reports on significant iterations of the sequencing technologies.
Modified Approach to Evaluate Column Test Data (1985)

In the conventional method of calculating the fractional removal of flocculent particles, it is assumed that the average settling velocity for different particle sizes in the lower depths in settling basins is the same as in the upper depths. This assumption is not quite correct, because the particles continuously flocculate or shear during the entire settling depth, and hence the average settling velocity changes both with depth and time. In the modified method, a different approach for calculating the fractional removal of particles is proposed to overcome the deficiency in the conventional method. Instead of considering a vertical constant time line, a horizontal constant depth line for that particular time is used. This approach is more reasonable because the settling velocities of different flocculating particles are all averaged over the same depth.