gebhart/patrepeval huggingface dataset:
An ice‐templated, linearly aligned chitosan‐alginate scaffold for neural tissue engineering (2013)

Several strategies have been investigated to enhance axonal regeneration after spinal cord injury, however, the resulting growth can be random and disorganized. Bioengineered scaffolds provide a physical substrate for guidance of regenerating axons towards their targets, and can be produced by freeze casting. This technique involves the controlled directional solidification of an aqueous solution or suspension, resulting in a linearly aligned porous structure caused by ice templating. In this study, freeze casting was used to fabricate porous chitosan-alginate (C/A) scaffolds with longitudinally oriented channels. Chick dorsal root ganglia explants adhered to and extended neurites through the scaffold in parallel alignment with the channel direction. Surface adsorption of a polycation and laminin promoted significantly longer neurite growth than the uncoated scaffold (poly-L-ornithine + Laminin = 793.2 ± 187.2 μm; poly-L-lysine + Laminin = 768.7 ± 241.2 μm; uncoated scaffold = 22.52 ± 50.14 μm) (P < 0.001). The elastic modulus of the hydrated scaffold was determined to be 5.08 ± 0.61 kPa, comparable to reported spinal cord values. The present data suggested that this C/A scaffold is a promising candidate for use as a nerve guidance scaffold, because of its ability to support neuronal attachment and the linearly aligned growth of DRG neurites.
Metabolomics: A Global Biochemical Approach to Drug Response and Disease (2008)

Metabolomics is the study of metabolism at the global level. This rapidly developing new discipline has important potential implications for pharmacologic science. The concept that metabolic state is representative of the overall physiologic status of the organism lies at the heart of metabolomics. Metabolomic studies capture global biochemical events by assaying thousands of small molecules in cells, tissues, organs, or biological fluids-followed by the application of informatic techniques to define metabolomic signatures. Metabolomic studies can lead to enhanced understanding of disease mechanisms and to new diagnostic markers as well as enhanced understanding of mechanisms for drug or xenobiotic effect and increased ability to predict individual variation in drug response phenotypes (pharmacometabolomics). This review outlines the conceptual basis for metabolomics as well as analytical and informatic techniques used to study the metabolome and to define metabolomic signatures. It also highlights potential metabolomic applications to pharmacology and clinical pharmacology.
Perpendicular patterned media in an (Al0.9Ga0.1)2O3/GaAs substrate for magnetic storage (1999)

By using electron beam lithography, chemically assisted ion beam etching, and electroplating, we have fabricated high aspect ratio magnetic columns, 60–170 nm in diameter, embedded in an aluminum–gallium–oxide/gallium–arsenide [(Al0.9Ga0.1)2O3/GaAs] substrate. In our previous work, we demonstrated storage of data in individual columns spaced 2 μm apart. Here the electroplated Ni columns are in the form of tracks (0.5 and 0.25 μm in the down-track direction, and 1 μm in the cross-track direction), corresponding to areal densities of 1.3 and 2.6 Gbits/in.2, respectively. In this report we describe in more detail the issues in the fabrication of patterned media samples, such as dry etching and oxidation of AlGaAs, and electrodeposition of Ni into GaAs substrate. Initial characterization of the resulting magnets using magnetic force microscopy are also presented.
AccelWord (2015)

Voice control has emerged as a popular method for interacting with smart-devices such as smartphones, smartwatches etc. Popular voice control applications like Siri and Google Now are already used by a large number of smartphone and tablet users. A major challenge in designing a voice control application is that it requires continuous monitoring of user?s voice input through the microphone. Such applications utilize hotwords such as "Okay Google" or "Hi Galaxy" allowing them to distinguish user?s voice command and her other conversations. A voice control application has to continuously listen for hotwords which significantly increases the energy consumption of the smart-devices.
Development of a bionanobattery for distributed power storage systems (2004)

Currently available power storage systems, such as those used to supply power to microelectronic devices, typically consist of a single centralized canister and a series of wires to supply electrical power to where it is needed in a circuit. As the size of electrical circuits and components become smaller, there exists a need for a distributed power system to reduce Joule heating, wiring, and to allow autonomous operation of the various functions performed by the circuit. Our research is being conducted to develop a bio-nanobattery using ferritins reconstituted with both an iron core (Fe-ferritin) and a cobalt core (Co-ferritin). Both Co-ferritin and Fe-ferritin were synthesized and characterized as candidates for the bio-nanobattery. The reducing capability was determined as well as the half-cell electrical potentials, indicating an electrical output of nearly 0.5 V for the battery cell. Ferritins having other metallic cores are also being investigated, in order to increase the overall electrical output. Two dimensional ferritin arrays were also produced on various substrates, demonstrating the necessary building blocks for the bio-nanobattery. The bio-nanobattery will play a key role in moving to a distributed power storage system for electronic applications.
Design of a high-resolution and high-sensitivity scintillation crystal array for PET with nearly complete light collection (2002)

Spatial resolution improvements in positron emission tomography (PET) can be achieved by developing detector arrays with finer resolution elements. To maintain high sensitivity and image quality, the challenge is to develop a finely pixellated scintillation crystal array with both high detection efficiency and high light collection. High detection efficiency means the crystals must be relatively long and tightly packed. Extracting a high fraction of the available scintillation light from the ends of long and skinny crystals proves to be very difficult and there is a strong variation with light source depth. The result is inadequate energy resolution. To facilitate light collection, the crystals must be highly polished, which significantly increases costs and complexity. In this paper, we examine this poor light collection phenomenon in more detail. We also describe a novel solution we are developing for readout of an array of 1 mm crystals using avalanche photodiodes (APD). We demonstrate through optical photon tracking simulations that the crystal light collection for this new design is nearly perfect (/spl ges/ 95 %) and is independent of the crystal length, width, and surface treatment and origin of the light created.
On the Backbone VLAN Identifier (BVID) Allocation in 802.1Qay Provider Backbone Bridged — Traffic Engineered Networks (2014)

Carrier Ethernet is rapidly being deployed in the metropolitan and core segments of the transport network. One of the emerging flavors of Carrier Ethernet is the IEEE 802.1Qay PBB-TE or Provider Backbone Bridging-Traffic Engineering standard. PBB-TE relies on the assignment of a network-specific Virtual Local Area Network (VLAN) tag, called the Backbone VLAN ID or BVID that is used in conjunction with a backbone Media Access Control (MAC) address for forwarding. The 12-bit BVID along with 48-bit Backbone MAC address are used to forward an Ethernet frame. The assignment of BVIDs in a network is critical, given that there are only 4094 possible assignments, especially for those paths that are overlapping in the network graph and incident at the same destination. While the only way to scale is to reuse BVIDs, this method can lead to a complication if the same BVID is allocated to an overlapping path. To the best of our knowledge, this is the first instance of isolating this problem of limited BVID availability which rises only due to graphical overlap between services. We formulate and solve this as a constrained optimization problem. We present optimal and heuristic algorithms to solve the BVID problem. The optimal approach solves the `static' case, while the heuristic can solve both the `static' and the `dynamic' cases of the BVID allocation problem. Results show that the developed heuristics perform close to the optimal and can be used in commercial settings for both the static and dynamic cases.
Simulator evaluation of a display for a Takeoff Performance Monitoring System (1989)

A Takeoff Performance Monitoring System (TOPMS) has been developed to provide the pilot with graphic and numeric information pertinent to his decision to continue or abort a takeoff. The TOPMS information display consists primarily of a runway graphic overlaid with symbolic status, situation, and advisory information including: (1) current position and airspeed; (2) predicted locations for reaching decision speed (V sub 1) and rotation speed (V sub R); (3) groundroll limit for reaching (V sub R); (4) predicted stop point for an aborted takeoff from current conditions; (5) engine-status flags; and (6) an overall situation advisory flag that recommends continuation or rejection of the takeoff. In this study, 32 experienced multi-engine pilots evaluated the TOPMS on the Langley B-737 real-time research simulator. They rated the system satisfactory - good and judged it to be suitable for implementation on an aircraft. The TOPMS, the TOPMS simulation, and the results of the simulator evaluation are described here. Appendices contain the pilot's prebriefing package (written explanation of the TOPMS--sent to the pilots prior to their visit), evaluation instructions, debriefing questions, and rating criteria (organized into a flow diagram similar to the Cooper-Harper diagram for evaluation of aircraft handling qualities).
Injection seeded THz-wave parametric generator with 100 MHz linewidth (2001)

Summary form only given. Our research focuses on the development of widely tunable (1-3 THz) THz-wave source with high temporal and spatial coherence. In the paper, an injection-seeded THz-wave parametric generator (TPG) was demonstrated using nonlinear crystals that were pumped by a Nd:YAG laser. Spectrum narrowing to the Fourier transform limit was achieved by injection seeding to the idler wave (near-infrared Stokes). Without injection seeding, the THz-wave linewidth is normally >500 GHz for a conventional TPG.
Large-Area Optical Proximity Correction with a Combination of Rule-Based and Simulation-Based Methods (1996)

We have developed a practical one-dimensional (1D) optical proximity correction (OPC) system based on a combination method. Our OPC system integrates a rule-based and a simulation-based method so that correction time can be reduced to a minimum, while maintaining sufficient accuracy for the correction. The correction accuracy depends on a simulator implemented in the system. By incorporating the 1D context within the range of the proximity effect into the rule table, higher accuracy in the OPC is obtained as compared with conventional methods which involve looking up tables based on duty ratio, or distance to the nearest neighbor. We applied this system to the linewidth correction of 0.3-µm rule logic gates, and obtained width specifications within ±10% and DOF ±0.4 µm. Since correction is basically carried out at the speed of a rule-based correction, our OPC method is applicable to large area layouts. The correction time for a layout of 116 mm 2 was only 64.2 min. The results of OPC for real devices such as SRAMs and DRAMs are also given, demonstrating the feasibility of large-area 1D OPC.
Development of wavelength-shifting-fiber neutron image detector with a fiber-optic taper with a high spatial resolution (2011)

The neutron image detector that was based on wavelength-shifting-fibers (WLS fibers) equipped with the fiber-optic taper was developed. By inserting the FOT in between the scintillator and WLS fibers the measured neutron image was magnified on the WLS fibers. We have tested two FOTs; a square-shaped one with a size of 2.6 × 2.6 mm and a round shaped with a diameter of 20 mm. Both FOTs have identical magnification ratios of 3.1. By implementing the larger FOT the detector has the neutron-sensitive area of 314 mm2 with the effective pixel size of 0.17 × 0.17 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> while the light transmission rate decreased 20% less compared to that with the small FOT. The detector equipped with the larger FOT exhibited a spatial resolution of 0.26 ±0.07 mm, which was similar to that of the one with the small FOT.
Inhibition of Vascular Smooth Muscle Cell Migration by Cytochrome P450 Epoxygenase-Derived Eicosanoids (2002)

Vascular smooth muscle cell (SMC) migration and proliferation contribute to neointimal hyperplasia and restenosis after vascular injury. The epoxyeicosatrienoic acids (EETs), which are products of cytochrome P450 (CYP) epoxygenases, possess vasodilatory, antiinflammatory, and fibrinolytic properties. To determine whether these compounds also possess antimigratory and antiproliferative properties, we stimulated rat aortic SMCs with either 20% serum or platelet-derived growth factor (PDGF-BB, 20 ng/mL). In a concentration-dependent manner, treatment with EETs, particularly 11,12-EET, inhibited SMC migration through a modified transwell filter by 53% to 60%. EETs, however, have no inhibitory effects on PDGF-stimulated SMC proliferation. Adenoviral-mediated overexpression of the CYP isoform, CYP2J2, in SMCs also inhibited serum- and PDGF-induced SMC migration by 32% and 26%, respectively; both effects of which were reversed by the CYP inhibitors SKF525A or clotrimazole, but not by the K(Ca) channel blocker, charybdotoxin, or the cyclooxygenase inhibitor, diclofenac. The effect of EETs correlated with increases in intracellular cAMP levels. Indeed, forskolin and 8-bromo-cAMP exert similar inhibitory effects on SMC migration as 11,12-EET and the effects of 11,12-EET were blocked by cAMP and protein kinase A (PKA) inhibitors. These findings indicate that EETs possess antimigratory effects on SMCs through the cAMP-PKA pathway and suggest that CYP epoxygenase-derived eicosanoids may play important roles in vascular disease and remodeling.
Polyurethane–urea anionomer dispersions. I (1994)

Abstract Polyurethane–urea anionomer dispersions with different stoichiometric DMPA/polyol and NCO/OH ratios were preapred from poly(oxypropylene)glycol, toluene diisocyanate (TDI), dimethylolpropionic acid (DMPA), and ethylenediamine (EDA). The dispersion‐cast films were prepared and characterized by mechanical properties, dynamic mechanical analysis (DMA), and differential scanning calorimetry (DSC). Increasing the hard‐segment content by either increasing the DMPA/polyol or the NCO/OH ratios affects the glass transition temperature (T g ) of the soft segments. © 1994 John Wiley & Sons, Inc.
Variational Reconstruction of Left Cardiac Structure from CMR Images (2015)

Cardiovascular Disease (CVD), accounting for 17% of overall deaths in the USA, is the leading cause of death over the world. Advances in medical imaging techniques make the quantitative assessment of both the anatomy and function of heart possible. The cardiac modeling is an invariable prerequisite for quantitative analysis. In this study, a novel method is proposed to reconstruct the left cardiac structure from multi-planed cardiac magnetic resonance (CMR) images and contours. Routine CMR examination was performed to acquire both long axis and short axis images. Trained technologists delineated the endocardial contours. Multiple sets of two dimensional contours were projected into the three dimensional patient-based coordinate system and registered to each other. The union of the registered point sets was applied a variational surface reconstruction algorithm based on Delaunay triangulation and graph-cuts. The resulting triangulated surfaces were further post-processed. Quantitative evaluation on our method was performed via computing the overlapping ratio between the reconstructed model and the manually delineated long axis contours, which validates our method. We envisage that this method could be used by radiographers and cardiologists to diagnose and assess cardiac function in patients with diverse heart diseases.
In vivo Functional Imaging Using Photoacoustic Microscopy (2006)

Photoacoustic microscopy extends the current depth limit of the high resolution optical imaging modalities while maintaining a comparable ratio of imaging depth to axial resolution. Based on spectral measurements, functional imaging is achieved in vivo.
Synthesis and antitumor activity of 2-.beta.-D-ribofuranosylselenazole-4-carboxamide and related derivatives (1983)

Treatment of 2,3,5-tri-O-benzoyl-beta-D-ribofuranosyl-1-carbonitrile with hydrogen selenide provided 2,5-anhydro-3,4,6-tri-O-benzoyl-D-allonselenoamide (3). Compound 3 was treated with ethyl bromopyruvate to provide ethyl 2-(2,3,5-tri-O-benzoyl-D-ribofuranosyl)selenazole-4-carboxylates, which after ammonolysis were converted to 2-beta-D-ribofuranosylselenazole-4-carboxamide (6) and its alpha-analogue 7, respectively. Acetylation of nucleoside 6 provided 2-(2,3,5-tri-O-acetyl-beta-D-ribofuranosyl)selenazole-4-carboxamide, and phosphorylation of 6 provided the corresponding 5'-phosphate 9. Compounds 6 and 9 were found to be cytotoxic toward P388 and L1210 cells in culture and effective against Lewis lung carcinoma in mice.
A hierarchical approach to deep learning and its application to tomographic reconstruction (2019)

Deep learning (DL) has shown unprecedented performance for many image analysis and image enhancement tasks. Yet, solving large-scale inverse problems like tomographic reconstruction remains challenging for DL. These problems involve non-local and space-variant integral transforms between the input and output domains, for which no efficient neural network models have been found. A prior attempt to solve such problems with supervised learning relied on a brute-force fully connected network and applied it to reconstruction for a $128^4$ system matrix size. This cannot practically scale to realistic data sizes such as $512^4$ and $512^6$ for three-dimensional data sets. Here we present a novel framework to solve such problems with deep learning by casting the original problem as a continuum of intermediate representations between the input and output data. The original problem is broken down into a sequence of simpler transformations that can be well mapped onto an efficient hierarchical network architecture, with exponentially fewer parameters than a generic network would need. We applied the approach to computed tomography (CT) image reconstruction for a $512^4$ system matrix size. To our knowledge, this enabled the first data-driven DL solver for full-size CT reconstruction without relying on the structure of direct (analytical) or iterative (numerical) inversion techniques. The proposed approach is applicable to other imaging problems such as emission and magnetic resonance reconstruction. More broadly, hierarchical DL opens the door to a new class of solvers for general inverse problems, which could potentially lead to improved signal-to-noise ratio, spatial resolution and computational efficiency in various areas.
Direct Synthesis of Amides from Alcohols and Amines with Liberation of H <sub>2</sub> (2007)

Given the widespread importance of amides in biochemical and chemical systems, an efficient synthesis that avoids wasteful use of stoichiometric coupling reagents or corrosive acidic and basic media is highly desirable. We report a reaction in which primary amines are directly acylated by equimolar amounts of alcohols to produce amides and molecular hydrogen (the only products) in high yields and high turnover numbers. This reaction is catalyzed by a ruthenium complex based on a dearomatized PNN-type ligand [where PNN is 2-(di-tert-butylphosphinomethyl)-6-(diethylaminomethyl)pyridine], and no base or acid promoters are required. Use of primary diamines in the reaction leads to bis-amides, whereas with a mixed primary-secondary amine substrate, chemoselective acylation of the primary amine group takes place. The proposed mechanism involves dehydrogenation of hemiaminal intermediates formed by the reaction of an aldehyde intermediate with the amine.
Field demonstration of coupling ion-exchange resin with electrochemical oxidation for enhanced treatment of per- and polyfluoroalkyl substances (PFAS) in groundwater (2021)

This pilot-scale field demonstration evaluated the remediation of poly- and perfluoroalkyl substances (PFAS) from groundwater contaminated with aqueous film-forming foam (AFFF) from a coupled regenerable ion exchange resin (IXR) and electrochemical oxidation (EO) treatment train. A pilot-scale IXR system was used that incorporates a novel resin regeneration process, and recovers and reuses the majority of the regenerant solution using distillation. The pilot system removed PFAS from ∼1,000,000 L (approximately 260,000 gallons) of contaminated groundwater from a fire training area, and treated effluent from the IXR system was non-detect for PFOA and PFOS. The concentrated waste stream (i.e., still bottom) from IXR was treated on-site by an EO system with Ti4O7 electrodes, achieving 80–98% destruction of PFOA and PFOS. The surface area normalized first-order rate constants (kSA) were 3.96 × 10−7 m s−1 and 7.92 × 10−7 m s−1 for PFOA and PFOS, respectively, with short-chain perfluoroalkyl acids (PFAAs) identified as intermediate degradation products. Based on the fluoride recovered and PFAS mass loss measured at the end of EO treatment, fluoride release ratios were 130% for still bottom sample 1 (SB1) and 215% for still bottom sample 2 (SB2), indicating mineralization of unquantified fluorinated compounds in the waste stream. Overall, the electric energy consumed per order of magnitude reduction in concentration (EE/O) for treating PFOA and PFOS in groundwater by the IXR-EO treatment train was 0.131–0.161 kWh/m3 for PFOA and 0.071–0.094 kWh/m3 for PFOS, which was orders of magnitude lower than the reported EE/O values for stand-alone electrochemical treatment. The results of this field demonstration show the promise of coupling regenerable IXR with EO for cost-effective removal, concentrating, and destroying PFAS from groundwater.
Robust Model-Based 3D Head Pose Estimation (2015)

We introduce a method for accurate three dimensional head pose estimation using a commodity depth camera. We perform pose estimation by registering a morphable face model to the measured depth data, using a combination of particle swarm optimization (PSO) and the iterative closest point (ICP) algorithm, which minimizes a cost function that includes a 3D registration and a 2D overlap term. The pose is estimated on the fly without requiring an explicit initialization or training phase. Our method handles large pose angles and partial occlusions by dynamically adapting to the reliable visible parts of the face. It is robust and generalizes to different depth sensors without modification. On the Biwi Kinect dataset, we achieve best-in-class performance, with average angular errors of 2.1, 2.1 and 2.4 degrees for yaw, pitch, and roll, respectively, and an average translational error of 5.9 mm, while running at 6 fps on a graphics processing unit.
Drug Delivery: Vaults Engineered for Hydrophobic Drug Delivery (Small 10/2011) (2011)

The frontispiece of the Full Papers section (right) shows a single-particle electron microscope tomography reconstruction, which reveals that a fully assembled drug-loaded nanodisk (red) can be packaged into the vault lumen (green) as a viable method for vault-mediated drug delivery. The electron micrograph in the background shows negatively stained vaults containing nanodisks. For more information, please read the Full Paper “Vaults Engineered for Hydrophobic Drug Delivery” by L. H. Rome and co-workers, beginning on page 1431.