gebhart/patrepeval huggingface dataset:
Direct space-to-time pulse shaping and applications in arbitrary electromagnetic waveform generation (2003)

Direct space-to-time (DST) pulse shaping, with its straightforward mapping of an input spatial pattern to an output temporal pattern, has been shown to be an effective method to create ultrafast optical data packets. To our knowledge, we introduce the first DST pulse shaper operating in the 1.5 μm lightwave communications band, which is compatible with high-speed (≥100 Gb/s) optical communication systems. Novel features of our pulse shaper include polarization-independent operation, utilization of diffractive optical elements for spatial pattern generation, and a telescopic, fiber-coupled configuration. These features collectively enable the creation of equal intensity optical pulse sequences over a time aperture in excess of 100 ps and at rates of ∼100 GHz. These pulse sequences enable us to overcome electrical limitations and generate arbitrary electromagnetic waveforms in the GHz to multiple tens of GHz range through a novel optical technique. Although creation of arbitrary optical waveforms is achievable through established methods—such as Fourier transform pulse shaping—arbitrary waveform generation capabilities in the microwave and millimeter-wave range are quite limited. We demonstrate, for the first time to our knowledge, cycle-by-cycle generation of broadband burst and continuous electromagnetic waveforms at center frequencies from ∼2–50 GHz. Our simple, reconfigurable method uses tailored optical pulse sequences from our 1.5 μm DST pulse shaper to drive a high-speed optical-to-electrical converter. By appropriately tailoring the input optical spatial pattern of the pulse shaper, arbitrarily phase- and frequency-modulated electromagnetic waveforms are achieved.
Pharmacological Effects of Withanolides (2020)

Withanolides is a class of active compounds widely found in Solanaceae plants. In traditional applications, it has a long history and a wide range of functions. With the progress of drug structure and pharmacological research, more and more reports point to its excellent anticancer effect. Solanaceae is widely distributed, providing a large number of sources for the structure and pharmacological research of its natural products. At the same time, in the light of market demand, the circulation of such medicinal materials is enormous. Based on the pharmacological action of inhibiting NF-κB signaling pathway, withanolides has become a research hotspot in natural medicine. Perhaps combining traditional clinical practice will point out a new research direction to provide basic information for the development of new drugs for difficult cases.
Cross Coupling Reactions (2017)

Palladium-catalyzed coupling reactions have emerged as powerful tools for the formation of new carbon-carbon bonds. In comparison with other more cost-effective metals such as copper, nickel, and iron, palladium catalysts usually show higher activities and turnover numbers. This makes palladium play an essential role in contemporary chemistry, and has led to its application in the production of pharmaceuticals and fine chemicals. The palladium-catalyzed cross-coupling reaction constitutes one of the most versatile and powerful tools for synthetic organic chemists. Structurally similar, yet diversified, organic molecules can be assembled through a modular approach. This protocol offers a relatively straightforward route for preparing pharmaceutically useful and materially interesting compounds. This chapter summarizes the recent developments of phosphine ligands that enable effective palladium-catalyzed aromatic carbon-nitrogen and carbon-oxygen bond-forming reactions from aryl halides, tosylates, and mesylates. It also describes selected representative examples from mainly 2002-2012.
Synthesis of Diamond Using Fe Catalysts by RF Plasma Chemical Vapor Deposition Method (1992)

Diamond growth was examined on a Fe/Si substrate in rf CH 4 plasma. The Fe film, evaporated on a Si wafer, promotes the growth of diamond. Although the density of the diamond particle grown on a Si substrate was on the order of 10 6 cm -2 , the Fe film enhanced the density to an order of 10 7 cm -2 . The particle size was increased with the increase in the Fe film thickness, and indicated a maximum value at around 500 Å. At an initial stage in the diamond growth, it was confirmed that C and Fe atoms diffused deeply into the Fe film and the Si substrate, respectively, which was confirmed by X-ray photoelectron spectroscope measurements. It was also observed that the diamond particles exist at the interface between the Fe film and Si substrate.
Efficient and accurate modeling of electrically large dielectric lens antennas using full-wave analysis (2014)

Two efficient analysis methods for the accurate modeling of electrically large dielectric lens antennas are presented. The first method is based on Double Physical Optics (PO), which takes into account an additional set of reflections within the lens, whereas the conventional PO method only accounts for one set. The second method relies on a higher-order Body of Revolution Method of Moments and is capable of providing a full-wave solution of a 100-wavelength dielectric lens antenna within 2 minutes on a laptop computer.
Formation of Tantalum Carbide and Nitride Phases in Atomic Layer Deposition Using Hydrogen Plasma and tert‐Butylimido‐tris(diethylamido)‐tantalum (TBTDET), and its Effect on Material Properties (2008)

Abstract TaCN films are deposited with plasma‐enhanced atomic layer deposition (PEALD) using tert‐butylimido‐tris(diethylamido)‐tantalum and hydrogen. It is confirmed that the film is a homogeneous mixture of TaC, TaN, Ta 3 N 5 , and Ta 2 O 5 with the oxide phase formed from the post‐deposition uptake of oxygen from the air. It is shown that the electrical properties of TaCN film are affected by the phase composition in the film. The effects of process parameters, such as deposition temperature, plasma power, and cycle time, on the film composition and electronic properties are evaluated. With the increase of the TaC and TaN phases over the Ta 3 N 5 phase, the resistivity of the film is decreased. As the deposition temperature, plasma power, and plasma cycle time are increased, the carbide and TaN phases in the film are increased and the film resistivity is decreased. The uptake of oxygen after deposition is up to 10 at.‐%, and the resistivity of TaCN film deposited using PEALD is as low as 350 µΩ · cm.
Biochemical and Structural Characterization of the Human TL1A Ectodomain, (2009)

TNF-like 1A (TL1A) is a newly described member of the TNF superfamily that is directly implicated in the pathogenesis of autoimmune diseases, including inflammatory bowel disease, atherosclerosis, and rheumatoid arthritis. We report the crystal structure of the human TL1A extracellular domain at a resolution of 2.5 A, which reveals a jelly-roll fold typical of the TNF superfamily. This structural information, in combination with complementary mutagenesis and biochemical characterization, provides insights into the binding interface and the specificity of the interactions between TL1A and the DcR3 and DR3 receptors. These studies suggest that the mode of interaction between TL1A and DcR3 differs from other characterized TNF ligand/receptor complexes. In addition, we have generated functional TL1A mutants with altered disulfide bonding capability that exhibit enhanced solution properties, which will facilitate the production of materials for future cell-based and whole animal studies. In summary, these studies provide insights into the structure and function of TL1A and provide the basis for the rational manipulation of its interactions with cognate receptors.
Toward the Photoinduced Reactivity of 1,5-Diphenylpenta-1,4-diyn-3-one (DPD): Real-Time Investigations by Magnetic Resonance (2009)

The reactivity of 1,5-diphenylpenta-1,4-diyn-3-one (DPD) upon photolysis in acetonitrile and propan-2-ol was followed by continuous-wave time-resolved EPR (TR-EPR) and 1H CIDNP (chemically induced dynamic nuclear polarization) spectroscopy. It was found that radical polymerizations using DPD can only be accomplished if an efficient hydrogen donor, such as propan-2-ol, is present, reflecting an analogous reaction pathway as the related benzophenone (BP). The same behavior was also established for ODPD, the bis(p-methoxy) derivative of DPD. In contrast to parent BP, where the steric hindrance of the ortho phenyl protons causes a twisted geometry, DPD and ODPD adopt an essentially planar minimum geometry which is also conserved in the corresponding radicals of type C as revealed by density functional theory calculations. This planarity is possibly one important factor for the considerable efficiency of DPD and its derivatives to act as initiators for two-photon-induced radical polymerizations.
Abstract 4090: Preclinical pharmacokinetics of CASC-578, a novel, selective, potent, and orally bioavailable small molecule checkpoint kinase 1 inhibitor (2017)

Abstract Introduction: Checkpoint kinase 1 (Chk1) is a serine/threonine protein kinase that regulates cell division in response to genotoxic stress by arresting cell cycle progression in the S &amp; G2 phases. Pharmacological inhibition of Chk1 is proposed to selectively uncouple the completion of DNA replication from G2/M phase transition in tumor cells that have impaired DNA damage response networks, resulting in mitotic catastrophe and cell death. CASC-578 is a novel small molecule inhibitor of Chk1 that is selective, highly potent and orally bioavailable in multiple preclinical species. Methods: The in vitro ADME properties of CASC-578 were evaluated, including in vitro intrinsic microsomal clearance, Caco2 permeability, plasma protein binding and stability, blood to plasma partitioning, cytochrome P450 inhibition and induction, and transporter inhibition. Pharmacokinetic studies of CASC-578 were conducted in mice, rats, and cynomolgus monkeys as either single dose (IV and/or PO) or repeat dose (PO only). Multiple oral dose pharmacokinetic studies were conducted in mice, rats and cynomolgus monkeys for 5-7 days. Results: CASC-578 is highly bound in plasma protein across all species. The apparent permeability is high in Caco2 bi-directional transport study and correlated well with a rapid absorption profile observed in vivo. CASC-578 is not a substrate of P-glycoporotein (efflux =1). There was no direct nor time dependent inhibition on human CYP450 enzymes, and only a slight induction of CYP3A4 was seen at 10 uM drug concentration in a transporter cell-based induction assay. In all animal species, CASC-578 exhibited species-dependent systemic clearance resulting from both phase I and phase II metabolism, and a moderate to high volume of distribution. The elimination kinetics appeared to be monophasic. Oral bioavailability was high in all species studied (&amp;gt;60% F). There was no significant difference in the pharmacokinetics of the drug between genders. Maximal plasma concentration and total drug exposure (AUC) appeared to be proportional from repeat dose studies. Overall, CASC-578 has very desirable drug-like properties and ideal pharmacokinetics for an oral once daily drug, and represents a suitable candidate for clinical development as a novel potential therapeutic approach for the treatment of solid and hematological malignancies Citation Format: Dina Leviten, Teresa Sierra, Ashley Dozier, Richard Boyce, Bob Boyle, Scott Peterson, Alex C. Vo. Preclinical pharmacokinetics of CASC-578, a novel, selective, potent, and orally bioavailable small molecule checkpoint kinase 1 inhibitor [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4090. doi:10.1158/1538-7445.AM2017-4090
Supplementary material from "Reorganization of complex ciliary flows around regenerating Stentor coeruleus" (2019)

The phenomenon of ciliary coordination has garnered increasing attention in recent decades and multiple theories have been proposed to explain its occurrence in different biological systems. While hydrodynamic interactions are thought to dictate the large-scale coordinated activity of epithelial cilia for fluid transport, it is rather basal coupling that accounts for synchronous swimming gaits in model microeukaryotes such as <i>Chlamydomonas.</i> Unicellular ciliates present a fascinating yet understudied context in which coordination is found to persist in ciliary arrays positioned across millimetre scales on the same cell. Here, we focus on the ciliate <i>Stentor coeruleus</i>, chosen for its large size, complex ciliary organization, and capacity for cellular regeneration. These large protists exhibit ciliary differentiation between cortical rows of short body cilia used for swimming, and an anterior ring of longer, fused cilia called the membranellar band (MB). The oral cilia in the MB beat metachronously to produce strong feeding currents. Remarkably, upon injury, the MB can be shed and regenerated de novo. Here, we follow and track this developmental sequence in its entirety to elucidate the emergence of coordinated ciliary beating: from band formation, elongation, curling and final migration towards the cell anterior. We reveal a complex interplay between hydrodynamics and ciliary restructuring in <i>Stentor</i>, and highlight for the first time the importance of a ring-like topology for achieving long-range metachronism in ciliated structures.This article is part of the Theo Murphy meeting ‘Unity and diversity of ciliary systems in locomotion and transport’.
Brain natriuretic peptide predicts successful cardioversion in patients with atrial fibrillation and maintenance of sinus rhythm. (2004)

In patients with persistent atrial fibrillation, BNP levels are associated with successful cardioversion and maintenance of sinus rhythm two weeks after cardioversion.
Automated LC-HRMS(/MS) Approach for the Annotation of Fragment Ions Derived from Stable Isotope Labeling-Assisted Untargeted Metabolomics (2014)

Structure elucidation of biological compounds is still a major bottleneck of untargeted LC-HRMS approaches in metabolomics research. The aim of the present study was to combine stable isotope labeling and tandem mass spectrometry for the automated interpretation of the elemental composition of fragment ions and thereby facilitate the structural characterization of metabolites. The software tool FragExtract was developed and evaluated with LC-HRMS/MS spectra of both native (12)C- and uniformly (13)C (U-(13)C)-labeled analytical standards of 10 fungal substances in pure solvent and spiked into fungal culture filtrate of Fusarium graminearum respectively. Furthermore, the developed approach is exemplified with nine unknown biochemical compounds contained in F. graminearum samples derived from an untargeted metabolomics experiment. The mass difference between the corresponding fragment ions present in the MS/MS spectra of the native and U-(13)C-labeled compound enabled the assignment of the number of carbon atoms to each fragment signal and allowed the generation of meaningful putative molecular formulas for each fragment ion, which in turn also helped determine the elemental composition of the precursor ion. Compared to laborious manual analysis of the MS/MS spectra, the presented algorithm marks an important step toward efficient fragment signal elucidation and structure annotation of metabolites in future untargeted metabolomics studies. Moreover, as demonstrated for a fungal culture sample, FragExtract also assists the characterization of unknown metabolites, which are not contained in databases, and thus exhibits a significant contribution to untargeted metabolomics research.
Approach to multifunctional device platform with epitaxial graphene on transition metal oxide (2015)

Heterostructures consisting of two-dimensional materials have shown new physical phenomena, novel electronic and optical properties, and new device concepts not observed in bulk material systems or purely three dimensional heterostructures. These new effects originated mostly from the van der Waals interaction between the different layers. Here we report that a new optical and electronic device platform can be provided by heterostructures of 2D graphene with a metal oxide (TiO2). Our novel direct synthesis of graphene/TiO2 heterostructure is achieved by C60 deposition on transition Ti metal surface using a molecular beam epitaxy approach and O2 intercalation method, which is compatible with wafer scale growth of heterostructures. As-grown heterostructures exhibit inherent photosensitivity in the visible light spectrum with high photo responsivity. The photo sensitivity is 25 times higher than that of reported graphene photo detectors. The improved responsivity is attributed to optical transitions between O 2p orbitals in the valence band of TiO2 and C 2p orbitals in the conduction band of graphene enabled by Coulomb interactions at the interface. In addition, this heterostructure provides a platform for realization of bottom gated graphene field effect devices with graphene and TiO2 playing the roles of channel and gate dielectric layers, respectively.
SMALL RING COMPOUNDS-III. A STUDY ON [4.3.2]-, [5.3.2]-, AND [4.4.1]PROPELLANONE ACETALS (1974)

Abstract The particular mass spectral behavior of [4.3.2]propellan-7-one and [5.3.2]propellan-2-one ethylene acetals, and 11,11-dimethoxy and diethoxy[4.4.1]propellanes is discussed.
DeepVO: A Deep Learning approach for Monocular Visual Odometry (2016)

Deep Learning based techniques have been adopted with precision to solve a lot of standard computer vision problems, some of which are image classification, object detection and segmentation. Despite the widespread success of these approaches, they have not yet been exploited largely for solving the standard perception related problems encountered in autonomous navigation such as Visual Odometry (VO), Structure from Motion (SfM) and Simultaneous Localization and Mapping (SLAM). This paper analyzes the problem of Monocular Visual Odometry using a Deep Learning-based framework, instead of the regular 'feature detection and tracking' pipeline approaches. Several experiments were performed to understand the influence of a known/unknown environment, a conventional trackable feature and pre-trained activations tuned for object classification on the network's ability to accurately estimate the motion trajectory of the camera (or the vehicle). Based on these observations, we propose a Convolutional Neural Network architecture, best suited for estimating the object's pose under known environment conditions, and displays promising results when it comes to inferring the actual scale using just a single camera in real-time.
The Refractivity of Air (1981)

The air density equation of Jones, Edlén's dispersion formula for standard air, and Edlén's empirically-derived expressions for the effects of Co<sub>2</sub> abundance and water vapor partial pressure on refractivity have been combined into a simplified equation for the refractivity of air, and estimates have been made of uncertainties in calculated refractivity. Under ambient conditions typical of metrology laboratories, the agreement between the simplified equation and Edlén's formulation is well within the uncertainty in each. The simplified equation is valid in the visible region.
Peroxidase-Catalyzed Halogenation (1976)

Peroxidase-catalyzed halogenation reactions have been established as being important in the biosynthesis of the hormone thyroxine and in biological defense mechanisms. Recently these reactions have been recognized as valuable tools for the study of proteins as well as their arrangement in macromolecular structures. The pathways of peroxidase catalyses can be accommodated within the framework of the classical Chance-George mechanism. This implies that the initial steps of the reaction invariably involve oxidation of peroxidases by peroxides--and that the resulting derivative, compound I, is the oxidant of the halide ions. Such reactions may result either in the formation of hypohalous acids, or in halogenation of the enzyme apoprotein, followed by transhalogenation to substrate for halogenation. Chloro- and myeloperoxidases catalyze oxidation of all halide ions, except F-; oxidation of bromide and iodide is mediated by lactoperoxidase, but horseradish peroxidase only oxidizes iodide. All of the above enzymes except horseradish will oxidize the pseudo halide thiocyanate. The origins of this differentiation remain to be defined, but they presumably reflect significant variation in oxidation potential of different peroxidase-peroxide derivatives, rather than constraints on the peroxidase-donor interactions. As pointed out above, halogenation of the amino acids tyrosine and histidine or these residues in proteins can take place on the enzyme. This makes lactoperoxidase-catalyzed iodination selective. The amino acid residues in proteins that are iodinated depend not only on reactivity of the amino acid residue but also on its geometric location. Thus lactoperoxidase-catalyzed iodination can be a useful tool in the study of protein structure and function. It is also useful in establishing the geometric position of proteins within macromolecular structures. Thyroid peroxidase catalyzes iodination of thyroglobulin and is involved in a second important step, the coupling of the iodotyrosines to form thyroxine or triiodothyronine. A proposed mechanism for this reaction suggests that the oxidation is mediated by the iodoenzyme derivative mentioned above followed by a prototropic rearrangement and scission to form the ether bound of thyronine and a serine residue on thyroglobulin.
Purification and Characterization of Schwann Cells from Adult Human Skin and Nerve (2017)

Despite its modest capacity for regeneration, peripheral nervous system injury often results in significant long-term disability. Supplementing peripheral nervous system injury with autologous Schwann cells (SCs) may serve to rejuvenate the postinjury environment to enhance regeneration and ultimately improve functional outcomes. However, human nerve-derived SC (hN-SC) collection procedures require invasive surgical resection. Here, we describe the characterization of SCs from adult human skin (hSk-SCs) of four male donors ranging between 27 and 46 years old. Within five weeks of isolating and culturing adherent mixed skin cells, we were able to obtain 3-5 million purified SCs. We found that hSk-SCs appeared transcriptionally indistinguishable from hN-SCs with both populations exhibiting expression of SC genes including: <i>SOX10</i>, <i>SOX9</i>, <i>AP2A1</i>, <i>CDH19</i>, <i>EGR1</i>, <i>ETV5</i>, <i>PAX3</i>, <i>SOX2</i>, <i>CX32</i>, <i>DHH</i>, <i>NECL4</i>, <i>NFATC4</i>, <i>POU3F1</i>, <i>S100B</i>, and <i>YY1</i>. Phenotypic analysis of hSk-SCs and hN-SCs cultures revealed highly enriched populations of SCs indicated by the high percentage of NES<sup>+ve</sup>, SOX10<sup>+ve</sup>, s100<sup>+ve</sup> and p75<sup>+ve</sup> cells, as well as the expression of a battery of other SC-associated proteins (PAX3, CDH19, ETV5, SOX2, POU3F1, S100B, EGR2, and YY1). We further show that both hSk-SCs and hN-SCs are capable of promoting axonal growth to similar degrees and that a subset of both associate with regenerating axons and form myelin following transplantation into the injured mouse sciatic nerve. Interestingly, although the majority of both hSk-SCs and hN-SCs maintained SOX10 immunoreactivity following transplant, only a subset of each activated the promyelinating factor, POU3F1, and were able to myelinate. Taken together, we demonstrate that adult hSk-SCs are genetically and phenotypically indistinguishable to hN-SCs.