gebhart/patrepeval huggingface dataset:
High-sensitivity integrated fluorescence analysis for microfluidic lab-on-a-chip (2007)

Microfluidics studies the behavior of fluids at the microscale and the design of systems to take advantage of such behavior. A multidisciplinary field encompassing physics, chemistry, engineering, and biotechnology, microfluidics integrates sensors, actuators, and other electronics to create new applications.1–3 Importantly, new principles of fluid manipulation have enabled detection and handling of nanoliter fluid samples. In recent years, these principles have been applied to the development of lab-on-a-chip (LOC) systems.4, 5 A substantial challenge for such miniaturized systems—the size of a credit card—for point-of-care and on-site analysis lies in developing their ability to effectively detect analytes of interest. Small sample volumes and low concentrations common to microfluidic LOCs make high-sensitivity detection of critical importance. While conventional microscopy tools can easily meet these demands in a laboratory, developing portable systems requires integrated miniaturized detectors. Fluorescence is one of the most commonly used analytic techniques in the biosciences. It is based on emission of a dye at one wavelength when it is illuminated by another, shorter wavelength. Lack of integrated fluorescence detection is a major roadblock for many biotechnological assays in portable LOC format. In a typical microfluidic fluorescence immunoassay assay, fluorescently labeled antibodies are used to tag a specific antigen (e.g., bacteria, viruses, or other organic molecules of interest) in a microfluidic device. The excitation light stimulates the dye to fluoresce, and the characteristic emission wavelength, or color, is observed through a filter that suppresses excitation light, enbling the dye emission to be seen clearly. As shown in Figure 1, the orange light represents the dye emission and the green light Figure 1. Schematic of a lab-on-a-chip (LOC) for fluorescence analysis. PDMS: Poly(dimethylsiloxane).
Synthesis and Evaluation of 8,10-Dideazatetrahydrofolic Acid and Derivatives (1993)

Syntheses of 8,10-dideazatetrahydrofolic acid and its 5-N-methyl and 5-N-formyl derivatives are reported. Hydrolysis of 2,4-diamino-4-deoxy-8,10-dideazapteroic acid in hot alkali afforded 8, 10-dideazapteroic acid. Coupling with diethyl L-glutamate followed by saponification gave 8,10-dideazafolic acid. Hydrogenation in acidic media gave the tetrahydro compound, while hydrogenation in the presence of formaldehyde yielded the 5-N-CH 3 analog. The 5-N-CH 3 compound was more potent than 5,10-DDTHF as an inhibitor of growth for L1210 cells in culture. In contrast to 5,10-DDTHF, the locus of action was apparently unrelated to inhibition of GAR formyltransferase. Unfortunatly, 5-CH 3 -8,10-DDTHF was not active in vivo against an L1210 challenge in mice
A Packaging Technique for Polymer Microfluidic Platforms (2004)

A new technique, resin−gas injection, has been developed for bonding and surface modification of polymer microfluidic devices. This method can easily bond biochips with complex flow patterns. A cascade micromixer and a multichannel DNA sequencing chip were demonstrated experimentally. By adding surface modification agents, the interfacial free energy of the substrate with water can be controlled. Local modification of the channel surface can also be achieved through sequential resin−gas injection in conjunction with a masking technique. For application, this technique is used to form a layer of dry monolithic stationary hydrogel on the walls of a microchannel, serving as a sieving material for electrophoresis separation of DNA fragments. The reagent loading and the electrophoresis separation efficiency of this technique were compared experimentally with the conventional linear polymer solution method used in the microchannel-based DNA sequencing process. It is found that our method has the advantages of more user-friendly operation, easier and faster sample loading, but slightly less separation efficiency.
A ferromagnetic model for the action of electric and magnetic fields in cryopreservation (2013)

Recent discussions in the literature have questioned the ability of electromagnetic exposure to inhibit ice crystal formation in supercooled water. Here we note that strong electric fields are able to disrupt the surface boundary layer of inert air on the surface of materials, promoting higher rates of heat transport. We also note that most biological tissues contain ferromagnetic materials, both biologically precipitated magnetite (Fe3O4) as well as environmental contaminants that get accidentally incorporated into living systems. Although present at trace levels, the number density of these particulates is high, and they have extraordinarily strong interactions with weak, low-frequency magnetic fields of the sort involved in claims of electromagnetic cryopreservation. Magnetically-induced mechanical oscillation of these particles provides a plausible mechanism for the disruption of ice-crystal nucleation in supercooled water.
Optical Integrating Sphere for Vacuum Ultraviolet (1986)

Optical integrating sphere with integral sliding sample holder saves time by allowing radiometric measurements made on each of four samples without breaking vacuum. Designed to operate with interior evacuated so dye samples illuminated with short-wavelength ultraviolet strongly absorbed by air; need not be evacuated when using longer wavelengths. Device mounts on monochromator and evacuated through port that admits light from monochromator.
Methods for improving transition delay fault coverage using broadside tests (2006)

Testing of delay faults require two pattern tests. Broadside and skewed-load testing are two approaches to test for delay faults in scan designs. The broadside approach is often preferred over the skewed-load approach in designs that also use the system clock for scan operations, since skewed-load requires a fast (at-speed) scan enable signal while broadside testing does not. In this paper, we propose new scan flip-flops to improve delay fault coverage for circuits with scan using broadside tests. The proposed flip-flops do not require a control signal to switch at-speed. This is a distinct advantage as the design effort required for timing closure of such control signals is significant. We also propose a circuit topology based flip-flop selection procedure that offers a scalable method for increasing the transition fault coverage. Experimental results on industrial circuits are included
Precision SAR processing using chirp scaling (1994)

A space-variant interpolation is required to compensate for the migration of signal energy through range resolution cells when processing synthetic aperture radar (SAR) data, using either the classical range/Doppler (R/D) algorithm or related frequency domain techniques. In general, interpolation requires significant computation time, and leads to loss of image quality, especially in the complex image. The new chirp scaling algorithm avoids interpolation, yet performs range cell migration correction accurately. The algorithm requires only complex multiplies and Fourier transforms to implement, is inherently phase preserving, and is suitable for wide-swath, large-beamwidth, and large-squint applications. This paper describes the chirp scaling algorithm, summarizes simulation results, presents imagery processed with the algorithm, and reviews quantitative measures of its performance. Based on quantitative comparison, the chirp scaling algorithm provides image quality equal to or better than the precision range/Doppler processor. Over the range of parameters tested, image quality results approach the theoretical limit, as defined by the system bandwidth.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
ChemInform Abstract: SYNTHESIS OF UNSYMMETRICAL 1,4‐BIS((AMINOALKYL)AMINO)ANTHRACENE‐9,10‐DIONES FOR ANTINEOPLASTIC EVALUATION (1985)

Abstract Aus I,4‐Dimethoxy‐anthrachinon (I) erhält man durch stufenweise Umsetzung mit den Aminen (II) bzw. (IV) die unsymmetrischen Substitutionsprodukte (III) bzw. (V) sowie ein Cyclisierungsprodukt (VI).
EFSIM: AN INTEGRATED CIRCUIT EARLY FAILURE SIMULATOR (1996)

Early failures are the dominant concern as integrated circuit technology matures into consistently producing systems of high reliability. These failures are attributed to the presence of randomly occurring defects in elementary objects (contacts, vias, metal runs, gate oxides, bonds etc.) that result in extrinsic rather than intrinsic (wearout-related) mortality. A model relating system failure to failure at the elementary object level has been developed. Reliability is modelled as a function of circuit architecture, mask layout, material properties, life-test data, worst-case use-conditions and the processing environment. The effects of competing failure mechanisms, and the presence of redundant sub-systems are accounted for. Hierarchy is exploited in the analysis, allowing large scale designs to be simulated. Experimental validation of the modelling of oxide leakage related failure, based on a correlation between actual failures reported for a production integrated circuit and Monte Carlo simulations that incorporate wafer-level test results and process defect monitor data, is presented. The state of the art in IC reliability simulation is advanced in that a methodology that provides the capability to design-in reliability while accounting for early failures has been developed; applications include process qualification, design assessment and fabrication monitoring.
On-stream measurement of coal quality, composition and flow (1982)

This paper presents results of research conducted to develop technology based on the magnetic resonance properties of coal for on-stream measurement of the quality, mass flow and composition. Twenty-four types of coal were researched from both the eastern and western regions of the U.S., ranging in rank from lignite to anthracite. Techniques for using these magnetic resonance data to continuously measure the percentages of moisture, carbon, hydrogen and volatiles and the calorific value have been developed. These methods were applied in the development of an experimental instrument suitable for on-stream measurement of the quality, composition and flow of pneumatically transported coal into a fluidized bed combustor or process system. Evaluation results are discussed as is the application to larger flow streams.
Evolution of a 193-nm bilayer resist for manufacturing (2002)

As 193 nm resist moves into production with minimum feature sizes approaching 100nm, bilayer resist is being evaluated more closely for certain applications. Our polymer design has been evolving to meet tighter outgassing requirements. Optical density, etch resistance and dissolution behavior are other considerations. The protecting group used in our 248 nm bilayer is not useful for 193 nm lithography because of the high optical density contribution from Si-Si linkage. Silicon was incorporated into a COMA platform for the first generation polymer. Maleic anhydride is used to modulate dissolution characteristics. The first generation 193 nm bilayer was optimized to print 120 nm L/S patterns with an attenuated PSM on a 0.6 NA Nikon S302. We will describe next generation platforms that address silicon outgassing concern. The lithographic performance of these resists was evaluated on a 0.6 NA Nikon S302 with a dark field mask. Results for 280nm pitch (1:1 L/S) and 245 nm pitch (105 nm L, 140 nm S) lithography are presented. Also shown is result for a 245 nm pitch (1:1 L/S) and 210 nm pitch (1:1 L/S) on a 0.75 NA ASML PAS 5500/1100. Outgassing data generated at MIT Lincoln Laboratory will be discussed.
PN code acquisition using smart antenna for DS-CDMA wireless communications (2002)

In our paper, a PN code acquisition scheme using a smart antenna is proposed. The basic structure is the combination of an adaptive beamformer and a conventional PN correlation searcher. The weight vector of the smart antenna is updated with a least mean square (LMS) algorithm. All array element outputs are employed in the PN correlation searcher. Performance of the proposed scheme is theoretically analyzed and also simulated in terms of detection probability P/sub d/ and average acquisition time T/sub acq/ under additive white Gaussian noise (AWGN) and Rayleigh mobile fading environment. Results show that the proposed scheme can significantly improve PN code acquisition performance.
A Recent Update of Pharmacogenomics in Drug-induced Severe Skin Reactions (2011)

In some adverse drug reactions (ADRs), genetic predisposition plays a significant role in pathogenesis, and the skin is the most frequently reported target. These severe cutaneous ADRs include bullous fixed drug eruptions (FDE), acute generalized exanthematous pustulosis (AGEP), drug-induced hypersensitivity syndrome (HSS), Stevens-Johnson syndrome (SJS), and toxic epidermal necrolysis (TEN). The putative contribution of individual effector cells in drug hypersensitivity is briefly mentioned. To trigger these drug hypersensitivities, certain class I HLA alleles (e.g., HLA-A and HLA-B alleles) and certain class II HLA alleles (e.g., HLA-DR alleles) have been recently found to be the genetic determinants. One of the best characterized examples mentioned in this article is HLA-B*1502 to determine the incidence of carbamazepine-induced SJS. How drugs are processed and presented by these HLA alleles to activate immune responses has been explained by several hypotheses. Further implication of pharmagenomic findings to prevent drug-induced severe skin reactions can be achieved by pre-screening putative risk HLA alleles before using drugs.
Heterogeneous patterns of DNA methylation-based field effects in histologically normal prostate tissue from cancer patients (2017)

Prostate cancer (PC) diagnosis is based on histological evaluation of prostate needle biopsies, which have high false negative rates. Here, we investigated if cancer-associated epigenetic field effects in histologically normal prostate tissue may be used to increase sensitivity for PC. We focused on nine genes (AOX1, CCDC181 (C1orf114), GABRE, GAS6, HAPLN3, KLF8, MOB3B, SLC18A2, and GSTP1) known to be hypermethylated in PC. Using quantitative methylation-specific PCR, we analysed 66 malignant and 134 non-malignant tissue samples from 107 patients, who underwent ultrasound-guided prostate biopsy (67 patients had at least one cancer-positive biopsy, 40 had exclusively cancer-negative biopsies). Hypermethylation was detectable for all genes in malignant needle biopsy samples (AUC: 0.80 to 0.98), confirming previous findings in prostatectomy specimens. Furthermore, we identified a four-gene methylation signature (AOX1xGSTP1xHAPLN3xSLC18A2) that distinguished histologically non-malignant biopsies from patients with vs. without PC in other biopsies (AUC = 0.65; sensitivity = 30.8%; specificity = 100%). This signature was validated in an independent patient set (59 PC, 36 adjacent non-malignant, and 9 normal prostate tissue samples) analysed on Illumina 450 K methylation arrays (AUC = 0.70; sensitivity = 40.6%; specificity = 100%). Our results suggest that a novel four-gene signature may be used to increase sensitivity for PC diagnosis through detection of epigenetic field effects in histologically non-malignant prostate tissue samples.
CSVideoNet: A Real-time End-to-end Learning Framework for High-frame-rate Video Compressive Sensing (2016)

This paper addresses the real-time encoding-decoding problem for high-frame-rate video compressive sensing (CS). Unlike prior works that perform reconstruction using iterative optimization-based approaches, we propose a non-iterative model, named "CSVideoNet". CSVideoNet directly learns the inverse mapping of CS and reconstructs the original input in a single forward propagation. To overcome the limitations of existing CS cameras, we propose a multi-rate CNN and a synthesizing RNN to improve the trade-off between compression ratio (CR) and spatial-temporal resolution of the reconstructed videos. The experiment results demonstrate that CSVideoNet significantly outperforms the state-of-the-art approaches. With no pre/post-processing, we achieve 25dB PSNR recovery quality at 100x CR, with a frame rate of 125 fps on a Titan X GPU. Due to the feedforward and high-data-concurrency natures of CSVideoNet, it can take advantage of GPU acceleration to achieve three orders of magnitude speed-up over conventional iterative-based approaches. We share the source code at https://github.com/PSCLab-ASU/CSVideoNet.
Evaluation of the effects of dietary supplementation with fish oil omega-3 fatty acids on weight bearing in dogs with osteoarthritis (2010)

At least in the short term, dietary supplementation with fish oil omega-3 fatty acids resulted in an improvement in weight bearing in dogs with osteoarthritis.
Protein Imprinting by Means of Alginate-Based Polymer Microcapsules (2010)

Molecular imprinting is a promising technology that, although successfully used to recognize small molecules, has had many difficulties in recognizing macromolecules such as peptides and proteins. The current technologies used to achieve the macromolecular imprinting are incompatible with diagnosis and recognition in many life sciences applications such as medical devices, food additives, or drug delivery systems that require biocompatible products. We present here a new, biocompatible technology of protein imprinting by means of calcium alginate-based polymer capsules using ionic gelation and without toxic chemicals other than sodium alginate and calcium chloride. These molecular imprinting capsules are capable of recognizing higher quantities of protein than the existing technologies developed until now, with a simple formulation.
Eradication of multidrug‐resistant pseudomonas biofilm with pulsed electric fields (2015)

Biofilm formation is a significant problem, accounting for over eighty percent of microbial infections in the body. Biofilm eradication is problematic due to increased resistance to antibiotics and antimicrobials as compared to planktonic cells. The purpose of this study was to investigate the effect of Pulsed Electric Fields (PEF) on biofilm-infected mesh. Prolene mesh was infected with bioluminescent Pseudomonas aeruginosa and treated with PEF using a concentric electrode system to derive, in a single experiment, the critical electric field strength needed to kill bacteria. The effect of the electric field strength and the number of pulses (with a fixed pulse length duration and frequency) on bacterial eradication was investigated. For all experiments, biofilm formation and disruption were confirmed with bioluminescent imaging and Scanning Electron Microscopy (SEM). Computation and statistical methods were used to analyze treatment efficiency and to compare it to existing theoretical models. In all experiments 1500 V are applied through a central electrode, with pulse duration of 50 μs, and pulse delivery frequency of 2 Hz. We found that the critical electric field strength (Ecr) needed to eradicate 100-80% of bacteria in the treated area was 121 ± 14 V/mm when 300 pulses were applied, and 235 ± 6.1 V/mm when 150 pulses were applied. The area at which 100-80% of bacteria were eradicated was 50.5 ± 9.9 mm(2) for 300 pulses, and 13.4 ± 0.65 mm(2) for 150 pulses. 80% threshold eradication was not achieved with 100 pulses. The results indicate that increased efficacy of treatment is due to increased number of pulses delivered. In addition, we that showed the bacterial death rate as a function of the electrical field follows the statistical Weibull model for 150 and 300 pulses. We hypothesize that in the clinical setting, combining systemic antibacterial therapy with PEF will yield a synergistic effect leading to improved eradication of mesh infections.
Geodesic Forests for Image Editing (2011)

III, retrospective diagnostic comparative study.
Transmission Line Resistance Compression Networks and Applications to Wireless Power Transfer (2014)

Microwave-to-dc rectification is valuable in many applications, including RF energy recovery, dc-dc conversion, and wireless power transfer. In such applications, it is desired for the microwave rectifier system to provide a constant RF input impedance. Consequently, variation in rectifier input impedance over varying incident power levels can hurt system performance. To address this challenge, we introduce multiway transmission line resistance compression networks (TLRCNs) for maintaining near-constant input impedance in RF-to-dc rectifier systems. A development of TLRCNs is presented, along with their application to RF-to-dc conversion and wireless power transfer. We derive analytical expressions for the behavior of TLRCNs, and describe two design methodologies applicable to both single and multistage implementations. A 2.45-GHz four-way TLRCN network is implemented and applied to create a 4-W resistance compressed rectifier system that has narrow-range resistive input characteristics over a 10-dB power range. It is demonstrated to improve the impedance match to mostly resistive but variable input impedance class-E rectifiers over a 10-dB power range. The resulting TLRCN plus rectifier system has >50% RF-to-dc conversion efficiency over a >10-dB input power range at 2.45 GHz (peak efficiency 70%), and standing wave ratio <;1.1 over a 7.7-dB range, despite a nonnegligible reactive component in the rectifier loads.
Possible Spin Pumping Effects on Spin Torque Induced Magnetization Switching in Magnetic Tunneling Junctions (2009)

Dependence of spin torque induced magnetization switching upon interfacial insulating layers properties of magnetic tunneling junctions (MTJ) are studied. For the same magnetic properties and patterning geometric dimensions, changes in MTJ interfacial insulating layers properties reveal interesting magnetization switching behaviors. These behaviors cannot be explained by conventional Landau-Lifshitz-Gilbert equation with a spin torque term and an intrinsic ferromagnetic relaxation damping. However the magnetization switching dynamics can be understood through assumption of spin pumping effects in magnetic tunneling junctions. This is not only important for fundamental understanding of spin and electronic transport in MTJ but also important for practical trade-offs between critical switching current and MTJ resistance for spin torque random access memory.
Bladder cancer detection by urinary extracellular vesicle mRNA analysis (2018)

Three urinary EV mRNA were discovered to be elevated in bladder cancer. Urinary EV mRNA are promising biomarkers of urothelial cancer and worth further investigation.