gebhart/patrepeval huggingface dataset:
Diffuse reflectance spectroscopy in Barrett’s Esophagus: developing a large field‐of‐view screening method discriminating dysplasia from metaplasia (2012)

We evaluated diffuse reflectance spectroscopy implemented as a small field-of-view technique for discrimination of dysplasia from metaplasia in Barrett's esophagus as an adjuvant to autofluorescence endoscopy. Using linear discriminant analysis on 2579 spectra measured in 54 patients identified an optimum a 4-wavelength classifier (at 485, 513, 598 and 629 nm). Sensitivity and specificity for a test data set were 0.67 and 0.85, respectively. Spectroscopic results show that this technique could be implemented in wide-field imaging mode to improve the accuracy of existing endoscopy techniques for finding early pre-malignant lesions in Barrett's esophagus. Results show that the discrimination occurs likely due to redistribution of blood content in the tissue sensed by the optical probing with the wavelength-dependent sampling depth.
Strategies for efficient and fast wave optics simulation of coded-aperture and other x-ray phase-contrast imaging methods (2013)

We derive a Fourier formulation of coded-aperture x-ray phase-contrast imaging, based on the wave theory of optics in the Fresnel approximation. We use this model to develop a flexible, efficient, and general simulation algorithm that can be easily adapted to other implementations of x-ray phase contrast imaging. Likewise, the algorithm enables a simple extension to 2D aperture designs, different acquisition schemes, etc. Problems related to numerical implementation of the algorithm are analyzed in detail, and simple rules are derived that enable us to avoid or at least mitigate them. Finally, comparisons with experimental data and data obtained with a different simulation algorithm are presented to validate the model and demonstrate its advantages in practical implementations. This also enabled us to demonstrate an increase in computational speed of more than one order of magnitude over a previous algorithm.
Adaptive Compensation of Piezoelectric Sensoriactuators (1994)

An adaptive filter is used to estimate the feedthrough capacitance of a piezoelectric sensoriactuator in this work. The mechanical response of the piezostructure is resolved from the electrical response of the piezoelectric device through standard adaptive signal processing tech niques. Two common adaptive algorithms are reviewed for the given application: the LMS and the RLS. For spectrally white inputs the adaptation of the digital compensator yields a filter output which is proportional to the electrical response of the piezoelectric device. Thus, the remaining elec trical signal consists of the charge due to the mechanical response of the piezostructure. The adap tive filter converges to a combination of the feedthrough capacitance and the real portion of the mechanical piezostructure response, and the filter error is the quadrature component of the mechanical response. Preliminary results from the theoretical analysis and numerical simulations indicate that, under certain conditions, adaptive signal processing can be employed to realize an adaptive, sensoriactuator for simultaneous strain actuation and sensing.
Ultrasonic transducer array shading (1984)

Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Twitter Facebook Reddit LinkedIn Tools Icon Tools Reprints and Permissions Cite Icon Cite Search Site Citation Lowell S. Smith, Axel F. Brisken, Michael S. Horner; Ultrasonic transducer array shading. J. Acoust. Soc. Am. 1 June 1984; 75 (6): 1935. https://doi.org/10.1121/1.390919 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAcoustical Society of AmericaThe Journal of the Acoustical Society of America Search Advanced Search |Citation Search
Rhodol-based thallium sensors for cellular imaging of potassium channel activity (2018)

Thallium (Tl+) flux assays enable imaging of potassium (K+) channel activity in cells and tissues by exploiting the permeability of K+ channels to Tl+ coupled with a fluorescent Tl+ sensitive dye. Common Tl+ sensing dyes utilize fluorescein as the fluorophore though fluorescein exhibits certain undesirable properties in these assays including short excitation wavelengths and pH sensitivity. To overcome these drawbacks, the replacement of fluorescein with rhodols was investigated. A library of 13 rhodol-based Tl+ sensors was synthesized and their properties and performance in Tl+ flux assays evaluated. The dimethyl rhodol Tl+ sensor emerged as the best of the series and performed comparably to fluorescein-based sensors while demonstrating greater pH tolerance in the physiological range and excitation and emission spectra 30 nm red-shifted from fluorescein.
Performance evaluation of an algorithm for fast optimization of beam weights in anatomy-based intensity modulated radiotherapy (2010)

This study aims to evaluate the performance of a new algorithm for optimization of beam weights in anatomy-based intensity modulated radiotherapy (IMRT). The algorithm uses a numerical technique called Gaussian-Elimination that derives the optimum beam weights in an exact or non-iterative way. The distinct feature of the algorithm is that it takes only fraction of a second to optimize the beam weights, irrespective of the complexity of the given case. The algorithm has been implemented using MATLAB with a Graphical User Interface (GUI) option for convenient specification of dose constraints and penalties to different structures. We have tested the numerical and clinical capabilities of the proposed algorithm in several patient cases in comparison with KonRad((R)) inverse planning system. The comparative analysis shows that the algorithm can generate anatomy-based IMRT plans with about 50% reduction in number of MUs and 60% reduction in number of apertures, while producing dose distribution comparable to that of beamlet-based IMRT plans. Hence, it is clearly evident from the study that the proposed algorithm can be effectively used for clinical applications.
Immunotoxins against a non-tandem repeat epitope on the membrane bound MUC1 kill tumor cells (2007)

C268 MUC1 is a tumor-associated antigen over-expressed in breast cancer tissues, and therefore provides an attractive marker for targeting and killing tumor cells.  To date most of the antibodies generated against MUC1 are directed against the highly immunogenic tandem repeat array on its α subunit. Since the α subunit is shed into the peripheral circulation this epitope may turn out to be problematic for targeting the tumor cells, as circulating MUC1 protein can sequester anti tandem repeat antibodies and prevent them from binding to the cells.  Methods: We immunized mice with MUC1 cDNA and with alternatively-spliced MUC1/X protein isoform, which lacks the tandem repeat array, thereby circumventing the immunogenicity of the α-chain tandem repeat array. Using this novel immunization protocol we isolated antibodies that recognize the α/β junction, an epitope present only on the membrane bound protein.  Results: DMC209, a monoclonal IgM antibody, specifically binds the MUC1 α/β junction on full-length MUC1 expressed by breast and ovarian cancer cells, and on MUC1-positive malignant plasma cells of multiple myeloma. DMC209 did not recognize proteins with mutations that abrogated the cleavage site.  Immunotoxins against the α/β junction were formed with polyclonal antibodies generated in our cDNA/protein immunization protocol and PE38, a powerful pseudomonas exotoxin. When administered to malignant MUC1 expressing cells those immunotoxins proved to be potently cytocidal. In addition when a competitor was added (soluble MUC1/X protein) the cell killing was abrogated, highlighting that the cell-killing immunotoxin gains cell entry via the MUC1 α/β junction  Conclusions: The MUC1 α/β junction has been identified as an important cell-tethered MUC1 epitope against which highly specific antibodies can be generated capable of killing MUC1-expressing cells. These studies point to effective anti-MUC1-based immuno-therapeutic strategies.
Trigger-less and reconfigurable data acquisition system for positron emission tomography (2014)

Abstract This article is focused on data acquisition system (DAQ) designed especially to be used in positron emission tomography (PET) or single-photon emission computed tomography. The system allows for continuous registration of analog signals during measurement. It has been designed to optimize registration and processing of the information carried by signals from the detector system in PET scanner. The processing does not require any rejection of data with a trigger system. The proposed system possesses also an ability to implement various data analysis algorithms that can be performed in real time during data collection.
Transport in Thermal Dip Pen Nanolithography (2004)

The manufacture of nanoscale devices is at present constrained by the resolution limits of optical lithography and the high cost of electron beam lithography. Furthermore, traditional silicon fabrication techniques are quite limited in materials compatibility and are not well-suited for the manufacture of organic and biological devices. One nanomanufacturing technique that could overcome these drawbacks is dip pen nanolithography (DPN), in which a chemical-coated atomic force microscope (AFM) tip deposits molecular ‘inks’ onto a substrate [1]. DPN has shown resolution as good as 5 nm [2] and has been performed with a large number of molecules, but has limitations. For molecules to ink the surface they must be mobile at room temperature, limiting the inks that can be used, and since the inks must be mobile in ambient conditions, there is no way to stop the deposition while the tip is in contact with the substrate. In-situ imaging of deposited molecules therefore causes contamination of the deposited features.
Discovery of α,γ-Diketo Acids as Potent Selective and Reversible Inhibitors of Hepatitis C Virus NS5b RNA-Dependent RNA Polymerase (2003)

alpha,gamma-Diketo acids (DKA) were discovered from screening as selective and reversible inhibitors of hepatitis C virus NS5b RNA-dependent RNA polymerase. The diketo acid moiety proved essential for activity, while substitution on the gamma position was necessary for selectivity and potency. Optimization led to the identification of a DKA inhibitor of NS5b polymerase with IC(50) = 45 nM, one of the most potent HCV NS5b polymerase inhibitors reported.
Online parallel accumulation − serial fragmentation (PASEF) with a novel trapped ion mobility mass spectrometer (2018)

ABSTRACT In bottom-up proteomics, peptides are separated by liquid chromatography with elution peak widths in the range of seconds, while mass spectra are acquired in about 100 microseconds with time-of-fight (TOF) instruments. This allows adding ion mobility as a third dimension of separation. Among several formats, trapped ion mobility spectrometry (TIMS) is attractive due to its small size, low voltage requirements and high efficiency of ion utilization. We have recently demonstrated a scan mode termed parallel accumulation – serial fragmentation (PASEF), which multiplies the sequencing speed without any loss in sensitivity (Meier et al. , PMID: 26538118). Here we introduce the timsTOF Pro instrument, which optimally implements online PASEF. It features an orthogonal ion path into the ion mobility device, limiting the amount of debris entering the instrument and making it very robust in daily operation. We investigate different precursor selection schemes for shotgun proteomics to optimally allocate in excess of 100 fragmentation events per second. More than 800,000 fragmentation spectra in standard 120 min LC runs are easily achievable, which can be used for near exhaustive precursor selection in complex mixtures or re-sequencing weak precursors. MaxQuant identified more than 6,400 proteins in single run HeLa analyses without matching to a library, and with high quantitative reproducibility (R > 0.97). Online PASEF achieves a remarkable sensitivity with more than 2,900 proteins identified in 30 min runs of only 10 ng HeLa digest. We also show that highly reproducible collisional cross sections can be acquired on a large scale (R > 0.99). PASEF on the timsTOF Pro is a valuable addition to the technological toolbox in proteomics, with a number of unique operating modes that are only beginning to be explored.
Scalable uncertainty estimation for nonlinear inverse problems using parameter reduction, constraint mapping, and geometric sampling: Marine controlled-source electromagnetic examples (2011)

We have developed a new uncertainty estimation method that accounts for nonlinearity inherent in most geophysical problems, allows for the explicit search of model posterior space, is scalable, and maintains computational efficiencies on the order of deterministic inverse solutions. We accomplish this by combining an efficient parameter reduction technique, a parameter constraint mapping routine, a sparse geometric sampling scheme, and an efficient forward solver. In order to reduce our model domain and determine an independent basis, we implement both a typical principal component analysis, which factorizes the model covariance matrix, and an alternative compression method, based on singular-value decomposition, which acts on training models, directly, and is storage efficient. Once we have a reduced base, we map parameter constraints, from our original model domain, to this reduced domain to define a bounded geometric region of feasible model space. We utilize an optimal scheme to sample this reduced model space that uses Smolyak sparse grids and minimizes the number of forward solves by finding the sparsest sampling required to produce convergent uncertainty measures. The result is an ensemble of equivalent models, consistent with our inverse solution structure, which is used to infer inverse uncertainty. We tested our method with a 1D synthetic example, a comparison with a published Metropolis-Hastings sampling example, and an extension to 2D problems using a field data inversion.
Effect of anisotropy, color center concentration, and recording parameters on volumetric optical data storage in aluminum oxide single crystal media (2004)

Recording and readout in two-photon absorbing Al 2 O 3 :C,Mg optical data storage media was investigated for crystals having different concentrations of color centers and for two orientations of the crystal optical c-axis. The writing and reading efficiency of the media was increased by taking into account the anisotropy of optical absorption and by rotating the laser light polarization vector synchronously with the disk rotation. The parameters for writing and non-destructive reading of the bits in the volume of a single crystal disk are reported.
Adaptive General Scale Interpolation Based on Weighted Autoregressive Models (2014)

The autoregressive (AR) model has been widely used in signal processing for its effective estimation, especially in image processing. Many dedicated 2× interpolation algorithms adopt the AR model to describe the strong correlation between low-resolution (LR) pixels and high-resolution (HR) pixels. However, these AR model-based methods closely depend on the fixed relative position between LR pixels and HR pixels that are nonexistent in the general scale interpolation. In this paper, we present an adaptive general scale interpolation algorithm that is capable of arbitrary scaling factors considering the nonstationarity of natural images. Different from other dedicated 2× interpolation methods, the proposed AR terms are modeled by pixels with their adjacent unknown HR neighbors. To compensate for the information loss caused by mismatches of AR models, we consider a weighting scheme suitable for general scale situations based on the pixel similarity to increase accuracy of the estimation. Comprehensive experiments demonstrate the effectiveness of the proposed method on general scaling factors. The maximum gain of peak signal-to-noise ratio is 2.07 dB compared with segment adaptive gradient angle in 1.5× enlargements. To evaluate the performance in resolution adaptive video coding, we have also tested our method on Joint Scalable Video Model codec and obtained better subjective quality and rate-distortion performance.
Comparative Study of Acoustic Wave Devices Using Thin Piezoelectric Plates in the 3–5-GHz Range (2019)

This paper investigates the applicability of acoustic wave devices using an interdigital transducer placed on a thin piezoelectric crystal plate to the 3-5-GHz range, where significant performance degradation was expected in surface acoustic wave (SAW) devices. Three types of the SAW-like devices were fabricated by using a KrF stepper/scanner, and their performances are compared from various aspects: 1) a 3.5-GHz resonator using a rotated V-cut LiTaO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> plate attached on a Si substrate; 2) a 5-GHz resonator using a X-cut LiNbO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> plate on a Si substrate; and 3) a 5.4-GHz A <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sub> Lamb mode resonator on a free-standing Z-cut LiNbO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> plate. It is revealed that these devices offer excellent performances even in the 3-5-GHz range.
Modeling for structured system interconnect test (2002)

With the acceptance of test standards such as IEEE 1149.1, the potential for structured methods for system test is growing rapidly. In particular, interconnect testing based on standardized boundary scan structures will be an important component of a future structured system test methodology. A strategy based on building an interconnect topology model of the system under test and using that model to generate interconnect test patterns at test time provides for a level of system test coverage that is difficult or impossible to obtain from methods based on static stored test patterns. This paper discusses the problem of dynamically generating a model of system interconnect topology for use in structured interconnect test generation and analysis. A solution for the most general case is given and some simple system design for test rules that greatly simplify the process are proposed. Several additional solutions which explore some potential trade-offs are discussed. A practical algorithm that requires minimal storage and reasonable computation is proposed.
Text vectorization based on character recognition and character stroke modeling (2014)

In this paper, a text vectorization method is proposed using OCR (Optical Character Recognition) and character stroke modeling. This is based on the observation that for a particular character, its font glyphs may have different shapes, but often share same stroke structures. Like many other methods, the proposed algorithm contains two procedures, dominant point determination and data fitting. The first one partitions the outlines into segments and second one fits a curve to each segment. In the proposed method, the dominant points are classified as “major” (specifying stroke structures) and “minor” (specifying serif shapes). A set of rules (parameters) are determined offline specifying for each character the number of major and minor dominant points and for each dominant point the detection and fitting parameters (projection directions, boundary conditions and smoothness). For minor points, multiple sets of parameters could be used for different fonts. During operation, OCR is performed and the parameters associated with the recognized character are selected. Both major and minor dominant points are detected as a maximization process as specified by the parameter set. For minor points, an additional step could be performed to test the competing hypothesis and detect degenerated cases.
A novel three phase fluidized bed process for simultaneous selective flocculation and microbial desulfurization of high sulfur coal (1990)

The purpose of this work was to investigate the feasibility of recovery and reclamation of ultrafine coal particles generated during the processing of coal. 10--35% of the total annual tonnage of coal in atypical coal preparation plant is estimated to be lost in forms of ultrafine particles during the mining, shipping, handling, and preparation of the coal. The technical feasibility of the proposed system which consisted of an integrated circuit of selective flocculation followed by microbial desulfurization, has been tested. The results indicate that using selective flocculation/froth flotation circuit, coal recoveryis 85% with 75% pyritic sulfur and 60% ash rejections. The remaining pyritic sulfur in the coal slurry was treated using microbial desulfurization in a draft-tube fluidized bed bioreactor. Using this reactor scheme considerable enhancement of the bioleaching rate was obtained. The results indicate that 90% rejection of pyritic sulfur can be achieved in less than 24 hrs. Note that the previously reported data for the bioleaching rate are from 4 to 12 days for the same amount of pyritic rejection. The results obtained in this work closely reflects the anticipated outcomes which were projected in the original proposal. Consequently, the results of this work implies a significant improvement inmore » bioleaching process and the possibility for the commercialization of the microbial desulfurization process. Our results also indicate further improvement of this process by optimization of reactor sequence and operating conditions.« less
Role of Ttca of Citrobacter Werkmanii in Bacterial Growth, Biocides Resistance, Biofilm Formation and Swimming Motility (2018)

To screen, identify and study the genes involved in isothiazolone resistance and biofilm formation in <i>Citrobacter werkmanii</i> strain BF-6. A Tn5 transposon library of approximately 900 mutants of <i>C. werkmanii</i> strain BF-6 was generated and screened to isolate 1,2-benzisothiazolin-3-one (BIT) resistant strains. In addition, the tRNA 2-thiocytidine (32) synthetase gene (<i>ttcA</i>) was deleted through homologous recombination and the resulting phenotypic changes of the <i>ΔttcA</i> mutant were studied. A total of 3 genes were successfully identified, among which <i>ΔttcA</i> mutant exhibited a reduction in growth rate and swimming motility. On the other hand, an increase in biofilms formation in <i>ΔttcA</i> were observed but not with a significant resistance enhancement to BIT. This work, for the first time, highlights the role of <i>ttcA</i> gene of <i>C. werkmanii</i> strain BF-6 in BIT resistance and biofilm formation.