gebhart/patrepeval huggingface dataset:
Novel Insights into FH-associated Disease are KEAPing the Lid on Oncogenic HIF Signalling (2011)

Fumarate hydratase (FH) encodes a Krebs cycle enzyme which is mutated in hereditary leiomyomatosis and renal cell cancer (HLRCC). Fumarate is a potent inhibitor of a class of enzymes, 2-oxoglutarate (2OG) oxygenases, that require oxygen, non-haem Fe(II), and 2OG for activity. Importantly, loss of FH function has been shown to result in elevated levels of fumarate in cells and tumors. Recent work has demonstrated that fumarate-mediated inhibition of a sub-class of 2OG oxygenases, the hypoxia-inducible factor prolyl hydroxylase enzymes (HIF-PHDs), causes stabilisation of HIF and the upregulation of a broad range of HIF-target genes, including those that stimulate cell growth and angiogenesis, which may in turn contribute to tumorigenesis [1]. Previously we generated a conditional Fh1 (the ortholog of human FH) knockout mouse and showed that kidney-specific deletion of Fh1 recapitulated important aspects of the human disease, including activation of HIF and the development of hyperplastic renal cysts [2]. HIF dysregulation following inactivation of the FH tumor suppressor gene has therefore been hypothesised as a plausible mechanism for HLRCC tumorigenesis. In addition to inhibiting 2OG oxygenases, fumarate modifies cysteine residues in multiple proteins to form S-(2-succinyl)-cysteine (2SC) and this chemical modification, termed succination, can have important functional consequences, such as the inactivation of glyceraldehyde-3-phosphate dehydrogenase in both an in vivo and in vitro setting [3]. Of potential clinical importance, we have reported recently that FH-deficient cells and tumors specifically exhibit high levels of 2SC that are absent in normal cells and tissues, thus providing a potential diagnostic biomarker and an alternative candidate or parallel mechanism for tumorigenesis [4]. In last month’s edition of Cancer Cell, we demonstrate through multiple genetic crosses in mice, that neither the presence of Hif, nor the absence of Phds, are required for renal cyst formation in an Fh1-deficient background and that surprisingly, loss of Hif-1α actually exacerbates the cystic phenotype [5]. Furthermore, we show that murine Fh1 deficient renal cysts, mouse embryonic fibroblasts
Wavelength routers in WDM local area networks (2002)

This paper presents a novel scheme for scheduling packet traffic on a wavelength-division-multiplexed (WDM) local optical network which employs a wavelength router. An N-port latin router allows N/sup 2//spl times/N/sup 2/ connectivity via only N physical wavelengths. We propose TDM schedules for interconnecting MN nodes with a wavelength router. We show that for non-zero transceiver tuning time, throughput on the order of N can be achieved.
Safety and Efficacy of a Calcineurin Inhibitor Avoidance Regimen in Pediatric Renal Transplantation (2006)

Thirty-four children were entered into a pilot trial of calcineurin inhibitor avoidance after living-donor kidney transplantation, the CN-01 study. Patients were treated with anti-CD25 mAb, prednisone, mycophenolate mofetil, and sirolimus. Twenty patients were maintained on the protocol for up to 3 yr of follow-up. One enrolled patient did not receive the transplant because of a donor problem, eight terminated because of one or more rejection episodes, four terminated because of adverse events, and one was lost to follow-up. Two grafts were lost, one as a result of chronic rejection and the other as a result of posttransplantation lymphoproliferative disorder. There were no deaths. The 6- and 12-mo acute rejection rates were 21.8 and 31.5%, respectively. GFR were stable throughout the course of the study, with a slight downward trend by 6 mo after transplantation followed by a slight upward trend to a mean of 70 ml/min thereafter. Early surveillance graft biopsies frequently showed focal interstitial mononuclear cellular infiltrates without overt vasculitis or tubulitis, but these infiltrates disappeared without treatment. Anti-HLA class I and II antibodies were detected in three patients before transplantation, and all three had acute rejections, including the two patients who lost their grafts. De novo anti-HLA Ab production occurred in only one patient after transplantation. There were two episodes of Epstein Barr virus-related posttransplantation lymphoproliferative disorder, one of which developed after the patient had been terminated from the study. It is concluded that calcineurin inhibitor-free immunosuppression can be safe and effective in pediatric living-donor renal transplantation. However, further modifications that are designed to lessen early rejection rates and decrease complications should be tested before this approach is used routinely.
Sacral nervous function, hormonal levels and sexuality in premenopausal women before and after hysterectomy (1994)

Preoperative somatic findings including sacral nervous function and pelvic muscular strength cannot be used as predictors for sexuality after subtotal hysterectomy.
Statistical Characterization of Bit Patterning in SOAs: BER Prediction and Experimental Validation (2009)

We present a novel simulation tool for optical systems employing in-line nonlinear SOAs, able to correctly estimate the bit error rate even in the presence of significant SOA-induced intersymbol interference.
Archazolid‐7‐O‐β‐D‐glucopyranoside – Isolation, Structural Elucidation and Solution Conformation of a Novel V‐ATPase Inhibitor from the Myxobacterium Cystobacter violaceus (2007)

Abstract The novel polyketide macrolide archazolid‐7‐ O ‐β‐ D ‐glucopyranoside ( 3 ) has been isolated from the myxobacterium Cystobacter violaceus and the structure of this first archazolid‐glycoside has been determined by spectroscopic and degradative methods. A synthesis of simplified 7‐ O analogues, based on regioselective derivatisation of archazolid A, was elaborated. These structurally novel archazolids of natural and synthetic origin were evaluated in detail for V‐ATPase inhibition and their biological activities are discussed in terms of their solution conformations, as determined by high‐field NMR studies, including J ‐based conformation analysis and constrained molecular dynamics simulations. (© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2007)
Appearance of an Increment of Tyrosine Aminotransferase Activity in a Cell-free System* (1964)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAppearance of an Increment of Tyrosine Aminotransferase Activity in a Cell-free System*George P. Tryfiates and Gerald LitwackCite this: Biochemistry 1964, 3, 10, 1483–1487Publication Date (Print):October 1, 1964Publication History Published online1 May 2002Published inissue 1 October 1964https://pubs.acs.org/doi/10.1021/bi00898a016https://doi.org/10.1021/bi00898a016research-articleACS PublicationsRequest reuse permissionsArticle Views24Altmetric-Citations14LEARN 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
The Future of Computing Research: Industry-Academic Collaborations (2016)

IT-driven innovation is an enormous factor in the worldwide economic leadership of the United States. It is larger than finance, construction, or transportation, and it employs nearly 6% of the US workforce. The top three companies, as measured by market capitalization, are IT companies - Apple, Google (now Alphabet), and Microsoft. Facebook, a relatively recent entry in the top 10 list by market capitalization has surpassed Walmart, the nation's largest retailer, and the largest employer in the world. The net income of just the top three exceeds $80 billion - roughly 100 times the total budget of the NSF CISE directorate which funds 87% of computing research. In short, the direct return on federal research investments in IT research has been enormously profitable to the nation. The IT industry ecosystem is also evolving. The time from conception to market of successful products has been cut from years to months. Product life cycles are increasingly a year or less. This change has pressured companies to focus industrial R&amp;D on a pipeline or portfolio of technologies that bring immediate, or almost immediate, value to the companies. To defeat the competition and stay ahead of the pack, a company must devote resources to realizing gains that are shorter term, and must remain agile to respond quickly to market changes driven by new technologies, new startups, evolving user experience expectations, and the continuous consumer demand for new and exciting products. Amidst this landscape, the Computing Community Consortium convened a round-table of industry and academic participants to better understand the landscape of industry-academic interaction, and to discuss possible actions that might be taken to enhance those interactions. We close with some recommendations for actions that could expand the lively conversation we experienced at the round-table to a national scale.
Quantization of massive vector fields on ultrastatic spacetimes (1997)

A canonical quantization is developed for massive vector fields on ultrastatic spacetimes with compact Cauchy surfaces. At the classical level, the field equation is recast as an abstract Cauchy problem subject to a subsidiary condition. Time evolution is obtained as a unitary mapping of Cauchy data, and the subsidiary condition is satisfied by restricting the data. At the quantum level, field operators are constructed and a representation of the CCRs is obtained on a Fock space.
Local Ferroelectricity inSrTiO3Thin Films (2002)

The temperature-dependent polarization of SrTiO3 thin films is investigated using confocal scanning optical microscopy. A homogeneous out-of-plane and an inhomogeneous in-plane ferroelectric phase are identified from images of the linear electro-optic response. Both hysteretic and nonhysteretic behavior are observed under a dc bias field. Unlike classical transitions in bulk ferroelectrics, local ferroelectricity is observed at temperatures far above the dielectric permittivity maximum. The results demonstrate the utility of local probe experiments in understanding inhomogeneous ferroelectrics.
Recognizing Object by Components With Human Prior Knowledge Enhances Adversarial Robustness of Deep Neural Networks (2023)

Adversarial attacks can easily fool object recognition systems based on deep neural networks (DNNs). Although many defense methods have been proposed in recent years, most of them can still be adaptively evaded. One reason for the weak adversarial robustness may be that DNNs are only supervised by category labels and do not have part-based inductive bias like the recognition process of humans. Inspired by a well-known theory in cognitive psychology – recognition-by-components, we propose a novel object recognition model ROCK (Recognizing Object by Components with human prior Knowledge). It first segments parts of objects from images, then scores part segmentation results with predefined human prior knowledge, and finally outputs prediction based on the scores. The first stage of ROCK corresponds to the process of decomposing objects into parts in human vision. The second stage corresponds to the decision process of the human brain. ROCK shows better robustness than classical recognition models across various attack settings. These results encourage researchers to rethink the rationality of currently widely-used DNN-based object recognition models and explore the potential of part-based models, once important but recently ignored, for improving robustness.
Airway Management for Trauma Patients With Potential Cervical Spine Injuries (1991)

Department of Anesthesia, San Francisco General Hospital, University of California, San Francisco, California Address correspondence to Dr. Hastings, San Francisco General Hospital, Department of Anesthesia, 35--50, 1001 Potrero Avenue, San Francisco, CA 94110. We thank Hideyo Minagi, MD, for providing the C-spine roentgen- ograms; Brian Andrews, MD, Larry Pitts, MD, Heidi Jerome, MD, Jeffrey Katz, MD, Jeanine Wiener-Kronish, MD, and Paul Wood, MB, QIB, for helpful suggestions; Winifred Von Ehrenberg for editorial assistance; and Rachel Saidman for manuscript preparation. Accepted for publication June 5, 1991.
Threat Image Projection (TIP) into X-ray images of cargo containers for training humans and machines (2016)

We propose a framework for Threat Image Projection (TIP) in cargo transmission X-ray imagery. The method exploits the approximately multiplicative nature of X-ray imagery to extract a library of threat items. These items can then be projected into real cargo. We show using experimental data that there is no significant qualitative or quantitative difference between real threat images and TIP images. We also describe methods for adding realistic variation to TIP images in order to robustify Machine Learning (ML) based algorithms trained on TIP. These variations are derived from cargo X-ray image formation, and include: (i) translations; (ii) magnification; (iii) rotations; (iv) noise; (v) illumination; (vi) volume and density; and (vii) obscuration. These methods are particularly relevant for representation learning, since it allows the system to learn features that are invariant to these variations. The framework also allows efficient addition of new or emerging threats to a detection system, which is important if time is critical. We have applied the framework to training ML-based cargo algorithms for (i) detection of loads (empty verification), (ii) detection of concealed cars (ii) detection of Small Metallic Threats (SMTs). TIP also enables algorithm testing under controlled conditions, allowing one to gain a deeper understanding of performance. Whilst we have focused on robustifying ML-based threat detectors, our TIP method can also be used to train and robustify human threat detectors as is done in cabin baggage screening.
Dimeric Metal-Salphen Complexes Which Target Multimeric G-Quadruplex DNA (2023)

G-Quadruplex DNA structures have attracted increasing attention due to their biological roles and potential as targets for the development of new drugs. While most guanine-rich sequences in the genome have the potential to form monomeric G-quadruplexes, certain sequences have enough guanine-tracks to give rise to multimeric quadruplexes. One of these sequences is the human telomere where tandem repeats of TTAGGG can lead to the formation of two or more adjacent G-quadruplexes. Herein we report on the modular synthesis via click chemistry of dimeric metal-salphen complexes (with Ni<sup>II</sup> and Pt<sup>II</sup>) bridged by either polyether or peptide linkers. We show by circular dichroism (CD) spectroscopy that they generally have higher selectivity for dimeric vs monomeric G-quadruplexes. The emissive properties of the Pt<sup>II</sup>-salphen dimeric complexes have been used to study their interactions with monomeric and dimeric G-quadruplexes <i>in vitro</i> as well as to study their cellular uptake and localization.
Atomic model for the EL0 defect in GaAs (1987)

We propose atomic models for the stable and metastable configurations of the bi-stable, oxygen-related defect in GaAs known as EL0. They consist of an O on As site donor as a nearest neighbor to a divacancy for the stable configuration and an O on Ga site acceptor between two As vacancies for the metastable configuration. We discuss analogies and distinctions between EL0 and EL2, another important bi-stable complex. We suggest that this complex is prominent in O-containing GaAs because divacancies migrate relatively rapidly and so are prone to formation of complexes.
Thrombospondin-1 and neural crest cell migration (1999)

Using a monoclonal antibody raised against human platelet thrombospondin, we found anti-thrombospondin immunoreactivity in the extracellular matrix of avian embryos, coincident with the ventral pathways followed by trunk neural crest cells. To confirm that the antibody recognized thrombospondin-1 and to determine the tissue of origin of the thrombospondin matrix, a thrombospondin-1 cRNA probe was used for whole mount in situ hybridization. This probe revealed thrombospondin-1 mRNAs in the developing myotome before and during neural crest cell migration. The effect of thrombospondin-1 on neural crest cell migration, morphology, and adhesion was assayed in vitro. Quail trunk neural crest cells cultured on 4 microg/ml of thrombospondin-1 migrate at 1.14 +/- 0.54 microm/min, which is significantly greater than the rate of cell migration on tissue culture plastic. Using a shaker-based adhesion assay, a significantly greater number of neural crest cells remain attached to dishes coated with 4 microg/ml of thrombospondin-1 than to tissue culture plastic alone. The number of neural crest cells that remain attached to 4 microg/ml of thrombospondin-1 is similar to the number that remain attached to dishes coated with 10 microg/ml of fibronectin. These observations indicate that neural crest cells migrate through a thrombospondin-filled extracellular matrix, and that thrombospondin-1 promotes neural crest cell migration and adhesion. Thus, thrombospondin-1 is the first somite-derived extracellular matrix molecule with properties consistent with a role in the promotion of migration into the anterior somite, as opposed to the repulsion of neural crest cells from the posterior half of the somite.
High frequency optical subcarrier generator (1994)

The authors describe an electro-optical oscillator capable of generating high stability optical signals at frequencies up to 70 GHz. Signals as high as 9.2 GHz were generated with an optical wavelength of 1310 nm using the oscillator, and a comb of stable frequencies was produced by modelocking the oscillator.
Improved Synthesis of RO4858542, a 5-HT6 Receptor Antagonist (2010)

An improved synthesis of a 5-HT6 antagonist is described. A problematic amide reduction step was avoided by a reductive amination. Overall, 2.9 kg was produced over 6 steps with an overall yield of 56%.
An Exact Method to Determine the Photonic Resonances of Quasicrystals Based on Discrete Fourier Harmonics of Higher-Dimensional Atomic Surfaces (2016)

A rigorous method for obtaining the diffraction patterns of quasicrystals is presented. Diffraction patterns are an essential analytical tool in the study of quasicrystals, since they can be used to determine their photonic resonances. Previous methods for approximating the diffraction patterns of quasicrystals have relied on evaluating the Fourier transform of finite-sized super-lattices. Our approach, on the other hand, is exact in the sense that it is based on a technique that embeds quasicrystals into higher dimensional periodic hyper-lattices, thereby completely capturing the properties of the infinite structure. The periodicity of the unit cell in the higher dimensional space can be exploited to obtain the Fourier series expansion in closed-form of the corresponding atomic surfaces. The utility of the method is demonstrated by applying it to one-dimensional Fibonacci and two-dimensional Penrose quasicrystals. The results are verified by comparing them to those obtained by using the conventional super-lattice method. It is shown that the conventional super-cell approach can lead to inaccurate results due to the continuous nature of the Fourier transform, since quasicrystals have a discrete spectrum, whereas the approach introduced in this paper generates discrete Fourier harmonics. Furthermore, the conventional approach requires very large super-cells and high-resolution sampling of the reciprocal space in order to produce accurate results leading to a very large computational burden, whereas the proposed method generates accurate results with a relatively small number of terms. Finally, we propose how this approach can be generalized from the vertex model, which assumes identical particles at all vertices, to a more realistic case where the quasicrystal is composed of different atoms.
Highly uniform 4-inch diameter ingaas/inp epitaxial wafer for pin-pd application (2005)

InGaAs/InP epitaxial layers were grown on four-inch S-doped InP substrates using production-scale organometallic vapor-phase epitaxy (OMVPE) system. High uniformity has been obtained by optimizing the growth conditions. For example, thickness uniformity of 1.09% in InGaAs layer, 1.39% in InP layer has been obtained. Also low dark current (<0.3 nA/200 /spl mu/m /spl phi/ at V/sub R/=5 V) has been achieved in planar type PIN-PD device. These results will highlight the large-diameter InGaAs/InP epitaxial growth for device cost performance.
Effect of chitosan acetate bandage on wound healing in infected and noninfected wounds in mice (2008)

HemCon bandage is an engineered chitosan acetate preparation designed as a hemostatic dressing, and is under investigation as a topical antimicrobial dressing. We studied its effects on healing of excisional wounds that were or were not infected with Staphylococcus aureus, in normal mice or mice previously pretreated with cyclophosphamide (CY). CY significantly suppressed wound healing in both the early and later stages, while S. aureus alone significantly stimulated wound healing in the early stages by preventing the initial wound expansion. CY plus S. aureus showed an advantage in early stages by preventing expansion, but a significant slowing of wound healing in later stages. In order to study the conflicting clamping and stimulating effects of chitosan acetate bandage on normal wounds, we removed the bandage from wounds at times after application ranging from 1 hour to 9 days. Three days application gave the earliest wound closure, and all application times gave a faster healing slope after removal compared with control wounds. Chitosan acetate bandage reduced the number of inflammatory cells in the wound at days 2 and 4, and had an overall beneficial effect on wound healing especially during the early period where its antimicrobial effect is most important.
Wet Processing in State-of-the-Art Cu(In,Ga)(S,Se)<sub>2</sub> Thin Film Solar Cells (2018)

Interface quality plays a key role in solar cell applications. Interface recombination at the front and rear surfaces, which determine this quality, have significant effects on open circuit voltage and fill factor values. In this work, several surface treatments were applied on Cu(In,Ga)Se 2 (CIGS) surfaces to improve the interface quality. Besides, the passivation layer implementation was investigated to reduce interface recombination between the buffer and absorber layers.