gebhart/patrepeval huggingface dataset:
In Vivo Pharmacodynamic Imaging of Proteasome Inhibition (2009)

Inhibiting the proteolytic activity of the 26S proteasome has been shown to have selective apoptotic effects on cancer cells and to be clinically efficacious in certain malignancies. There is an unmet medical need for additional proteasome inhibitors, and their development will be facilitated by surrogate markers of proteasome function. Toward this end, ectopic fusion of the destruction domain from ornithine decarboxylase (ODC) to reporter proteins is often used for assessing proteasome function. For luciferase-based reporters, we hypothesized that the oxygen-dependent destruction domain (ODD) from hypoxia-inducible factor 1 alpha (HIF-1 alpha) may provide improved sensitivity over luciferase-ODC, owing to its extremely rapid turnover by the proteasome (HIF-1 alpha has a half-life of less than 5 minutes). In the current study, we show that ODD-luciferase affords a greater dynamic range and faster kinetics than luciferase-ODC in sensing proteasome inhibition in vitro. Importantly, ODD-luciferase also serves as an effective in vivo marker of proteasome function in xenograft tumor models, with inhibition being detected by noninvasive imaging within 3 hours of bortezomib administration. These data establish ODD-luciferase as a surrogate marker of proteasome function that can be used both in vitro and in vivo for the development of novel proteasome inhibitors.
Integrated Si 3 N 4 Soliton Microcomb Driven by a Compact Ultra-Low-Noise Laser (2019)

We generate 100-GHz soliton microcombs in a photonic integrated high-Q Si 3 N 4 microresonator using an ultra-compact, high-power and low-frequency-noise semiconductor-based laser. The soliton is initiated via direct current tuning of the laser. © 2019 The Author(s)
Combining long-range dependencies with phase information in Natural Stochastic Texture enhancement (2014)

Enhancement of Natural Stochastic Textures (NST) is of special interest in image processing. These textures are considered to be realizations of random processes, and exhibit different statistical properties than those characteristic of cartoontype natural images or of structured textures. NSTs are interesting due to their fine details, which pose a challenge to enhancement algorithms. Existing algorithms, based on models of natural images, do not produce satisfactory results on NST. The long-range dependence (LRD) property of NST is explored and substantiated in this paper. An optimization scheme, implemented in the frequency domain, is then proposed. This scheme exploits the LRD as a property of the frequency magnitude, while a desired phase, extracted from the degraded image, is imposed. The scheme is general and can be further used in other image processing tasks. Zero-phase filters are of special interest in this context.
Comparison of Corrosion-Fatigue Cracking of Al-Li Alloy AA 2090-T8E41 and Alloy AA 7075-T651 in Salt Water (1989)

The corrosion-fatigue cracking behavior of aluminum-lithium alloy AA(1) 2090-T8E41 (UNS(2) A92090) and alloy AA 7075-T651 (UNS A97505) in air and 3.5% NaCl solution were investigated, using a fracture mechanics approach. The 2090-T8E41 alloy, as fatigued in air, was found to exhibit a very tortuous fracture-surface morphology and high crack-closure levels that led to fatigue-crack growth rates about 10 times lower than counterpart growth rates for alloy 7075-T651. Such roughness-induced crack closure was greatly reduced for specimens tested in 3.5% NaCl solution, as the conjoint action of salt water corrosion and mechanical fretting greatly diminshed the fracture surface tortuosity; consequently, fatigue-crack growth rates were elevated approximately 6-fold relative to those in air. Fatigue-crack growth rates of alloy 7075-T651 in salt water in the intermediate stress intensity range (ΔK) region were 2 to 3 times higher than those in air. However, in the low ΔK region, the crack-growth rates in salt water were comparable or even lower than those in air. This unusual phenomenon was attributed to the corrosion product induced crack closure.
High quantum efficiency and narrow absorption bandwidth of the wafer-fused resonant In/sub 0.53/Ga/sub 0.47/As photodetectors (1994)

We demonstrate greater than 90% quantum efficiency in an In/sub 0.53/Ga/sub 0.47/As photodetector with a thin (900 /spl Aring/) absorbing layer. This was achieved by inserting the In/sub 0.53/Ga/sub 0.47/As/InP epitaxial layer into a microcavity composed of a GaAs/AlAs quarter-wavelength stack (QWS) and a Si/SiO/sub 2/ dielectric mirror. The 900-/spl Aring/-thick In/sub 0.53/Ga/sub 0.47/As layer was wafer fused to a GaAs/AlAs mirror, having nearly 100% power reflectivity. A Si/SiO/sub 2/ dielectric mirror was subsequently deposited onto the wafer-fused photodiode to form an asymmetric Fabry-Perot cavity. The external quantum efficiency and absorption bandwidth for the wafer-fused RCE photodiodes were measured to be 94/spl plusmn/3% and 14 nm, respectively. To our knowledge, these wafer-fused RCE photodetectors have the highest external quantum efficiency and narrowest absorption bandwidth ever reported on the long-wavelength resonant-cavity-enhanced photodetectors.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
HTR: A framework for interconnecting wireless heterogeneous devices (2012)

The last two decades have witnessed major advances in the wireless communication area, which have been supported by the increasing capabilities of portable devices, such as notebooks, tablets, cellular phones, smart phones and personal digital assistants (PDAs). Today, they provide a rich computing environment and incorporate different radio technologies. Despite of network diversity, a great deal of research in the field of mobile ad hoc networks focuses on a single and isolated wireless technology at a time, with homogeneous elements identified by IP addresses. This work proposes a Heterogeneous Technology Routing Framework (HTR), targeted towards scenarios where the heterogeneity of devices and networking technologies is present. Our contribution is twofold. It consists of a framework, which encompasses a process for bootstrapping networks, and a routing protocol capable of dealing with multiple network interfaces. We then evaluate the performance of this protocol by taking measurements in a real test-bed.
An APD-CMOS image sensor toward high sensitivity and wide dynamic range (2016)

We present a sensitivity-boosting technique by incorporating an avalanche photodiode into a normal photo-conversion region. Under a dark scene, an avalanche photodiode operation is selected, where the photo-electrons are multiplied up to 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5</sup> electrons. Under a bright scene, a photodiode operation is selected, where photo-electrons in proportional to light intensity are generated in a similar way to conventional CMOS image sensors. Alternating the two operations enables wide operational range extending to dark conditions.
Accelerating in-system FPGA debug of high-level synthesis circuits using incremental compilation techniques (2017)

High-Level Synthesis has emerged as a promising technology for improving FPGA designer productivity, but will only be successful if it is accompanied by a debug ecosystem. Recent efforts have presented in-system debug techniques which allow a designer to debug an implementation, running on an FPGA, in the context of the original source code. These techniques typically store a history of all user variables on chip. To maximize the effectiveness of the on-chip memory, it is desirable to store only selected user variables. Unfortunately, this may lead to multiple debug runs. In existing frameworks, changing the variables to be stored between runs requires a full recompile. In this paper, we propose several flows that use incremental compilation to reduce the debug turn-around time. The first flow, in which the user circuit and instrumentation are co-optimized during compilation, gives the fastest debug clock speeds but suffers in user circuit performance once the debug instrumentation is removed. In the second flow, the optimization of the user circuit is sacrosanct. It is placed and routed first without having any constraints and the debug instrumentation is added later leading to the fastest user circuit clock speeds, but performance suffers slightly during debug. Using either flow, we achieve 40% reduction in debug turn-around times, on average.
Intravesical Delivery of Small Activating RNA Formulated into Lipid Nanoparticles Inhibits Orthotopic Bladder Tumor Growth (2012)

Practical methods for enhancing protein production in vivo remain a challenge. RNA activation (RNAa) is emerging as one potential solution by using double-stranded RNA (dsRNA) to increase endogenous gene expression. This approach, although related to RNA interference (RNAi), facilitates a response opposite to gene silencing. Duplex dsP21-322 and its chemically modified variants are examples of RNAa-based drugs that inhibit cancer cell growth by inducing expression of tumor suppressor p21(WAF1/CIP1) (p21). In this study, we investigate the therapeutic potential of dsP21-322 in an orthotopic model of bladder cancer by formulating a 2'-fluoro-modified derivative (dsP21-322-2'F) into lipid nanoparticles (LNP) for intravesical delivery. LNP composition is based upon clinically relevant formulations used in RNAi-based therapies consisting of PEG-stabilized unilamellar liposomes built with lipid DLin-KC2-DMA. We confirm p21 induction, cell-cycle arrest, and apoptosis in vitro following treatment with LNP-formulated dsP21-322-2'F (LNP-dsP21-322-2'F) or one of its nonformulated variants. Both 2'-fluoro modification and LNP formulation also improve duplex stability in urine. Intravesical delivery of LNP-dsP21-322-2'F into mouse bladder results in urothelium uptake and extends survival of mice with established orthotopic human bladder cancer. LNP-dsP21-322-2'F treatment also facilitates p21 activation in vivo leading to regression/disappearance of tumors in 40% of the treated mice. Our results provide preclinical proof-of-concept for a novel method to treat bladder cancer by intravesical administration of LNP-formulated RNA duplexes.
Abstract 741: Combined inhibition of MDM2 and MEK for KRAS mutant non-small cell lung cancer (2014)

Abstract There are currently no effective targeted therapies for KRAS mutant NSCLC. Combination drug strategies that target downstream pathways activated by mutant KRAS are currently being investigated, however efficacy may be limited by inability to induce a sufficient apoptotic response. MDM-2 (murine double minute 2) is a ubiquitin ligase that negatively regulates p53 function by promoting its degradation. Inhibitors of the MDM2-p53 interaction lead to p53 activation and transcription of genes promoting cell cycle arrest and apoptosis. We investigated the efficacy of combined MEK and MDM2 inhibition for KRAS mutant NSCLC. In KRAS mutant NSCLC cell lines with wild-type p53, pimasertib (MEKi) and SAR405838 (MDM-2i) led to upregulation of BIM and PUMA respectively. Induction of apoptosis and cell cycle arrest correlated with in vitro efficacy, and the combination exhibited marked in vivo activity against KRAS mutant p53 wild-type NSCLC xenograft tumors. These studies provide rationale for future clinical investigation of combined MEK and MDM-2 inhibition for KRAS mutant NSCLC. Citation Format: Aaron N. Hata, Hannah L. Archibald, Maria D. Gomez-Caraballo, Laurent R. DeBussche, Sukhvinder Sidhu, James Watters, Jeffrey A. Engelman. Combined inhibition of MDM2 and MEK for KRAS mutant non-small cell lung cancer. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 741. doi:10.1158/1538-7445.AM2014-741
Protein-lipid interactions. Studies of the M13 coat protein in dimyristoylphosphatidylcholine vesicles using parinaric acid (1979)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTProtein-lipid interactions. Studies of the M13 coat protein in dimyristoylphosphatidylcholine vesicles using parinaric acidDavid Kimelman, Evelyn S. Tecoma, Paul K. Wolber, Bruce S. Hudson, William T. Wickner, and Robert D. SimoniCite this: Biochemistry 1979, 18, 26, 5874–5880Publication Date (Print):December 1, 1979Publication History Published online1 May 2002Published inissue 1 December 1979https://pubs.acs.org/doi/10.1021/bi00593a018https://doi.org/10.1021/bi00593a018research-articleACS PublicationsRequest reuse permissionsArticle Views41Altmetric-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
Performance assessment across different care settings of a heart failure hospitalisation risk-score for type 2 diabetes using administrative claims (2022)

Predicting the risk of cardiovascular complications, in particular heart failure hospitalisation (HHF), can improve the management of type 2 diabetes (T2D). Most predictive models proposed so far rely on clinical data not available at the higher Institutional level. Therefore, it is of interest to assess the risk of HHF in people with T2D using administrative claims data only, which are more easily obtainable and could allow public health systems to identify high-risk individuals. In this paper, the administrative claims of > 175,000 patients with T2D were used to develop a new risk score for HHF based on Cox regression. Internal validation on the administrative data cohort yielded satisfactory results in terms of discrimination (max AUROC = 0.792, C-index = 0.786) and calibration (Hosmer-Lemeshow test p value < 0.05). The risk score was then tested on data gathered from two independent centers (one diabetes outpatient clinic and one primary care network) to demonstrate its applicability to different care settings in the medium-long term. Thanks to the large size and broad demographics of the administrative dataset used for training, the proposed model was able to predict HHF without significant performance loss concerning bespoke models developed within each setting using more informative, but harder-to-acquire clinical variables.
Very Large Cooperative Effects in Heterobimetallic Titanium-Chromium Catalysts for Ethylene Polymerization/Copolymerization (2014)

The heterobimetallic complexes, (η(5)-indenyl)[1-Me2Si((t)BuN)TiCl2]-3-CnH2n-[N,N-bis(2-(ethylthio)ethyl)amine]CrCl3 (n = 0, Ti-C0-Cr(SNS); n = 2, Ti-C2-Cr(SNS); n = 6, Ti-C6-Cr(SNS)), (η(5)-indenyl)[1-Me2Si((t)BuN)TiCl2]-3-C2H4-[N,N-bis((o-OMe-C6H4)2P)amine]CrCl3 (Ti-C2-Cr(PNP)), and (η(5)-indenyl)[1-Me2Si((t)BuN)TiCl2]-3-C2H4-[N,N-bis((diethylamine)ethyl)-amine]CrCl3 (Ti-C2-Cr(NNN)), are synthesized, fully characterized, and employed as olefin polymerization catalysts. With ethylene as the feed and MAO as cocatalyst/activator, SNS-based complexes Ti-C0-Cr(SNS), Ti-C2-Cr(SNS), and Ti-C6-Cr(SNS) afford linear low-density polyethylenes (LLDPEs) with exclusive n-butyl branches (6.8-25.8 branches/1000 C), while under identical polymerization conditions Ti-C2-Cr(PNP) and Ti-C2-Cr(NNN) produce polyethylenes with heterogeneous branching (C2, C4, and C≥6) or negligible branching, respectively. Under identical ethylene polymerization conditions, Ti-C0-Cr(SNS) produces polyethylenes with higher activity (4.5× and 6.1×, respectively), Mn (1.3× and 1.8×, respectively), and branch density (1.4× and 3.8×, respectively), than Ti-C2-Cr(SNS) and Ti-C6-Cr(SNS). Versus a CGC(Et)Ti + SNSCr tandem catalyst, Ti-C0-Cr(SNS) yields polyethylene with somewhat lower activity, but with 22.6× higher Mn and 4.0× greater branching density under identical conditions. In ethylene +1-pentene competition experiments, Ti-C0-Cr(SNS) yields 5.5% n-propyl branches and 94.5% n-butyl branches at [1-pentene] = 0.1 M, and the estimated effective local concentration of 1-hexene is ∼8.6 M. In contrast, the tandem CGC(Et)Ti + SNSCr system yields 91.0% n-propyl branches under identical reaction conditions. The homopolymerization and 1-pentene competition results argue that close Ti···Cr spatial proximity together with weak C-H···Ti and C-H···S interactions significantly influence relative 1-hexene enchainment and chain transfer rates, supported by DFT computation, and that such effects are conversion insensitive but cocatalyst and solvent sensitive.
Fate of phthalic acid esters during digestion of municipal solid waste under landfill conditions (1997)

The objective of this thesis has been to investigate whether anaerobic microorganisms developing in acidogenic and methanogenic landfill environments have the potential to degrade phthalic acid esters (PAEs) and what kinds of intermediates may be formed, assuming PAE degradation. PAEs form a group of compounds widely used in huge amounts worldwide, mainly as plasticiser in PVC-plastics. PAEs are presently entering Swedish landfills, mostly via PVC-plastics deposited as refuse, but also via other products. At landfills they are subjected to an anaerobic environment and may be stored for several decades and centuries under such conditions. Diluted and homogenised municipal solid waste (MSW) samples from different landfill environments were used as inocula in an assay developed for the purpose to determine the potential of microbial PAE degradation. The results showed that the microorganisms present in the MSW-samples were able to transform almost all PAEs investigated. However, the degradation of PAEs may give rise to compounds which are more chemically inert than the parental compounds. As an example bis(2-ethylhexyl) phthalate (DEHP) was observed to be degraded to mono(2-ethylhexyl) phthalate during 300 days of incubation. Monoesters of PAEs were observed in leachate from methanogenic landfill lysimeters in concentrations up to 12 mg per litre during MSW degradation. Ten fold amounts of PVC-plastic were also added to landfill lysimeters to investigate whether PAEs or degradation intermediates could be detected in the lysimeter leachate above the indigenous concentrations of PAEs. This was shown not to be the case for methanogenic conditions. However, the PVC-plastics subjected to methanogenic conditions were shown to be leached of PAEs, which did not occur for samples under acidogenic conditions. The results imply that microbial degradation enhanced the loss of PAEs from the PVC-plastics incubated under methanogenic conditions
Recurrent Neural Network based MPC for Process Industries (2019)

Autonomous operation of industrial plants requires a cheap and efficient way of creating dynamic process models, which can then be used to either be part of the autonomous systems or to serve as simulators for reinforcement learning. The trends of digitalization, cheap storage, and industry 4.0 enable the access to more and more historical data that can be used in data driven methods to perform system identification. Model predictive control (MPC) is a promising advanced control framework, which might be part of autonomous plants or contribute to some extent to autonomy. In this article, we combine data-driven modeling with MPC and investigate how to train, validate, and incorporate a special recurrent neural network (RNN) architecture into an MPC framework. The proposed structure is designed for being scalable and applicable to a wide range of multiple-input multiple-output (MIMO) systems encountered in industrial applications. The training, validation, and closed-loop control using RNNs are demonstrated in an industrial simulation case study. The results show that the proposed framework performs well dealing with challenging practical conditions such as MIMO control, nonlinearities, noise, and time delays.
A New Algorithm for estimating three-phase relative permeability from unsteady-state core experiments (2010)

We present a new history matching method based on a Genetic Algorithm to estimate three-phase k
 r (relative permeability) from unsteady-state coreflood experiments. In this method, relative permeabilities (k
 r) are represented by quadratic B-Spline functions. Adjustable coefficients in k
 r functions are changed in an iterative process to minimize an objective function. The objective function is defined as the difference between the measures and simulated values of the pressure drop across the core and fluids recovery during the experiment. One of the main features of this approach is that water and gas relative permeabilities (k
 rw and k
 rg) are assumed to be functions of two independent saturations as opposed to most of the existing empirical k
 r models in which k
 rw and k
 rg are assumed to be only dependent of their own saturations. Another important aspect of this algorithm is that it considers inequality constrains to ensure that physically acceptable k
 r curves are maintained throughout the iterative optimization process. A three-phase coreflood simulator has been developed based on this methodology that generates best k
 r values by matching experimental data. The integrity of the developed software was first successfully verified by using two sets of experimental three-phase k
 r data published in the literature. Then, the results of some three-phase coreflood experiments carried out in our laboratory were used to obtain three-phase k
 r curves by this approach.
Synthesis of poly(8-aminopyrene-1,3,6-trisulfonic acid)/CNT Nanocomposite for Electrochemical Detection of Caffeine (2016)

We synthesized nanocomposite of polymerized 8-aminopyrene-1,3,6-trisulfonic acid (APTA) and single-walled carbon nanotubes (SWCNTs). To prepare the nanocomposite, SWCNTs were dispersed in aqueous solution of APTA (monomers) using a probe sonicator. The as-prepared APTA/SWCNTs dispersion was characterized using Raman, FT-IR, and UV-visible-near infrared (UV-vis-NIR) spectroscopies. Cyclic voltammetry measurements indicated that polymerization of APTA occurred during probe sonication due to the oxidation of APTA molecules. Using the poly(APTA)/SWCNTs dispersion, a conducting thin film was prepared on a glassy carbon electrode (GCE) and its electrochemical and catalytic properties were studied. The poly(APTA)/SWCNTs film coated electrode exhibited excellent electrochemical catalytic activity toward the oxidation of caffeine (CAF) with a linear range from 10 μM to 0.76 mM with a linear regression equation; Ipa (mA) = 0.015 mM + 5.84 × 10−7 (R2 = 0.993). In addition, the other common electroactive biomolecules such as dopamine (DA) and ascorbic acid (AA) did not interfere with the CAF oxidation peak. Well-defined oxidation peaks (with high catalytic currents) of AA (+0.49 V), DA (+0.53 V) and CAF (+1.47 V) were simultaneously observed at the poly(APTA)/SWCNTs sensor. Selective detection of CAF in fruit juices was also demonstrated.