gebhart/patrepeval huggingface dataset:
The <i>ade6</i> Gene of the Fission Yeast as a Target for Antisense and Ribozyme RNA-Mediated Suppression (1995)

A genetic system for the analysis of antisense and ribozyme mechanisms is a much needed experimental tool, and yeast represent a favorable organism on which to base such a system. We have shown previously that the fission yeast Schizosaccharomyces pombe has potential to satisfy the requirements of such a system. This report describes experiments designed to determine if antisense and ribozyme RNA-mediated gene suppression will be generally applicable to other genes in S. pombe. Antisense and ribozyme RNAs designed to suppress the ade6 gene were expressed at high levels from episomal expression vectors. The ade6 gene was chosen as a target as mutations within the gene confer adenine auxotrophy and a red colony phenotype, and it was expected that antisense or ribozyme RNA-mediated mutant phenocopies would exhibit the same readily detectable phenotype. No phenotypic indication of ade6 suppression was detected in transformed yeast, and ade6 target mRNA was analyzed by primer extension and Northern analysis. Initially, conflicting results were obtained from these techniques, which were determined to be due to duplex formation between antisense and target RNA in vitro. No detectable reduction in the ade6 mRNA levels was found, and it was concluded that the gene was not suppressed by the antisense or ribozyme RNAs tested. These results confirm that in S. pombe as with other organisms, the susceptibility of genes to RNA-mediated suppression may be gene specific and that design of antisense and ribozyme genes will be an empirical process.
Physiological problems in patients undergoing autologous and allogeneic hematopoietic stem cell transplantation (2014)

Autologous and allogeneic patients experienced most of physical problems due to they receive high doses of chemotherapy. Therefore, it is recommended that an interdisciplinary support team approach should be usedtohelp reduce and manage the problems that may arise during patient care.
RNAIII-Inhibiting Peptide Enhances Healing of Wounds Infected with Methicillin-Resistant <i>Staphylococcus aureus</i> (2008)

Quorum sensing is a mechanism through which a bacterial population receives input from neighboring cells and elicits an appropriate response to enable survival within the host. Inhibiting quorum sensing by RNAIII-inhibiting peptide (RIP) has been demonstrated as a very effective mode of prevention and therapy for device-associated staphylococcal infections and was tested here for healing of wounds that are otherwise resistant to conventional antibiotics. Wounds, established through the panniculus carnosus of BALB/c mice, were inoculated with 5 x 10(7) CFU of methicillin-resistant Staphylococcus aureus. Mice were treated with Allevyn, RIP-soaked Allevyn (containing 20 microg RIP), daily intraperitoneal teicoplanin (7 mg/kg of body weight), Allevyn and teicoplanin, and RIP-soaked Allevyn and daily intraperitoneal teicoplanin. The main outcome measures were quantitative bacterial culture and histological examination with assessment of microvessel density and of vascular endothelial growth factor (VEGF) expression in tissue sections. Treatment with RIP-soaked Allevyn together with teicoplanin injection greatly reduced the bacterial load to 13 CFU/g (control untreated animals had 10(8) CFU/g bacteria). All other treatments were also significantly effective but only reduced the bacterial load to about 10(3) CFU/ml. Histological examination indicated that only treatment with RIP-soaked Allevyn with teicoplanin injection restored epithelial, granulation, and collagen scores, as well as microvessel density and VEGF expression, to the levels found with uninfected mice. In conclusion, we observed that RIP may be useful for the management of infected wounds and that it could represent an exciting and future alternative to the conventional antibiotics, at present considered the gold-standard treatments for methicillin-resistant S. aureus infections.
A context-aware machine learning-based approach (2018)

It is known that training a general and versatile Machine Learning (ML)-based model is more cost-effective than training several specialized ML-models for different operating contexts. However, as the volume of training information grows, the higher the probability of producing biased results. Learning bias is a critical problem for many applications, such as those related to healthcare scenarios, environmental monitoring and air traffic control. In this paper, we compare the use of a general model that was trained using all contexts against a system that is composed of a set of specialized models that was trained for each particular operating context. For this purpose, we propose a local learning approach based on context-awareness, which involves: (i) anticipating, analyzing and representing context changes; (ii) training and finding machine learning models to maximize a given scoring function for each operating context; (iii) storing trained ML-based models and associating them with corresponding operating contexts; and (iv) deploying a system that is able to select the best-fit ML-based model at runtime based on the context. To illustrate our proposed approach, we reproduce two experiments: one that uses a neural network regression-based model to perform predictions and another one that uses an evolutionary neural network-based approach to make decisions. For each application, we compare the results of the general model, which was trained based on all contexts, against the results of our proposed approach. We show that our context-aware approach can improve results by alleviating bias with different ML tasks.
Neuroscience Runs on GNU/Linux (2011)

OPINION article Front. Neuroinform., 07 July 2011 Volume 5 - 2011 | https://doi.org/10.3389/fninf.2011.00008
Transbilayer Phospholipid Movements in ABCA1-Deficient Cells (2007)

Tangier disease is an inherited disorder that results in a deficiency in circulating levels of HDL. Although the disease is known to be caused by mutations in the ABCA1 gene, the mechanism by which lesions in the ABCA1 ATPase effect this outcome is not known. The inability of ABCA1 knockout mice (ABCA1-/-) to load cholesterol and phospholipids onto apoA1 led to a proposal that ABCA1 mediates the transbilayer externalization of phospholipids, an activity integral not only to the formation of HDL particles but also to another, distinct process: the recognition and clearance of apoptotic cells by macrophages. Expression of phosphatidylserine (PS) on the surface of both macrophages and their apoptotic targets is required for efficient engulfment of the apoptotic cells, and it has been proposed that ABCA1 is required for transbilayer externalization of PS to the surface of both cell types. To determine whether ABCA1 is responsible for any of the catalytic activities known to control transbilayer phospholipid movements, these activities were measured in cells from ABCA1-/- mice and from Tangier individuals as well as ABCA1-expressing HeLa cells. Phospholipid movements in either normal or apoptotic lymphocytes or in macrophages were not inhibited when cells from knockout and wildtype mice or immortalized cells from Tangier individuals vs normal individuals were compared. Exposure of PS on the surface of normal thymocytes, apoptotic thymocytes and elicited peritoneal macrophages from wildtype and knockout mice or B lymphocytes from normal and Tangier individuals, as measured by annexin V binding, was also unchanged. No evidence was found of ABCA1-stimulated active PS export, and spontaneous PS movement to the outer leaflet in the presence or absence of apoA1 was unaffected by the presence or absence of ABCA1. Normal or Tangier B lymphocytes and macrophages were also identical in their ability to serve as targets or phagocytes, respectively, in apoptotic cell clearance assays. No evidence was found to support the suggestion that ABCA1 is involved in transport to the macrophage cell surface of annexins I and II, known to enhance phagocytosis of apoptotic cells. These results show that mutations in ABCA1 do not measurably reduce the rate of transbilayer movements of phospholipids in either the engulfing macrophage or the apoptotic target, thus discounting catalysis of transbilayer movements of phospholipids as the mechanism by which ABCA1 facilitates loading of phospholipids and cholesterol onto apoA1.
The role of proteases in regulating Eph/ephrin signaling (2014)

Proteases regulate a myriad of cell functions, both in normal and disease states. In addition to protein turnover, they regulate a range of signaling processes, including those mediated by Eph receptors and their ephrin ligands. A variety of proteases is reported to directly cleave Ephs and/or ephrins under different conditions, to promote receptor and/or ligand shedding, and regulate receptor/ligand internalisation and signaling. They also cleave other adhesion proteins in response to Eph-ephrin interactions, to indirectly facilitate Eph-mediated functions. Proteases thus contribute to Eph/ephrin mediated changes in cell-cell and cell-matrix interactions, in cell morphology and in cell migration and invasion, in a manner which appears to be tightly regulated by, and co-ordinated with, Eph signaling. This review summarizes the current literature describing the function and regulation of protease activities during Eph/ephrin-mediated cell signaling.
Pubo-Urethral Ligament Transection Causes Stress Urinary Incontinence in the Female Rat: A Novel Animal Model of Stress Urinary Incontinence (2007)

Our results demonstrate that deficiency of the pubo-urethral ligament in the female rat induces stress urinary incontinence comparable to that in a previously established model of pudendal nerve transection induced stress urinary incontinence. This novel rat model could be used to investigate the mechanisms of urethral hypermobility in female stress urinary incontinence or potential therapeutic interventions for stress urinary incontinence.
Arc-fusion splicing of single-mode fibers 1: Optimum splice conditions (1982)

The optimum conditions for arc-fusion splicing of single-mode fibers with core eccentricity of a few microns are investigated in detail. A narrow, quick fusion method, where the fiber-fused region is restricted by the narrowing of the electrode gap and the arc-discharge time is short compared with the conventional multi-mode fiber splice, is presented that will reduce the surface tension effect. The optimum values of electrode gap, prefusion time, and discharge duration are found to be 0.7 mm, 0.2 sec, and 1 sec, respectively, when the discharge current is 18 mA. The optimum pressing stroke of a fiber after the fiber end faces contact each other is determined to be 20 microm. Splice loss <0.1 dB is achieved in the present conditions for fibers with 2-microm core eccentricity and +/-3-microm o.d. discrepancy.
The Rate of Fermentation by Growing Yeast Cells (1913)

Research Article| March 01 1913 The Rate of Fermentation by Growing Yeast Cells Arthur Slator Arthur Slator Search for other works by this author on: This Site PubMed Google Scholar Author and article information Publisher: Portland Press Ltd © 1913 Cambridge: at the University Press1913 Biochem J (1913) 7 (2): 197–203. https://doi.org/10.1042/bj0070197 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn Email Cite Icon Cite Get Permissions Citation Arthur Slator; The Rate of Fermentation by Growing Yeast Cells. Biochem J 1 March 1913; 7 (2): 197–203. doi: https://doi.org/10.1042/bj0070197 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBiochemical Journal Search Advanced Search This content is only available as a PDF. © 1913 Cambridge: at the University Press1913 Article PDF first page preview Close Modal You do not currently have access to this content.
Demonstration of tumor necrosis factor in human amniotic fluids and supernatants of placental and decidual tissues. (1988)

Human amniotic fluid samples obtained from normal pregnancies and supernatants of normal full-term placental and decidual tissues were assayed in a specific radioimmunoassay (RIA) and in a sensitive bioassay for tumor necrosis factor (TNF). TNF was detected in 91% of amniotic fluid samples and in all placental and decidual supernatants assayed by the RIA. Amniotic fluid samples collected during the second trimester of pregnancy contained significantly higher concentrations of TNF than samples collected during the third trimester, average concentrations being 2.5 ng/ml and 0.9 ng/ml, respectively. Parallel testing in the bioassay showed that most of the amniotic fluid TNF is biologically inactive, whereas placental and decidual supernatants had biologic activity correlating with TNF levels detected by the RIA. The quantities of TNF detected by the RIA ranged from 1.1 to 2.8 ng/ml in placental supernatants and from 3.9 to 8.5 ng/ml in decidual supernatants. The presence of TNF in normal amniotic fluids and in placental and decidual supernatants suggest that this cytokine has a physiologic role in human pregnancy.
Redox- and Calmodulin-dependent S-Nitrosylation of the KCNQ1 Channel (2009)

Nitric oxide (NO) is a gaseous signal mediator showing numerous important biological effects. NO has been shown in many instances to exhibit its action via the protein S-nitrosylation mechanism, in which binding of NO to Cys residues regulate protein function independently of activation of soluble guanylate cyclase. The direct link between protein S-nitrosylation and functional modulation, however, has been demonstrated only in limited examples. Furthermore, although most proteins have more than one Cys residue, the mechanism by which a certain Cys becomes a specific target residue of S-nitrosylation is poorly understood. We have previously reported that NO regulates currents through the cardiac slowly activating delayed rectifier potassium channel (I(Ks)) irrespective of soluble guanylate cyclase activation. Here we demonstrate using a biotin-switch assay that NO induced S-nitrosylation of the alpha-subunit of the I(Ks) channel, KCNQ1, at Cys(445) in the C terminus. A redox motif flanking Cys(445) and the interaction of KCNQ1 with calmodulin are required for preferential S-nitrosylation of Cys(445). A patch clamp experiment shows that S-nitrosylation of Cys(445) modulates the KCNQ1/KCNE1 channel function. Our data provide a molecular basis of NO-mediated regulation of the I(Ks) channel. This novel regulatory mechanism of the I(Ks) channel may play a role in previously demonstrated NO-mediated phenomenon in cardiac electrophysiology, including shortening in action potential duration in response to intracellular Ca(2+) or sex hormones.
Dual-channel surface plasmon resonance sensor withspectral discriminationof sensing channels using dielectric overlayer (1999)

A novel dual-channel surface plasmon resonance sensor is described which uses a high refractive index overlayer to spectrally separate sensing channels, allowing for their simultaneous interrogation using a single spectrograph. A theoretical analysis of the sensor is presented as well as experimental results demonstrating its capability as a biosensor.
Transposon Tn<i>5</i> (2008)

Tn5 was one of the first transposons to be identified ( 10 ). As a result of Tn5's early discovery and its simple macromolecular requirements for transposition, the Tn5 system has been a very productive tool for studying the molecular mechanism of DNA transposition. These studies are of broad value because they offer insights into DNA transposition in general, because DNA transposition is a useful model with which to understand other types of protein-DNA interactions such as retroviral DNA integration and the DNA cleavage events involved in immunoglobulin gene formation, and because Tn5-derived tools are useful adjuncts in genetic experimentation.
Performance of a dual, solid-state intraoperative probe system with 18F, 99mTc, and (111)In. (2001)

The results from this investigation demonstrate the flexibility and versatility of the dual, solid-state probe system used in this study. These capabilities may be used to improve existing techniques or lead to new methods for performing radionuclide-guided surgeries.
Macrophage activation for tumor cytotoxicity: induction of macrophage tumoricidal activity by lymphokines from EL-4, a continuous T cell line. (1982)

Supernatant culture fluids from a phorbol myristate acetate (PMA) stimulated variant of the murine EL-4 thymoma cell line activated inflammatory macrophages for nonspecific tumoricidal activity in vitro; active supernatants fluids were not directly toxic to tumor target cells in the absence of macrophages. Macrophages treated with culture fluids of unstimulated and concanavalin A-stimulated EL-4 or PMA-stimulated cells derived from any of ten other continuous T cell lines were not cytotoxic. The titer of activity in lymphokines from PMA-stimulated EL-4 was similar to that from antigen-stimulated spleen cell cultures. Spleen cell and EL-4 derived activities were both retained within a dialysis membrane and destroyed by heating at 100 degrees C for 15 min. However, unlike the activity in spleen cell-derived LK, activity in EL-4 culture fluids was stable to dialysis against pH 2 buffer. Further physicochemical characterization of the EL-4 activity showed two different factors that activated macrophages for cytotoxicity: one was indistinguishable from gamma interferon (IFN) (antiviral activity, 50,000 m.w., pI 4.2 to 6.0, pH 2 labile and neutralized by anti-gamma IFN serum); the other was clearly distinct (no antiviral activity, 23,000 m.w., pH 2 stable and unaffected by anti-gamma IFN serum). These results suggest that the EL-4 cell line may produce one or more of the macrophage activation factors present in spleen cell-derived lymphokines.
The design of efficient, broadband ultrasonic transducers (1979)

Expression of alpha-, beta-, or gamma-catenin can be used as a prognostic indicator in patients with surgically resected stage I non-small cell lung cancers of 3 cm or less in size.
The art of taming light: ultra-slow and stopped light (2004)

I n 1998, laser pulses were slowed [1] in a Bose-Einstein condensate (BEe) [2] ofsodium to only 17 m/s, more than seven orders of magnitude lower than the speed of light in vacuum. Associated with the dramatic reduction factor for the light speed was a spatial compression of the pulses by the same large factor. A light pulse, which was more than 1 km long in vacuum, was compressed to a size of -50 flm, and at that point was completely contained within the condensate [1]. This allowed the light-slowing experiments to be brought to their ultimate extreme [3]: in the summer of 2000, light pulses were completely stopped, stored, and subsequently revived in an atomic medium, with millisecond storage times [4]. The initial ultra-slow light experiments spurred a flurry of slow light investigations, and slow or partially stopped light has now been observed in limited geometries in warm rubidium vapours [5-7], liquid-nitrogen cooled crystals [8], and recently in room temperature crystals [9]. Here, we begin with a discussion ofultra-slow and stopped light. We describe how cold atoms and Bose-Einstein condensates have been manipulated to generate media with extreme optical properties. While the initial experiments concentrated on the light propagation, we have recently begun a number of investigations of the effects that slow light has on the medium in which it propagates. Effects are profound because both the velocity and length scales associated with propagating light pulses have been brought down to match the characteristic velocity and length scales of the medium. With the most recent extension, the light roadblock [10], we have compressed light pulses to a length ofonly 2 f!ill. Here, we describe the use of ultra-compressed light pulses to probe superfluidity and the creation of quantized vortices in BEes through formation of'superfluid shock. waves'. We also present the observation of an ultra-slow-light-based, pulsed atom laser. Furthermore, we demonstrate the use of slow and stopped light for manipulation of optical information, in particular in Bose-Einstein condensates that allow for phase coherent processing of three-dimensional, compressed patterns of stored optical information.
Cis-Trans Isomers of 6-Methyl-3-cyclohexene-1-carboxylic Acid and Their sec-Butyl Esters (1959)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCis-Trans Isomers of 6-Methyl-3-cyclohexene-1-carboxylic Acid and Their sec-Butyl EstersNATHAN GREEN and MORTON BEROZACite this: J. Org. Chem. 1959, 24, 6, 761–764Publication Date (Print):June 1, 1959Publication History Published online1 May 2002Published inissue 1 June 1959https://pubs.acs.org/doi/10.1021/jo01088a008https://doi.org/10.1021/jo01088a008research-articleACS PublicationsRequest reuse permissionsArticle Views176Altmetric-Citations7LEARN 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
Multi-level p+ tri-gate SONOS NAND string arrays (2006)

Tri-gate silicon-oxide-nitride-oxide-silicon (SONOS) NAND string arrays with p+ gate for multi-level high density data flash applications have been fabricated down to 50 nm gate length for the first time. Thick nitride and top oxide layers have been chosen to achieve large threshold voltage shifts of DeltaV <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">th</sub> = 6 V at NAND flash compatible times and voltages. In spite of the thick dielectric stack device scalability is not compromised, as shown by simulation for 30 nm gate length. In addition, excellent program inhibit and retention properties as well as tight multi-level threshold voltage distributions have been found
Anti-herbivore Structures of Paulownia tomentosa: Morphology, Distribution, Chemical Constituents and Changes During Shoot and Leaf Development (2008)

The results indicate that P. tomentosa protects young and/or reproductive organs from herbivores through the distribution and allocation of small structures, the nature of which depends on the developmental stage of leaves and shoots.
The Reliability and Patient Acceptability of the SmartTrack Device: A New Electronic Monitor and Reminder Device for Metered Dose Inhalers (2012)

The ST has acceptable reliability and utility comparable to other electronic monitoring devices. Its remote data upload capability, reminder functions for missed doses, and graphical display of medication use for patient- and physician-feedback are useful additional features.