gebhart/patrepeval huggingface dataset:
Large-scale Analyses of Disease Biomarkers and Apremilast Pharmacodynamic Effects (2020)

Finding biomarkers that provide shared link between disease severity, drug-induced pharmacodynamic effects and response status in human trials can provide number of values for patient benefits: elucidating current therapeutic mechanism-of-action, and, back-translating to fast-track development of next-generation therapeutics. Both opportunities are predicated on proactive generation of human molecular profiles that capture longitudinal trajectories before and after pharmacological intervention. Here, we present the largest plasma proteomic biomarker dataset available to-date and the corresponding analyses from placebo-controlled Phase III clinical trials of the phosphodiesterase type 4 inhibitor apremilast in psoriasis (PSOR), psoriatic arthritis (PsA), and ankylosing spondylitis (AS) from 526 subjects overall. Using approximately 150 plasma analytes tracked across three time points, we identified IL-17A and KLK-7 as biomarkers for disease severity and apremilast pharmacodynamic effect in psoriasis patients. Combined decline rate of KLK-7, PEDF, MDC and ANGPTL4 by Week 16 represented biomarkers for the responder subgroup, shedding insights into therapeutic mechanisms. In ankylosing spondylitis patients, IL-6 and LRG-1 were identified as biomarkers with concordance to disease severity. Apremilast-induced LRG-1 increase was consistent with the overall lack of efficacy in ankylosing spondylitis. Taken together, these findings expanded the mechanistic knowledge base of apremilast and provided translational foundations to accelerate future efforts including compound differentiation, combination, and repurposing.
Leveraging query logs and machine learning for parametric query optimization (2021)

Parametric query optimization (PQO) must address two problems: identify a relatively small number of plans to cache for a parameterized query (populateCache), and efficiently select the best cached plan to use for executing any instance of the parameterized query (getPlan). Our approach decouples these two decisions. We formulate populateCache as an optimization problem with the goal of identifying a set of plans that minimizes the optimizer estimated cost of queries in the log, and present an efficient algorithm. For getPlan, we leverage query logs to train machine learning (ML) models to choose the lowest optimizer-estimated cost plan from the cached plans. We conduct extensive experiments using complex parameterized queries from benchmarks and real workloads. Our algorithm for populateCache achieves low geometric mean sub-optimality (1.2) even for complex queries using relatively few plans, and scales well to large query logs. The mean latency of our ML model based getPlan technique (~ 210μ sec ) is between one to four orders of magnitude faster compared to prior PQO techniques. The mean sub-optimality is low (1.05), and the 95 th percentile sub-optimality (1.3) is between 1.1× and 25× lower compared to prior techniques. Finally, we present an efficient algorithm for getPlan that leverages execution time information in query logs to circumvent inaccuracies of the query optimizer's cost estimates.
A hardware-oriented dynamically adaptive disparity estimation algorithm and its real-time hardware (2013)

The computational complexity of disparity estimation algorithms and the need of large size and bandwidth for the external and internal memory make the real-time processing of disparity estimation challenging, especially for High Resolution (HR) images. This paper proposes a hardware-oriented adaptive window size disparity estimation (AWDE) algorithm and its real-time reconfigurable hardware implementation that targets HR video with high quality disparity results. The proposed algorithm is a hybrid solution involving the Sum of Absolute Differences and the Census cost computation methods to vote and select the best suitable disparity candidates. It utilizes a pixel intensity based refinement step to remove faulty disparity computations. The AWDE algorithm dynamically adapts the window size considering the local texture of the image to increase the disparity estimation quality. The proposed reconfigurable hardware of the AWDE algorithm enables handling 60 frames per second on Virtex-5 FPGA at a 1024×768 XGA video resolution for a 120 pixel disparity range.1
Compatibility Studies of Some Azo Polymer Blends (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCompatibility Studies of Some Azo Polymer BlendsShuang Xie, Almeria Natansohn, and Paul RochonCite this: Macromolecules 1994, 27, 6, 1489–1492Publication Date (Print):March 1, 1994Publication History Published online1 May 2002Published inissue 1 March 1994https://pubs.acs.org/doi/10.1021/ma00084a033https://doi.org/10.1021/ma00084a033research-articleACS PublicationsRequest reuse permissionsArticle Views299Altmetric-Citations27LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
SSIM-Motivated Rate-Distortion Optimization for Video Coding (2011)

We propose a rate-distortion optimization (RDO) scheme based on the structural similarity (SSIM) index, which was found to be a better indicator of perceived image quality than mean-squared error, but has not been fully exploited in the context of image and video coding. At the frame level, an adaptive Lagrange multiplier selection method is proposed based on a novel reduced-reference statistical SSIM estimation algorithm and a rate model that combines the side information with the entropy of the transformed residuals. At the macroblock level, the Lagrange multiplier is further adjusted based on an information theoretical approach that takes into account both the motion information content and perceptual uncertainty of visual speed perception. Finally, the mode for H.264/AVC coding is selected by the SSIM index and the adjusted Lagrange multiplier. Extensive experiments show that the proposed scheme can achieve significantly better rate-SSIM performance and provide better visual quality than conventional RDO coding schemes.
Automatic Retinal Oximetry (2007)

This paper presents a method for automating the evaluation of hemoglobin oxygen saturation in the retina. This method should prove useful for monitoring ischemic retinal diseases and the effect of treatment. In order to obtain saturation values automatically, spectral images must be registered in pairs, the vessels of the retina located and measurement points must be selected. The registration algorithm is based on a data driven approach that circumvents many of the problems that have plagued previous methods. The vessels are extracted using an algorithm based on morphological profiles and supervised classifiers. Measurement points on retinal arterioles and venules as well as reference points on the adjacent fundus are automatically selected. Oxygen saturation values along vessels are averaged to arrive at a more accurate estimate of the retinal vessel oxygen saturation. The system yields reproducible results as well as being sensitive to changes in oxygen saturation.
Evaluation of the Characteristics of Small Linear Electromagnetic Actuators. (2003)

Linear actuators have been used in a wide range of fields in the recent years. A linear actuator has a simple structure and is easy to miniaturize. The small size and high thrust of linear actuators are essential for office and factory automation.This paper discusses a comparison of the characteristic evaluations of linear actuators. The type of small linear actuator to be investigated is defined as one having an input power of 100 W or less. The expressions of the motor constant of moving-magnet- type and moving-coil-type linear actuators were examined theoretically and compared.
Motion analysis method for determining cardiomyocyte beating properties based on digital image correlation and templates (2014)

Video-based analysis of cardiomyocytes provides a non-invasive and label-free method of analyzing their beating characteristics. Here, we aim to demonstrate that defining averaged signal templates can improve the determination of cardiomyocyte beating characteristics.
Exploring the Feasibility of Face Video Based Instantaneous Heart-Rate for Micro-Expression Spotting (2018)

Facial micro-expressions (ME) are manifested by human reflexive behavior and thus they are useful to disclose the genuine human emotions. Their analysis plays a pivotal role in many real-world applications encompassing affective computing, biometrics and psychotherapy. The first and foremost step for ME analysis is ME spotting which refers to detection of ME affected frames from a video. ME spotting is a highly challenging research problem and even human experts cannot correctly perform it because MEs are manifested using subtle face deformations and that too for a short duration. It is well established that changes in the human emotions, not only manifest ME but it also introduces changes in instantaneous heart rate. Thus, the manifestation of ME and changes in the instantaneous heart rate are related to the change in human expressions and both of them are estimated using temporal deformations of the face. This provides the motivation of this paper that aims to explore the feasibility of variations in the instantaneous heart rate for performing the correct the ME spotting. Experimental results conducted on a publicly available spontaneous ME spotting dataset, reveal that the variations in instantaneous heart rate can be utilized to improve the ME spotting.
Nanoparticle Ag-enhanced textured-powder Bi-2212/Ag wire technology (2015)

A new approach to the preparation of cores for Bi-2212/Ag wire is being developed. Nanoparticle Ag is homogeneously dispersed in Bi-2212 fine powder, and the mixture is uniaxially compressed to form highly textured, cold-sintered core rods. The rods can be assembled in a silver matrix, drawn to form multifilament wire, and restacked and drawn to form multifilament wire. Preliminary studies using tablet geometry demonstrate that a non-melt heat treatment produces densification, grain growth, intergrowth among grains, and macroscopic current transport. The status of the development is reported.
Geometric Calibration of Third-Generation Computed Tomography Scanners from Scans of Unknown Objects using Complementary Rays (2007)

To achieve good image quality for computed tomography scans, it is important to accurately know the geometrical relationship between the x-ray source, detector, and axis of rotation. Conventional geometric calibration algorithms generally require particular calibration phantoms, such as a small pin or wire, which may not be practical for all scanner types, particularly for large industrial scanners. This paper presents an alternative framework to calibrate system geometry from scans of arbitrary objects, without prior knowledge of the object's form. This lessens physical construction requirements, and permits post-scan geometric calibration from any arbitrary scan data. Experimental results show that central ray calibration using this approach can give results accurate to 0.01 channels for low-noise conditions, or 0.1-0.45 channels under higher noise levels.
Strategy for Synthesizing Porous Cellulose Nanocrystal Supported Metal Nanocatalysts (2016)

This paper describes a novel platform to prepare small and uniformly distributed metal nanoparticles (MNPs) on cellulose nanocrystals for use as high performance sustainable nanocatalysts. The model platinum or palladium NPs (1–2 nm in size) were immobilized and chemically reduced onto melamine-formaldehyde (MF) coated cellulose nanocrystals (MFCNCs). The MF coating was critical for the uniform generation and size-control of MNPs. The contribution of MF resin to optimal MNP synthesis includes: (1) increased surface area with its spongelike structure, (2) enhanced affinity to metals through chelation with nitrogen functionalities, and (3) effective MNP size control due to the mesoporous structure. The MNP/MFCNC system significantly improved catalytic activity as demonstrated by the reduction of 4-nitrophenol with Pd/MFCNCs with a turnover frequency of 3168 h–1. Our synthesis does not require any complicated apparatus or harsh reaction conditions. The proposed strategy is well-suited for the synthesis of a wide range of metal nanocatalysts characterized by a particle size of 1 to 2 nm and superior catalytic activity.
Expression of <i>Escherichia coli</i>β‐galactosidase in <i>Mycobacterium bovis</i> BCG using an expression system isolated from <i>Mycobacterium paratuberculosis</i> which induced humoral and cellular immune responses (1992)

A promoter sequence, PAN, was isolated from Mycobacterium paratuberculosis and characterized. This promoter lies adjacent to, and outside, the 3' end of an IS900 insertion element. IS900 contains an open reading frame, ORF2, on the complementary strand which codes for the putative transposase of this insertion sequence. A DNA fragment containing PAN and part of ORF2 was fused to the lacZ gene and inserted into the replicative shuttle vector pRR3. Mycobacterium smegmatis and Mycobacterium bovis BCG (BCG) transformed with this plasmid exhibited beta-galactosidase activity. However, lacZ was only expressed in Escherichia coli under the control of PAN, when ORF2 was deleted. Immunization of mice with the recombinant M. bovis BCG expressing lacZ resulted in the induction of a high humoral and cellular response directed against beta-galactosidase. The PAN-ORF2 expression system may prove to be particularly useful for cloning and expression of heterologous genes in the BCG vaccine strain.
Design and Analyses of Efficient Chaotic Generators for Crypto-systems (2008)

In this paper, we design and implement under Matlab/Simulink some efficient digital chaotic generators for data encryption/decryption process. Some of these generators (logistic, PWLCM, Frey) are known, the others xcos(x), xexp[cos(x)], 2-D Tmap) are proposed. A number of designed generators contain cascaded layer to improve the statistical properties of the generated sequences. We introduce and demonstrate the importance of the perturbing orbit technique to avoid the dynamical degradation caused by the 2N-dimensional finite state space. This technique increases also the orbit cycle length. Finally, to quantify the security level of the proposed generators, we analyze their global dynamical properties using system and signal processing tools (Lyapunov exponents, bifurcation diagrams, distribution, pseudo phase space, autonotcorrelation, cross correlation, NIST tests ldquoNational Institute of Standards and Technology ldquo). Experimental and theoretical analyses show that the proposed generators have good cryptographic properties.
Splitting of active contour models based on crossing detection for extraction of multiple objects (1997)

With previous active contour models (Snakes), separate extraction of multiple objects inside a contour was impossible, and thus the number of initial contours to be set was the same as that of objects. This paper aims at automatic extraction of multiple objects using Snakes, so that those objects can be extracted separately by means of a single initial contour that includes them all. For this purpose, a splitting contour model is proposed; specifically, a contraction-type Snake is split into multiple contours wherever self-crossing is detected during deformation by means of area term. With the proposed method, smaller contour models generated in splitting are extinguished, so that noise or nonrelevant tiny objects within the image are prevented from capturing; hence, stable extraction of objects is ensured even though the initial contour is placed well apart from the objects. Particularly, multiple objects may be extracted automatically with the initial contour set as the image border. Evaluation tests were carried out to prove the effectiveness of the proposed method, after which the method was applied successfully to actual images, namely, to extracting multiple cells from a microphotograph, and to extracting/tracing multiple objects from moving images. © 1998 Scripta Technica, Syst Comp Jpn, 28(11): 34–42, 1997
Multimode Quasistatic Cavity Resonators for Wireless Power Transfer (2017)

The majority of existing wireless power transfer (WPT) solutions are limited to two-dimensional (2-D) configurations, which limits mobility when charging electronic devices. What is needed are systems capable of 3-D WPT, which can deliver power everywhere throughout large volumes. Prior work on quasistatic cavity resonance (QSCR) showed promising results for ubiquitous WPT at room scales or larger. However, many challenges remain for QSCR, such as the need for a conductive pole in the middle of the room and the power efficiency that is not high over the entire cavity volume. To address these two issues, this letter introduces a room-scale resonator that possesses a “pole independent” (PI) mode, which can be operated without a pole. It is shown by finite-element simulations that by using the PI mode alone, power can be delivered to 93% of the 54 m <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> volume with over 50% efficiency. Moreover, the PI mode and the “pole dependent” (PD) mode, which was used in previous QSCR work, can coexist in the same resonator. These two modes can be selectively stimulated by shifting the operation frequency by less than 1%, and no physical switching components are required. It is shown by simulations that power can be delivered with over 66% efficiency to any location in the room by using this dual-mode operation.
Near-infrared fluorescence molecular imaging of amyloid beta species and monitoring therapy in animal models of Alzheimer’s disease (2015)

Near-infrared fluorescence (NIRF) molecular imaging has been widely applied to monitoring therapy of cancer and other diseases in preclinical studies; however, this technology has not been applied successfully to monitoring therapy for Alzheimer's disease (AD). Although several NIRF probes for detecting amyloid beta (Aβ) species of AD have been reported, none of these probes has been used to monitor changes of Aβs during therapy. In this article, we demonstrated that CRANAD-3, a curcumin analog, is capable of detecting both soluble and insoluble Aβ species. In vivo imaging showed that the NIRF signal of CRANAD-3 from 4-mo-old transgenic AD (APP/PS1) mice was 2.29-fold higher than that from age-matched wild-type mice, indicating that CRANAD-3 is capable of detecting early molecular pathology. To verify the feasibility of CRANAD-3 for monitoring therapy, we first used the fast Aβ-lowering drug LY2811376, a well-characterized beta-amyloid cleaving enzyme-1 inhibitor, to treat APP/PS1 mice. Imaging data suggested that CRANAD-3 could monitor the decrease in Aβs after drug treatment. To validate the imaging capacity of CRANAD-3 further, we used it to monitor the therapeutic effect of CRANAD-17, a curcumin analog for inhibition of Aβ cross-linking. The imaging data indicated that the fluorescence signal in the CRANAD-17-treated group was significantly lower than that in the control group, and the result correlated with ELISA analysis of brain extraction and Aβ plaque counting. It was the first time, to our knowledge, that NIRF was used to monitor AD therapy, and we believe that our imaging technology has the potential to have a high impact on AD drug development.
Scanning Fluorescent Microthermal Imaging (1997)

Abstract We have developed scanning fluorescent microthermal imaging (SFMI), a new failure analysis technique. The fluorescent microthermal imaging (FMI) technique has been used for over a decade in its original form [1-2]. FMI normally relies on the use of a cooled, slow-scan CCD camera and a flood beam fluorescence pump source, usually an ultraviolet arc lamp. Interest in FMI has grown greatly over the past few years [3-9] due largely to its unique combination of high spatial and thermal resolution. In this paper, we demonstrate that the existing infrastructure found on a scanning laser microscope (SLM) is capable of acquiring the necessary images for SFMI using its scanned laser source and a point detector. The implications ofthis work are significant in that now high spatial and thermal resolution images can be made using an SLM without the need of additional, expensive hardware.
<title>Partial rotation invariance in retinal pattern recognition</title> (1994)

We desire to have a joint transform correlator track features in the image of a human retina. Previous binarized digital methods indicated unacceptable limitations in tracking through torsion motions of the eye. To create an extended range of response to eyeball rotation we tried several methods of processing the reference image. We compared laboratory measurements with digital simulations. Based on small statistics and our noiseless models, the results disagree; the digital method has less range, and the optical method has sufficient range (+/- 5 degree(s)) for our purpose.
Localization and Diagnostic Application of Immunodominant Domains of the BFRF3-Encoded Epstein-Barr Virus Capsid Protein (1994)

The Epstein-Barr virus (EBV) open reading frame BFRF3 encodes a viral structural capsid protein or tegument protein, VCA p18, that is highly immunogenic in humans. In this study, a cluster of immunodominant epitopes in the C-terminus of VCA p18 has been identified. These epitopes were combined into a single synthetic peptide that was analyzed for diagnostic value in an ELISA. This VCA combined peptide appeared to be an excellent VCA marker with remarkable applications for IgG- and IgM-related EBV diagnostics. The combined peptide reacted with 95% of 159 sera that were IgG VCA-positive by immunofluorescence assay. In addition, 95% of sera from 67 persons with confirmed infectious mononucleosis were positive for IgM antibodies to this VCA combined peptide. An IgG-specific seroconversion could be demonstrated by subsequent serum samples during the acute phase of primary EBV infections. Although 97% of the tested sera from nasopharyngeal carcinoma patients had IgG antibodies reacting positively with the VCA combined peptide, only 61% contained IgA anti-VCA combined peptide.