gebhart/patrepeval huggingface dataset:
Deep Lesion Tracker: Monitoring Lesions in 4D Longitudinal Imaging Studies (2021)

Monitoring treatment response in longitudinal studies plays an important role in clinical practice. Accurately identifying lesions across serial imaging follow-up is the core to the monitoring procedure. Typically this incorporates both image and anatomical considerations. However, matching lesions manually is labor-intensive and time-consuming. In this work, we present deep lesion tracker (DLT), a deep learning approach that uses both appearance- and anatomical-based signals. To incorporate anatomical constraints, we propose an anatomical signal encoder, which prevents lesions being matched with visually similar but spurious regions. In addition, we present a new formulation for Siamese networks that avoids the heavy computational loads of 3D cross-correlation. To present our network with greater varieties of images, we also propose a self-supervised learning (SSL) strategy to train trackers with unpaired images, overcoming barriers to data collection. To train and evaluate our tracker, we introduce and release the first lesion tracking benchmark, consisting of 3891 lesion pairs from the public DeepLesion database. The proposed method, DLT, locates lesion centers with a mean error distance of 7mm. This is 5% better than a leading registration algorithm while running 14 times faster on whole CT volumes. We demonstrate even greater improvements over detector or similarity-learning alternatives. DLT also generalizes well on an external clinical test set of 100 longitudinal studies, achieving 88% accuracy. Finally, we plug DLT into an automatic tumor monitoring workflow where it leads to an accuracy of 85% in assessing lesion treatment responses, which is only 0.46% lower than the accuracy of manual inputs.
Thermal‐aided phosvitin extraction from egg yolk (2015)

A purity of 88.0% and a yield of 23.5 g kg(-1) yolk dry matter were obtained at 90 °C. The purity and yield were comparable to or higher than those of previously methods. The method developed in this study is simple, including mainly two steps, i.e. water dilution of egg yolk and NaCl extraction with heating, and can be scaled up for industrial production.
<title>Classification, simplification, and dynamic visualization of scene transition graphs for video browsing</title> (1997)

The scene transition graph (STG) is a directed graph structure that compactly captures both image content and temporal flow of video. An STG offers a condensed view of the story content, serves as the summary of the clip represented, and allows nonlinear access to its story element. It can serve as a valuable tool for both the analysis of video structure and presentation of high level visual summary for video browsing applications. In this paper, we study new techniques for classification and simplification of the STG, and present better means of visualizing the graph through dynamic visual display and simplified structures. In other words, our techniques improve significantly the existing graph structure to enable more succinct presentation of the graphs which leads to more efficient utilization of the screen spaces. In addition, a technique that captures and presents visually the temporal dynamics of the video sequence is described. We have tested the graph visualization techniques on various programming types and the new tools are found to effectively handle video from a wider variety than the existing STG structure.
Small field of view scintimammography gamma camera integrated to a stereotactic core biopsy digital X-ray system (2002)

A small field of view gamma camera has been developed for integration with a commercial stereotactic core biopsy system. The goal is to develop and implement a dual-modality imaging system utilizing scintimammography and digital radiography to evaluate the reliability of scintimammography in predicting the malignancy of suspected breast lesions from conventional X-ray mammography. The scintimammography gamma camera is a custom-built mini gamma camera with an active area of 5.3 cm /spl times/ 5.3 cm and is based on a 2 /spl times/ 2 array of Hamamatsu R7600-C8 position-sensitive photomultiplier tubes. The spatial resolution of the gamma camera at the collimator surface is < 4 mm full-width at half-maximum and a sensitivity of /spl sim/ 4000 Hz/mCi. The system is also capable of acquiring dynamic scintimammographic data to allow for dynamic uptake studies. Sample images of preliminary clinical results are presented to demonstrate the performance of the system.
Oligonucleotide derivatives in nucleic acid hybridization analysis. III. Synthesis and investigation of properties of oligonucleotides, bearing bifunctional non-nucleotide insertion (2012)

Non-nucleotide phosporamidites were synthetized, having branched backbone with different position of functional groups. Obtained phosphoramidite monomers contain intercalator moiety--6-chloro-2-methoxyacridine, and additional hydroxyl residue protected with dimethoxytrityl group or with tert-butyldimethylsilyl group for post-synthetic modification. Synthesized oligothymidilates contain one or more modified units in different positions of sequence. Melting temperature and thermodynamic parameters of formation of complementary duplexes formed by modified oligonucleotides was defined (change in enthalpy and entropy). The introduction of intercalating residue causes a significant stabilization of DNA duplexes. It is shown that the efficiency of the fluorescence of acridine residue in the oligonucleotide conjugate significantly changes upon hybridization with DNA.
Multicomponent glass fibers for optical communications (1980)

The preparation of low-loss multicomponent glasses, and the methods by which both step- and graded-index fibers can be drawn from them are described. The optical performance of fiber prepared by each technique is discussed.
Crystal Structure of the TSH Receptor in Complex with a Thyroid-Stimulating Autoantibody (2007)

It is remarkable that the thyroid-stimulating autoantibody shows almost identical receptor-binding features to TSH although the structures and origins of these two ligands are very different. Furthermore, our structure of the TSHR and its complex with M22 provide foundations for developing new strategies to understand and control both glycoprotein hormone receptor activation and the autoimmune response to the TSHR.
Metalorganic Chemical Vapor Deposition of Ferroelectric Pb(Zr,Ti)O <sub>3</sub> Thin Films (1994)

Ferroelectric Pb(Zr x T 1–x )O 3 , films were successfully and reproducibly deposited by both hot–wall metalorganic chemical vapor deposition (MOCVD) and cold‐wall MOCVD. One of the important problems associated with the MOCVD techniques is the selection of ideal precursors. After an intensive investigation for the most suitable precursors for MOCVD PZT films, the safe and stable precursors, namely lead tetramethylheptadione [Pb(thd) 2 ], zirconium tetramethylheptadione [Zr(thd) 4 ], and titanium ethoxide [Ti(OEt) 4 ], were chosen. The films were deposited at temperatures as low as 550°C and were single‐phase perovskite in the as‐deposited state. Also, the films were smooth, specular, crack‐free, and uniform, and adhered well to the substrates. The stoichiometry of the films can be easily controlled by varying the individual precursor temperature and/or the flow rate of the carrier gas. Auger electron spectroscopic (AES) depth profile showed good compositional uniformity through the thickness of the films. The AES spectra also showed no carbon contamination in the bulk of the films. As‐deposited films were dense and showed uniform and fine grains (≅0.1 μm).The optical properties of the films on the sapphire disks showed high refractive index ( n = 2.413) and low extinction coeflicient ( k = 0.0008) at a wavelength of 632.8 nm. The PZT (82/18) film annealed at 600°C showed a spontaneous polarization of 23.3 μC/cm 2 and a coercive field of 64.5 kV/cm.
Optimization of a PEGylated Glucuronide-Monomethylauristatin E Linker for Antibody–Drug Conjugates (2016)

The emergence of antibody-drug conjugates (ADC), such as brentuximab vedotin and ado-trastuzumab emtansine, has led to increased efforts to identify new payloads and develop improved drug-linker technologies. Most antibody payloads impart significant hydrophobicity to the ADC, resulting in accelerated plasma clearance and suboptimal in vivo activity, particularly for conjugates with high drug-to-antibody ratios (DAR). We recently reported on the incorporation of a discrete PEG<sub>24</sub> polymer as a side chain in a β-glucuronidase-cleavable monomethylauristatin E (MMAE) linker to provide homogeneous DAR 8 conjugates with decreased plasma clearance and increased antitumor activity in xenograft models relative to a non-PEGylated control. In this work, we optimized the drug-linker by minimizing the size of the PEG side chain and incorporating a self-stabilizing maleimide to prevent payload de-conjugation in vivo Multiple PEG-glucuronide-MMAE linkers were prepared with PEG size up to 24 ethylene oxide units, and homogeneous DAR 8 ADCs were evaluated. A clear relationship was observed between PEG length and conjugate pharmacology when tested in vivo Longer PEG chains resulted in slower clearance, with a threshold length of PEG<sub>8</sub> beyond which clearance was not impacted. Conjugates bearing PEG of sufficient length to minimize plasma clearance provided a wider therapeutic window relative to faster clearing conjugates bearing shorter PEGs. A lead PEGylated glucuronide-MMAE linker was identified incorporating a self-stabilizing maleimide and a PEG<sub>12</sub> side chain emerged from these efforts, enabling highly potent, homogeneous DAR 8 conjugates and is under consideration for future ADC programs. Mol Cancer Ther; 16(1); 116-23. ©2016 AACR.
A model-driven transformation method (2004)

Model-driven architectures (MDA) separate the business or application logic from the underlying platform technology and represent this logic with precise semantic models. These models are supposed to span the entire life cycle of a software system and ease the software production and maintenance tasks. Consequently, tools will be needed that support these tasks. In this paper, we present a method that implements model-driven transformations between particular platform-independent (business view) and platform-specific (IT architectural) models. On the business level, we focus on business view models expressed in ADF or UML2, whereas on the IT architecture side we focus on service-oriented architectures with Web service interfaces and processes specified in business process protocol languages such as BPEL4WS.
Hybrid Check Node Architectures for NB-LDPC Decoders (2018)

This paper proposes a unified framework to describe the check node architectures of non-binary low-density parity-check (NB-LDPC) decoders. Forward-backward, syndrome-based, and pre-sorting approaches are first described. Then, they are hybridized in an effective way to reduce the amount of computation required to perform a check node. This paper is specially impacting check nodes of high degrees (or high coding rates). Results of 28-nm ASIC post-synthesis for a check node of degree 12 (i.e., a code rate of 5/6 with a degree of variable equal to 2) are provided for NB-LDPC over GF(64) and GF(256). While simulations show almost no performance loss, the new proposed hybrid implementation check node increases the hardware and the power efficiency by a factor of six compared with the classical forward-backward architecture. This leads to the first ever reported implementation of a degree 12 check node over GF(256), and these preliminary results open the road to high decoding throughput, high rate, and high-order Galois field NB-LDPC decoder with a reasonable hardware complexity.
Recombinant Ebolavirus antigens from insect cells are potent immunogens inducing cellular and humoral immunity in rodents and non-human primates and provide protection against virus challenge (P4325) (2013)

Abstract Soluble recombinant Filovirus surface glycoproteins (GP) and matrix proteins (VP24 and VP40) were generated in the Drosophila S2 cell expression system and purified by immunoaffinity chromatography. The immunogenicity of individual recombinant Zaire ebolavirus (ZEBOV) subunits and admixtures with or without adjuvants was evaluated in mice, guinea pigs and macaques. Strong antigen-specific IgG responses were observed, includng Ebola virus neutralization responses. In mice and macaques subunit proteins were shown to elicit cell mediated immunity, as significant B- and T-cell stimulation was observed in immune lymphocytes after antigen re-stimulation. Analysis of secreted cytokines in batch-cultured, antigen-stimulated splenocytes or PBMC’s demonstrated Th1 and Th2 type responses. Vaccine candidates were tested in mice and guinea pigs for direct protection against challenge with species-adapted ZEBOV. All vaccine formulations containing ZEBOV GP were protective in mice and serum transfer from such animals into naïve mice demonstrated that humoral immunity alone can be fully protective. Furthermore, the transfer of immune splenocytes into naïve mice showed that recombinant GP and VP24 subunits elicit functional T cell responses that lead to protection against live virus challenge. In guinea pigs, lead vaccine formulations consistently produced high antibody responses and demonstrated 100% protective efficacy in the ZEBOV challenge model.
Localization optoacoustic tomography (2018)

Localization-based imaging has revolutionized fluorescence optical microscopy and has also enabled unprecedented ultrasound images of microvascular structures in deep tissues. Herein, we introduce a new concept of localization optoacoustic tomography (LOT) that employs rapid sequential acquisition of three-dimensional optoacoustic images from flowing absorbing particles. We show that the new method enables breaking through the spatial resolution barrier of acoustic diffraction while further enhancing the visibility of structures under limited-view tomographic conditions. Given the intrinsic sensitivity of optoacoustics to multiple hemodynamic and oxygenation parameters, LOT may enable a new level of performance in studying functional and anatomical alterations of microcirculation.
Botulinum toxin type A (BOTOX) for treatment of migraine (2001)

An open-label study and 2 double-blind, placebo-controlled studies have provided supporting evidence of botulinum toxin type A (BTX-A) as an effective, well-tolerated treatment for migraine. Observed durations of benefit were consistent with known properties of BTX-A. Findings suggest that response may vary by features of preinjection headaches, such as migraine frequency. The precise mechanism by which BTX-A provides pain relief is hypothesized to be related not only to acetylcholine inhibition but also to a blocking action on the parasympathetic nervous system. Additional studies that control factors likely to be related to response may lead to better understanding of the BTX-A effect on migraine and an optimal treatment protocol.
Systematic Synthesis of Sialoglycoconjugates "Gangliosides" Towards the Elucidation of their Biological Functions. (1992)

The facile regio- and stereo-controlled α-glycosidations of sialic acid (Neu5Ac) are now well studied by using the thioglycosides of Neu5Ac as glycosyl donors, and suitably protected sugar residues as glycosyl acceptors. High yields of desired products are possible either by using DMTST or NIS/TfOH as thiophilic promoters in acetonitrile. A variety of gangliosides, such as GM4, GM3, GM2, GM1a, GM1b, GD1a, GD1α, GD3, lacto- and neolacto-series gangliosides, and their isomers, have systematically been synthesized by a series of reactions which start from the condensation of sialo-oligosaccharides and 2-azido-sphingosine. Various analogs and derivatives of gangliosides containing thioglycosidic linkage (s), modified sialic acids and pseudo-ceramides have also been synthesized. Recent advance in the biomedical studies using synthetic gangliosides, especially sialyl Lex and its related carbohydrate ligands, is also described.
Synthesis of 2-, 3- and 9-substituted 11-oxo-11H-pyrrolo[2,1-b][3]benzazepines (1983)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis of 2-, 3- and 9-substituted 11-oxo-11H-pyrrolo[2,1-b][3]benzazepinesPatrice C. Belanger, Joseph G. Atkinson, C. Stanley Rooney, Susan F. Britcher, and David C. RemyCite this: J. Org. Chem. 1983, 48, 19, 3234–3241Publication Date (Print):September 1, 1983Publication History Published online1 May 2002Published inissue 1 September 1983https://pubs.acs.org/doi/10.1021/jo00167a016https://doi.org/10.1021/jo00167a016research-articleACS PublicationsRequest reuse permissionsArticle Views505Altmetric-Citations26LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Don't trust the cloud, verify (2015)

Cloud services have turned remote computation into a commodity and enable convenient online collaboration. However, they require that clients fully trust the service provider in terms of confidentiality, integrity, and availability. Towards reducing this dependency, this paper introduces a protocol for verification of integrity and consistency for cloud object storage (VICOS), which enables a group of mutually trusting clients to detect data-integrity and consistency violations for cloud storage. It aims at services where multiple clients cooperate on data stored remotely on a potentially misbehaving service. VICOS enforces the consistency notion of fork-linearizability, supports wait-free client semantics for most operations, and reduces the computation and communication overhead compared to previous protocols. VICOS is based in a generic way on any authenticated data structure. A prototype of VICOS that works with the key-value store interface of commodity cloud storage has been implemented, and an evaluation demonstrates its advantage compared to existing systems.
Towards Real-Time Estimation of Solar Generation From Micro-Synchrophasor Measurements (2016)

This paper presents a set of methods for estimating the renewable energy generation downstream of a measurement device using real-world measurements. First, we present a generation disaggregation scheme where the only information available for estimation is the micro-synchrophasor measurements obtained at the substation or feeder head. We then propose two strategies in which we use measurements from the substation as well as a proxy solar irradiance measurement. Using these two measurement points, we first propose a multiple linear regression strategy, in which we estimate a relationship between the measured reactive power and the load active power consumption, which are then used in disaggregation. Finally, we expand this strategy to strategically manage the reconstruction errors in the estimators. We simultaneously disaggregate the solar generation and load. We show that it is possible to disaggragate the generation of a 7.5 megawatt photovoltaic site with a root-mean-squared error of approximately 450 kilowatts.
Tunneling gate oxide approach to ultra-high current drive in small geometry MOSFETs (2002)

Ultra-high performance n-MOSFETs were fabricated with a tunneling gate oxide 1.5 nm thick. It was found that these devices operate well when the gate length is around 0.1 /spl mu/m, because gate leakage current falls in proportion to the gate length and the drain current increases in inverse proportion. A very high drivability of 1.1 mAspl mu/m at 15 V was obtained, even in devices with a 0.14 pm gate length. A record high transconductance, 1,010 mS/mm at room temperature was also obtained in 0.09 /spl mu/m MOSFETs. Confirmation was obtained that hot-carrier reliability improves as the gate oxide thickness is reduced, even in the 1.5 nm case. High current drive at the low supply voltage of 0.5 V was also demonstrated. We made clear that very high performance is obtained in Si MOSFETs, if we can use a high capacitance gate insulator. In future devices, the tunnel gate oxide may be a good candidate for such a gate film, depending upon their applications.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Improved Interactive Medical-Imaging System (2003)

An improved computational-simulation system for interactive medical imaging has been invented. The system displays high-resolution, three-dimensional-appearing images of anatomical objects based on data acquired by such techniques as computed tomography (CT) and magnetic-resonance imaging (MRI). The system enables users to manipulate the data to obtain a variety of views for example, to display cross sections in specified planes or to rotate images about specified axes. Relative to prior such systems, this system offers enhanced capabilities for synthesizing images of surgical cuts and for collaboration by users at multiple, remote computing sites.
A conformation-switching fluorescent protein probe for detection of alpha synuclein oligomers (2013)

We engineered the structural flexibility of an α synuclein (αS) variant, PG65, together with conformation-sensitive fluorescence to create a molecular probe for rapid, specific and quantitative detection of αS oligomers, which are the major toxic aggregate forms in Parkinson's disease.
Acquaintance: A Novel Vector-Space N-Gram Technique for Document Categorization. (1994)

Acquaintance is the name of a novel vector-space n-gram technique for categorizing documents. The technique is completely language independent, highly garble resistant, and computationally simple. An unoptimized version of the algorithm was used to process the TREC database in a very short time.
Molecular characterization of prostate-specific antigen messenger RNA expressed in breast tumors. (1994)

Prostate-specific antigen (PSA) is considered a highly specific biochemical marker of the prostate gland and is currently used for prostate cancer diagnosis and monitoring of patients with prostate adenocarcinoma. We recently demonstrated, however, that about 30% of female breast tumors produce a M(r) 33,000 protein that has striking similarities to seminal PSA. In this study we characterized the presence of PSA in 6 breast tumors and in the testosterone-stimulated T47D breast cancer cell line at the mRNA level. Using reverse transcriptase-polymerase chain reaction and DNA sequencing techniques we identified PSA mRNA in immunoreactive PSA-positive breast tumors but not in immunoreactive PSA-negative breast tumors. The sequence of the generated polymerase chain reaction products was identical to the sequence of the PSA complementary DNA derived from prostate tissue. The data presented here support the notion that breast tumors produce a M(r) 33,000 protein which is identical to PSA produced by the prostate gland. Our study suggests that the presence of PSA in breast tumors may be used as a new additional biochemical marker for breast cancer prognosis, for the spreading of hematogenous micrometastases, and/or for response to adjuvant treatment.