gebhart/patrepeval huggingface dataset:
SopE, a secreted protein of Salmonelladublin, is translocated into the target eukaryotic cell via a sip‐dependent mechanism and promotes bacterial entry (1996)

The entry of Salmonella into cultured epithelial cells is dependent on genes located in several adjacent chromosomal loci. One of these loci encodes the recently identified secretory proteins, denoted Sips ( Salmonella invasion proteins). SipB,C,D proteins are essential for the ability of the pathogen to invade epithelial cells. To examine if additional invasion‐associated proteins were secreted by Salmonella dublin , the genes encoding already characterized secretory proteins were inactivated to facilitate this analysis. The proteins produced and secreted by a double fliM /polar sipB mutant of S. dublin were analysed; this revealed a set of novel secreted proteins. These proteins, which we denoted Sops ( Salmonella outer proteins), formed large filamentous aggregates in the medium of bacterial culture growing at 37°C. These aggregates contained five predominant proteins. Here we report the identification and characterization of one of these proteins, SopE, which is a novel invasion‐associated secretory protein of S. dublin . A specific sopE mutant of S. dublin was found to be defective for invasion into epithelial cells. Upon interaction of Salmonella with HeLa cells, SopE was found to be translocated into the cytoplasm of the target cell by extracellular bacteria. The translocation of SopE was shown to be dependent on the Sip proteins because a polar sipB mutant did not translocate SopE across the HeLa cell membrane.
Asymmetric synthesis via axially dissymmetric molecules. A binaphthol-modified complex aluminum hydride reagent possessing extremely high ability of chiral recognition (1981)

Abstract
Replication-defective vectors of reticuloendotheliosis virus transduce exogenous genes into somatic stem cells of the unincubated chicken embryo (1989)

Replication-defective vectors derived from reticuloendotheliosis virus were used to transduce exogenous genes into early somatic stem cells of the chicken embryo. One of these vectors transduced and expressed the chicken growth hormone coding sequence. The helper cell line, C3, was used to generate stocks of vector containing about 10(4) transducing units per ml. Injection of 5- to 20-microliters volumes of vector directly beneath the blastoderm of unincubated chicken embryos led to infection of somatic stem cells. Infected embryos and adults contained unrearranged integrated proviral DNAs. Embryos expressed the transduced chicken growth hormone gene and contained high levels of serum growth hormone. Blood, brain, muscle, testis, and semen contained from individuals injected as embryos contained vector DNA. Replication-defective vectors of the reticuloendotheliosis virus transduced exogenous genes into chicken embryonic stem cells in vivo.
A novel connector linkage applicable in prodrug design (1981)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA novel connector linkage applicable in prodrug designPhilip L. Carl, Prasun K. Chakravarty, and John A. KatzenellenbogenCite this: J. Med. Chem. 1981, 24, 5, 479–480Publication Date (Print):May 1, 1981Publication History Published online1 May 2002Published inissue 1 May 1981https://doi.org/10.1021/jm00137a001Request reuse permissionsArticle Views4072Altmetric-Citations269LEARN 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 InReddit PDF (239 KB) Get e-Alertsclose Get e-Alerts
Cyclic Nucleotide–Gated Channels Colocalize with Adenylyl Cyclase in Regions of Restricted Camp Diffusion (2000)

Cyclic AMP is a ubiquitous second messenger that coordinates diverse cellular functions. Current methods for measuring cAMP lack both temporal and spatial resolution, leading to the pervasive notion that, unlike Ca(2+), cAMP signals are simple and contain little information. Here we show the development of adenovirus-expressed cyclic nucleotide-gated channels as sensors for cAMP. Homomultimeric channels composed of the olfactory alpha subunit responded rapidly to jumps in cAMP concentration, and their cAMP sensitivity was measured to calibrate the sensor for intracellular measurements. We used these channels to detect cAMP, produced by either heterologously expressed or endogenous adenylyl cyclase, in both single cells and cell populations. After forskolin stimulation, the endogenous adenylyl cyclase in C6-2B glioma cells produced high concentrations of cAMP near the channels, yet the global cAMP concentration remained low. We found that rapid exchange of the bulk cytoplasm in whole-cell patch clamp experiments did not prevent the buildup of significant levels of cAMP near the channels in human embryonic kidney 293 (HEK-293) cells expressing an exogenous adenylyl cyclase. These results can be explained quantitatively by a cell compartment model in which cyclic nucleotide-gated channels colocalize with adenylyl cyclase in microdomains, and diffusion of cAMP between these domains and the bulk cytosol is significantly hindered. In agreement with the model, we measured a slow rate of cAMP diffusion from the whole-cell patch pipette to the channels (90% exchange in 194 s, compared with 22-56 s for substances that monitor exchange with the cytosol). Without a microdomain and restricted diffusional access to the cytosol, we are unable to account for all of the results. It is worth noting that in models of unrestricted diffusion, even in extreme proximity to adenylyl cyclase, cAMP does not reach high enough concentrations to substantially activate PKA or cyclic nucleotide-gated channels, unless the entire cell fills with cAMP. Thus, the microdomains should facilitate rapid and efficient activation of both PKA and cyclic nucleotide-gated channels, and allow for local feedback control of adenylyl cyclase. Localized cAMP signals should also facilitate the differential regulation of cellular targets.
ChemInform Abstract: Kahalalides: Bioactive Peptides from a Marine Mollusk Elysia rufescens and Its Algal Diet Bryopsis sp. (1997)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Phase III Study of Immediate Compared With Delayed Docetaxel After Front-Line Therapy With Gemcitabine Plus Carboplatin in Advanced Non–Small-Cell Lung Cancer (2008)

We observed a statistically significant improvement in PFS and a nonstatistically significant increase in OS when docetaxel was administered immediately after front-line GC, without increasing toxicity or decreasing QOL.
Apparent velocities in relativity theory (1989)

The problem of measuring the velocity of separation of distant objects is considered. It is shown that, in the framework of general relativity, apparent velocities of separation may exceed 2c without implying physical velocities greater than c in standard cosmological models. The contribution due to this effect in measurements of distant superluminal expansions is calculated.
Immune responses against hepatitis C virus structural proteins following genetic immunisation. (1998)

We have used direct DNA inoculation to study the in vivo induction of both humoral and cellular immune responses to hepatitis C virus (HCV) encoded structural antigens. Following immunisation of mice, immune responses were compared using plasmids encoding full-length or partial HCV gene sequences for the nucleocapsid and envelope E2 proteins. Plasmids encoding secreted or non-secreted forms of the immunogens, including constructs expressing HCV sequences fused with the hepatitis B virus surface antigen (HCV-HBV chimeras), were evaluated. Results indicate that: (i) all constructs induced specific anti-HCV antibodies; (ii) antibody titres ranged from 1:100 to > 1:100,000; (iii) all HCV DNA immunogens induced a predominant Th1 response with the induction of IgG2a antibodies; (iv) the secretion level of the antigens and immune responses was not always correlated and (v) CTL could be detected against both HCV and HBV determinants.
The place of women and the perils of biblical interpretation (2011)

With regard to exegesis of the Bible, Niall Martin argues persuasively that we pause to think objectively about whether or not the Bible contains only explicit teaching and instruction with regard to life. Accepting that there are, of course, explicit teachings in the New Testament, he argues that the Scriptures can also be used to illuminate our thinking rather than to provide for regulated conduct. For example, with regard to the Law, Martin juxtaposes the fascinating story of Ruth with the approach of the Book of Ezra. What emerges is a much greater emphasis on contrast or dialectic in our Scriptural exegesis.
Large field of view scanning fluorescence lifetime imaging system for multimode optical imaging of small animals (2008)

We describe a scanning fluorescence lifetime imaging (SFLIM) system that provides a large field of view (LFOV), using a femtosecond (fs) pulsed laser, for multi-mode optical imaging of small animals. Fluorescence lifetime imaging (FLIM) can be a useful optical method to distinguish between fluorophores inside small animals. However, difficulty arises when LFOV is required in FLIM using a fs pulsed laser for the excitation of the fluorophores at low wavelengths (<500nm), primarily because the field of view of the pulsed blue excitation light generated from the second harmonic of the fs pulsed light is limited to about a centimeter in diameter due to the severe scattering and absorption of the light inside tissues. Here, we choose a scanning method in order to acquire a FLIM image with LFOV as one alternative. In the SFLIM system, we used a conventional cooled CCD camera coupled to an ultra-fast time-gated intensifier, a tunable femtosecond laser for the excitation of fluorophores, and an x-y moving stage for scanning. Images acquired through scanning were combined into a single image and then this reconstructed image was compared with images obtained by spectral imaging. The resulting SFLIM system is promising as an alternative method for the FLIM imaging of small animals, containing fluorophores exited by blue light, for LFOV applications such as whole animal imaging.
Iterative Learning Control: Brief Survey and Categorization (2007)

In this paper, the iterative learning control (ILC) literature published between 1998 and 2004 is categorized and discussed, extending the earlier reviews presented by two of the authors. The papers includes a general introduction to ILC and a technical description of the methodology. The selected results are reviewed, and the ILC literature is categorized into subcategories within the broader division of application-focused and theory-focused results.
Study on Recognition Characteristics of Acoustic Emission Based on Fractal Dimension (2008)

It is difficult to recognise acustic emission (AE) signal because of serious pollution by noise. Fractal dimension is a new method to describe the characteristics of AE singal. According to the complex computation and low precision of box counting dimension, correlation dimension and Katz dimension, an algorithm of logarithmic fractal dimension based on waveform length was proposed in this paper the deduction process was introduced. The experiment datas was rub impact AE signals sampled from rotating test stand. Gaussian white noise and non-stationary noise were added to simulate the field AE signal which polluted seriously by noise. Then, three algorithms based on box counting dimension, Katz dimension and logarithmic fractal dimension were compared in AE signal recognition. The results show that the algorithm of logarithmic dimension distinguishes rub impact AE signals from strong noise is more effectively, and has lower computation and higher precision than others. It provides a new approach to identify characteristics of AE signal and detect rub impact fault of rotating machinery.
Site-specific functionalization of RNA molecules by an unnatural base pair transcription system via click chemistry (2012)

Toward new biotechnology by genetic alphabet expansion, we developed an efficient site-specific labeling method for large RNA molecules. The combination of unnatural base pair transcription and post-transcriptional modification by click chemistry enables simple RNA labeling with a wide variety of functional groups at desired positions, in a one-pot reaction.
Expression, Purification, and Initial Kinetic Characterization of the Large Subunit of the Human Mitochondrial DNA Polymerase (1998)

Faulty replication of the human mitochondrial genome is thought to be the cause of many diseases; moreover, the low selectivity of the mitochondrial DNA polymerase has been implicated as the cause of many side effects observed in the treatment of viral infections such as HIV. To better understand how the mitochondrial genome is replicated, we cloned a cDNA encoding the large subunit of human DNA polymerase gamma, the enzyme that replicates the mitochondrial genome. The large subunit was recombinantly expressed and purified to near homogeneity. The purified enzyme demonstrated both polymerase and 3'-5' exonuclease activity. The purified protein was examined in single nucleotide incorporation assays, demonstrating that the enzyme had a maximum polymerization rate of 3.5 s-1 and a dissociation rate from the DNA substrate of 0.03 s-1, affording a calculated processivity of 116. The dissociation constants for the enzyme binding to DNA and nucleoside triphosphate were 39 nM and 14 microM, respectively. The 3'-5' exonuclease rate was measured at 0. 18 s-1. Though the slow rate of polymerization suggests that the large subunit of human DNA polymerase gamma may require accessory factors to increase its processivity of polymerization, the kinetic parameters indicate that the large subunit of DNA polymerase gamma could replicate the mitochondrial genome in a physiologically relevant time frame. This study provides the initial characterization of the large subunit of DNA polymerase gamma and establishes the baseline for examination of the effects of accessory proteins such as the putative small subunit.
Micro-spectrometer for NMR: analysis of small quantitiesin vitro (2004)

International audience
Colloidal Two‐Dimensional Systems: CdSe Quantum Shells and Wells (2003)

Dünne CdSe-Schichten („Quantenschalen“) wurden epitaktisch auf CdS-Nanokristalltemplaten gezüchtet. Ihre optischen Eigenschaften werden trotz unterschiedlicher Bandlücken und Templatgrößen fast ausschließlich von der Schalendicke bestimmt. Durch Variieren der Schalendicke kann die Emission der CdSe-Quantenschalen zwischen 520 und 650 nm abgestimmt werden (siehe Bild); die Quantenausbeute lässt sich durch epitaktische Beschichtung der Quantenschalen mit dünnen CdS-Schichten auf über 40 % steigern.
A Streptomyces glaucescens endodeoxyribonuclease which shows a strong preference for CC dinucleotide (1992)

We have characterized a deoxyribonuclease from Streptomyces glaucescens that cleaves double-stranded DNA preferably between the dinucleotide 5'-CC-3'. The cleavage specificity was demonstrated by both analysis of the terminal nucleotides of the generated fragments and DNA sequencing of partially digested DNA. Digestion of lambda DNA with this enzyme resulted in the production of double-stranded fragments with 5' and/or 3'-protruding single-stranded tails. DNase I footprinting experiments indicated that the nuclease specifically binds to its cleavage sites on the DNA under non-catalytic conditions. The enzyme is not affected by cytosine methylation in hemimethylated DNA.
Evolutionary arbitrage for FTSE-100 index options and futures (2002)

The objective in this paper is to develop and implement FGP-2 (Financial Genetic Programming) on intra daily tick data for stock index options and futures arbitrage in a manner that is suitable for online trading when windows of profitable arbitrage opportunities exist for short periods from one to ten minutes. Our benchmark for FGP-2 is the textbook rule for detecting arbitrage profits. This rule has the drawback that it awaits a contemporaneous profitable signal to implement an arbitrage in the same direction. A novel methodology of randomised sampling is used to train FGP-2 to pick up the fundamental arbitrage patterns. Care is taken to fine tune weights in the fitness function to enhance performance. As arbitrage opportunities are few, missed opportunities can be as costly as wrong recommendations to trade. Unlike conventional genetic programs, FGP-2 has a constraint satisfaction feature supplementing the fitness function that enables the user to train the FGP to specify a minimum and a maximum number of profitable arbitrage opportunities that are being sought. Historical sample data on arbitrage opportunities enables the user to set these minimum and maximum bounds. Good FGP rules for arbitrage are found to make a 3-fold improvement in profitability over the textbook rule. This application demonstrates the success of FGP-2 in its interactive capacity that allows experts to channel their knowledge into machine discovery.
Pathophysiology, diagnosis and treatment of endometriosis. (2004)

Endometriosis is generally a benign condition. However, there is a tendency towards progression and in part deep infiltrating processes occur, which can lead to obstruction and even silent loss of organ function such as kidney failure. Hereditary, genetic and immunological peculiarities have been found. Important are symptoms such as pain and infertility, which burden the life of the women involved. In spite of extensive research in the past the pathogenesis and epidemiology of the disease are not definitely clarified as yet. The estimated prevalence of endometriosis ranges between 10% and even more than 50% depending on the underlying problems of the women studied. Besides the main location of the disease within the pelvis also extra pelvic locations have been found (lung, lymph nodes, scars). The diagnosis should be established by histological verification. The main therapeutic modalities consist of surgery and medical treatment or combinations, which need to be individually adjusted, because of the high risk of recurrence and progression of the disease. The aim should be early detection and treatment as complete as possible, since symptom relief, resolution or prevention of infertility and decrease of recurrences are at their best under these circumstances.
Validation of an Independent Web-Based Tool for Measuring Visual Acuity and Refractive Error (the Manifest versus Online Refractive Evaluation Trial): Prospective Open-Label Noninferiority Clinical Trial. (2019)

Clinicaltrials.gov NCT03313921; https://clinicaltrials.gov/ct2/show/NCT03313921.
Cramér–Rao lower bound of basis image noise in multiple-energy x-ray imaging (2009)

We present an analytical method to compute the basis image noise in the context of multi-energy x-ray imaging based on the Cramér-Rao lower bound (CRLB). The proposed formalism extends the original idea of Alvarez and Macovski (1976 Phys. Med. Biol. 21 733) to estimate the noise in the photo-effect and Compton-effect basis images in the case of dual-energy imaging. It includes an arbitrary number of independent, spectrally distinct attenuation measurements and also goes beyond the two-dimensional decomposition of the attenuation, including, e.g., a contrast agent as a third basis material. To illustrate our method, we consider three simple applications. The first application is to study the influence of the exact values for the energy thresholds on the basis image noise for a binned photon-counting system. The second application relates to the same detector system as the first and is an investigation of the dependence of the basis image noise on the energy resolution of the detector system. Finally, the third application provides an example for the case of an energy-integrating detector: the aim is to optimize the front-scintillator layer thickness of a dual-crystal detector for dual-energy imaging. The CRLB is used to minimize the noise of a photo-effect/Compton-effect basis material decomposition.
A Common Requirement for the Catalytic Activity and Both SH2 Domains of SHP-2 in Mitogen-activated Protein (MAP) Kinase Activation by the ErbB Family of Receptors (1998)

The ErbB family of receptors, which include the epidermal growth factor receptor (EGFR), ErbB2, ErbB3, and ErbB4 mediate the actions of a family of bioactive polypeptides. EGF signals through EGFR, whereas heregulin (HRG) signaling is initiated through binding to either ErbB3 or ErbB4. In this report we studied the role of protein-tyrosine phosphatase SHP-2 in ErbB-mediated activation of mitogen-activated protein kinase (MAPK) by overexpressing SHP-2 mutants in COS-7 cells. We demonstrate that enzymatic activity and both NH2- and COOH-terminal SH2 domains of SHP-2 are required for EGF-induced MAPK activation, but not for c-Jun amino-terminal kinase stimulation or MAPK activation which occurred in response to myristoylated son of sevenless, activated Ras, or phorbol ester. Dominant-negative forms of SHP-2 had no effect on EGF-stimulated interaction of GRB2 with EGFR or SHC, nor did they influence phosphorylation of SHC and SHC/EGFR association. The same mutant SHP-2 structures that inhibited EGF-mediated stimulation of MAPK also blocked HRG alpha/beta-induced MAPK activation. EGF or HRG beta caused SHP-2 SH2 domains to engage multiple phosphotyrosine proteins, and mutation of either domain disrupted these associations. These results demonstrate that SHP-2 performs a common and essential function(s) in ligand-stimulated MAPK activation by the ErbB family of receptors.
Chitosan/double‐stranded RNA nanoparticle‐mediated RNA interference to silence chitin synthase genes through larval feeding in the African malaria mosquito ( Anopheles gambiae ) (2010)

The purpose of this study was to examine whether the expression of two chitin synthase genes, AgCHS1 and AgCHS2, can be repressed by chitosan/AgCHS dsRNA-based nanoparticles through larval feeding in Anopheles gambiae. The AgCHS1 transcript level and chitin content were reduced by 62.8 and 33.8%, respectively, in the larvae fed on chitosan/AgCHS1 dsRNA nanoparticles compared with those of the control larvae fed on chitosan/GFP dsRNA nanoparticles. Our study suggested for the first time that RNA interference (RNAi) in mosquito larvae is systemic, and demonstrated that the larvae fed on the nanoparticles assembled from AgCHS1 and AgCHS2 dsRNA increased larval susceptibilities to diflubenzuron, and calcofluor white (CF) or dithiothreitol, respectively. These results suggest great potential for using such a nanoparticle-based RNAi technology for high-throughput screening of gene functions and for developing novel strategies for pest management.