gebhart/patrepeval huggingface dataset:
Transcription Factor Decoy to Study the Molecular Mechanism of Negative Regulation of Renin Gene Expression in the Liver In Vivo (1999)

Renin is synthesized in high quantities in the juxtaglomerular cells of the kidney, but little or none is synthesized in the liver. Our previous in vitro and biochemical studies have demonstrated that tissue-specific expression of the mouse renin gene is regulated by the specific interaction between negative regulatory element (NRE) in the 5'-flanking region of the renin gene and NRE binding protein (NREB). In this study, we examined the hypothesis that this interaction between the NRE in the promoter region of the rat renin gene and the NREB in the liver contributes to the suppressed renin gene expression in this tissue in vivo. We used in vivo transfection of NRE transcription factor decoy (TFD) double-stranded oligonucleotide into the rat liver via portal vein infusion. A gel mobility shift assay showed that transfected NRE TFD blocked endogenous NREB binding with the rat renin gene. This resulted in enhanced hepatic renin mRNA expression, immunohistochemical detection of renin in the liver, and consequently, increased plasma renin concentration. Taken together, these results document the importance of NREB in the inhibition of renin gene expression in rat liver in vivo and suggest the possibility of in vivo renin gene modulation by the TFD approach.
Efficient Charge Separation in Li+@C60 Supramolecular Complexes with Electron Donors (2014)

Lithium-ion-encapsulated fullerene (Li(+) @C60 ) exhibits greatly enhanced reactivity in photoinduced electron-transfer reduction with electron donors compared with pristine C60 . The enhanced reactivity of Li(+) @C60 results from the more positive one-electron reduction potential of Li(+) @C60 (+0.14 V versus a standard calomel electrode (SCE)) than that of C60 (-0.43 V versus SCE), whereas the reorganization energy of electron transfer of Li(+) @C60 (1.01 eV) becomes larger than that of C60 (0.73 eV) because of the change in electrostatic interactions of encapsulated Li(+) upon electron transfer. Li(+) @C60 can form strong supramolecular complexes with various anionic electron donors through electrostatic interactions. Li(+) @C60 can also form strong supramolecular π complexes with various electron donors, such as cyclic porphyrin dimers, corannulene, and crown ether fused monopyrrolotetrathiafulvalenes. Photoinduced electron transfer from electron donors to Li(+) @C60 afforded long-lived charge-separated states of supramolecular complexes between electron donors and Li(+) @C60 . A photoelectrochemical solar cell composed of supramolecular nanoclusters of Li(+) @C60 and zinc sulfonated meso-tetraphenylporphyrin exhibits significant enhancement in the photoelectrochemical performance than that of the reference system containing only a single component.
Lymphangiogenesis guidance by paracrine and pericellular factors (2017)

Lymphatic vessels are important for tissue fluid homeostasis, lipid absorption, and immune cell trafficking and are involved in the pathogenesis of several human diseases. The mechanisms by which the lymphatic vasculature network is formed, remodeled, and adapted to physiological and pathological challenges are controlled by an intricate balance of growth factor and biomechanical cues. These transduce signals for the readjustment of gene expression and lymphatic endothelial migration, proliferation, and differentiation. In this review, we describe several of these cues and how they are integrated for the generation of functional lymphatic vessel networks.
The potential cost savings of implementing an inter-utility NO{sub x} trading program (1995)

Technology based standards such as RACT, which require the installation of a (R)easonably (A)vailable (C)ontrol (T)echnology on a boiler by boiler basis have been the dominant factor driving electric utility NO{sub x} compliance plans. In this paper, the authors examine the cost savings of implementing NO{sub x} trading, an alternative market based strategy for reducing the emissions of nitrogen oxides (NO{sub x}) to achieve NO{sub x} reduction goals set under Title IV of the 1990 Clean Air Act. In order to estimate the potential cost savings of inter-utility NO{sub x} trading, they use a combinatorial optimization approach to identify boiler retrofits and operating parameters which yield efficient (i.e., the most cost effective) NO{sub x} abatement strategies. In their formulation, annual emissions at individual boilers which are expensive to abate may exceed RACT levels by up to a factor of two thus allowing for trades with boilers which can abate in a more cost effective manner. They constrain total emissions in a trading region to be at or below the level obtained had all the boilers adopted RACT. Increasing the flexibility with which trades can occur has two main effects: (1) the cost effectiveness of meeting an aggregate reduction goal increasesmore » and (2) the spatial distribution of emissions shift relative to what it would have been under a strict RACT based compliance strategy. They estimate the magnitude of these effects for two Eastern electric utilities making intra- and inter-utility NO{sub x} trades. Results indicate that the cost effectiveness of meeting RACT level reduction can be increased by as much as 38% under certain trading regimes.« less
Sample-profile estimate for fast atomic force microscopy (2005)

In this letter, a design scheme that achieves an optimal tip-sample force regulation with an ideal topography image reconstruction is presented. It addresses the problem of obtaining accurate sample profiles when scanning at high bandwidth while maintaining a constant cantilever-tip sample force in atomic force microscopes. In this design scheme, the objective of maintaining a constant tip-sample force while scanning at high bandwidth does not impose limitations on the reconstruction of the sample topography. It is shown that the proposed scheme provides a faithful replica of the sample at all relevant scanning speeds limited only by the inaccuracy in the model for the atomic force microscope. This provides an improvement over existing designs where the sample profile reconstruction is typically bandwidth limited. Comparison with the existing methods of using the control signal as the image is provided. The experimental results corroborate the theoretical development.
Magnetic resonance imaging of hepatic fibrosis: Emerging clinical applications (2007)

Chronic liver disease and cirrhosis remains a major public health problem worldwide. While the majority of complications from chronic liver disease result from progressive hepatic fibrosis, the available diagnostic tests used in clinical practice are not sensitive or specific enough to detect occult liver injury at early or intermediate stages. While liver biopsy can stage the extent of fibrosis at diagnosis, its utility as a tool for longitudinal monitoring will be limited at the population level. To date, a number of methods including serum marker panels and ultrasound-based transient elastrography have been proposed for the non-invasive identification of hepatic fibrosis. Novel techniques including magnetic resonance (MR) spectroscopy, diffusion weighted MR, and MR elastography have also emerged for detecting fibrosis. In contrast to other non-invasive methods, MR imaging holds the promise of providing functional and biological information about hepatic pathophysiology as it relates to the natural history and future treatment of hepatic fibrosis. (HEPATOLOGY 2007.).
Design optimization of the distributed modal filtering rod fiber for increasing single mode bandwidth (2012)

High-power fiber amplifiers for pulsed applications require large mode area (LMA) fibers having high pump absorption and near diffraction limited output. This improves the limiting factor of nonlinear effects, while maintaining good beam quality. Photonic crystal fibers allow realization of short LMA fiber amplifiers having high pump absorption through a pump cladding that is decoupled from the outer fiber. However, achieving ultra low NA for single-mode (SM) guidance is challenging, and thus different design strategies must be applied to filter out higher order modes (HOMs). The novel distributed modal filtering (DMF) design presented here enables SM guidance, and previous results have shown a SM mode field diameter of 60 &mu;m operating in a 20 nm SM bandwidth. The DMF rod fiber has high index ring-shaped inclusions acting as resonators enabling SM guidance through modal filtering of HOMs. Large preform tolerances are compensated during the fiber draw resulting in ultra low NA fibers with very large cores. In this paper, design optimization of the SM bandwidth of the DMF rod fiber is presented. Analysis of band gap properties results in a fourfold increase of the SM bandwidth compared to previous results, achieved by utilizing the first band of cladding modes. This covers of a large fraction of the Yb emission band, where wavelengths of 1030 nm and 1064 nm can be included.
Simultaneous perception of prosthetic and natural vision in AMD patients (2022)

Loss of photoreceptors in atrophic age-related macular degeneration (AMD) results in severe visual impairment. Since the low-resolution peripheral vision is retained in such conditions, restoration of central vision should not jeopardize the surrounding healthy retina and allow for simultaneous use of the natural and prosthetic sight. This interim report, prespecified in the study protocol, presents the first clinical results with a photovoltaic substitute of the photoreceptors providing simultaneous use of the central prosthetic and peripheral natural vision in atrophic AMD. In this open-label single group feasibility trial (NCT03333954, recruitment completed), five patients with geographic atrophy have been implanted with a wireless 2 x 2 mm-wide 30 µm-thick device, having 378 pixels of 100 µm in size. All 5 patients achieved the primary outcome of the study by demonstrating the prosthetic visual perception in the former scotoma. The four patients with a subretinal placement of the chip demonstrated the secondary outcome: Landolt acuity of 1.17 ± 0.13 pixels, corresponding to the Snellen range of 20/460-20/565. With electronic magnification of up to a factor of 8, patients demonstrated prosthetic acuity in the range of 20/63-20/98. Under room lighting conditions, patients could simultaneously use prosthetic central vision and their remaining peripheral vision in the implanted eye and in the fellow eye.
Batterie convenzionali ed avanzate, sistemi efficienti di accumulo e conversione dell'energia (2007)

Il sistema energetico di oggi basato principalmente sull’energia da combustibili fossili non è più sostenibile per i previsti danni ambientali, per gli aumenti dei costi dovuti alla crescita della richiesta ed il calo delle risorse e per la dipendenza economica dai Paesi produttori di petrolio, destinato per il 30% alla quasi totalità (90%) del trasporto con macchine a combustione interna a bassa efficienza energetica. A livello internazionale vi è un crescente impegno per un nuovo piano energetico sostenibile che vede anche aumentare gli investimenti per lo sfruttamento di energia da fonti rinnovabili, in particolare per le tecnologie più mature come quelle eolica e solare, ed è proprio in tale ambito che emerge il ruolo chiave dei sistemi elettrochimici per un uso efficiente dell’energia [1]. Infatti tali fonti rinnovabili hanno carattere di intermittenza, pertanto risultano di fondamentale importanza i sistemi elettrochimici di accumulo e conversione ad alto rendimento energetico, quali batterie ricaricabili e supercapacitori che accumulano l’energia per poi erogarla e distribuirla efficientemente in base alle richieste e alla potenza desiderata.
Universal cancer screening: revolutionary, rational, and realizable (2018)

Cancer remains the second leading cause of mortality worldwide, and overall cancer-related deaths are increasing. Despite the survival benefit from early detection, screening has to date targeted only those few organs that harbor tumors of sufficient prevalence to show cost-effectiveness at population levels, leaving most cancer types unscreened. In this perspective overview, a case is made for universal cancer screening as a logical and more inclusive approach with potentially high impact. The centrally important conceptual drivers to universal screening are biological and epidemiological. The shared biology of tumor marker release into a common distant medium, like blood, can be exploited for multi-cancer detection from a single test. And, by aggregating prevalence rates, universal screening allows all cancers (including less common ones) to be included as targets, increases screening efficiency and integration across tumor types, and potentially improves cost-effectiveness over single-organ approaches. The identification of new tumor marker classes with both broad expression across tumor types and site-prediction, remarkable advances in assay technologies, and compelling early clinical data increase the likelihood of actualizing this new paradigm. Multi-organ screening could be achieved by targeting markers within or stemming from the circulation (including blood, urine, saliva, and expired breath) or those exfoliated into common excretory pathways (including the gastrointestinal and female reproductive tracts). Rigorous clinical studies in intended use populations and collaborations between academia, industry, professional societies, and government will be required to bring this lofty vision to a population application.
Concurrent fault detection for a multiple-plane packet switch (2003)

In high-speed and high-capacity packet switches, system reliability is critical to avoid loss of huge amounts of information and retransmission of traffic. We propose a series of concurrent fault-detection mechanisms for a multiple-plane crossbar-based packet switch. Our switch model, called the m+z model, has m active planes and z spare planes. This switch has distributed arbiters on each plane. The spare planes, used for substitution of faulty active ones, are also used in the fault-detection mechanism, thus providing fault detection and fault location for all switching planes. Our detection schemes are able to detect a single fault quickly without increasing transmission overhead. The proposed schemes can be used for switches with different numbers of active planes and a small number of spare planes.
High-Density Chemical Intercalation of Zero-Valent Copper into Bi2Se3 Nanoribbons (2012)

A major goal of intercalation chemistry is to intercalate high densities of guest species without disrupting the host lattice. Many intercalant concentrations, however, are limited by the charge of the guest species. Here we have developed a general solution-based chemical method for intercalating extraordinarily high densities of zero-valent copper metal into layered Bi(2)Se(3) nanoribbons. Up to 60 atom % copper (Cu(7.5)Bi(2)Se(3)) can be intercalated with no disruption to the host lattice using a solution disproportionation redox reaction.
Modulation of Synaptic Transmission by G Protein βγ Subunits (2009)

Synaptic transmission is characterized by exocytotic events which mediate the release of chemical transmitters to facilitate neuronal communication. Gi/Go coupled GPCRs play an important role in controlling exocytosis. In addition to direct interaction with voltage‐gated calcium channels to inhibit calcium influx, Gβγ subunits bind directly to SNARE proteins in the regulation of fusion events. The current study is aimed at developing small, druglike molecules which target the βγ /SNARE interaction to elucidate details involved in this novel mode of neuromodulation. Compound libraries were screened using a novel, label free detection method, Corning Epic®, which identifies protein‐protein interactions as changes in the local index of refraction due to binding events. Using these signals, we evaluated the ability of small molecules to modulate the Gβγ /SNARE interaction. Initial screening identified five lead compounds. By further application of an iterative analog library synthesis approach, we will develop analogs with improved physiochemical properties to serve as tools to dissect the therapeutic relevance of the Gβγ /SNARE interaction. This work was supported by the National Institutes of Health (EY010291).
Preparation and application of a waterborne acrylic copolymer-siloxane composite: improvement on the corrosion resistance of zinc-coated NdFeB magnets (2015)

In order to improve the corrosion resistance of the zinc coating on NdFeB, a novel siloxane functionalised waterborne acrylic copolymer was prepared by combining the self-produced waterborne acrylic copolymer coating with the silica sol precursor.
Cover Feature: Total Synthesis of the Antitumor Depsipeptide FE399 and Its S‐Benzyl Derivative: A Macrolactamization Approach (Eur. J. Org. Chem. 32/2020) (2020)

The Cover Feature shows schematically each reaction step in the total synthesis of a depsipeptidic natural product, FE399, with time. In the presence of MNBA combined with a nucleophilic catalyst DMAP or DMAPO, the ester bond formation and the subsequent peptide bond formation smoothly proceeded to afford the cyclic precursor, which was then subjected to the MNBA-mediated macrolactamization to afford the desired macrolactam core of FE399 in high yield. Eventually, the total synthesis of FE399 was successfully achieved. More information can be found in the Communication by T. Tonoi, I. Shiina et al.
Symposium on Psychophysics and Clinical Aspects of Vision (1982)

University of Houston, College of Optometry, Houston, Texas Presented by Dr. Levi on December 14, 1980 at the Symposium: Psychophysics and Clinical Aspects of Clinical Vision hosted by the Section on Visual Science at the Annual Meeting of the American Academy of Optometry in Chicago, Illinois. Received December 29, 1981. * Optometrist, Ph.D., Member of Faculty, F.A.A.O. AUTHOR'S ADDRESS: Dennis M. Levi University of Houston College of Optometry Central Campus Houston, Texas 77004
Lower Plasma Vitamin E Levels Are Associated With the Frailty Syndrome: The InCHIANTI Study (2006)

Our findings show an association between low circulating levels of one of the most important components of the human antioxidant system and the presence of frailty.
SoftNER: Mining Knowledge Graphs From Cloud Incidents (2021)

The move from boxed products to services and the widespread adoption of cloud computing has had a huge impact on the software development life cycle and DevOps processes. Particularly, incident management has become critical for developing and operating large-scale services. Prior work on incident management has heavily focused on the challenges with incident triaging and de-duplication. In this work, we address the fundamental problem of structured knowledge extraction from service incidents. We have built SoftNER, a framework for mining Knowledge Graphs from incident reports. First, we build a novel multi-task learning based BiLSTM-CRF model which leverages not just the semantic context but also the data-types for extracting factual information in the form of named entities. Next, we present an approach to mine relations between the named entities for automatically constructing knowledge graphs. We have deployed SoftNER at Microsoft, a major cloud service provider and have evaluated it on more than 2 months of cloud incidents. We show that the unsupervised machine learning pipeline has a high precision of 0.96. Our multi-task learning based deep learning model also outperforms the state-of-the-art NER models. Lastly, using the knowledge extracted by SoftNER, we are able to build accurate models for applications such as incident triaging and recommending entities based on their relevance to incident titles.
A Multiple Regression-Enhanced Convolution Estimator for the Density of a Response Variable in the Presence of Additional Covariate Information (2021)

In this paper we propose a convolution estimator for estimating the density of a response variable that employs an underlying multiple regression framework to enhance the accuracy of density estimates through the incorporation of auxiliary information. Suppose we have a sample consisting of $N$ complete case observations of a response variable and an associated set of covariates, along with an additional sample consisting of $M$ observations of the covariates only. We show that the mean square error of the multiple regression-enhanced convolution estimator converges as $O(N^{-1})$ towards zero, and moreover, for a large fixed $N$, that the mean square error converges as $O(M^{-4/5})$ towards an $O(N^{-1})$ constant. This is the first time that the convergence of a convolution estimator with respect to the amount of additional covariate information has been established. In contrast to convolution estimators based on the Nadaraya-Watson estimator for a nonlinear regression model, the multiple regression-enhanced convolution estimator proposed in this paper does not suffer from the curse of dimensionality. It is particularly useful for scenarios in which one wants to estimate the density of a response variable that is challenging to measure, while being in possession of a large amount of additional covariate information. In fact, an application of this type from the field of ophthalmology motivated our work in this paper.
Targetable genetic features of primary testicular and primary central nervous system lymphomas (2015)

Primary central nervous system lymphomas (PCNSLs) and primary testicular lymphomas (PTLs) are extranodal large B-cell lymphomas (LBCLs) with inferior responses to current empiric treatment regimens. To identify targetable genetic features of PCNSL and PTL, we characterized their recurrent somatic mutations, chromosomal rearrangements, copy number alterations (CNAs), and associated driver genes, and compared these comprehensive genetic signatures to those of diffuse LBCL and primary mediastinal large B-cell lymphoma (PMBL). These studies identify unique combinations of genetic alterations in discrete LBCL subtypes and subtype-selective bases for targeted therapy. PCNSLs and PTLs frequently exhibit genomic instability, and near-uniform, often biallelic, CDKN2A loss with rare TP53 mutations. PCNSLs and PTLs also use multiple genetic mechanisms to target key genes and pathways and exhibit near-uniform oncogenic Toll-like receptor signaling as a result of MYD88 mutation and/or NFKBIZ amplification, frequent concurrent B-cell receptor pathway activation, and deregulation of BCL6. Of great interest, PCNSLs and PTLs also have frequent 9p24.1/PD-L1/PD-L2 CNAs and additional translocations of these loci, structural bases of immune evasion that are shared with PMBL.
From conceptual design to process design optimization: a review on flowsheet synthesis (2019)

This paper presents the authors’ perspectives on some of the open questions and opportunities in Process Systems Engineering (PSE) focusing on process synthesis. A general overview of process synthesis is given, and the difference between Conceptual Design (CD) and Process Design (PD) is presented using an original ternary diagram. Then, a bibliometric analysis is performed to place major research team activities in the latter. An analysis of ongoing work is conducted and some perspectives are provided based on the analysis. This analysis includes symbolic knowledge representation concepts and inference techniques, i.e. , ontology, that is believed to become useful in the future. Future research challenges that process synthesis will have to face, such as biomass transformation, shale production, response to spaceflight demand, modular plant design, and intermittent production of energy, are also discussed.