gebhart/patrepeval huggingface dataset:
Positive and negative regulation of the Mu operator by Mu repressor and Escherichia coli integration host factor. (1986)

Bacteriophage Mu utilizes two converging promoters to regulate the lytic and lysogenic pathways. Messenger RNA encoding the repressor gene is synthesized leftward from a promoter (PcM) located 1066 base pairs from the Mu left end. This transcript overlaps and is complementary to RNA synthesized rightward from the early promoter (PE) for transposase and replication proteins which initiates transcription at base pair 1028. Purified Mu repressor binds to three distinct operator sites (O1, O2, and O3); repressor binding at O2 blocks RNA polymerase binding at PE and repressor binding at O3 blocks RNA polymerase binding at PcM. O1 and O2 have higher affinity for repressor than O3, and transcription from PE is blocked at repressor concentrations that do not affect PcM. Thus, maintenance of the lysogenic state and autoregulation of the repressor gene is achieved by RNA polymerase transcription through DNA-repressor ensembles at O1 and O2. Integration host factor (IHF) encoded by the Escherichia coli him A and him D genes binds to Mu operator DNA between sites O1 and O2. IHF enhances transcription from PE 3-5-fold on supercoiled plasmid substrates in vitro and in Mu monolysogens in vivo. In vitro, IHF simultaneously decreases transcription from PcM 5-10-fold which results in a 25-fold change in lytic transcription relative to repressor transcription. A model for regulating the Mu lysis-lysogeny decision is presented.
Parsing to Stanford Dependencies: Trade-offs between Speed and Accuracy. (2010)

We investigate a number of approaches to generating Stanford Dependencies, a widely used semantically-oriented dependency representation. We examine algorithms specifically designed for dependency parsing (Nivre, Nivre Eager, Covington, Eisner, and RelEx) as well as dependencies extracted from constituent parse trees created by phrase structure parsers (Charniak, Charniak-Johnson, Bikel, Berkeley and Stanford). We found that phrase structure parsers systematically outperform algorithms designed specifically for dependency parsing. The most accurate method for generating dependencies is the Charniak-Johnson reranking parser, with 89 % (labeled) attachment F1 score. The fastest methods are Nivre, Nivre Eager, and Covington. When used with a linear classifier to make local parsing decisions, these methods can parse the entire Penn Treebank development set (section 22) in less than 10 seconds on an Intel Xeon E5520. However, this speed comes with a substantial drop in F1 score (about 76 % for labeled attachment) compared to competing methods. By tuning how much of the search space is explored by the Charniak-Johnson parser, we are able to arrive at a balanced configuration that is both fast and nearly as good as the most accurate approaches. 1.
Quantitative Analysis of Collagen Lamellae in the Normal and Keratoconic Human Cornea by Second Harmonic Generation Imaging Microscopy (2014)

In the normal human cornea, collagen lamellae adjacent to BL are narrow and form a steep angle with BL, whereas they increase in width and their angle relative to BL flattens with progression toward DM. These properties of collagen lamellae are altered in keratoconus and are likely related to abnormalities of corneal shape.
Design of a performance technology infrastructure to support the construction of responsive software (2000)

Article Design of a performance technology infrastructure to support the construction of responsive software Share on Author: E. Papaefstathiou Microsoft Research Limited, St. George House, 1 Guildhall Street, Cambridge CB2 3NH, UK Microsoft Research Limited, St. George House, 1 Guildhall Street, Cambridge CB2 3NH, UKView Profile Authors Info & Claims WOSP '00: Proceedings of the 2nd international workshop on Software and performanceSeptember 2000 Pages 96–104https://doi.org/10.1145/350391.350414Online:01 September 2000Publication History 5citation392DownloadsMetricsTotal Citations5Total Downloads392Last 12 Months2Last 6 weeks0 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
Ionization Potential, Electron Affinity, Electronegativity, Hardness, and Electron Excitation Energy:  Molecular Properties from Density Functional Theory Orbital Energies (2003)

Representative atomic and molecular systems, including various inorganic and organic molecules with covalent and ionic bonds, have been studied by using density functional theory. The calculations were done with the commonly used exchange-correlation functional B3LYP followed by a comprehensive analysis of the calculated highest-occupied and lowest-unoccupied Kohn−Sham orbital (HOMO and LUMO) energies. The basis set dependence of the DFT results shows that the economical 6-31+G* basis set is generally sufficient for calculating the HOMO and LUMO energies (if the calculated LUMO energies are negative) for use in correlating with molecular properties. The directly calculated ionization potential (IP), electron affinity (EA), electronegativity (χ), hardness (η), and first electron excitation energy (τ) are all in good agreement with the available experimental data. A generally applicable linear correlation relationship exists between the calculated HOMO energies and the experimental/calculated IPs. We have also found satisfactory linear correlation relationships between the calculated LUMO energies and experimental/calculated EAs (for the bound anionic states), between the calculated average HOMO/LUMO energies and χ values, between the calculated HOMO−LUMO energy gaps and η values, and between the calculated HOMO−LUMO energy gaps and experimental/calculated first excitation energies. By using these linear correlation relationships, the calculated HOMO and LUMO energies can be employed to semiquantitatively estimate ionization potential, electron affinity, electronegativity, hardness, and first excitation energy.
Hyaluronic acid dermal fillers: can adjunctive lidocaine improve patient satisfaction without decreasing efficacy or duration? (2011)

Hyaluronic acid (HA) dermal fillers are the most widely used injectables to augment facial volume without surgery. HA dermal fillers are popular because of their ease of administration, predictable effectiveness, good safety profile, and quick patient recovery. The most common patient complaint is pain. Our goal is to review the current literature on HA fillers and compare outcomes with and without lidocaine. We found adjunctive lidocaine significantly decreases pain during injection and postinjection with corresponding increased patient satisfaction. The efficacy and safety profile appears unchanged. Rare complications with HA fillers and those associated with constituents of the product, contaminants, and lidocaine are reviewed. The corrective effects of HA fillers are temporary; repeat treatment is required to maintain results. Minimizing pain is crucial to optimize patient satisfaction.
Wavefront aberration measurements and corrections through thick tissue using fluorescent microsphere reference beacons (2010)

We present a new method to directly measure and correct the aberrations introduced when imaging through thick biological tissue. A Shack-Hartmann wavefront sensor is used to directly measure the wavefront error induced by a Drosophila embryo. The wavefront measurements are taken by seeding the embryo with fluorescent microspheres used as "artificial guide-stars." The wavefront error is corrected in ten millisecond steps by applying the inverse to the wavefront error on a micro-electro-mechanical deformable mirror in the image path of the microscope. The results show that this new approach is capable of improving the Strehl ratio by 2 times on average and as high as 10 times when imaging through 100 microm of tissue. The results also show that the isoplanatic half-width is approximately 19 microm resulting in a corrected field of view 38 microm in diameter around the guide-star.
Synthesis and characterization of vanadium-containing silsesquioxanes (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis and characterization of vanadium-containing silsesquioxanesFrank J. Feher and John F. WalzerCite this: Inorg. Chem. 1991, 30, 8, 1689–1694Publication Date (Print):April 1, 1991Publication History Published online1 May 2002Published inissue 1 April 1991https://pubs.acs.org/doi/10.1021/ic00008a005https://doi.org/10.1021/ic00008a005research-articleACS PublicationsRequest reuse permissionsArticle Views533Altmetric-Citations116LEARN 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
AID from bony fish catalyzes class switch recombination (2005)

Class switch recombination was the last of the lymphocyte-specific DNA modification reactions to appear in the evolution of the adaptive immune system. It is absent in cartilaginous and bony fish, and it is common to all tetrapods. Class switching is initiated by activation-induced cytidine deaminase (AID), an enzyme expressed in cartilaginous and bony fish that is also required for somatic hypermutation. Fish AID differs from orthologs found in tetrapods in several respects, including its catalytic domain and carboxy-terminal region, both of which are essential for the switching reaction. To determine whether evolution of class switch recombination required alterations in AID, we assayed AID from Japanese puffer and zebra fish for class-switching activity in mouse B cells. We find that fish AID catalyzes class switch recombination in mammalian B cells. Thus, AID had the potential to catalyze this reaction before the teleost and tetrapod lineages diverged, suggesting that the later appearance of a class-switching reaction was dependent on the evolution of switch regions and multiple constant regions in the IgH locus.
Regional ventricular wall thickening reflects changes in cardiac fiber and sheet structure during contraction: quantification with diffusion tensor MRI (2005)

Dynamic changes of myocardial fiber and sheet structure are key determinants of regional ventricular function. However, quantitative characterization of the contraction-related changes in fiber and sheet structure has not been reported. The objective of this study was to quantify cardiac fiber and sheet structure at selected phases of the cardiac cycle. Diffusion tensor MRI was performed on isolated, perfused Sprague-Dawley rat hearts arrested or fixed in three states as follows: 1) potassium arrested (PA), which represents end diastole; 2) barium-induced contracture with volume (BV+), which represents isovolumic contraction or early systole; and 3) barium-induced contracture without volume (BV-), which represents end systole. Myocardial fiber orientations at the base, midventricle, and apex were determined from the primary eigenvectors of the diffusion tensor. Sheet structure was determined from the secondary and tertiary eigenvectors at the same locations. We observed that the transmural distribution of the myofiber helix angle remained unchanged as contraction proceeded from PA to BV+, but endocardial and epicardial fibers became more longitudinally orientated in the BV- group. Although sheet structure exhibited significant regional variations, changes in sheet structure during myocardial contraction were relatively uniform across regions. The magnitude of the sheet angle, which is an index of local sheet slope, decreased by 23 and 44% in BV+ and BV- groups, respectively, which suggests more radial orientation of the sheet. In summary, we have shown for the first time that geometric changes in both sheet and fiber orientation provide a substantial mechanism for radial wall thickening independent of active components due to myofiber shortening. Our results provide direct evidence that sheet reorientation is a primary determinant of myocardial wall thickening.
Plasma gas discharge deposited fluorocarbon polymers exhibit reduced elutability of adsorbed albumin and fibrinogen (1989)

The adsorption and subsequent detergent elutability of fibrinogen and albumin were measured on various treated and untreated polymer films in order to determine whether the relative adsorption of these proteins was responsible for the enhanced thromboresistance of Dacron vascular grafts treated with tetrafluoroethylene in a radio frequency glow discharge (RFGD) apparatus. Fluorocarbon-coated surfaces varying in the relative proportions of CF, CF2, and CF3 groups and in the ratio of fluorine to carbon were prepared by RFGD treatment of poly(ethylene terephthalate) (PET) films with tetrafluoroethylene or perfluoropropane. The adsorption of fibrinogen and albumin to these fluorocarbon-coated surfaces was comparable to the adsorption of the proteins to polytetrafluoroethylene (PTFE) and PET. However, the elutability of fibrinogen and albumin from the RFGD fluorocarbon surfaces with sodium dodecyl sulfate was much lower than that from PTFE or PET. Other RFGD treatments of PET, such as ethylene deposition or argon etching, did not reduce the extent of albumin elutability as dramatically as did the RFGD fluorocarbon treatments. The strong albumin binding to RFGD fluorocarbon surfaces may be exploited clinically to enhance the retention of albumin preadsorbed to blood-contacting surfaces to render them thromboresistant.
Low-dose Cyclophosphamide Treatment Impairs Regulatory T Cells and Unmasks AFP-specific CD4+ T-cell Responses in Patients With Advanced HCC (2010)

Immunotherapy represents a potential therapeutic option for patients with hepatocellular carcinoma (HCC). However, CD4CD25Foxp regulatory T cells, which suppress potential antigen-specific T-cell responses, are increased in patients with HCC and might impair the effect of an immune-based therapeutic approach. In this study, we demonstrate that depletion of regulatory T cells in vitro unmasks alpha-fetoprotein-specific T-cell responses in HCC patients. On the basis of these results, we performed a clinical trial, in which 13 patients with advanced HCC ineligible for any other type of treatment were treated with 150, 250, or 350 mg/m cyclophosphamide on day 1 and 29 to suppress regulatory T cells in these patients (NCT00396682). The primary end point of this trial was regulatory T-cell number and function. Low-dose cyclophosphamide treatment (150 and 250 mg/m) induced a decrease in the absolute and relative frequency of CD4CD25Foxp regulatory T cells in peripheral blood on days 8 and 29. Suppressor function of regulatory T cells was impaired after treatment of patients with 250 mg/m on days 8 and 21. Finally, alpha-fetoprotein-specific T-cell responses were unmasked in 6/13 treated patients. In summary, systemic treatment of HCC patients with low-dose cyclophosphamide decreases the frequency and suppressor function of circulating CD4CD25Foxp regulatory T cells in peripheral blood and could be used in combination with immunotherapeutic approaches in HCC.
Salmonella bacteraemia in England and Wales, 1981-1990. (1992)

Salmonella septicaemia is rare in England and Wales in other than a few serotypes of limited epidemiological importance.
Inkjet Printed, Self Powered, Wireless Sensors for Environmental, Gas, and Authentication-Based Sensing (2011)

In this paper, inkjet-printed flexible sensors fabricated on paper substrates are introduced as a system-level solution for ultra-low-cost mass production of UHF Radio Frequency Identification (RFID) Tags and wireless sensor nodes in a “green” approach that could be easily extended to other microwave and wireless applications. The authors briefly touch up the state-of-the-art area of fully integrated wireless sensor modules on paper and show several active and power scavenging platforms to power on wireless sensors that could potentially set the foundation for the truly convergent wireless sensor ad hoc networks of the future.
Layered Coding Transport (LCT) Building Block (2009)

Layered Coding Transport (LCT) provides transport level support for reliable content delivery and stream delivery protocols. LCT is specifically designed to support protocols using IP multicast, but also provides support to protocols that use unicast. LCT is compatible with congestion control that provides multiple rate delivery to receivers and is also compatible with coding techniques that provide reliable delivery of content.
Influence of dislocation density on recombination at grain boundaries in multicrystalline silicon (1993)

This paper reports a study of the causes of room-temperature recombination activity of grain boundaries in annealed multicrystalline silicon using the methods of electron-beam-induced current (EBIC) and transmission electron microscopy. It is found that the recombination activity is related to the density of dislocations in the boundary, with decoration by precipitates producing additional activity. Grain boundaries without dislocations and precipitates show only very low EBIC contrast.
Microcavity GalaAs/GaAs surface-emitting laser with I th = 6 mA (1987)

A circular buried microcavity 7 μm long and 6 μm in diameter has been realised. We obtained Ith = 6mA, ηd = 9% and peak power ≥1 mW at 20.5°C at single mode. The first CW operation of a GaAlAs/GaAs surface-emitting laser with Ith = 4.5 mA at 77 K was also realised.
Thrombopoietin-Mediated Sustained Activation of Extracellular Signal-Regulated Kinase in UT7-Mpl Cells Requires Both Ras–Raf-1- and Rap1–B-Raf-Dependent Pathways (2001)

Thrombopoietin (TPO) regulates growth and differentiation of megakaryocytes. We previously showed that extracellular signal-regulated kinases (ERKs) are required for TPO-mediated full megakaryocytic maturation in both normal progenitors and a megakaryoblastic cell line (UT7) expressing the TPO receptor (Mpl). In these cells, intensity and duration of TPO-induced ERK signal are controlled by several regions of the cytoplasmic domain of Mpl. In this study, we explored the signaling pathways involved in this control. We show that the small GTPases Ras and Rap1 contribute together to TPO-induced ERK activation in UT7-Mpl cells and that they do so by activating different Raf kinases as downstream effectors: a Ras-Raf-1 pathway is required to initiate ERK activation while Rap1 sustains this signal through B-Raf. Indeed, (i) in cells expressing wild-type or mutant Mpl, TPO-induced Ras and Rap1 activation correlates with early and sustained phases of ERK signal, respectively; (ii) interfering mutants of Ras and Rap1 both inhibit ERK kinase activity and ERK-dependent Elk1 transcriptional activation in response to TPO; (iii) the kinetics of activation of Raf-1 and B-Raf by TPO follow those of Ras and Rap1, respectively; (iv) RasV12-mediated Elk1 activation was modulated by the wild type or interfering mutants of Raf-1 but not those of B-Raf; (v) Elk1 activation mediated by a constitutively active mutant of Rap1 (Rap1V12) is potentiated by B-Raf and inhibited by an interfering mutant of this kinase. UT7-Mpl cells represent the second cellular model in which Ras and Rap1 act in concert to modulate the duration of ERK signal in response to a growth factor and thereby the differentiation program. This is also, to our knowledge, the first evidence suggesting that Rap1 may play an active role in megakaryocytic maturation.
Oxidative DNA damage induces the ATM-mediated transcriptional suppression of the Wnt inhibitor WIF-1 in systemic sclerosis and fibrosis (2014)

Systemic sclerosis (SSc) is an autoimmune disease characterized by extensive visceral organ and skin fibrosis. SSc patients have increased production of autoreactive antibodies and Wnt signaling activity. We found that expression of the gene encoding Wnt inhibitor factor 1 (WIF-1) was decreased in fibroblasts from SSc patient biopsies. WIF-1 deficiency in SSc patient cells correlated with increased abundance of the Wnt effector β-catenin and the production of collagen. Knocking down WIF-1 in normal fibroblasts increased Wnt signaling and collagen production. WIF-1 loss and DNA damage were induced in normal fibroblasts by either SSc patient immunoglobulins or oxidative DNA-damaging agents, such as ultraviolet light, hydrogen peroxide, or bleomycin. The DNA damage checkpoint kinase ataxia telangiectasia mutated (ATM) mediated WIF-1 silencing through the phosphorylation of the transcription factor c-Jun, which in turn activated the expression of the gene encoding activating transcription factor 3 (ATF3). ATF3 and c-Jun were recruited together with histone deacetylase 3 (HDAC3) to the WIF-1 promoter and inhibited WIF-1 expression. Preventing the accumulation of reactive oxygen species or inhibiting the activation of ATM, c-Jun, or HDACs restored WIF-1 expression in cultured SSc patient cells. Trichostatin A, an HDAC inhibitor, prevented WIF-1 loss, β-catenin induction, and collagen accumulation in an experimental fibrosis model. Our findings suggest that oxidative DNA damage induced by SSc autoreactive antibodies enables Wnt activation that contributes to fibrosis.
Norovirus and Histo-Blood Group Antigens: Demonstration of a Wide Spectrum of Strain Specificities and Classification of Two Major Binding Groups among Multiple Binding Patterns (2005)

Noroviruses, an important cause of acute gastroenteritis, have been found to recognize human histo-blood group antigens (HBGAs) as receptors. Four strain-specific binding patterns to HBGAs have been described in our previous report. In this study, we have extended the binding patterns to seven based on 14 noroviruses examined. The oligosaccharide-based assays revealed additional epitopes that were not detected by the saliva-based assays. The seven patterns have been classified into two groups according to their interactions with three major epitopes (A/B, H, and Lewis) of human HBGAs: the A/B-binding group and the Lewis-binding group. Strains in the A/B binding group recognize the A and/or B and H antigens, but not the Lewis antigens, while strains in the Lewis-binding group react only to the Lewis and/or H antigens. This classification also resulted in a model of the norovirus/HBGA interaction. Phylogenetic analyses showed that strains with identical or closely related binding patterns tend to be clustered, but strains in both binding group can be found in both genogroups I and II. Our results suggest that noroviruses have a wide spectrum of host range and that human HBGAs play an important role in norovirus evolution. The high polymorphism of the human HBGA system, the involvement of multiple epitopes, and the typical protein/carbohydrate interaction between norovirus VLPs and HBGAs provide an explanation for the virus-ligand binding diversities.