gebhart/patrepeval huggingface dataset:
Pharmacological activation of the Sonic hedgehog pathway with a Smoothened small molecule agonist ameliorates the severity of alcohol‐induced morphological and behavioral birth defects in a zebrafish model of fetal alcohol spectrum disorder (2022)

Ethanol exposure during the early stages of embryonic development can lead to a range of morphological and behavioral differences termed fetal alcohol spectrum disorders (FASDs). In a zebrafish model, we have shown that acute ethanol exposure at 8-10 hr postfertilization (hpf), a critical time of development, produces birth defects similar to those clinically characterized in FASD. Dysregulation of the Sonic hedgehog (Shh) pathway has been implicated as a molecular basis for many of the birth defects caused by prenatal alcohol exposure. We observed in zebrafish embryos that shh expression was significantly decreased by ethanol exposure at 8-10 hpf, while smo expression was much less affected. Treatment of zebrafish embryos with SAG or purmorphamine, small molecule Smoothened agonists that activate Shh signaling, ameliorated the severity of ethanol-induced developmental malformations including altered eye size and midline brain development. Furthermore, this rescue effect of Smo activation was dose dependent and occurred primarily when treatment was given after ethanol exposure. Markers of Shh signaling (gli1/2) and eye development (pax6a) were restored in embryos treated with SAG post-ethanol exposure. Since embryonic ethanol exposure has been shown to produce later-life neurobehavioral impairments, juvenile zebrafish were examined in the novel tank diving test. Our results further demonstrated that in zebrafish embryos exposed to ethanol, SAG treatment was able to mitigate long-term neurodevelopmental impairments related to anxiety and risk-taking behavior. Our results indicate that pharmacological activation of the Shh pathway at specific developmental timing markedly diminishes the severity of alcohol-induced birth defects.
In vivo characterization of the antinociceptive effects of UFP‐512 and BG‐156: Selective Delta Opioid Receptor Ligands (2009)

Delta opioid receptor (DOR) agonists have demonstrated efficacy in several preclinical models of pain. In addition, several groups have demonstrated novel antidepressant and anxiolytic effects for this class of compounds. Modification of the N‐terminal tyrosine by 2',6′‐dimethyl‐L‐tyrosine (Dmt) can have significant effects on opioid peptide affinity, selectivity, and efficacy at the DOR. The studies presented here assess the in vivo activity of two structurally related peptides that possess DOR‐selectivity (UFP‐512 and BG‐156). Both compounds produced dose‐related antinociception in the mouse 55°C tail‐flick assay (i.c.v. A50 values of 8.0 and 5.4 nmol, respectively). I.v. administration of these compounds produced limited antinociception (&lt;20% MPE). In contrast, systemic administration of UFP‐512 produced potent, dose‐related antinociception in the mouse acetic acid writhing assay. In Rhesus monkeys, the intramuscular administration of UFP‐512 dose‐dependently reversed capsaicin‐induced thermal hyperalgesia, with a 10 mg/kg dose producing ~50% reversal. The data indicates that these peptides produce antinociception and antihyperalgesia in both rodents and monkeys, and that systemic injections of the compound may act primarily at peripheral DORs. Additional studies are being conducted to confirm receptor selectivity and site(s) of action in vivo.
Control of in‐plane epitaxial relationship of c ‐plane AlN layers grown on a ‐plane sapphire substrates by hydride vapor phase epitaxy (2011)

Abstract Control of the in‐plane epitaxial relationship of a c ‐plane AlN layer grown at 1450 °C by hydride vapor phase epitaxy on an a ‐plane sapphire substrate is achieved. In addition, two in‐plane epitaxial relationships are compared. It was possible to grow a c ‐plane AlN layer on an a ‐plane sapphire substrate with selectable in‐plane matching: AlN [10 $ \bar 1 $ 0]//sapphire [0001] could be obtained by growing an intermediate AlN layer at 1065 °C, whereas AlN [11 $ \bar 2 $ 0] // sapphire [0001] could be grown on the intermediate AlN layer at a low temperature of 700 °C. The full‐width at half‐maximums of X‐ray rocking curves for the (0002) and (10 $ \bar 1 $ 0) planes were respectively 313.2 and 543.6 arcsec from the AlN layer with the AlN [10 $ \bar 1 $ 0]//sapphire [0001] relationship and 428.4 and 788.0 arcsec from the AlN layer with the AlN [11 $ \bar 2 $ 0] // sapphire [0001] relationship. (© 2011 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
Blocked diisocyanate‐modified epoxy resin: Mechanism and mechanical properties (1996)

The modification of bisphenol-A-based epoxy resin with isocyanates was investigated. To increase the crosslinking density by a urethane reaction and to conduct the normal cross-linking reaction between the epoxide and the amine during the cure cycle, blocking the isocyanates with active hydrogens is necessary, which may be deblocked and reacted at elevated temperature. The modified reactions involving diisocyanates and hydroxyl groups generated from epoxy cured with an amine system were studied. This mechanism can be identified by the variations of infrared spectra in the carbonyl group stretching region. Furthermore, the effect of the blocked isocyanate incorporation with amine on the reactivity of epoxy was also studied. The thermal and the mechanical properties were characterized. It was found that the glass transition temperature increased with an aromatic blocked-diisocyanate content. The mechanical properties were improved by blocked diisocyanate. The morphology was also investigated, which showed that a homogeneous structure existed in the modified system. © 1996 John Wiley & Sons, Inc.
Superconducting Electromagnetic Suspension (EMS) system for Grumman Maglev concept (1994)

The Grumman developed Electromagnetic Suspension (EMS) Maglev system has the following key characteristics: a large operating airgap--40 mm; levitation at all speeds; both high speed and low speed applications; no deleterious effects on SC coils at low vehicle speeds; low magnetic field at the SC coil--less than 0.35 T; no need to use non-magnetic/non-metallic rebar in the guideway structure; low magnetic field in passenger cabin--approximately 1 G; low forces on the SC coil; employs state-of-the-art NbTi wire; no need for an active magnet quench protection system; and lower weight than a magnet system with copper coils. The EMS Maglev described in this paper does not require development of any new technologies. The system could be built with the existing SC magnet technology.
Typing of acute leukemia by intelligent optical time-stretch imaging flow cytometry on a chip (2023)

Acute leukemia (AL) is one of the top life-threatening diseases. Accurate typing of AL can significantly improve its prognosis. However, conventional methods for AL typing often require cell staining, which is time-consuming and labor-intensive. Furthermore, their performance is highly limited by the specificity and availability of fluorescent labels, which can hardly meet the requirements of AL typing in clinical settings. Here, we demonstrate AL typing by intelligent optical time-stretch (OTS) imaging flow cytometry on a microfluidic chip. Specifically, we employ OTS microscopy to capture the images of cells in clinical bone marrow samples with a spatial resolution of 780 nm at a high flowing speed of 1 m s<sup>-1</sup> in a label-free manner. Then, to show the clinical utility of our method for which the features of clinical samples are diverse, we design and construct a deep convolutional neural network (CNN) to analyze the cellular images and determine the AL type of each sample. We measure 30 clinical samples composed of 7 acute lymphoblastic leukemia (ALL) samples, 17 acute myelogenous leukemia (AML) samples, and 6 samples from healthy donors, resulting in a total of 227 620 images acquired. Results show that our method can distinguish ALL and AML with an accuracy of 95.03%, which, to the best of our knowledge, is a record in label-free AL typing. In addition to AL typing, we believe that the high throughput, high accuracy, and label-free operation of our method make it a potential solution for cell analysis in scientific research and clinical settings.
Synthesis of In1–xGaxP Quantum Dots in Lewis Basic Molten Salts: The Effects of Surface Chemistry, Reaction Conditions, and Molten Salt Composition (2022)

Inorganic molten salts are emerging as versatile solvents for high-temperature processing of colloidal nanocrystals. Molten alkali bromide eutectics can serve as a convenient solvent for the transformation of InP quantum dots (QDs) to In1–xGaxP QDs, with simultaneous tuning of the composition and band gap. Here, we explore various aspects of this molten salt indium-to-gallium cation exchange in-depth, including the nanocrystal surface chemistry, reaction conditions, and salt composition, to obtain a more detailed understanding and finer control over the transformation. InP QDs capped with (DDA)2S, (NH4)2S, Li2Se, GaCl3, or InCl3 can be homogenously dispersed in a molten bromide salt mixture. We demonstrate that chalcogenide capping ligands improve the high temperature stability of InP QDs through the formation of a chalcogen-rich layer which prevents InP decomposition. For each surface chemistry studied, the indium-to-gallium cation exchange proceeds similarly, yielding colloidal In1–xGaxP QDs with an increased band gap and decreased lattice constant. By carefully engineering the reaction conditions and protecting the nanoparticles from oxidative exposure, we achieve a narrow emission linewidth of 41 nm full width at half maximum from the alloyed In1–xGaxP colloidal QDs. These insights provide the design space for colloidal synthesis in molten inorganic salts and introduce synthetic methods for In1–xGaxP QDs with tunable composition and properties. Our work demonstrates the development of nontoxic QD emitters with optimized stability, color purity, and luminescence quantum efficiency.
NEBULIZER DELIVERY OF OLIGOSACCHARIDE SOLUTION AEROSOLS (1997)

ABSTRACT Oligosaccharides may be employed to inhibit lung infections. Since these molecules are water soluble they may be administered directly to the lungs as aerosol droplets delivered by nebulizer. Two oligosaccharides, 3'-sialyflactose and lacto-N-neotetraose, were prepared as 1% w/v solutions and delivered using each of two nebulizers, the Acorn II or Aerotech II. The output characteristics of these nebulizers were characterized in terms of total mass output (208–253 ug/mL), mass median aerodynamic diameter (0.6–1.1 urn), fine particle fraction (83–95%) and ACGIH respirable fraction (72–86%). The nebulizer output was also evaluated following administration via a ventilator unit employed to administer aerosols to animals. The ventilator was employed in preliminary experiments to deliver aerosols to rabbits in preparation for subsequent experiments in which oligosaccharide administration to an animal model of infection may be studied.
Quantitative sequence basis for the E. coli transcriptional regulatory network (2022)

Abstract The transcriptional regulatory network (TRN) of E. coli consists of thousands of interactions between regulators and DNA sequences. Inherently the DNA sequence is the primary determinant of the TRN; however, it is well established that the presence of a DNA binding motif does not guarantee a functional regulatory protein binding site. Thus, the extent to which the TRN architecture can be predicted by the genome DNA sequence alone remains unclear. Here, we developed machine learning models that predict the TRN structure of E. coli based on genome sequence. Models were constructed successfully (cross-validation AUROC &gt;= 0.8) for 84% (57/68) of valid E. coli regulons identified from top-down analysis of RNA-seq data. We found that: 1) While regulatory motif strength is the most important sequence feature for determining regulon membership, additional features such as DNA shape substantially influence membership; 2) complex regulons involving multiple interacting regulators could be unraveled by machine learning; 3) investigating regulons where initial ML models failed revealed new regulator-specific sequence features that improved model accuracy. Finally, while regulon structure can appear to be variable across estimation methods and strains, we found that strong regulatory sequence features underlie both the genes that appear most consistently in regulons across estimation methods as well as the core regulon genes in the Fur pan-regulon. This work develops a quantitative understanding of the sequence basis of the TRN and suggests a path towards computationally-guided control of transcriptional regulation for synthetic biology applications.
Cavity-enhanced measurements for determining dielectric-membrane thickness and complex index of refraction (2014)

The material properties of silicon nitride (SiN) play an important role in the performance of SiN membranes used in optomechanical applications. An optimum design of a subwavelength high-contrast grating requires accurate knowledge of the membrane thickness and index of refraction, and its performance is ultimately limited by material absorption. Here we describe a cavity-enhanced method to measure the thickness and complex index of refraction of dielectric membranes with small, but nonzero, absorption coefficients. By determining Brewster's angle and an angle at which reflection is minimized by means of destructive interference, both the real part of the index of refraction and the sample thickness can be measured. A comparison of the losses in the empty cavity and the cavity containing the dielectric sample provides a measurement of the absorption.
Pathogenic variants of sphingomyelin synthase SMS2 disrupt lipid landscapes in the secretory pathway (2022)

Sphingomyelin is a dominant sphingolipid in mammalian cells. Its production in the <i>trans-</i>Golgi traps cholesterol synthesized in the ER to promote formation of a sphingomyelin/sterol gradient along the secretory pathway. This gradient marks a fundamental transition in physical membrane properties that help specify organelle identify and function. We previously identified mutations in sphingomyelin synthase SMS2 that cause osteoporosis and skeletal dysplasia. Here, we show that SMS2 variants linked to the most severe bone phenotypes retain full enzymatic activity but fail to leave the ER owing to a defective autonomous ER export signal. Cells harboring pathogenic SMS2 variants accumulate sphingomyelin in the ER and display a disrupted transbilayer sphingomyelin asymmetry. These aberrant sphingomyelin distributions also occur in patient-derived fibroblasts and are accompanied by imbalances in cholesterol organization, glycerophospholipid profiles, and lipid order in the secretory pathway. We postulate that pathogenic SMS2 variants undermine the capacity of osteogenic cells to uphold nonrandom lipid distributions that are critical for their bone forming activity.
In-depth characterization of the microRNA transcriptome in a leukemia progression model (2008)

MicroRNAs (miRNAs) have been shown to play important roles in physiological as well as multiple malignant processes, including acute myeloid leukemia (AML). In an effort to gain further insight into the role of miRNAs in AML, we have applied the Illumina massively parallel sequencing platform to carry out an in-depth analysis of the miRNA transcriptome in a murine leukemia progression model. This model simulates the stepwise conversion of a myeloid progenitor cell by an engineered overexpression of the nucleoporin 98 (NUP98)-homeobox HOXD13 fusion gene (ND13), to aggressive AML inducing cells upon transduction with the oncogenic collaborator Meis1. From this data set, we identified 307 miRNA/miRNA species in the ND13 cells and 306 miRNA/miRNA species in ND13+Meis1 cells, corresponding to 223 and 219 miRNA genes. Sequence counts varied between two and 136,558, indicating a remarkable expression range between the detected miRNA species. The large number of miRNAs expressed and the nature of differential expression suggest that leukemic progression as modeled here is dictated by the repertoire of shared, but differentially expressed miRNAs. Our finding of extensive sequence variations (isomiRs) for almost all miRNA and miRNA species adds additional complexity to the miRNA transcriptome. A stringent target prediction analysis coupled with in vitro target validation revealed the potential for miRNA-mediated release of oncogenes that facilitates leukemic progression from the preleukemic to leukemia inducing state. Finally, 55 novel miRNAs species were identified in our data set, adding further complexity to the emerging world of small RNAs.
Phase Transitions in Frequency Agile Radar Using Compressed Sensing (2021)

Frequency agile radar (FAR) has improved anti-jamming performance over traditional pulse-Doppler radars under complex electromagnetic circumstances. To reconstruct the range-Doppler information in FAR, many compressed sensing (CS) methods including standard and block sparse recovery have been applied. In this paper, we study phase transitions of range-Doppler recovery in FAR using CS. In particular, we derive closed-form phase transition curves associated with block sparse recovery and complex Gaussian matrices, based on prior results of standard sparse recovery under real Gaussian matrices. We further approximate the obtained curves with elementary functions of radar and target parameters, facilitating practical applications of these curves. Our results indicate that block sparse recovery outperforms the standard counterpart when targets occupy more than one range cell, which are often referred to as extended targets. Simulations validate the availability of these curves and their approximations in FAR, which benefit the design of the radar parameters.
EDLCs Based on Solvent‐Free Ionic Liquids (2013)

High-power supercapacitors are key energy storage/conversion systems for applications ranging from sustainable transportation to grid-connected renewable energy plants. Research activity worldwide is focused currently on developing systems of increased specific energy without sacrificing power capability and cycling stability. Here, we shall focus on the use of ionic liquids (ILs) as solvent-free electrolytes in electric double-layer capacitors (EDLCs), which represent a powerful strategy for the development of safe, high-energy supercapacitors. The features of solvent-free IL/electrode interface are reported and an overview of the physicochemical properties of the most investigated ILs is given to highlight the main requirements for the effective use of ILs in supercapacitors. The properties of carbon electrode materials for IL-based EDLCs, which should be tailored in relation to the nature of the IL, are discussed and particular emphasis is given to carbon porosity and surface chemistry. Cell configurations of IL-based EDLCs, which make possible high voltages and high specific energy, are also described in some detail and the most recent advances in IL-based EDLCs are reviewed.
Coating and spark plasma sintering of nano-sized TiN on alumina particles of different size, shape and structure (2009)

TiN-coated Al2O3 particles of different size, shape and crystal structure were prepared by depositing nano-size TiO2 on the Al2O3 surfaces from Ti(O-i-C3H7)4 solution (TiO2 precursor) by controlled hydrolysis, then nitrided with NH3 at 1000°C. Irrespective of the source of Al2O3 particles, a homogeneous TiO2 coating was achieved by heating from 10 to 40°C an ultrasonic suspension of the Al2O3 particles containing the precursor with 1.0 vol% H2O. After nitridation, the Al2O3 grains were coated with 10-20 nm TiN particles. Spark plasma sintering of the TiN/Al2O3 particles at 1500°C and 1600°C yielded the composite ceramics with a relative density of 94-97%. Composite TiN/Al2O3 ceramics with an electrical resistivity of ∼10-2 Ω cm were obtained at 25 vol% TiN composition.
A microwave and millimeter wave planar circuit with PBG structure and analysis using the FDTD method. (2001)

Recently, the demand of information and telecommunication systems has been growing rapidly. In order to realize these systems with small, lightweight and multi-function capabilities, planar circuit and antenna technology have been used. However, these technologies have problems such as low gain and surface wave loss. Photonic band-gap technology is believed to be a promising new solution to these problems. In this paper, simulation results using the FDTD method for photonic band-gap structure on a microwave and a millimeter wave circuit substrate made by etching are presented. The analysis of a Microstrip line and a millimeter wave active integrated antenna with PBG structure are also presented.
M. P. Schützenberger. On context-free languages and push-down automata. Information and control, vol. 6 (1963), pp. 246–264. (1969)

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GRACE-FO: The Gravity Recovery and Climate Experiment Follow-On Mission (2019)

The Gravity Recovery and Climate Experiment Follow-On mission was conceived to continue the successful legacy of the recently decommissioned Gravity Recovery and Climate Experiment mission and, at the same time, serve as a platform to demonstrate the first-ever in-space intersatellite laser ranging interferometer as a technology pathfinder for future gravity mapping missions. Launched in May of 2018, the Gravity Recovery and Climate Experiment Follow-On observatory builds on the design of the original Gravity Recovery and Climate Experiment satellites, but incorporates a number of improvements based on lessons learned, and features significantly increased complexity due to the accommodation of the laser ranging interferometer. This paper provides an overview of the challenging requirements levied on the observatory, and the mission and spacecraft design necessary to meet them. As the original Gravity Recovery and Climate Experiment spacecraft design has not been, to date, broadly discussed in the engineering literature, this paper further highlights original design rationales, where still applicable. As future satellite-based geodesy missions with similar constraints and challenges emerge, the implementation of the Gravity Recovery and Climate Experiment Follow-On observatory described herein can serve as a pathfinder and guide for the successful realization of these endeavors.
A Trial System for 5G Wireless Access (2015)

5G is the next step in the evolution of mobile communication and a key component of the future networked society. With capabilities such as massive system capacity, higher data rates, very low latency and ultra-high reliability, 5G will provide significantly enhanced mobile-broadband experience but also support a wide range of new wireless applications and use cases. In this paper, a trial system for 5G mobile broadband operating at 15 GHz is outlined, together with initial experimental results showing that multi-Gbps data rates are possible.