gebhart/patrepeval huggingface dataset:
RGS proteins reconstitute the rapid gating kinetics of Gβγ-activated inwardly rectifying K<sup>+</sup> channels (1997)

G protein-gated inward rectifier K + (GIRK) channels mediate hyperpolarizing postsynaptic potentials in the nervous system and in the heart during activation of Gα(i/o)-coupled receptors. In neurons and cardiac atrial cells the time course for receptor-mediated GIRK current deactivation is 20–40 times faster than that observed in heterologous systems expressing cloned receptors and GIRK channels, suggesting that an additional component(s) is required to confer the rapid kinetic properties of the native transduction pathway. We report here that heterologous expression of “regulators of G protein signaling” (RGS proteins), along with cloned G protein-coupled receptors and GIRK channels, reconstitutes the temporal properties of the native receptor → GIRK signal transduction pathway. GIRK current waveforms evoked by agonist activation of muscarinic m 2 receptors or serotonin 1A receptors were dramatically accelerated by coexpression of either RGS1, RGS3, or RGS4, but not RGS2. For the brain-expressed RGS4 isoform, neither the current amplitude nor the steady-state agonist dose-response relationship was significantly affected by RGS expression, although the agonist-independent “basal” GIRK current was suppressed by ≈40%. Because GIRK activation and deactivation kinetics are the limiting rates for the onset and termination of “slow” postsynaptic inhibitory currents in neurons and atrial cells, RGS proteins may play crucial roles in the timing of information transfer within the brain and to peripheral tissues.
Development of a biomimetic collagen‐hydroxyapatite scaffold for bone tissue engineering using a SBF immersion technique (2009)

The objective of this study was to develop a biomimetic, highly porous collagen-hydroxyapatite (HA) composite scaffold for bone tissue engineering (TE), combining the biological performance and the high porosity of a collagen scaffold with the high mechanical stiffness of a HA scaffold. Pure collagen scaffolds were produced using a lyophilization process and immersed in simulated body fluid (SBF) to provide a biomimetic coating. Pure collagen scaffolds served as a control. The mechanical, material, and structural properties of the scaffolds were analyzed and the biological performance of the scaffolds was evaluated by monitoring the cellular metabolic activity and cell number at 1, 2, and 7 days post seeding. The SBF-treated scaffolds exhibited a significantly increased stiffness compared to the pure collagen group (4-fold increase), while a highly interconnected structure (95%) was retained. FTIR indicated that the SBF coating exhibited similar characteristics to pure HA. Micro-CT showed a homogeneous distribution of HA. Scanning electron microscopy also indicated a mineralization of the collagen combined with a precipitation of HA onto the collagen. The excellent biological performance of the collagen scaffolds was maintained in the collagen-HA scaffolds as demonstrated from cellular metabolic activity and total cell number. This investigation has successfully developed a biomimetic collagen-HA composite scaffold. An increase in the mechanical properties combined with an excellent biological performance in vitro was observed, indicating the high potential of the scaffold for bone TE.
Label-free Bio-aerosol Sensing Using On-Chip Holographic Microscopy and Deep Learning (2019)

We present automated and label-free bio-aerosol sensing using a portable and cost-effective device, enabled by on-chip digital holographic microscopy and deep-learning.
Detecting Targeted Attacks By Multilayer Deception (2013)

Over the past few years, enterprises are facing a growing number of highly customized and targeted attacks that use sophisticated techniques and seek after important company assets, such as customer data and intellectual property. Unlike conventional attacks, targeted attacks are operated by experts who use multiple steps to gain access to sensitive assets, and most of time, leave very few network traces behind for detection. In this paper, we propose a multi-layer deception system that provides an in depth defense against such sophisticated targeted attacks. Specifically, based on previous knowledge and patterns of such attacks, we model the attacker as trying to compromising an enterprise network via multiple stages of penetration and propose defenses at each of these layers using deception based detection. Due to multiple layers of deception, the probability of detecting such an attack will be greatly enhanced. We present a proof of concept implementation of one of the key deception methods proposed. Due to various financial constraints of an enterprise, we also model the design of the deception system as an optimization problem in order to minimize the total expected loss due to system deployment and asset compromise.We find that there is an optimal solution to deploy deception entities,and even over spending budget on more entities will only increase the total expected loss to the enterprise. Such a system can be coupled with existing detection techniques to protect enterprises from sophisticated attacks.
MR temperature mapping of focused ultrasound surgery (1994)

Deep lying soft tissue tumors may be treated by a nonincisional surgical procedure executed inside an MR imaging system using a thermal effect delivered by a focused ultrasound transducer. A prototype system is constructed to assess MRI thermal monitoring and the localization of the heat zone in muscle. The temperature distribution of the focal spot is imaged with MRI while mechanically moving the transducer with an hydraulic 3-axis positioner. Acoustic power is applied with a spherical shell transducer using 1- to 10-s duration pulses at frequencies of 1.5 MHz to selectively coagulate tissue at 60-70 degrees C. The procedure is monitored with a series of fast second gradient echo, T1-weighted, temperature sensitive MR sequences. Acquisitions are optimized for high temperature sensitive images that yield the thermal diffusivity, heat flow time constant and the focal spot size in muscle. MR temperature maps of muscle provide localization and dosimetry both in the focal region and near field.
A high density overlapping gate charge coupled device array (1973)

In this talk a technique for constructing a high density overlapping gate charge coupled device array is described and experimental verification of the concept is presented. The technique involves forming an asymmetrical well within each gate region. A bit density advantage of nearly four to one compared with a standard poly-silicon overlapping gate structure is achieved; this comparison is based upon serpentine arrays using identical mask design rules in each case. A density greater than <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">6\times10^{6}</tex> bits/inch <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> results using a minimum geometry length of five microns. The array structure will be described and array characteristics will be given and compared to standard overlapping gate arrays.
Capillarity-based switchable adhesion (2010)

Drawing inspiration from the adhesion abilities of a leaf beetle found in nature, we have engineered a switchable adhesion device. The device combines two concepts: The surface tension force from a large number of small liquid bridges can be significant (capillarity-based adhesion) and these contacts can be quickly made or broken with electronic control (switchable). The device grabs or releases a substrate in a fraction of a second via a low-voltage pulse that drives electroosmotic flow. Energy consumption is minimal because both the grabbed and released states are stable equilibria that persist with no energy added to the system. Notably, the device maintains the integrity of an array of hundreds to thousands of distinct interfaces during active reconfiguration from droplets to bridges and back, despite the natural tendency of the liquid toward coalescence. We demonstrate the scaling of adhesion strength with the inverse of liquid contact size. This suggests that strengths approaching those of permanent bonding adhesives are possible as feature size is scaled down. In addition, controllability is fast and efficient because the attachment time and required voltage also scale down favorably. The device features compact size, no solid moving parts, and is made of common materials.
Welding of 3D-printed carbon nanotube–polymer composites by locally induced microwave heating (2017)

Additive manufacturing through material extrusion, often termed three-dimensional (3D) printing, is a burgeoning method for manufacturing thermoplastic components. However, a key obstacle facing 3D-printed plastic parts in engineering applications is the weak weld between successive filament traces, which often leads to delamination and mechanical failure. This is the chief obstacle to the use of thermoplastic additive manufacturing. We report a novel concept for welding 3D-printed thermoplastic interfaces using intense localized heating of carbon nanotubes (CNTs) by microwave irradiation. The microwave heating of the CNT-polymer composites is a function of CNT percolation, as shown through in situ infrared imaging and simulation. We apply CNT-loaded coatings to a 3D printer filament; after printing, microwave irradiation is shown to improve the weld fracture strength by 275%. These remarkable results open up entirely new design spaces for additive manufacturing and also yield new insight into the coupling between dielectric properties and radio frequency field response for nanomaterial networks.
Effect of glucose supplements on the fermentation of xylose by <i>Pachysolen tannophilus</i> (1985)

Hemicellulosic sugars, predominantly D-xylose, comprise about one-half the total carbohydrate that can be obtained from hardwoods and agricultural residues through dilute acid hydrolysis. Because rates and yields in the xylose fermentation are low, economic utilization of these materials as fermentation feedstocks is difficult. Pachysolen tannophilus formed 5.5% ethanol from 12% glucose but only 2% ethanol from 12% xylcose. Aeration doubled the specific rate of D-glucose fermentation by P. tannophilus, as compared to anaerobic fermentation, but the specific rate of the xylose fermentation remained unchanged. Periodic additions of 0.5% D-glucose to aerobic fermentations of 3% xylose increased the yield of ethanol from 0.28 g/g xylose to greater than 0.41 g/g xylose utilized. The rate of xylose utilization remained unchanged, and radiotracer studies showed that addition of 0.5% glucose did not inhibit xylose utilization under aerobic or anaerobic conditions. No enhancement was observed anaerobically, nor was enhancement observed with acid hydrolysates, apparently because of the presence of acetic acid which inhibited growth and fermentation.
An <i>R</i>‐Selective Hydroxynitrile Lyase from <i>Arabidopsis thaliana</i> with an α/β‐Hydrolase Fold (2007)

Folding and selectivity: The noncyanogenic plant Arabidopsis thaliana contains a new hydroxynitrile lyase, which was cloned and characterized. This enzyme is readily available form a recombinant source, has a broad range of substrates, and enantioselectively transforms aliphatic and aromatic aldehydes as well as ketones into the corresponding R-cyanohydrins.
Abstract 19546: Retinoblastoma Regulates Cardiac and Mesenchymal Stem Cell Niches during Adult Heart Regeneration (2012)

Introduction: Cardiac (CSCs) and mesenchymal stem cells (MSCs) stimulate cardiac repair, both primarily and secondarily by stimulating endogenous cardiac regeneration; however, the mechanisms underlying successful cardiac repair remain elusive and controversial. We addressed this issue in a porcine model of cell therapy by quantifying levels of Ser-608 hyperphosphorylated retinoblastoma (Rbser608+), which marks actively regenerating cardiomyocytes (CM) in adult newt hearts, and Ink4aARF (alternate reading frame of Ink4a), which inhibits cell cycle. Hypothesis: Interactions between CSCs and MSCs regulate Rbser608 and Ink4aARF expression in endogenous progenitors and CM to enhance cardiac regeneration. Methods: Twenty adult swine underwent myocardial infarction (MI), followed 2 weeks later by intramyocardial injection of 200M human (h)MSCs (n=5), 1M hCSCs (n=5), 200M hMSC plus 1M hCSC (MCC, n=5) or placebo (n=5). Tissue from immunosuppressed animals were analyzed 4 weeks later for exogenous cell engraftment (human Alu). Ink4aARF and Rbser608 were assessed in GATA4+ progenitors and mitotic CMs (phosphoH3+). Results: In situ hybridization demonstrated Alu+ cells in all groups. Engraftment was ∼7-fold greater in the MCC group compared to hCSCs or hMSCs (7.8±4.6, 0.2±0.2, 1.4±0.7 Alu+/cm3 respectively, p=0.0003) and infarct size was reduced 2-fold in MCC vs either cell type alone. Interestingly, Rbser608+ was expressed both in porcine GATA4+ progenitors as well as mature CM. There were 3 times as many Rbser608+/GATA4+ progenitors (150M/cm3) in the MCC hearts compared to the other 3 groups (p<0.0001). In addition ∼20% of the CM were Rbser608+/Ink4a(-), suggesting that the MCC hearts contained CM capable of completing the cell-cycle (p<0.0001). There was also a 46-fold increase in mitotic CMs in MCC hearts vs. either cell alone (P<0.0001). Importantly, MCC recipients contained a subpopulation of Ink4aARF(−)/phosphoH3+ CM, supporting the existence of transient amplifying CM with the capacity to undergo multiple cell divisions. Conclusions: Together these findings demonstrate a novel mechanism of heart regeneration, where hMSC and hCSC interactions propagate Rbser608 in CM and CSCs to regulate cell-cycle and stem cell fate decisions.
AC Modulated Magneto-Optic Sensor for Remote Investigation of Surface Deformation (2005)

A new magneto‐optic technique based on the domain wall motion in a transparent magneto‐optic (MO) thin film has been developed for nondestructive evaluation of surface deformation created by subsurface or internal defects in non‐magnetic and non‐conducting materials. Investigation of defects in non‐conducting and non‐magnetic materials cannot be performed using conventional electromagnetic techniques such as eddy current or magnetic flux leakage. The new method utilizes the displacement of a single domain wall in the MO thin film created using a field gradient from by two permanent magnets and under an ac sinusoidal external magnetic field applied perpendicular to the surface of the MO film. The new technique can measure mechanical deformation of a surface of any type of material from the changing reflected intensity of a polarized light beam.
Experimental Evaluation of a Two-Stage Pulse Detonation Combustor (2005)

A two -stage pulsed detonation device was assembled and examined in an experimental program. The device consisted of a precombustor, used to mix and burn a fuel-rich mixture, and a resonator designed to sustain high-frequency repeating detonations. The device was evaluated over a range of operating conditions and with a variety of fuels including natural gas, ethylene and liquid Jet-A. It was found that the addition of an initiator, consisting of a small tube PDE firing directly into the resonator, was necessary to produce high-speed wave combustion processes in the device. The addition of the initiator enabled the device to produce supersonic combustion waves at the resonator exit, however, the resulting wave speeds were not as high as calculated detonation speeds for the mixtures.
[IC‐P‐192]: PRECLINICAL CHARACTERIZATION OF PI‐2620, A NOVEL TAU PET TRACER FOR DETECTION OF TAU IN AD AND OTHER TAUOPATHIES (2017)

Tau aggregates represent a critical pathology in Alzheimer's disease (AD) and other forms of dementia. The spreading of Tau neurofibrillary tangles across defined brain regions corresponds to the observed level of cognitive decline in AD. Positron emission tomography has proved to be an important tool for the detection of amyloid-beta aggregates in the brain and is currently explored for detection of Tau in AD and other tauopathies. Several tracers targeting Tau have been discovered and tested in humans so far. However, limitations have been reported especially regarding their selectivity and off-target binding e.g. binding to MAO A and B. Here we present data on the new tracer PI-2620 with improved characteristics specifically targeting Tau in AD and non-AD tauopathies. PI-2620 was tested for affinity to aggregated Tau using human brain homogenates, isolated PHFs as well as recombinant fibrils. Off-target binding was evaluated in competition assays using radiolabeled MAO A / B and beta-amyloid binders. Binding to AD and non-AD brain tissue was performed using autoradiography (ARG) on human brain sections. The specific binding was compared to the corresponding signals on brain tissues of non-demented control subjects. The pharmacokinetic profiles of 18F-PI-2620 were evaluated in mice and non-human primates. PI-2620 displayed a high affinity for Tau in AD brain homogenate competition-assays (IC50: 1.8 nM). In addition to its high affinity binding to Tau, the compound showed excellent selectivity with no detectable off-target binding to beta-amyloid or MAO A/B. Specific binding to Tau deposits was demonstrated by ARG on AD brain sections (Braak I-VI), Pick's and PSP pathology indicating detection of both 3R and 4R Tau deposits. No specific tracer binding was detected on brain slices from non-demented donors. Good brain uptake and fast wash-out was observed in healthy mice and non-human primates. PI-2620 demonstrated improved characteristics in preclinical models with high affinity, good selectivity and excellent preclinical PK properties. The compound is currently being evaluated in clinical studies.
Charged-particle emission tomography (2017)

We proposed a new volumetric imaging technique for charged-particle-emitting radionuclides, which we have called charged-particle emission tomography (CPET). We also proposed a new class of charged-particle detectors, which we have called particle-processing detectors (PPDs). When a PPD is used to measure the direction and/or energy attributes along with the position attributes, CPET is feasible.
HapSeat (2012)

We introduce a novel way of simulating sensations of motion which does not require an expensive and cumbersome motion platform. Multiple force-feedbacks are applied to the seated user's body to generate a sensation of motion experiencing passive navigation. A set of force-feedback devices such as mobile armrests or headrests are arranged around a seat so that they can apply forces to the user. We have dubbed this new approach HapSeat. A proof of concept has been designed which uses three low-cost force-feedback devices, and two control models have been implemented. Results from the first user study suggest that subjective sensations of motion are reliably generated using either model. Our results pave the way to a novel device to generate consumer motion effects based on our prototype.
Characterization of Immunodominant and Potentially Protective Epitopes of<i>Mannheimia haemolytica</i>Serotype 1 Outer Membrane Lipoprotein PlpE (2004)

Mannheimia haemolytica serotype 1 (S1) is the most common bacterial isolate found in shipping fever pneumonia in beef cattle. Currently used vaccines against M. haemolytica do not provide complete protection against the disease. Research with M. haemolytica outer membrane proteins (OMPs) has shown that antibodies to one particular OMP from S1, PlpE, may be important in immunity. In a recently published work, members of our laboratory showed that recombinant PlpE (rPlpE) is highly immunogenic when injected subcutaneously into cattle and that the acquired immunity markedly enhanced resistance to experimental challenge (A. W. Confer, S. Ayalew, R. J. Panciera, M. Montelongo, L. C. Whitworth, and J. D. Hammer, Vaccine 21:2821-2829, 2003). The objective of this work was to identify epitopes of PlpE that are responsible for inducing the immune response. Western blot analysis of a series of rPlpE with nested deletions on both termini with bovine anti-PlpE hyperimmune sera showed that the immunodominant region is located close to the N terminus of PlpE. Fine epitope mapping, in which an array of overlapping 13-mer synthetic peptides attached to a derivatized cellulose membrane was probed with various affinity-purified anti-PlpE antibodies, identified eight highly reactive regions, of which region 2 (R2) was identified as the specific epitope. The R2 region is comprised of eight imperfect repeats of a hexapeptide (QAQNAP) and is located between residues 26 and 76. Complement-mediated bactericidal activity of affinity-purified anti-PlpE bovine antibodies confirmed that antibodies directed against the R2 region are effective in killing M. haemolytica.
Natural products with antifungal activity fromPseudomonas biocontrol bacteria (2000)

It is now well established that some bacteria and fungi are aggressive colonizers of soil and the roots of plants, and are able to protect plants from infection by soil-borne fungal pathogens. In most cases that have been well studied, the biological mechanisms underlying this phenomenon, known as biocontrol, include the production of antifungal compounds, involving both metabolites and enzymes. Bacteria of the genus Pseudomonas comprise a large group of the active biocontrol strains as a result of their general ability to produce a diverse array of potent antifungal metabolites. These include simple metabolites such as 2,4-diacetylphloroglucinol, phenazine-1-carboxylic acid and pyrrolnitrin [3-chloro-4-(2′- nitro-3′-chlorophenyl)-pyrrole], as well as the complex macrocyclic lactone, 2,3-de-epoxy-2,3-didehydro-rhizoxin. Study of the biochemistry and mechanism of formation of these metabolites has proved useful in several ways. Pyrrolnitrin is active against Rhizoctonia spp, Fusarium spp, and other plant pathogenic fungi, and it has been used as a lead structure in the development of a new phenylpyrrole agricultural fungicide. In addition, pyrrolnitrin has been used for years as a model for the study of the mechanisms involved in the chlorination of organic molecules. We have cloned a four-gene cluster from a P fluorescens biocontrol strain that encodes the enzymes required for the production of pyrrolnitrin. Using these genes and strains mutated in the individual genes, we have elucidated the biochemical pathway by which pyrrolnitrin is synthesized. Studies of the genes involved in pyrrolnitrin biosynthesis have demonstrated that a new class of halogenase enzyme is involved in the chlorination reactions in pyrrolnitrin biosynthesis. The P fluorescens mutants that do not produce pyrrolnitrin have been used to demonstrate clearly the important role of pyrrolnitrin in the overall biocontrol activity shown by the strain. In addition, we have modified the pyrrolnitrin genes within the P fluorescens strain, which has resulted in significant increases in the production of this metabolite. The strains which overproduce pyrrolnitrin are also significantly more active than the wild-type strain in biocontrol. These studies suggest that the biocontrol activity of bacteria can be dramatically increased to rival the activity of commercial chemical fungicides through directed genetic modification. Bacteria remain important sources of natural products with diverse activities. In order to capture the full potential of these compounds, it will be necessary in the future to take a multi-disciplinary approach to their study and development. © 2000 Society of Chemical Industry