gebhart/patrepeval huggingface dataset:
Mitomycin immunoblot colony assay for detection of Shiga-like toxin-producing Escherichia coli in fecal samples: comparison with DNA probes (1993)

We developed a direct screening immunoblot assay for the detection of Shiga-like toxin (SLT)-producing organisms in stool samples. The assay takes advantage of the phage-mediated nature of SLT production in Escherichia coli and the phage-inducing effects of mitomycin. The addition of mitomycin significantly enhanced the amount of toxin available for immunologic detection. By using the mitomycin-enhanced immunoblot assay, SLT-producing E. coli could be distinguished from non-toxin-producing E. coli and normal stool flora in ratios of 1:1,000 to 1:5,000. The immunoblot assay was examined in a field setting and compared with direct DNA probing for SLT-I and SLT-II. The assay was able to detect SLT-producing E. coli with a high level of sensitivity and specificity. Specificity was markedly improved by using a monoclonal antibody which cross-reacts with both SLT-I and SLT-II B subunits in place of the polyclonal antitoxin sera. We conclude that the mitomycin-enhanced immunoblot colony assay is a rapid and reliable alternative to DNA probing for the detection of phage-mediated SLT-producing organisms in stool samples, especially when the production and use of nucleic acid probes are not feasible. In addition, it permits isolation of positive colonies for further study and confirmation.
Abstract LB-247: Early detection of gastric cancer using global and gene-specific promoter DNA methylation in endoscopic biopsies (2017)

Abstract Clinically useful molecular tools to triage gastric cancer patients are not currently available. We aimed to develop a molecular tool to predict gastric cancer risk in endoscopy-driven biopsies obtained from high-risk gastric cancer clinics in low resource settings. We discovered and validated a DNA methylation biomarker panel in endoscopic samples obtained from 362 patients seen between 2004 and 2009 in three high-risk gastric cancer clinics in Lima, Perú, and validated it in 306 samples from the Cancer Genome Atlas project (“TCGA”). Global, genome wide and gene-specific DNA methylation analyses were used in a Phase I Biomarker Development Trial to identify a continuous biomarker panel that combines a Global DNA Methylation Index (GDMI) and promoter DNA methylation levels of IRF4, ELMO1, CLIP4 and MSC. We observed an inverse association between the GDMI and histological progression to gastric cancer, when comparing gastritis patients without metaplasia (mean= 5.74, 95% CI, 4.97-6.50), gastritis patients with metaplasia (mean= 4.81, 95% CI, 3.77-5.84), and gastric cancer cases (mean=3.38, 95% CI, 2.82-3.94), respectively (p&lt;0.0001). Promoter methylation of IRF4 (p &lt;0.0001), ELMO1 (p &lt;0.0001), CLIP4 (p &lt;0.0001), and MSC (p &lt;0.0001), is also associated with increasing severity from gastritis with no metaplasia to gastritis with metaplasia and gastric cancer. Our findings suggest that promoter methylation of IRF4, ELMO1, CLIP4 and MSC and a GDMI &gt; 4, is a useful molecular tool for gastric cancer risk stratification in endoscopic biopsies. Citation Format: Francesca Pirini, Sassan Noazin, Martha Jahuira Arias, Sebastian Rodriguez-Torres, Leah Friess, Christina Michailidi, Jaime Cok, Juan Combe, Goria Vargas, William Prado, Ethan Soudry, Jimena Perez, Tikki Yudin, Andrea Mancinelli, Helen Unger, Carmen Ili, Priscilla Brebi, Douglas Berg, Masamichi Hayashi, David Sidransky, Robert Gilman, Rafael E. Guerrero-Preston. Early detection of gastric cancer using global and gene-specific promoter DNA methylation in endoscopic biopsies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr LB-247. doi:10.1158/1538-7445.AM2017-LB-247
<title>Spectral/spatial annealing of hyperspectral imagery initialized by a supervised classification method</title> (2002)

A simulated annealing method of partitioning hyperspectral imagery, initialized by a supervised classification method, is investigated to provide spatially smooth class labeling for terrain mapping applications. The method is used to obtain an estimate of the mode a Gibbs distribution defined over a symmetric spatial neighborhood system that is based on an energy function characterizing spectral disparities in Euclidean distance and spectral angle. Experiments are conducted on a 210-band HYDICE scene that contains a diverse range of terrain features and that is supported with ground truth. Both visual and quantitative results demonstrate a clear benefit of this method as compared to spectral-only supervised classification or unsupervised annealing that has been initialized randomly.
Anodic iridium oxide films: A new electrochromic (1979)

We review the preparation and properties of a new electrochromic material, an anodically grown iridium oxide film (AIROF), and describe three new developments: 1) a heat treatment which improves response times and greatly improves stability; 2) the observation that the maximum coloration and the speed of response are independent of pH, i.e., essentially the same for acidic, neutral, or alkaline electrolytes, and 3) the development of a transmission device in which the AIROF is grown on a semitransparent conducting substrate. We have also observed a new electrochromism isotherm in AIROF's, and shown that there are two distinct electrochromic processes with different isotherms. Since the two distinct processes cannot both be simple proton injection, our results show clearly that other processes can accomplish coloration in AIROF's. Moreover, both isotherms are dominated by internal entropy changes of noninteracting particles. Such isotherms are qualitatively different from that of the proton-injection process in WO <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</inf> electrochromics.
Disparity-compensated inter-layer motion prediction using standardized HEVC extensions (2015)

The scalable and multiview extensions of the High Efficiency Video Coding share the same high-level syntax coding structure. For the scalable extension, the motion field of the inter-layer reference picture is modified through Motion Field Mapping before used for motion vector prediction. However, the motion field of the inter-layer reference picture is used without modification in the multiview extension. In this paper, a disparity-compensated inter-layer motion prediction is proposed for multiview video coding to achieve disparity compensation in inter-layer motion prediction using the scaled reference layer offset. The experimental results show that comparing with the multiview extension anchor, the proposed method achieves an average of 1.1% bitrate reduction.
Ultrasensitive detection enabled by nonlinear magnetization of nanomagnetic labels (2018)

Geometrically confined magnetic particles due to their unique response to external magnetic fields find a variety of applications, including magnetic guidance, heat and drug delivery, magneto-mechanical actuation, and contrast enhancement. Highly sensitive detection and imaging techniques based on the nonlinear properties of nanomagnets were recently proposed as innovative strong-translational potential methods applicable in complex, often opaque, biological systems. Here we report on the significant enhancement of the detection capability using optical-lithography-defined, ferromagnetic iron-nickel alloy disk-shaped particles. We show that an irreversible transition between strongly non-collinear (vortex) and single domain states, driven by an alternating magnetic field, translates into a nonlinear magnetic response that enables ultrasensitive detection of these particles. The record sensitivity of ∼3.5 × 10-9 emu, which is equivalent to ∼39 pg of magnetic material is demonstrated at room temperature for arrays of patterned disks. We also show that unbound disks suspended in the aqueous buffer can be successfully detected and quantified in real-time when administered into a live animal allowing for tracing of their biodistribution. The use of nanoscale ferromagnetic particles with engineered nonlinear properties opens prospects for further enhancing the sensitivity, scalability, and tunability of noise-free magnetic tag detection in high-background environments for various applications spanning from biosensing and medical imaging to anti-counterfeiting technologies.
Keep it Unreal: Bridging the Realism Gap for 2.5D Recognition with\n Geometry Priors Only (2018)

With the increasing availability of large databases of 3D CAD models,\ndepth-based recognition methods can be trained on an uncountable number of\nsynthetically rendered images. However, discrepancies with the real data\nacquired from various depth sensors still noticeably impede progress. Previous\nworks adopted unsupervised approaches to generate more realistic depth data,\nbut they all require real scans for training, even if unlabeled. This still\nrepresents a strong requirement, especially when considering\nreal-life/industrial settings where real training images are hard or impossible\nto acquire, but texture-less 3D models are available. We thus propose a novel\napproach leveraging only CAD models to bridge the realism gap. Purely trained\non synthetic data, playing against an extensive augmentation pipeline in an\nunsupervised manner, our generative adversarial network learns to effectively\nsegment depth images and recover the clean synthetic-looking depth information\neven from partial occlusions. As our solution is not only fully decoupled from\nthe real domains but also from the task-specific analytics, the pre-processed\nscans can be handed to any kind and number of recognition methods also trained\non synthetic data. Through various experiments, we demonstrate how this\nsimplifies their training and consistently enhances their performance, with\nresults on par with the same methods trained on real data, and better than\nusual approaches doing the reverse mapping.\n
Development and Validation of a Transient Event Detector (1993)

The nonintrusive load monitor (NILM) determines the operating schedule of the major electrical loads in a building from measurements made at the utility service entry. This paper describes techniques used to develop, test, and implement a transient event detector that extends the applicability of NILM to challenging commercial and industrial sites. Software has been developed that can flexibly and quickly simulate the electrical harness and loads in a building. Data from this simulator were used to design a transient event detection algorithm. This algorithm has been implemented on a real-time digital signal processing system that can be used to monitor actual loads in operation. The performance of the algorithm is illustrated with results from the prototype transient event detector.
Laser‐based microfocused x‐ray source for mammography: Feasibility study (1997)

A laser-produced plasma (LPP) x-ray source with possible application in mammography was created by focusing a laser beam on a Mo target. A Table-Top-Terawatt (TTT) laser operating at 1 J energy per pulse was employed. A dual pulse technique was used. Maximum energy transfer (approximately 10%) from laser light to hot electrons was reached at a 150 ps delay between pulses and the conversion efficiency (hard x-ray yield/laser energy input) was approximately 2 x 10(-4). The created LPP x-ray source is characterized by a very small focal spot size (tens of microns), Gaussian brightness distribution, and a very short pulse duration (a few ps). The spectral distribution of the generated x rays was measured. Images of the focal spot, using a pinhole camera, and images of a resolution pattern and a mammographic phantom were obtained. The LPP focal spot modulation transfer function for different magnification factors was calculated. We have shown that the LPP source in conjunction with a spherically bent, high throughput, crystal monochromator in a fixed-exit Rowland circle configuration can be used to created a narrow band tunable mammography system. Tunability to a specific patient breast tissue thickness and density would allow one to significantly improve contrast and resolution (exceeding 20 lp/mm) while lowering the exposure up to 50% for thicker breasts. The prospects for the LPP x-ray source for mammographic application are discussed.
Quantum measurement with a positive operator-valued measure (2003)

In the quantum theory of measurement, the positive operator-valued measure (POVM) is an important concept, and its implementation can be useful. A POVM consists of a set of non-negative quantum-mechanical Hermitian operators that add up to the identity. The probability that a quantum system is in a particular state is given by the expectation value of the POVM operator corresponding to that state. Following a brief review of the mathematics and mention of the history of POVMs in quantum theory, a particular implementation of a POVM for use in the measurement of nonorthogonal photon polarization states is reviewed. The implementation consists simply of a Wollaston prism, a mirror, two beam splitters, a polarization rotator and three phototubes arranged in an interferometric configuration, and it is shown analytically that the device faithfully represents the POVM. Based on Neumark's extension theorem, the two-dimensional Hilbert space of the POVM implementation can be embedded in the three-dimensional Hilbert space of an ordinary projective-valued measure. Also, analytical expressions are given for the maximum Renyi information loss from the device to a disturbing probe, and for the error and inconclusive rates induced by the probe. Various aspects of the problem of probe optimization are elaborated.
The Effect of Error Propagation on the Performance of Polar Codes Utilizing Successive Cancellation Decoding Algorithm (2019)

In this paper, we discuss and analyze the effect of error propagation on the performance polar codes decoded using the successive cancellation algorithm. We show that error propagation due to erroneous bit decision is a catastrophic issue for the successive cancellation decoding of polar codes. Even a wrong decision on a single bit may cause an abundance of successor bits to be wrongly decoded. Furthermore, we observe that the performance of polar codes is significantly improved if even single bit errors are detected and corrected before the decoding of successor bits.
Detecting malicious ADS-B transmitters using a low-bandwidth sensor network (2015)

Automatic Dependent Surveillance Broadcast (ADS-B) has been proposed as both an extension and an alternative to Primary and Secondary Surveillance RADAR. Although ADS-B has many advantages, security was not a key issue in its design. Packets are sent in clear text, making it vulnerable to many attacks. A main concern is that some of these attacks can be easily implemented using inexpensive ADS-B transmitters. For instance, ADS-B is vulnerable to injection attacks, which introduce ghost aircraft into an surveillance system. In this paper we propose a method that addresses these issues by detecting malicious ADS-B transmitters using a network of sensors with an associated data fusion center. A key aspect of our solution is that the data fusion process has a low message exchange overhead, enabling its applicability to current constrains of ADS-B sensors. Our method can be implemented using commercial off-the-shelf ADS-B receivers.
Loading of a Unilateral Temporomandibular Joint Prosthesis: A Three-dimensional Mathematical Study (1998)

The load on the prosthetic side and the influence of the design on the remaining natural contralateral TMJ must be known before a unilateral temporomandibular joint (TMJ) prosthesis can be developed. The aim of the present study was to determine the maximum loading of the TMJ prosthetic side and the natural contralateral TMJ and to investigate the influence of the location of the center of rotation of the prosthesis on the maximum loading. For this purpose, a mathematical model of the mandible with a unilateral TMJ prosthesis with a fixed center of rotation (CR) was developed. The location of the CR of the TMJ prosthesis was varied from the middle of the natural mandibular condyle to 15 mm inferior to this location. Although the maximum joint reaction forces changed as a result of a unilateral TMJ prosthesis, the trend of the loading curves was similar to that of an intact mandible. A unilateral TMJ prosthesis resulted in a 50% higher loading of the prosthetic side, while the load on the natural contralateral TMJ remained within normal limits. The maximum load on the prosthetic side occurred during molar bites and could reach 100 N in the cranial direction, 30 N in the ventral direction, and 25 N in the medio-lateral direction. The location of the CR did not have a significant influence on the loading of the TMJ prosthesis and the natural contralateral TMJ.
Late-Onset Friedreich Ataxia (2005)

Patients with gait and limb ataxias, dysarthria, loss of vibration sense, and fixational instability after age 25 years should be considered for molecular testing for GAA expansion in the FA gene. In contrast to previous studies, cerebellar vermian atrophy is not an uncommon finding.
Advanced processing of n (100) GaAs with femtosecond laser treatment (1999)

Gallium arsenide (GaAs) is an important compound semiconductor, especially in view of its applicability to wireless as well as opto-electronic devices. However, it is known that GaAs, unlike silicon (Si), does not possess a stable native oxide that can passivate and protect the surface. This letter reports for the first time, the use of ultrashort laser treatment of the GaAs surface for realizing passivating effects. In this work, femtosecond laser-based processing was shown to be effective and more convenient compared to conventional capping processes, due to the laser’s inherent properties that include an almost non-existent heat affected zone (HAZ). The absence of a HAZ implies that there is virtually no thermal damage to the volume of material surrounding a processed region. The surface passivating effects were confirmed by depth-profiling x-ray photoelectron spectroscopic (XPS) measurements. In addition, scanning electron microscopy (SEM) measurements lead to a possible explanation of the mechanism responsible for the passivation.
A New Efficient Synthesis of Both Enantiomers of Macrosphelide Core: A Potential Precursor for Functionalized Macrosphelides (2003)

The asymmetric synthesis of a macrosphelide core (1) and its enantiomer was achieved from (S)-or (R)-3-hydroxybutyrate in excellent yields.These compounds are potentially useful precursors for the preparation of biologically important macrosphelide analogues.Recently macrosphelides A-L, isolated from Microsphaeropsis sp.FO-5050 and Periconia byssoides, have been well recognized as important potential lead compounds for a new drug against cancer due to their strong inhibitory activities on the adhesion of human cells. 1 These natural products possess characteristic 16-membered macrocyclic lactone structures and oxygen-functionalities at their 8 and/or 14 positions (Figure 1).
Cowpea Mosaic Virus-Based Systems for the Expression of Antigens and Antibodies in Plants (2009)

This chapter describes the use of Cowpea mosaic virus-based vectors for the production of foreign proteins such as antigens and antibodies in plants. The systems include vectors based on both full-length and deleted versions of RNA-2. In both cases, the modified RNA-2 is replicated by coinoculation with RNA-1. The constructs based on full-length RNA-2 retain the ability to spread systemically throughout an inoculated plant and the infection can be passaged. The vector based on a deleted version of RNA-2 can stably incorporate larger inserts but lacks the ability to move systemically. However, it has the added advantage of biocontainment. In both cases, vector constructs modified to contain a foreign gene of interest can be delivered by agroinfiltration to obtain transient expression of the foreign protein. If required, the same constructs can also be used for stable nuclear transformation. Both types of vector have proved effective for the production in plants of a diverse range of proteins including antigens and antibodies.
State-of-charge and parameter estimation of lithium-ion battery using dual adaptive filter (2017)

In this paper, we propose a cross-referring approach using a dual adaptive filter to estimate the state-of-charge (SOC), full charge capacity (FCC), and resistance of a battery in a real-time manner. Although conventional SOC estimation methods such as the Coulomb counting and the open-circuit voltage (OCV) estimation are commonly used for battery systems, accuracy of their SOC estimates are deteriorated by the presence of errors on the current and voltage measurements of the battery. Moreover, the methods depend on parameters such as the FCC and resistance, both of them gradually vary as the battery degrades, resulting in large SOC estimation errors. In our approach, the FCC and current sensor offset in the Coulomb counting method are estimated by referring the OCV estimation method, while the resistance in the OCV estimation method is estimated by referring the Coulomb counting method, resulting in accurate SOC estimation. The performance of the proposed method is verified through numerical examples based on both simulated and experimental data of a lithium-ion battery (LIB).
Low-profile, integrated radiator tiles for wideband, circular-polarized phased array applications (2002)

A versatile planar, low-profile radiating element for phased array applications has been developed that can provide excellent scan and axial ratio performance over a very wide frequency bandwidth. The design is based on a stacked-disc configuration where the lower disc is fed by a pair of probes per linear polarisation. The stacked-disc radiator has since been integrated with its feed circuits in a very compact and versatile package. This package, referred to as an integrated radiator tile, is the building block for a very low-profile phased array aperture that can provide dual circular polarization. The radiator tile's form factor lends itself well to many conformal applications and tile array architectures in general. This paper presents an integrated radiator tile design that was developed for an active array antenna for submarine satellite communication. It describes the packaging scheme and shows the measured performance of the various components. A small test array was built using the radiator tiles to demonstrate its element performance. Its results are also discussed.
Electro-optic mode-displacement silicon light modulator (1991)

A new type of guided-wave electro-optical intensity modulator is proposed and analyzed. The waveguide consists of an N-type Si core layer on a P-type Si substrate. Foward bias on the N+-N-P-P+ diode decreases the refractive index of the core and displaces the fundamental guided mode downward into the substrate. However, the mode is not extinguished because the substrate is bounded by a P+ contact. A spatial filter at the output converts the mode displacement into optical intensity modulation. A Poisson and continuity equation solver and multilayer waveguide simulation were used to obtain numerical estimates of mode displacement in a realistic structure.