gebhart/patrepeval huggingface dataset:
Bladder and Sphincter Behavior in Patients With Spinal Cord Lesions (1991)

To ascertain the relationship between the clinical neurological level, and bladder and sphincter behavior, the video-urodynamic studies of 489 patients with spinal cord lesions due to a variety of causes were retrospectively analyzed. Patients were classified based on the clinical neurological level, etiology of the lesion and presence or absence of signs of sacral cord involvement. Urodynamic findings were classified as either detrusor hyperreflexia, detrusor-external sphincter dyssynergia, detrusor areflexia or normal. The results indicate that although there was a general correlation between the neurological level of injury and the expected vesicourethral function, it was neither absolute nor specific. For example, 20 of 117 cervical cord lesions had detrusor areflexia, 42 of 156 lumbar cord lesions had detrusor-external sphincter dyssynergia and 26 of 84 sacral cord had either detrusor hyperreflexia or detrusor-external sphincter dyssynergia. However, if one considers the presence of neurological abnormalities, 84% of the suprasacral cord lesions with detrusor areflexia have sacral cord signs. In contrast, all suprasacral cord lesions with no evidence of sacral cord involvement have either detrusor hyperreflexia or detrusor-external sphincter dyssynergia. The positive predictive value for positive sacral cord signs and detrusor areflexia was 87%. The positive predictive value for negative sacral cord signs and detrusor hyperreflexia/detrusor-external sphincter dyssynergia was 81%. These data suggest that the clinical neurological examination alone is not an adequate barometer to predict neurourological dysfunction and that video-urodynamic evaluation provides a more precise diagnosis for each patient.
Characterization of the terahertz near-field output of parallel-plate waveguides (2011)

We experimentally characterize the field confinement properties of various parallel-plate waveguide (PPWG) geometries in the terahertz spectral range. In contrast to infinite-width PPWGs with free-space diffraction along the unshielded direction, finite-width (and also tapered) PPWGs show well-confined THz fields at the output facet. Both the transverse field component, perpendicular to the inside surfaces, and the longitudinal component, parallel to the propagation direction, exhibit strong lateral confinement. We also observe an antisymmetric longitudinal field distribution across the air gap, analogous to the symmetric surface plasmon polariton mode observed in optical slot waveguides.
Hollow Mesoporous Carbon Nanospheres Decorated with Metal Oxide Nanoparticles as Efficient Earth‐Abundant Zinc‐Air Battery Catalysts (2021)

Abstract Invited for this month's cover picture are the research teams of Jonathan G. C. Veinot and Douglas G. Ivey at the University of Alberta (Canada). The cover picture provides an artistic representation of a new class of bifunctional Zn‐air battery catalysts consisting of hollow mesoporous carbon nanospheres decorated with various precious‐metal‐free transition‐metal oxide nanoparticles. Read the full text of the Article at 10.1002/celc.202001526 .
Heavy-Duty Truck Emissions in the South Coast Air Basin of California (2013)

California and Federal emissions regulations for 2007 and newer heavy-duty diesel engines require an order of magnitude reduction in particulate matter and oxides of nitrogen spurring the introduction of new aftertreatment systems. Since 2008, four emission measurement campaigns have been conducted at a Port of Los Angeles location and an inland weigh station in the South Coast Air Basin of California. Fuel specific oxides of nitrogen emissions at the Port have decreased 12% since 2010 while infrared opacity (a measure of particulate matter) remained low, showing no diesel particulate filter deterioration. The weigh station truck’s fuel specific oxides of nitrogen emission reductions since 2010 (18.5%) almost double the previous three year’s reductions and are the result of new trucks using selective catalytic reduction systems. Trucks at the weigh station equipped with these systems have a skewed oxides of nitrogen emissions distribution (half of the emissions were from 6% of the measurements) and had significantly lower emissions than similarly equipped Port trucks. Infrared thermographs of truck exhaust pipes revealed that the mean temperature observed at the weigh station (225 ± 4.5 °C) was 70 °C higher than for Port trucks, suggesting that the catalytic aftertreatment systems on trucks at our Port site were often below minimum operating temperatures.
Extraction of polyphenols from grape seeds by unconventional methods and extract concentration through polymeric membrane (2011)

International audience
Grand Challenges in Soft Matter Science: Prospects for Microgravity Research (2021)

At the suggestion of NASA’s Physical Science Research Program in the Space Life and Physical Science Research and Application Division, Paul Chaikin, Noel Clark, and Sidney Nagel organized a focus session and workshop for the 2020 American Physical Society (APS) March meeting under the auspices of the Division of Soft Matter. Three overarching themes emerged from the workshop and are presented with additional details:

•Machines made out of machines
•Scalable self-sustaining ecosystems
•Active materials and metamaterials

This report lays out only some of the potential directions for soft matter dynamics over the next two decades. It also lays out the role that gravity plays in the organization of the basic building blocks of matter. Not only will research on soft matter have tremendous application towards understanding its behavior in our terrestrial environment, but also potentially in other NASA programs such as planetary science, exploration, robotics, etc.
High-Q Nanocavities based on Two-Dimensional Photonic Crystals (2017)

A heterostructure-type nanocavity based on a two-dimensional photonic crystal slab made from a silicon-on-insulator wafer can realize an experimental Q factor exceeding 11 million. Fundamental properties and applications of such nanocavities are discussed.
Supplementary Figure 1 from Gene Expression Profiling in Uveal Melanoma Reveals Two Molecular Classes and Predicts Metastatic Death (2023)

Supplementary Figure 1 from Gene Expression Profiling in Uveal Melanoma Reveals Two Molecular Classes and Predicts Metastatic Death
Abstract 3489: TNK1 is a ubiquitin sensing kinase that can be targeted in vivo to block tumor growth (2023)

Abstract Thirty eight negative kinase 1 (TNK1) is an understudied non-receptor tyrosine kinase with no established function or mechanism of regulation. Our recent publication reported TNK1 as the primary kinase driver of cell survival in subsets of patient blood cancer samples. In an effort to understand TNK1 function and regulation, we discovered that it has an unusual C-terminal ubiquitin-association (UBA) domain that binds with high affinity to multiple poly-ubiquitin linkages. A 1.5 angstrom crystal structure of the TNK1 UBA shows an atypical five helix UBA domain with two ubiquitin-binding interfaces. Our data suggest that TNK1 relies on its UBA domain to localize to phase-separated ubiquitin-rich condensates and becomes fully active at these sites. To our knowledge, this feature of TNK1 (a bona-fide ubiquitin-association domain that promotes kinase activation) makes TNK1 unique across the human kinome. We also show that the phospho-binding protein 14-3-3 interacts with a MARK-mediated phosphorylation at S502 within the proline-rich domain of TNK1 to sequester TNK1 away from ubiquitin condensates and inhibit kinase activation. In this way, TNK1 toggles between poly-ubiquitin bound (active) and 14-3-3-bound (inactive) states. Our preliminary data suggest that the interaction with poly-ubiquitin at condensates tethers TNK1 to substrates involved in the lysosomal degradation of the condensates via aggrephagy. Furthermore, we found that patient mutations that truncate the 14-3-3 binding site and UBA domain convert TNK1 into a cancer driver with an altered substrate profile, skewed toward pro-growth substrates like STAT3. Finally, we show that mutant TNK1-driven tumors can be targeted in vivo with an anti-TNK1 small molecule. Together, our data provide a first mechanism of regulation and role for TNK1 as a ubiquitin sensor and implicate TNK1 as a candidate for targeted cancer therapy. 1. Chan TY*, Egbert CM*, Maxson JE, Siddiqui A, Larsen LJ, Kohler K, Balasooriya ER, Pennington KL, Tsang TM, Frey M, Soderblom EJ, Geng H, Müschen M, Forostyan TV, Free S, Mercenne G, Banks CJ, Valdoz J, Whatcott CJ, Foulks JM, Bearss DJ, O'Hare T, Huang DCS, Christensen KA, Moody J, Warner SL, Tyner JW, Andersen JL. (2021) TNK1 is a ubiquitin-binding and 14-3-3-regulated kinase that can be targeted to block tumor growth. Nature Communications, Sept 9;12(1):5337, PMID: 34504101, *co-first authors Citation Format: Tania Lopez-Palacios, Tsz-Yin Chan, Christina M. Egbert, Spencer Ashworth, Alec Vaughan, Tanya V. Forostyan, Adam Siddiqui, Jason M. Foulks, James Moody, Julia E. Maxson, Jeffrey W. Tyner, Steven L. Warner, Joshua Lyon Andersen. TNK1 is a ubiquitin sensing kinase that can be targeted in vivo to block tumor growth [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3489.
Functional Maturation of Induced Pluripotent Stem Cell Hepatocytes in Extracellular Matrix—A Comparative Analysis of Bioartificial Liver Microenvironments (2016)

Through the use of novel technology to develop three-dimensional (3D) scaffolds, the present study demonstrated that hepatocyte-like cells derived via induced pluripotent stem cell (iPSC) technology mature on 3D extracellular matrix scaffolds as a result of 3D matrix structure and scaffold biology. The result is an improved hepatic phenotype with increased synthetic and catalytic potency, an improvement on the blunted phenotype of iPSC-derived hepatocytes, a critical limitation of iPSC technology. These findings provide insight into the influence of 3D microenvironments on the viability, proliferation, and function of iPSC hepatocytes to yield a more mature population of cells for cell toxicity studies and disease modeling.
Isolation and Characterization of a Novel IgD-Binding Protein from Moraxella catarrhalis (2001)

A novel surface protein of the bacterial species Moraxella catarrhalis that displays a high affinity for IgD (MID) was solubilized in Empigen and isolated by ion exchange chromatography and gel filtration. The apparent molecular mass of monomeric MID was estimated to approximately 200 kDa by SDS-PAGE. The mid gene was cloned and expressed in Escherichia coli. The complete mid nucleotide gene sequence was determined, and the deduced amino acid sequence consists of 2123 residues. The sequence of MID has no similarity to other Ig-binding proteins and differs from all previously described outer membrane proteins of M. catarrhalis. MID was found to exhibit unique Ig-binding properties. Thus, in ELISA, dot blots, and Western blots, MID bound two purified IgD myeloma proteins, four IgD myeloma sera, and finally one IgD standard serum. No binding of MID was detected to IgG, IgM, IgA, or IgE myeloma proteins. MID also bound to the surface-expressed B cell receptor IgD, but not to other membrane molecules on human PBLs. This novel Ig-binding reagent promises to be of theoretical and practical interest in immunological research.
A Quantitative NMR Method for Silyllithium Analysis (2017)

A rapid and extremely simple method for silyl anion analysis is presented. The progress of silyllithium reagent preparation can be determined by quenching an aliquot with neat chloro(trimethyl)silane, evaporation, dilution with CDCl3, and direct proton NMR analysis. This procedure is fast, simple, and allows for identification and relative quantification of the starting reagent, intermediates, and the silyllithium product.
Broadband microwave fiber optic link with a compact transmitter (1994)

A microwave fiber optic link is developed for operation from 8 to 18 GHz. Modulation of a 1.3-μm wavelength optical carrier is accomplished using a lithium niobate Mach-Zehnder interferometer modulator that was designed for broadband operation up to 19 GHz. The link transmitter components, which consist of a high-power semiconductor laser, an optical isolator, and a modulator with polarization-preserving fiber pigtails, are spliced together to fit into a 10.16- x 5.08- x 2.54-cm3 (4- x 2- x 1-in.) box for applications where space is critical. The average link electrical gain is 45 dB, the frequency response is flat to within ±4 dB across the 10-GHz band, and the spur-free dynamic range of the link is 84 dB.
Unraveling the molecular mechanism underlying ALS-linked astrocyte toxicity for motor neurons (2013)

Mutations in superoxide dismutase-1 (SOD1) cause a familial form of amyotrophic lateral sclerosis (ALS), a fatal paralytic disorder. Transgenic mutant SOD1 rodents capture the hallmarks of this disease, which is characterized by a progressive loss of motor neurons. Studies in chimeric and conditional transgenic mutant SOD1 mice indicate that non-neuronal cells, such as astrocytes, play an important role in motor neuron degeneration. Consistent with this non-cell autonomous scenario are the demonstrations that wild-type primary and embryonic stem cell-derived motor neurons selectively degenerate when cultured in the presence of either mutant SOD1-expressing astrocytes or medium conditioned with such mutant astrocytes. The work in this thesis rests on the use of an unbiased genomic strategy that combines RNA-Seq and "reverse gene engineering" algorithms in an attempt to decipher the molecular underpinnings of motor neuron degeneration caused by mutant astrocytes. To allow such analyses, first, mutant SOD1-induced toxicity on purified embryonic stem cell-derived motor neurons was validated and characterized. This was followed by the validation of signaling pathways identified by bioinformatics in purified embryonic stem cell-derived motor neurons, using both pharmacological and genetic techniques, leading to the discovery that nuclear factor kappa B (NF-κB) is instrumental in the demise of motor neurons exposed to mutant astrocytes in vitro. These findings demonstrate the usefulness of this novel genomic approach to study neurodegeneration and to point to NF-κB as a potential valuable therapeutic target for ALS.
Density Functional Theory Investigation into the Stereocontrol of the Syndiospecific Polymerization of Propylene Catalyzed byCs-Symmetric Zirconocenes (2007)

The mechanisms of the two most likely routes for the generation of stereodefects in the syndiospecific polymerization of propylene, mediated by the Cs-symmetric ansa-zirconocenes Me2CCpFluZrR+X- (1), Me2CCp(3,6-di-Me-Flu)ZrR+X- (2a), Me2SiCp(3,6-di-Me-Flu)ZrR+X- (2b), and Me2CCp(3,6-di-tBu-Flu)ZrR+X- (3) (X- = MeB(C6F5)3-, FAl(Bipf)3-, MAOMe-) are explored using density functional theory. Site epimerization events (also known as back-skip or missed insertion) generate defective single m dyads, while enantiomeric misinsertions are the main source of double mm triads. The most important factor affecting the frequency of enantiomeric misinsertion is the structure of the ligand, while the counterion and solvation have little effect. Site epimerization is also influenced by the nature of the ligand system, but the bulk and the charge distribution of the anion are more prominent factors. The inclusion of solvent effects in the modeling of the site epimerization is critical for explaining reactivity and to achieving at least qualitatively correct results. Application of the two-parameter probabilistic scheme developed by Farina and co-workers allows for the prediction of pentad distributions from the computed selectivities. The good agreement found between experiment and computations for the basic unsubstituted system invented by Ewen and Razavi validates the proposed model. Thus, the computed pentad distributions may be used for assessing the effectiveness of modifications to the ligands on syndioselectivity. Increasing the bulk of 3,6-substituents on the fluorenyl ligand leads to increased syndiotacticity, without significantly affecting the reactivity. By introducing a stereogenic center on the alkyl chain, it is possible to assess the influence of chain end control on stereoselectivity. The main effect of chain end control is to increase the stereoselectivity after a stereoerror.
Energy-efficient standby mode algorithm in short-range one-to-one millimeter wave communications (2012)

This paper proposes two energy-efficient standby mode algorithms in short-range one-to-one 60 GHz millimeter wave (mmWave) communications. Among the many usage scenarios for mmWave radio, file downloading from kiosk terminals or peer-to-peer sync service with portable terminals are of great interest. For these portable terminals, the power consumption of standby mode as well as connection setup time is important. Comparing the power consumption for a frame transmission with that for a frame reception in short-range one-to-one 60 GHz mmWave, the power consumption for a frame reception may become larger than that for a frame transmission. In this paper, two energy-efficient standby mode algorithms are proposed for one-to-one communications. In the proposed algorithms, each terminal operates based on Interval consisting of several Sub-intervals. One proposed algorithm (Prop1) is that a terminal transmits a connection request frame (CREQ) once at every Sub-interval and the other terminal waits for the CREQ during one Sub-interval per each Interval. Thus, Prop1 saves the power consumption for a CREQ transmission. The other proposed algorithm (Prop2) is that a terminal selects one Sub-interval randomly for each Interval and transmits CREQs repeatedly during that Sub-interval. The other terminal waits for a CREQ during this CREQ transmission period at every Sub-interval. Prop2 saves the power consumption for a CREQ reception. We evaluate the power consumption of standby mode and connection setup time for Prop1 and Prop2 by both numerical analysis and computer simulations. We compare these proposed algorithms under several ratio of the power consumption for transmission and reception.
Large Volume Sample-Pretreatment Microdevice Based on Sol-Gel 3D Matrix (2010)

Sample-pretreatment is of great interest for micro-total-analysis-system due to the needs of relevant sample concentration and separation techniques for efficient detection. In this study, we demonstrated a novel 3-dimensional sol-gel matrix based microdevice that can process a large volume of the sample and capture target cells with magnetic nanoparticles (MNPs)-mediated colorimetric signal. The antibody-MNP-DNA-Photocleavable linker complexes were immobilized on the sol-gel and the capture was enhanced by 3D matrix and flutter pumping scheme. The concentrated cells were released after UV irradiation, and analyzed based on MNP-mediated colorimetric detection. This novel platform suggests a simple biosensor device with sample-in-answer-out capability.
Fabrication of Nanostructures by Hydroxylamine Seeding of Gold Nanoparticle Templates (2001)

Hydroxylamine-seeding of colloidal gold particles has been used to fabricate gold nanostructures on a SiO2 substrate. Gold nanoparticles (15 nm diameter) were randomly deposited on a SiO2 surface that had been modified with aminopropyltrimethoxysilane (APTS). The nanoparticles were then manipulated using a scanning force microscope (SFM) tip to produce 1-D templates for gold deposition. We demonstrate the utility of this approach by fabricating a gold nanowire by using 13 nanoparticles as a template. The junction between joined (coated) particles was examined by mechanical manipulation, and homogeneous deposition was shown to form stable structures. This approach was also used to fabricate nanostructures in a small gap between two gold electrodes. Particles were pushed into the gap, and then gold deposition was used to “connect” the particles and electrodes. Although the particular structure tested was not electrically connected to the electrode, we suggest that this approach will be useful in tackling the difficult problems associated with electrically connecting nano- to microscale structures.
Emergent oscillations in unidirectionally coupled overdamped bistable systems (2004)

It is well known that overdamped unforced dynamical systems do not oscillate. However, well-designed coupling schemes, together with the appropriate choice of initial conditions, can induce oscillations when a control parameter exceeds a threshold value. In a recent publication [Phys. Rev. E 68, 045102 (2003)]], we demonstrated this behavior in a specific prototype system, a soft-potential mean-field description of the dynamics in a hysteretic "single-domain" ferromagnetic sample. The previous analysis of this work showed that N (odd) unidirectionally coupled elements with cyclic boundary conditions would, in fact, oscillate when a control parameter-in this case the coupling strength-exceeded a critical value. These oscillations are now finding utility in the detection of very weak "target" signals, via their effect on the oscillation characteristics, e.g., the frequency and asymmetry of the oscillation wave forms. In this paper we explore the underlying dynamics of this system. Scaling laws that govern the oscillation frequency in the vicinity of the critical point, as well as the zero-crossing intervals in the presence of a symmetry-breaking target dc signal, are derived; these quantities are germane to signal detection and analysis.
Low-Temperature Performance of a Ferroelectric Glass Electrolyte Rechargeable Cell (2019)

An electrochemical cell that powers all-electric road vehicles will likely have an alkali-metal anode and the ability to operate down to −20 °C. The traditional all-solid-state batteries can only perform well at temperatures above room temperature. We have shown elsewhere that an alkali-metal negative electrode can be plated dendrite-free from a ferroelectric amorphous-oxide (glass) Li+ or Na+ electrolyte having a room-temperature Li+ or Na+ conductivity σi ≈ 2.5 × 10–2 S cm–1 which is similar to that of a liquid electrolyte. Here, it is demonstrated that the ionic conductivity of the electrolyte is σi ≈ 10–2 S cm–1 at −20 °C after optimization, and the dielectric constant is ε′r ≈ 6 × 105 at −35 °C. Moreover, it is shown that the remanent polarization of the ferroelectric-electrolyte (polarization at zero potential) adds to the capacity of the cell. The electrochemical cycling performances between −35 and 25 °C of the Li+-glass electrolyte in gold and lithium symmetric cells and in full cells are presented. Furthermore, it is shown that a coin-cell with the ferroelectric Li-glass electrolyte at −35 °C with output current of 56 μA cm–2 can light a red LED at 1.5 V. Finally, it is concluded that the Li+-glass electrolyte performs very well in symmetric cells and performs reasonably well down to −20 °C in asymmetric cells that also rely on the performance of the cathode and on the electrolyte/cathode interface.