gebhart/patrepeval huggingface dataset:
Ultrasensitive Immunosensor Array for TNF-α Detection in Artificial Saliva using Polymer-Coated Magnetic Microparticles onto Screen-Printed Gold Electrode (2019)

Tumor necrosis factor-α (TNF-α) is a biomarker of inflammation that occurs in patients suffering from heart failure (HF). Saliva can be sampled in a non-invasive way, and it is currently gaining importance as matrix alternative to blood in diagnostic and therapy monitoring. This work presents the development of an immunosensor array based on eight screen-printed gold electrodes to detect TNF-α in saliva samples. Two different functionalization strategies of electrodes were compared. In the first, anti-TNF-α antibodies were chemically bonded onto the electrode by functionalization with 4-carboxymethylaniline. The other functionalization procedure involved the binding of antibodies onto polymer-coated magnetic microparticles, which were then deposited onto the electrode by pulsed chronoamperometry. Finally, the chronoamperometry technique was applied to characterize the modified SPEAu. The use of a secondary antibody anti-TNF-α (Ab-TNF-α-HRP) labelled with horseradish peroxidase (HRP, 2 µg·mL<sup>-1</sup>) was investigated using tetramethylbenzidine (TMB, pH = 3.75) as electrochemical substrate containing 0.2 mM of H₂O₂. A sandwich-type detection strategy with a secondary antibody anti-TNF-α provided chronoamperometric analyses in 10 s for each sample. Linearity, precision, limit of detection, and selectivity of devices were investigated. Interferences were evaluated by analyzing solutions containing other cytokine produced during the acute stage of inflammation. The immunosensor showed good performance within the clinically relevant concentration range, with a precision of 8%, and a limit of detection of 0.3 pg/mL. Therefore, it may represent a promising tool for monitoring HF in a non-invasive way.
The Safety and Efficacy of OP-1 (rhBMP-7) as a Replacement for Iliac Crest Autograft in Posterolateral Lumbar Arthrodesis (2008)

OP-1 Putty is a safe and effective alternative to autograft in the setting of uninstrumented posterolateral spinal arthrodesis performed for degenerative spondylolisthesis and symptomatic spinal stenosis.
Toward a widely tunable narrow linewidth RF source utilizing an integrated heterogenous silicon photonic module (2013)

A system for generating widely tunable, narrow-line RF signals from a pair of injection-locked lasers has been developed. By injection seeding one laser with a sideband obtained from a second laser that is phase modulated by a spectrally pure low-frequency RF reference oscillator and then mixing these coherent optical outputs on a fast photodiode, RF with the same linewidth and phase noise characteristics as the reference oscillator can be produced. By using harmonics of the reference oscillator the RF output can be tuned over a much wider range than the reference oscillator while maintaining its narrow linewidth.Here we present the results of our efforts to develop an integrated version of this system, based on a silicon-photonic integrated circuit coupled to III-V semiconductor gain chips.Towards that goal we have successfully demonstrated an integrated module and shown tunable RF generation with a 1 Hz linewidth.
Supplementary Figure 5 from Selectin Ligand Sialyl-Lewis x Antigen Drives Metastasis of Hormone-Dependent Breast Cancers (2023)

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Cholesteric liquid crystals: properties and applications (2014)

Cholesteric liquid crystals (CLCs) are a fascinating genre from the liquid crystalline material family, due, in large part, to the unique optical properties its mesoscopic helical structure imparts...
Mast cells and exosomes in hyperoxia-induced neonatal lung disease (2016)

Chronic lung disease of prematurity (CLD) is a frequent sequela of premature birth and oxygen toxicity is a major associated risk factor. Impaired alveolarization, scarring, and inflammation are hallmarks of CLD. Mast cell hyperplasia is a feature of CLD but the role of mast cells in its pathogenesis is unknown. We hypothesized that mast cell hyperplasia is a consequence of neonatal hyperoxia and contributes to CLD. Additionally, mast cell products may have diagnostic and prognostic value in preterm infants predisposed to CLD. To model CLD, neonatal wild-type and mast cell-deficient mice were placed in an O2 chamber delivering hyperoxic gas mixture [inspired O2 fraction (FiO2 ) of 0.8] (HO) for 2 wk and then returned to room air (RA) for an additional 3 wk. Age-matched controls were kept in RA (FiO2 of 0.21). Lungs from HO mice had increased numbers of mast cells, alveolar simplification and enlargement, and increased lung compliance. Mast cell deficiency proved protective by preserving air space integrity and lung compliance. The mast cell mediators β-hexosaminidase (β-hex), histamine, and elastase increased in the bronchoalveolar lavage fluid of HO wild-type mice. Tracheal aspirate fluids (TAs) from oxygenated and mechanically ventilated preterm infants were analyzed for mast cell products. In TAs from infants with confirmed cases of CLD, β-hex was elevated over time and correlated with FiO2 Mast cell exosomes were also present in the TAs. Collectively, these data show that mast cells play a significant role in hyperoxia-induced lung injury and their products could serve as potential biomarkers in evolving CLD.
MeV-proton channeling in crystalline silicon (2014)

Hydrogen implantation has become an important application in the fabrication of power semiconductor devices. With the product requirement of a well-defined implantation profile, adequate control of the incident beam angle is necessary in order to avoid channeling effects. With respect to the different scan systems of commercial implanters and the crystal alignment of the bulk material the implant tilt and twist angles have to be adapted. We used commercially available <100>-oriented silicon wafers to examine planar channeling along a {110}-plane for proton energies in the range of 0.5–2.5 MeV. The critical angle as a function of proton energy is determined from photothermal response measurements (TWIN).
Dixon water‐fat separation in PROPELLER MRI acquired with two interleaved echoes (2015)

The proposed method enables motion-insensitive PROPELLER MRI with robust fat suppression and reduced blurring. Additionally, fat images are available if desired.
Error rate estimation in a multi-channel active phased array (2002)

The symbol error rate (SER) degradation due to intermodulation and sidelobe (or co-channel) interference in a multi-channel active phased array satellite communication system is investigated. The intermodulation products are generated by the RF power amplifier nonlinearity, and the sidelobe interferences are introduced when multiple channels use the same carrier frequency. Traditionally, the far field power of the intermodulation and sidelobe signals are combined non-coherently with the thermal noise power at the receiver to form the total system noise (N+I). The SER is then estimated based on the carrier to total noise ratio, C/(N+I), by assuming the total noise to be white Gaussian and uncorrelated with the desired signal. The coherency effects of the interferences are therefore ignored. In this paper, we test the accuracy of this method. We develop expressions to calculate the intermodulation and sidelobe far-field powers, and we analytically estimate the symbol error rate (SER/sub est/). We also compute the symbol error rate (SER/sub c/) with a Monte Carlo simulation that includes filtered QPSK channels, the active phased array, and a coherent receiver with thermal noise. When we compared the results of the two methods, we observed a discrepancy in bit error rate that is caused by ignoring the coherent effects of the interferences in the analytical method. This discrepancy was larger when the interference consisted of only sidelobe signals than when the interference contained both sidelobe and intermodulation signals.
71 Removal of hypotaurine from porcine embryo culture medium decreases message for pro-apoptotic genes but does not affect development at low oxygen tension (2018)

Hypotaurine (HT) is a routine additive to embryo culture medium, acting primarily as an oxygen radical scavenger. However, the practice of culturing embryos at ~5% O2 has been widely adopted because this is more physiologically relevant to the oxygen tensions detected in the oviduct and uterus. Thus, the utility of HT may be diminished as fewer oxygen radicals are produced during culture at 5% O2. The objective here was to determine the effects of removing HT from our porcine embryo culture medium (MU2) on the development of embryos incubated at a lower oxygen tension (5% O2) compared with atmospheric oxygen (~20% O2). Porcine cumulus-oocyte complexes were aspirated, matured, and fertilized with standard procedures from our laboratory. Presumptive zygotes were cultured in 1 of 4 conditions: MU2 with 5 mM HT at 5% O2 (low O2 +HT; control), MU2 without HT at 5% O2 (low O2 -HT), MU2 with 5 mM HT at 20% O2 (high O2 +HT), or MU2 without HT at 20% O2 (high O2 -HT). The percentage of presumptive zygotes that developed to the blastocyst stage on Day 6 and total number of nuclei in the blastocysts were determined. The RNA was extracted from pools of 30 blastocysts, and cDNA was synthesised for quantitative PCR for genes associated with HT synthesis, oxidative stress, and apoptosis. Damage to DNA was assessed by TUNEL staining of Day 6 blastocysts. Data were analysed for normality by using a Shapiro-Wilk test, and differences between means were detected by using 2-way ANOVA followed by Tukey’s honest significant difference test with P &amp;lt; 0.05 considered significant. Embryos cultured with high O2 -HT had significantly decreased blastocyst development compared with all other groups (26.2 ± 2.5% v. 36.9-41.7 ± 3.3-4.3%). Embryos cultured with low O2 -HT had significantly more nuclei than those cultured with high O2 +HT (50.5 ± 1.5 v. 45.5 ± 1.2). Notably, differences in blastocyst development (41.7 ± 3.3% v. 36.9 ± 3.3%) or total number of nuclei (50.0 ± 1.8 v. 50.5 ± 1.5) were not detected between embryos cultured with low O2 +HT or low O2 -HT. The abundance of messages for genes involved in HT synthesis (cysteine sulfinic acid decarboxylase [CSAD]) and oxidative stress (superoxide dismutase 1 [SOD1] and glutathione peroxidase 6 [GPX6]) did not differ between groups. Contrarily, messages for 2 pro-apoptotic markers (BCL2 associated agonist of cell death [BAD] and caspase 3 [CASP3]) were significantly increased in embryos cultured with +HT regardless of oxygen tension; however, percentages of DNA-damaged nuclei in blastocysts after TUNEL staining were not different between groups (5.4-6.5 ± 0.5-1.0%). These results indicate that HT is not necessary for porcine pre-implantation development at 5% O2 but is beneficial at atmospheric oxygen tension. Further investigation is required to confirm if HT promotes apoptosis in pre-implantation embryos. This research was supported by Food for the 21st Century at the University of Missouri and R01 HD080636.
Future Microsystems for Information Processing: Limits and Lessons From the Living Systems (2013)

The paper examines the impact of the physics of extremely scaled information processing devices and systems, with a focus on energy minimization. Architectural implications are also discussed including the impact on system scaling. In order to comprehend the system-level scaling and performance limits, understanding of limiting behavior for many electronic components is needed, e.g., logic and memory devices, I/Os, communication, etc. In the second part of the paper, entirely new information processing concepts are discussed based on learning from examples in nature, specifically, the individual living cell will be considered in the context of information processing. In the paper, a bacterial cell, such as E.coli of about one cubic micrometer volume is shown to be a very efficient and powerful information processor, far surpassing conceivable performance in the same volume by an ultimately scaled semiconductor system. Advances in the science of synthetic biology are beginning to suggest possible pathways for future information processing technologies. It might be possible that some of the physical limits faced by semiconductor technology may in fact be overcome by borrowing from synthetic biology principles.
Research Data Supporting: Uncovering the Connection Between Low-Frequency Dynamics and Phase-Transformation Phenomena in Molecular Solids (2019)

Experimental and simulated structural data (powder x-ray diffraction and crystallographic information file (CIF) data), experimental and simulated terahertz spectra, and molecular displacements.
Horizontal toroidal response in three-dimensional plasmonic(Conference Presentation) (2016)

The toroidal dipole moments of natural molecules are hard to be detected so the artificial toroidal materials made by metamaterial attract more attentions. Metamaterial, the sub-wavelength artificial structures, can modulate reflection or transmission of light. The toroidal metamaterial can not only amplify the toroidal moment but also repress the electric and magnetic dipole so it can be used to study the properties of toroidal dipole moment. However, there are many limitations for the experiments, such as the lateral light is necessary to excite the toroidal response. Most of the toroidal dipole moments oscillate perpendicularly to the substrate, therefore it is difficult to couple it with other dipole moments and could be only excited in the microwave region. In this paper, we design a toroidal metamaterial consisting of dumbbell-shaped aperture and vertical split ring resonator (VSRR) vertically. The toroidal dipole moment of our metamaterial is excited in the optical region. The arrangement of our nanostructures is vertical instead of planar annular arrangement to reduce the size of the unit cell and increase the density of the toroidal dipole moment. Moreover, the direction of toroidal dipole moment is parallel to the substrate which can be used for the study of the coupling effect with other kinds of dipolar moments.
Generalized scanning and multiresolution image compression (2002)

Summary form only given. The authors present a technique which exploits the correlative nature of image attributes by multiresolution decomposition of data sets reduced from an image along a generalized scan trajectory. Scanning strategies are based either on Hamiltonian space-filling curves (of the proper fractal dimensions) or on the solutions of a set of linear congruences.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Analog GAAS optoelectronic integrated circuits for large scale arrays (2007)

This thesis focuses on the design and fabrication of large arrays of analog optoelectronic circuits where transistors and optoelectronic devices such as photodetectors and LEDs are monolithically integrated on a single substrate. This optoelectronic approach allows one to design complex functions with the transistors and use the optoelectronic devices to couple the optical signals in and out of the circuit. The specific application for the analog optoelectronic circuits is large scale neuron arrays for optical neural networks. A neural network has two main elements: nonlinear elements (neurons) and interconnections (synapses). The neurons perform a nonlinear operation on their incoming signals while the synapses provide the weighted connection between neurons. In an optical neural network, the neurons are arranged as two-dimensional arrays that are optically interconnected using the third dimension. Two approaches to the design and fabrication of a variety of optoelectronic GaAs neuron circuits will be described. In the first approach, GaAs MESFETs (Metal-Semiconductor-Field-Effect Transistors), double hetero-structure GaAs/A1GaAs LEDs, and photodetectors are fabricated on a GaAs substrate containing epitaxial layers for the different devices. In the other approach, the detector/transistor portion of the circuit is fabricated by Vitesse through MOSIS and the LEDs are integrated afterwards using MBE regrowth. This second approach produces circuits with high uniformity and allows one to fabricate more complex optoelectronic circuits at a reasonable cost and turn-around-time. Most of the circuits are based on high responsivity optical FET detectors, which make it possible to build high optical gain circuit with little electrical power dissipation and small surface area.
Parallel homodimer structures of the extracellular domains of the voltage-gated sodium channel β4 subunit explain its role in cell–cell adhesion (2017)

Voltage-gated sodium channels (VGSCs) are transmembrane proteins required for the generation of action potentials in excitable cells and essential for propagating electrical impulses along nerve cells. VGSCs are complexes of a pore-forming α subunit and auxiliary β subunits, designated as β1/β1B-β4 (encoded by <i>SCN1B-4B,</i> respectively), which also function in cell-cell adhesion. We previously reported the structural basis for the <i>trans</i> homophilic interaction of the β4 subunit, which contributes to its adhesive function. Here, using crystallographic and biochemical analyses, we show that the β4 extracellular domains directly interact with each other in a parallel manner that involves an intermolecular disulfide bond between the unpaired Cys residues (Cys<sup>58</sup>) in the loop connecting strands B and C and intermolecular hydrophobic and hydrogen-bonding interactions of the N-terminal segments (Ser<sup>30</sup>-Val<sup>35</sup>). Under reducing conditions, an N-terminally deleted β4 mutant exhibited decreased cell adhesion compared with the wild type, indicating that the β4 <i>cis</i> dimer contributes to the <i>trans</i> homophilic interaction of β4 in cell-cell adhesion. Furthermore, this mutant exhibited increased association with the α subunit, indicating that the <i>cis</i> dimerization of β4 affects α-β4 complex formation. These observations provide the structural basis for the parallel dimer formation of β4 in VGSCs and reveal its mechanism in cell-cell adhesion.
Supplementary Movie 5 from Depletion of the Ras Association Domain Family 1, Isoform A–Associated Novel Microtubule-Associated Protein, C19ORF5/MAP1S, Causes Mitotic Abnormalities (2023)

Supplementary Movie 5 from Depletion of the Ras Association Domain Family 1, Isoform A–Associated Novel Microtubule-Associated Protein, C19ORF5/MAP1S, Causes Mitotic Abnormalities
Sustained hyperammonemia induces TNF-a IN Purkinje neurons by activating the TNFR1-NF-κB pathway (2020)

Sustained (4 weeks) but not short-term hyperammonemia induces TNF-a in Purkinje neurons in rats. This is mediated by peripheral inflammation. TNF-a is also increased in the Purkinje neurons of patients who die with liver cirrhosis. The results suggest that hyperammonemia induces TNF-a in glial cells and that TNF-a released by glial cells activates TNFR1 in Purkinje neurons, leading to NF-κB nuclear translocation and the induction of TNF-a expression, which may contribute to the neurological alterations observed in hyperammonemia and hepatic encephalopathy.
Molecular glass resists for next generation lithography (2008)

The idea of using small molecules instead of polymers for next generation lithography may enable improved resolution and line edge roughness (LER). Rather than using polymeric materials we are focusing on a new class of materials known as molecular glasses (MGs). These are low molecular weight organic materials that demonstrate high glass transition temperatures despite their modest size. Unlike polymeric resists, these molecules have the added advantages of distinct size and uniformity. We have synthesized a series of molecular resists containing rigid aromatic backbones and phenolic moieties suited for electron beam and Extreme Ultraviolet (EUV) lithography as both positive tone and negative tone photoresists. An increase in glass transition temperature is observed with increasing size and rigidity. Glass transition temperatures (Tgs) between 80-130&deg;C have been observed for t- BOC protected positive tone resists with molecular weights within the range of 800-1200g/mol. MGs with branched, dense structures are explored to design high Tg resist systems with improved sensitivity and contrast. The effects of protection ratio, high and low activation protecting groups, post exposure bake conditions, etch resistance and outgassing have been tested using selected phenolic MG resists. These new resist architectures are synthesized and evaluated to attain sub 30nm feature sizes required of candidates for next generation lithography.
Development and deployment of an underwater mass spectrometer for quantitative measurements of dissolved gases (2009)

Manual collection and processing of seawater samples for dissolved gas analyses are technically challenging, time consuming and costly. Accordingly, in situ analysis techniques present attractive alternatives to conventional gas measurement procedures. To meet the demands of sustained, high-resolution chemical observations of the oceans, the University of South Florida and SRI International developed underwater mass spectrometer systems for quantitative measurements of dissolved gases and volatile organic compounds. This work describes the influence of variable in situ conditions on the performance of a membrane introduction mass spectrometer used for measurements in both the water column and sediment porewater.\nLaboratory experiments to simulate the effects of field conditions on the membrane were performed by varying sample flow rate, salinity, hydrostatic pressure, and chemistry. Data indicate that membrane permeability has a strong dependence on hydrostatic pressure, and a weak dependence on salinity. Under slow flow conditions bicarbonates in solution contributed to carbon dioxide instrument response as a result of carbon system equilibration processes in the boundary layer at the membrane interface. In addition, method development was undertaken to enable underwater sediment porewater analyses and quantitative (calibrated) measurements of total dissolved inorganic carbon (DIC). This work establishes the capability of membrane introduction mass spectrometry to measure two compatible variables (DIC and dissolved CO2) for comprehensive CO2-system characterizations.\nIn addition to laboratory studies three types of field observation were obtained in this work. High-resolution vertical profiles of dissolved gases in the Gulf of Mexico were obtained through system calibration and characterization of the influence of hydrostatic pressure on the behavior of polydimethylsiloxane membranes. In the South Atlantic Bight, sediment porewater profiles of dissolved gases were repeatedly obtained over a 54 hr period. Data trends were in agreement with high remineralization rates facilitated by porewater advection. Finally, time-series underwater DIC measurements that were undertaken proved to be in good accord with results obtained using conventional techniques. These measurements constitute the first quantitative observations of dissolved gas ocean profiles, sediment porewater profiles, and DIC measurements by underwater mass spectrometry.