gebhart/patrepeval huggingface dataset:
Rigidified A<sub>3</sub>Adenosine Receptor Agonists: 1-Deazaadenine Modification Maintains High in Vivo Efficacy (2015)

Substitution of rigidified A3 adenosine receptor (AR) agonists with a 2-((5-chlorothiophen-2-yl)ethynyl) or a 2-(4-(5-chlorothiophen-2-yl)-1H-1,2,3-triazol-1-yl) group provides prolonged protection in a model of chronic neuropathic pain. These agonists contain a bicyclo[3.1.0]hexane ((N)-methanocarba) ring system in place of ribose, which adopts a receptor-preferred conformation. N (6)-Small alkyl derivatives were newly optimized for A3AR affinity and the effects of a 1-deaza-adenine modification probed. 1-Deaza-N (6)-ethyl alkyne 20 (MRS7144, K i 1.7 nM) and 1-aza N (6)-propyl alkyne 12 (MRS7154, K i 1.1 nM) were highly efficacious in vivo. Thus, the presence of N1 is not required for nanomolar binding affinity or potent, long-lasting functional activity. Docking of 1-deaza compounds to a receptor homology model confirmed a similar binding mode as previously reported 1-aza derivatives. This is the first demonstration in nonribose adenosine analogues that the 1-deaza modification can maintain high A3AR affinity, selectivity, and efficacy.
Channel Waveguide of One-Dimensional Photonic Crystal (2006)

Channel waveguide of one-dimensional photonic crystal was fabricated and evaluated. Because of high order mode propagation on Brillouin zone boundary, light is strongly confined. Bending loss of right angle was 1.2dB.
Synchronous dynamic brain networks revealed by magnetoencephalography (2005)

We visualized synchronous dynamic brain networks by using prewhitened (stationary) magnetoencephalography signals. Data were acquired from 248 axial gradiometers while 10 subjects fixated on a spot of light for 45 s. After fitting an autoregressive integrative moving average model and taking the residuals, all pairwise, zero-lag, partial cross-correlations (PCC(ij)(0)) between the i and j sensors were calculated, providing estimates of the strength and sign (positive and negative) of direct synchronous coupling between neuronal populations at a 1-ms temporal resolution. Overall, 51.4% of PCC(ij)(0) were positive, and 48.6% were negative. Positive PCC(ij)(0) occurred more frequently at shorter intersensor distances and were 72% stronger than negative ones, on the average. On the basis of the estimated PCC(ij)(0), dynamic neural networks were constructed (one per subject) that showed distinct features, including several local interactions. These features were robust across subjects and could serve as a blueprint for evaluating dynamic brain function.
RF Sensor of a Novel NMR Apparatus (1993)

A novel NMR instrument to be used in holes drilled for geophysical exploration employs an unusual RF sensor which resembles one half of a coaxial cable that is split along its axis. The magnetic field and the efficiency of the sensor are computed by the method of moments.
FPGA implementation of Delta Sigma Modulation based all-digital RF transmitter for parallel magnetic resonance imaging (2015)

This paper presents an all-digital RF transmitter which enables frequency, phase, and amplitude modulation in a magnetic Resonance Imaging (MRI) system. Delta Sigma Modulation (DSM) is a very promising technique to generate digital modulated signals and gaining high interest for all-digital transmitter architectures in MRI. In an all-digital MRI transmitter, the switch mode RF power amplifiers amplifies the digital signal with high efficiency; and a narrowband RF coil filters the digital signal to recover the envelope information. So, high efficiency is maintained through the RF chain up to the RF coil. All-digital transmitter architecture seems a good candidate to a parallel MRI system. In this study, a novel delta sigma based digital modulator is proposed. Multi-band signal modulation with less than 1 Hz inter-carrier frequency resolution and digital single side band modulation with 50 dB side band suppression are achieved with the new modulator.
Photonic crystals with SiO2–Ag “post-cap” nanostructure coatings for surface enhanced Raman spectroscopy (2008)

We demonstrate that the resonant near fields of a large-area replica molded photonic crystal (PC) slab can efficiently couple light from a laser to SiO2–Ag “post-cap” nanostructures deposited on the PC surface by a glancing angle evaporation technique for achieving high surface enhanced Raman spectroscopy (SERS) enhancement factor. To examine the feasibility of the PC-SERS substrate, the simulated electric field around individual Ag particles and the measured Raman spectrum of trans-1,2-bis(4pyridyl)ethane on the PC-SERS substrate were compared with those from an ordinary glass substrate coated with the same SiO2–Ag nanostructures.
Impaired nigrostriatal function precedes behavioral deficits in a genetic mitochondrial model of Parkinson's disease (2011)

Parkinson's disease (PD) involves progressive loss of nigrostriatal dopamine (DA) neurons over an extended period of time. Mitochondrial damage may lead to PD, and neurotoxins affecting mitochondria are widely used to produce degeneration of the nigrostriatal circuitry. Deletion of the mitochondrial transcription factor A gene (Tfam) in C57BL6 mouse DA neurons leads to a slowly progressing parkinsonian phenotype in which motor impairment is first observed at ~12 wk of age. L-DOPA treatment improves motor dysfunction in these "MitoPark" mice, but this declines when DA neuron loss is more complete. To investigate early neurobiological events potentially contributing to PD, we compared the neurochemical and electrophysiological properties of the nigrostriatal circuit in behaviorally asymptomatic 6- to 8-wk-old MitoPark mice and age-matched control littermates. Release, but not uptake of DA, was impaired in MitoPark mouse striatal brain slices, and nigral DA neurons lacked characteristic pacemaker activity compared with control mice. Also, hyperpolarization-activated cyclic nucleotide-gated (HCN) ion channel function was reduced in MitoPark DA neurons, although HCN messenger RNA was unchanged. This study demonstrates altered nigrostriatal function that precedes behavioral parkinsonian symptoms in this genetic PD model. A full understanding of these presymptomatic cellular properties may lead to more effective early treatments of PD.
Expression of streptococcal M protein in mammalian cells. (1988)

The M protein encoded by group A streptococci is a cell-wall polypeptide that has the property of enabling these organisms to evade the phagocytic cells of the human host. Therefore, the M protein plays a major role in the pathogenesis of streptococcal diseases. As an initial step toward the use of this protein as a target antigen for the production of protective anti-streptococcal immunity, a live vaccinia virus recombinant containing the M-protein gene has been constructed (VV:M6 delta). The bacterial M-protein DNA sequence is stable within this genetic context and is actively transcribed by viral RNA polymerase. Furthermore, high levels of immunoreactive M protein were detected in vivo when the VV:M6 delta recombinant was used to infect mammalian cells in culture. Thus, in addition to providing a powerful approach for dissecting the immunodominant domains of the M protein, the VV:M6 delta recombinant appears to be an excellent candidate vaccine for animal trials.
Sticky Trap Design Considerations for Entrapping Bed Bugs (2019)

Little evidence has been presented on the usefulness of sticky traps for monitoring bed bugs, <i>Cimex lectularius</i>. We examined how the surface roughness around the adhesive of a sticky trap affects both bed bug behavior and adhesive entrapment. In the first assay, bed bugs were placed onto acetate paper discs with different roughness averages (R<sub>a</sub>). Each disc was surrounded by sticky trap adhesive and number of captured bed bugs were recorded. The second assay was set up similarly to the first assay except that the outer portion of the acetate disc had a different R<sub>a</sub> than the center. In the third assay, bed bugs were placed into circular acetate arenas where they were surrounded by different R<sub>a</sub> treatments. The number of times the bed bugs contacted the R<sub>a</sub> treatment but did not cross onto the treatment was recorded. Results of these assays showed that as the acetate surfaces got smoother (lower R<sub>a</sub>), bed bugs were more likely to get trapped in sticky trap adhesives but also less likely to travel across the smoother surfaces they encountered. A sticky trap design with a smooth plastic film around the adhesive was tested in the field to see if it could capture bed bugs in apartments with known bed bug activity. This trap was not only able to capture bed bugs but was also able to detect unknown German cockroach, <i>Blattela germanica,</i> infestations. Sticky trap designs with smooth surfaces around an adhesive could be used to monitor not only bed bugs but also German cockroaches.
Combining the converse humidity/resistance response behaviors of rGO films for flexible logic devices (2017)

We report the fabrication of a series of flexible logical devices based on the converse humidity/resistance response of rGO films.
Development and Application of New Computational Procedures for Modeling Miscible Gas Injection in Fractured Reservoirs (2007)

Abstract Detailed geological characterizations of naturally fractured reservoirs are commonly in the form of discrete fracture models, in which each fracture is defined explicitly. The efficient simulation of flow processes in such models poses a great challenge. In recent work, we developed systematic procedures for upscaling discrete fracture models to coarse-scale continuum descriptions referred to as multiple subregion (MSR) models. In this work, we extend these formulations to generate full dual-porosity, dual-permeability MSR models and additionally introduce the use of global single-phase flow information in the computation of the upscaled interblock transmissibilities required by the method. The resulting models are used for waterflood simulations and, more interestingly, for compositional simulations of first-contact-miscible gas injection. In a series of flow simulations involving both connected and disconnected fracture systems, it is shown that the MSR method provides results of reasonable accuracy, relative to the reference DFM solutions, for both oil-water and compositional oil-gas simulations with six pseudocomponents. Computational speedups of order 1000 are achieved for the compositional models.
Spatiotemporal Oxygen Sensing Using Dual Emissive Boron Dye–Polylactide Nanofibers (2014)

Oxygenation in tissue scaffolds continues to be a limiting factor in regenerative medicine despite efforts to induce neovascularization or to use oxygen-generating materials. Unfortunately, many established methods to measure oxygen concentration, such as using electrodes, require mechanical disturbance of the tissue structure. To address the need for scaffold-based oxygen concentration monitoring, a single-component, self-referenced oxygen sensor was made into nanofibers. Electrospinning process parameters were tuned to produce a biomaterial scaffold with specific morphological features. The ratio of an oxygen sensitive phosphorescence signal to an oxygen insensitive fluorescence signal was calculated at each image pixel to determine an oxygenation value. A single component boron dye-polymer conjugate was chosen for additional investigation due to improved resistance to degradation in aqueous media compared to a boron dye polymer blend. Standardization curves show that in fully supplemented media, the fibers are responsive to dissolved oxygen concentrations less than 15 ppm. Spatial (millimeters) and temporal (minutes) ratiometric gradients were observed in vitro radiating outward from the center of a dense adherent cell grouping on scaffolds. Sensor activation in ischemia and cell transplant models in vivo show oxygenation decreases on the scale of minutes. The nanofiber construct offers a robust approach to biomaterial scaffold oxygen sensing.
Compliant Modular Shape Memory Alloy Actuators (2010)

We have presented a simple but effective method to design flexible actuators. This process relies on understanding the behavior of a simple unit cell element built out of SMA sheet. The unit cell effectively uses the properties of flat SMA sheets: it operates in the bent region where more force is generated; it minimizes the nonbent SMA; and it heats up only the bent regions. However, the force generated by this unit cell does not scale up well, and an array of them is needed to increase the force generated. Building an actuator out of an array of unit cells increases its complexity but provides advantages, including the control of expansion length, trajectory, and generated force. Given the current technologies, including 3-D printing and laser cutting, a variety of support structures can be built to create an actuator with a given behavior. We have shown three types of configurations: linear, rotational, and surface. The linear actuator has been tested for endurance and can easily perform over 10,000 repetitions under load without breaking. These actuators have been tested in actual systems, such as the battery-operated HexRoller robot that uses six actuators connected in a chain. The robot demonstrates that this SMA actuator is power efficient compared with other SMA designs that cannot operate with batteries. We have also showed that a rotational version of this type of actuator is comparable with an electromagnetic motor.
"LINC-ing" the family (2006)

Families must continually organize, plan, and stay aware of the activities of their households in order to coordinate everyday life. Despite having organization schemes, many people still feel overwhelmed when it comes to family coordination. To help overcome this, we present our research efforts on LINC: an inkable family calendar designed for the kitchen. LINC was developed using a participatory design process involving interviews, paper prototyping, and a formative evaluation. Our work outlines key implications for digital family calendars and family coordination systems in general. We found that coordination is not typically done through the family calendar; rather, the family calendar is a tool that provides family members with an awareness of activities and changes that in turn enables coordination. Thus, digital family calendars should provide tools that enable families to use their own coordination routines which leverage the social affordances prominent in existing paper calendars.
Silk fibroin micro-particle scaffolds with superior compression modulus and slow bioresorption for effective bone regeneration (2018)

Silk fibroin (SF), a natural polymer produced by Bombyx mori silkworms, has been extensively explored to prepare porous scaffolds for tissue engineering applications. Here, we demonstrate, a scaffold made of SF, which exhibits compression modulus comparable to natural cancellous bone while retaining the appropriate porosities and interconnected pore architecture. The scaffolds also exhibit high resistance to in-vitro proteolytic degradation due to the dominant beta sheet conformation of the SF protein. Additionally, the scaffolds are prepared using a simple method of microparticle aggregation. We also demonstrate, for the first time, a method to prepare SF micro-particles using a Hexafluoroisopropanol-Methanol solvent-coagulant combination. SF microparticles obtained using this method are monodisperse, spherical, non-porous and extremely crystalline. These micro-particles have been further aggregated together to form a 3D scaffold. The aggregation is achieved by random packing of these microparticles and fusing them together using a dilute SF solution. Preliminary in-vitro cell culture and in-vivo implantation studies demonstrate that the scaffolds are biocompatible and they exhibit the appropriate early markers, making them promising candidates for bone regeneration.
Chopping of near- and mid-infrared radiation using a curled electrostatic MEMS actuator (2003)

An electrostatic MEMS actuator known as the “Artificial Eyelid” can be used as a micromechanical chopper for IR detectors. The actuator structure consists of a curled polymer/metal film stack which is microfabricated and released from an IR transparent substrate. The film stack is uncurled by applying an electric field between the curled film and the transparent fixed electrode on the substrate. These flexible film actuators can act as IR choppers, providing transmission of radiation to the sensor elements when open (curled) and reflection when closed (uncurled). Arrays of actuators were fabricated on ITO-coated glass substrates and ranged in size from 4 x 4 mm to 7.5 x 15 mm with individual elements ranging from 250 to 500 μm on a side. Actuation for devices with average radius of curvature of 120 μ was consistently achieved at 150-170 V operation with 98-100% of the elements functioning and long lifetimes. IR chopper characteristics were measured using a blackbody source and pyroelectric detector by applying sine and square wave voltage to the actuators at a frequency of 30 Hz. The capability of the artificial eyelid for chopping near- and mid-IR radiation, including future fabrication of devices using NiCo<sub>2</sub>O<sub>4</sub> or NiRh<sub>2</sub>O<sub>4</sub> films for IR transparent electrodes, will be discussed.
Intelligibility Prediction of Single-Channel Noise-Reduced Speech (2010)

In general, single-channel noise-reduction algorithms do not im-prove the speech intelligibility for normal-hearing listeners. A reliable objective intelligibility measure is therefore of great in-terest. It could be used for analysis and/or optimization of noise-reduction algorithms. For these applications it is important that the objective measure can correctly predict the difference in in-telligibility before and after noise reduction. Typically, exist-ing studies do not evaluate objective measures for this property. Twelve objective measures are evaluated in order to let them pre-dict the intelligibility before and after noise reduction. Best per-formance was obtained with a recently developed intelligibility predictor called STOI. Modest results were obtained with WSS and NSEC. The remaining measures significantly overestimated the intelligibility of the noise-reduced speech. 1
Near-infrared luminescent metallacrowns for combined in vitro cell fixation and counter staining (2017)

Cell fixation is an essential approach for preserving cell morphology, allowing the targeting and labelling of biomolecules with fluorescent probes. One of the key requirements for more efficient fluorescent labelling is the preservation of cell morphology, which usually requires a combination of several fixation techniques. In addition, the use of a counter stain is often essential to improve the contrast of the fluorescent probes. Current agents possess significant limitations, such as low resistance toward photobleaching and sensitivity to changes in the microenvironment. Luminescent Ln<sup>3+</sup> 'encapsulated sandwich' metallacrowns (MCs) overcome these drawbacks and offer complementary advantages. In particular, they emit sharp emission bands, possess a large difference between excitation and emission wavelengths and do not photobleach. Herein, MCs formed with pyrazinehydroxamic acid (Ln<sup>3+</sup>[Zn(ii)MC<sub>pyzHA</sub>], Ln<sup>3+</sup> = Yb, Nd) were used, combined with near-infrared (NIR) counter staining and fixation agents for HeLa cells upon an initial five minute exposure to UV-A light. The validity and quality of the cell fixation were assessed with Raman spectroscopy. Analysis of the NIR luminescence properties of these MCs was performed under different experimental conditions, including in a suspension of stained cells. Moreover, the high emission intensity of Ln<sup>3+</sup>[Zn(ii)MC<sub>pyzHA</sub>] in the NIR region allows these MCs to be used for imaging with standard CCD cameras installed on routine fluorescence microscopes. Finally, the NIR-emitting Ln<sup>3+</sup>[Zn(ii)MC<sub>pyzHA</sub>] compounds combine, within a single molecule, features such as cell fixation and staining abilities, good photostability and minimal sensitivity of the emission bands to the local microenvironment, and they are highly promising for establishing the next generation of imaging agents with a single biodistribution.
Generalized five‐dimensional dynamic and spectral factor analysis (2006)

We have generalized the spectral factor analysis and the factor analysis of dynamic sequences (FADS) in SPECT imaging to a five-dimensional general factor analysis model (5D-GFA), where the five dimensions are the three spatial dimensions, photon energy, and time. The generalized model yields a significant advantage in terms of the ratio of the number of equations to that of unknowns in the factor analysis problem in dynamic SPECT studies. We solved the 5D model using a least-squares approach. In addition to the traditional non-negativity constraints, we constrained the solution using a priori knowledge of both time and energy, assuming that primary factors (spectra) are Gaussian-shaped with full-width at half-maximum equal to gamma camera energy resolution. 5D-GFA was validated in a simultaneous pre-/post-synaptic dual isotope dynamic phantom study where 99mTc and 123I activities were used to model early Parkinson disease studies. 5D-GFA was also applied to simultaneous perfusion/dopamine transporter (DAT) dynamic SPECT in rhesus monkeys. In the striatal phantom, 5D-GFA yielded significantly more accurate and precise estimates of both primary 99mTc (bias=6.4 % +/- 4.3 %) and 1231 (-1.7% +/- 6.9%) time activity curves (TAC) compared to conventional FADS (biases = 15.5% +/- 10.6% in 99mTc and 8.3% +/- 12.7% in 123I, p < 0.05). Our technique was also validated in two primate dynamic dual isotope perfusion/DAT transporter studies. Biases of 99mTc-HMPAO and 123I-DAT activity estimates with respect to estimates obtained in the presence of only one radionuclide (sequential imaging) were significantly lower with 5D-GFA (9.4% +/- 4.3% for 99mTc-HMPAO and 8.7% +/-4.1% for 123I-DAT) compared to biases greater than 15% for volumes of interest (VOI) over the reconstructed volumes (p < 0.05). 5D-GFA is a novel and promising approach in dynamic SPECT imaging that can also be used in other modalities. It allows accurate and precise dynamic analysis while compensating for Compton scatter and cross-talk.
Large Dimeric Ligands with Favorable Pharmacokinetic Properties and Peroxisome Proliferator-Activated Receptor Agonist Activity in Vitro and in Vivo (2003)

Two potent nonselective, but PPARalpha-preferring, PPAR agonists 5 and 6 were designed and synthesized in high yields. The concept of dimeric ligands in transcription factors was investigated by synthesizing and testing the corresponding dimers 7, 8a, and 8b in PPAR transactivation assays. The three dimeric ligands all showed agonist activity on all three PPAR receptor subtypes, but with different profiles compared to the monomers 5 and 6. Despite breaking all the "rule of five" criteria, the dimers had excellent oral bioavailability and pharmacokinetic properties, resulting in good in vivo efficacy in db/db mice. X-ray crystal structure and modeling experiments suggested that the dimers interacted with the AF-2 helix as well as with amino acid residues in the lipophilic pocket close to the receptor surface.